Starting phenix.real_space_refine on Tue Mar 3 19:32:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rmh_24570/03_2026/7rmh_24570.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rmh_24570/03_2026/7rmh_24570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rmh_24570/03_2026/7rmh_24570.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rmh_24570/03_2026/7rmh_24570.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rmh_24570/03_2026/7rmh_24570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rmh_24570/03_2026/7rmh_24570.map" } resolution = 3.1 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= -0.002 sd= 0.314 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1082 atoms to isotropic. 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 55 5.16 5 C 4811 2.51 5 N 1267 2.21 5 O 1301 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7434 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1665 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 5, 'TRANS': 210} Chain breaks: 4 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 4, 'GLU:plan': 8, 'GLN:plan1': 2, 'ASP:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 99 Chain: "B" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2319 Classifications: {'peptide': 322} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 5, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 7, 'ASP:plan': 13, 'ASN:plan1': 5, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 113 Chain: "G" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 245 Classifications: {'peptide': 38} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "N" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 851 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 2269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2269 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 13, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "S" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 84 Classifications: {'peptide': 11} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 8} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.76, per 1000 atoms: 0.24 Number of scatterers: 7434 At special positions: 0 Unit cell: (75.68, 98.9, 131.58, 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 55 16.00 O 1301 8.00 N 1267 7.00 C 4811 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 180 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 295.9 milliseconds 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1876 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 11 sheets defined 40.8% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 14 through 38 removed outlier: 3.987A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.568A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.660A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 238 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.659A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 351 removed outlier: 4.214A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 4.073A pdb=" N ARG A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 25 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'G' and resid 14 through 23 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.608A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.705A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.733A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.759A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 60 removed outlier: 3.748A pdb=" N ILE R 32 " --> pdb=" O PRO R 28 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE R 42 " --> pdb=" O ALA R 38 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N HIS R 60 " --> pdb=" O ILE R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 67 No H-bonds generated for 'chain 'R' and resid 65 through 67' Processing helix chain 'R' and resid 68 through 85 removed outlier: 3.623A pdb=" N PHE R 84 " --> pdb=" O SER R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 94 Processing helix chain 'R' and resid 101 through 135 Proline residue: R 112 - end of helix Processing helix chain 'R' and resid 143 through 168 Proline residue: R 164 - end of helix removed outlier: 3.564A pdb=" N TYR R 168 " --> pdb=" O PRO R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 205 Processing helix chain 'R' and resid 205 through 224 Processing helix chain 'R' and resid 240 through 270 Proline residue: R 263 - end of helix Processing helix chain 'R' and resid 271 through 273 No H-bonds generated for 'chain 'R' and resid 271 through 273' Processing helix chain 'R' and resid 274 through 279 removed outlier: 3.817A pdb=" N LEU R 277 " --> pdb=" O ASN R 274 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYR R 278 " --> pdb=" O PRO R 275 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU R 279 " --> pdb=" O ASP R 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 274 through 279' Processing helix chain 'R' and resid 280 through 296 removed outlier: 4.103A pdb=" N GLN R 284 " --> pdb=" O LYS R 280 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 309 removed outlier: 3.953A pdb=" N ILE R 303 " --> pdb=" O MET R 299 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Processing helix chain 'R' and resid 309 through 320 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.238A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.119A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.123A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.063A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.890A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.911A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.773A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.785A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 5.496A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 169 through 174 370 hydrogen bonds defined for protein. 1059 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: 0.99 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2330 1.34 - 1.46: 1967 1.46 - 1.59: 3234 1.59 - 1.71: 0 1.71 - 1.83: 79 Bond restraints: 7610 Sorted by residual: bond pdb=" N GLN R 24 " pdb=" CA GLN R 24 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.33e-02 5.65e+03 8.92e+00 bond pdb=" C ARG S 1 " pdb=" N PRO S 2 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.41e+00 bond pdb=" CB PRO R 208 " pdb=" CG PRO R 208 " ideal model delta sigma weight residual 1.492 1.403 0.089 5.00e-02 4.00e+02 3.18e+00 bond pdb=" CA LEU R 262 " pdb=" C LEU R 262 " ideal model delta sigma weight residual 1.521 1.539 -0.017 1.08e-02 8.57e+03 2.62e+00 bond pdb=" C PHE R 163 " pdb=" N PRO R 164 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.25e-02 6.40e+03 2.24e+00 ... (remaining 7605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 9989 1.70 - 3.39: 323 3.39 - 5.09: 44 5.09 - 6.79: 14 6.79 - 8.49: 9 Bond angle restraints: 10379 Sorted by residual: angle pdb=" N PHE R 111 " pdb=" CA PHE R 111 " pdb=" C PHE R 111 " ideal model delta sigma weight residual 109.81 118.30 -8.49 2.21e+00 2.05e-01 1.47e+01 angle pdb=" N LEU R 270 " pdb=" CA LEU R 270 " pdb=" C LEU R 270 " ideal model delta sigma weight residual 112.75 116.95 -4.20 1.36e+00 5.41e-01 9.54e+00 angle pdb=" CA TRP B 169 " pdb=" CB TRP B 169 " pdb=" CG TRP B 169 " ideal model delta sigma weight residual 113.60 119.05 -5.45 1.90e+00 2.77e-01 8.23e+00 angle pdb=" N ASN R 301 " pdb=" CA ASN R 301 " pdb=" C ASN R 301 " ideal model delta sigma weight residual 109.81 115.85 -6.04 2.21e+00 2.05e-01 7.47e+00 angle pdb=" CA ARG R 141 " pdb=" CB ARG R 141 " pdb=" CG ARG R 141 " ideal model delta sigma weight residual 114.10 119.53 -5.43 2.00e+00 2.50e-01 7.38e+00 ... (remaining 10374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 3987 16.80 - 33.61: 340 33.61 - 50.41: 72 50.41 - 67.22: 8 67.22 - 84.02: 5 Dihedral angle restraints: 4412 sinusoidal: 1520 harmonic: 2892 Sorted by residual: dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -153.35 -26.65 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA VAL A 224 " pdb=" C VAL A 224 " pdb=" N GLY A 225 " pdb=" CA GLY A 225 " ideal model delta harmonic sigma weight residual 180.00 157.00 23.00 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -157.70 -22.30 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 4409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 806 0.043 - 0.086: 295 0.086 - 0.130: 86 0.130 - 0.173: 20 0.173 - 0.216: 3 Chirality restraints: 1210 Sorted by residual: chirality pdb=" CB VAL R 200 " pdb=" CA VAL R 200 " pdb=" CG1 VAL R 200 " pdb=" CG2 VAL R 200 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA PHE R 111 " pdb=" N PHE R 111 " pdb=" C PHE R 111 " pdb=" CB PHE R 111 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.03e-01 chirality pdb=" CG LEU B 284 " pdb=" CB LEU B 284 " pdb=" CD1 LEU B 284 " pdb=" CD2 LEU B 284 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.97e-01 ... (remaining 1207 not shown) Planarity restraints: 1294 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET R 174 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO R 175 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO R 175 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO R 175 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS N 87 " 0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO N 88 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO N 88 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO N 88 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 224 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.32e+00 pdb=" C VAL A 224 " 0.032 2.00e-02 2.50e+03 pdb=" O VAL A 224 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY A 225 " -0.011 2.00e-02 2.50e+03 ... (remaining 1291 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2015 2.81 - 3.33: 5941 3.33 - 3.86: 11584 3.86 - 4.38: 12745 4.38 - 4.90: 23751 Nonbonded interactions: 56036 Sorted by model distance: nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.290 3.040 nonbonded pdb=" O ALA R 36 " pdb=" OG1 THR R 40 " model vdw 2.307 3.040 nonbonded pdb=" OE1 GLN N 39 " pdb=" OH TYR N 95 " model vdw 2.354 3.040 nonbonded pdb=" O LEU B 168 " pdb=" OG1 THR B 177 " model vdw 2.368 3.040 nonbonded pdb=" NH1 ARG N 67 " pdb=" O SER N 85 " model vdw 2.406 3.120 ... (remaining 56031 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.500 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 7614 Z= 0.224 Angle : 0.747 8.487 10385 Z= 0.413 Chirality : 0.050 0.216 1210 Planarity : 0.005 0.051 1294 Dihedral : 13.417 84.023 2527 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.25), residues: 958 helix: -0.93 (0.23), residues: 366 sheet: 0.50 (0.34), residues: 228 loop : -1.60 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 64 TYR 0.012 0.001 TYR N 95 PHE 0.019 0.002 PHE R 264 TRP 0.021 0.002 TRP B 169 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 7610) covalent geometry : angle 0.74600 (10379) SS BOND : bond 0.00466 ( 3) SS BOND : angle 2.07929 ( 6) hydrogen bonds : bond 0.13088 ( 370) hydrogen bonds : angle 5.55496 ( 1059) Misc. bond : bond 0.10074 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 247 ASP cc_start: 0.7784 (p0) cc_final: 0.7549 (p0) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.0795 time to fit residues: 15.5370 Evaluate side-chains 95 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 24 GLN R 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.116367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.095631 restraints weight = 13793.784| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 3.61 r_work: 0.3208 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7614 Z= 0.174 Angle : 0.587 7.894 10385 Z= 0.316 Chirality : 0.043 0.138 1210 Planarity : 0.004 0.032 1294 Dihedral : 4.399 25.654 1059 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.65 % Allowed : 9.09 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.26), residues: 958 helix: 0.65 (0.27), residues: 361 sheet: 0.76 (0.34), residues: 214 loop : -1.53 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 389 TYR 0.014 0.001 TYR N 95 PHE 0.017 0.002 PHE R 264 TRP 0.019 0.001 TRP B 169 HIS 0.003 0.001 HIS R 95 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 7610) covalent geometry : angle 0.58542 (10379) SS BOND : bond 0.00477 ( 3) SS BOND : angle 1.86516 ( 6) hydrogen bonds : bond 0.05827 ( 370) hydrogen bonds : angle 4.22877 ( 1059) Misc. bond : bond 0.00055 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8387 (pp30) cc_final: 0.8169 (pp30) REVERT: R 250 MET cc_start: 0.7884 (mtt) cc_final: 0.7625 (mtt) REVERT: R 285 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7959 (mt0) REVERT: S 5 GLN cc_start: 0.8528 (mp10) cc_final: 0.7899 (mp10) outliers start: 12 outliers final: 6 residues processed: 110 average time/residue: 0.0680 time to fit residues: 10.6615 Evaluate side-chains 99 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 266 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 19 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.118163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.097893 restraints weight = 13768.300| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.58 r_work: 0.3246 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7614 Z= 0.111 Angle : 0.510 7.369 10385 Z= 0.271 Chirality : 0.042 0.184 1210 Planarity : 0.003 0.032 1294 Dihedral : 4.131 28.144 1059 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.65 % Allowed : 11.85 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.27), residues: 958 helix: 1.26 (0.28), residues: 366 sheet: 0.80 (0.34), residues: 215 loop : -1.41 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 389 TYR 0.011 0.001 TYR N 95 PHE 0.012 0.001 PHE R 264 TRP 0.017 0.001 TRP B 169 HIS 0.002 0.000 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 7610) covalent geometry : angle 0.50894 (10379) SS BOND : bond 0.00324 ( 3) SS BOND : angle 1.31014 ( 6) hydrogen bonds : bond 0.04591 ( 370) hydrogen bonds : angle 3.96361 ( 1059) Misc. bond : bond 0.00036 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: B 175 GLN cc_start: 0.8361 (pp30) cc_final: 0.8096 (pp30) REVERT: N 68 PHE cc_start: 0.7596 (m-80) cc_final: 0.7095 (m-80) REVERT: R 104 TYR cc_start: 0.7832 (t80) cc_final: 0.7621 (t80) outliers start: 12 outliers final: 7 residues processed: 108 average time/residue: 0.0730 time to fit residues: 11.1321 Evaluate side-chains 96 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 266 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 80 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.115804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.095879 restraints weight = 14261.787| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.58 r_work: 0.3183 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7614 Z= 0.174 Angle : 0.562 6.007 10385 Z= 0.305 Chirality : 0.043 0.202 1210 Planarity : 0.004 0.038 1294 Dihedral : 4.234 27.052 1059 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.34 % Allowed : 13.50 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.27), residues: 958 helix: 1.45 (0.27), residues: 361 sheet: 0.73 (0.33), residues: 206 loop : -1.51 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 389 TYR 0.013 0.001 TYR N 95 PHE 0.019 0.002 PHE R 264 TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS R 95 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 7610) covalent geometry : angle 0.56101 (10379) SS BOND : bond 0.00474 ( 3) SS BOND : angle 1.69352 ( 6) hydrogen bonds : bond 0.05728 ( 370) hydrogen bonds : angle 4.14288 ( 1059) Misc. bond : bond 0.00063 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.261 Fit side-chains REVERT: A 209 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8197 (mt-10) REVERT: A 210 THR cc_start: 0.7476 (OUTLIER) cc_final: 0.6808 (p) REVERT: A 286 SER cc_start: 0.9308 (p) cc_final: 0.9086 (p) REVERT: A 293 LYS cc_start: 0.8138 (mmtt) cc_final: 0.7912 (mtpp) REVERT: B 175 GLN cc_start: 0.8345 (pp30) cc_final: 0.8075 (pp30) REVERT: B 273 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7846 (mp) REVERT: R 104 TYR cc_start: 0.8026 (t80) cc_final: 0.7745 (t80) REVERT: S 5 GLN cc_start: 0.8557 (mp10) cc_final: 0.8009 (mp10) outliers start: 17 outliers final: 7 residues processed: 111 average time/residue: 0.0705 time to fit residues: 11.1621 Evaluate side-chains 100 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 266 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 24 GLN R 309 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.117982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.098067 restraints weight = 14108.971| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.56 r_work: 0.3227 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7614 Z= 0.120 Angle : 0.525 6.483 10385 Z= 0.281 Chirality : 0.042 0.184 1210 Planarity : 0.003 0.035 1294 Dihedral : 4.213 30.423 1059 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.20 % Allowed : 15.01 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.27), residues: 958 helix: 1.75 (0.28), residues: 361 sheet: 0.72 (0.33), residues: 210 loop : -1.39 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 389 TYR 0.010 0.001 TYR N 95 PHE 0.021 0.001 PHE N 68 TRP 0.015 0.001 TRP B 169 HIS 0.002 0.000 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 7610) covalent geometry : angle 0.52382 (10379) SS BOND : bond 0.00338 ( 3) SS BOND : angle 1.77384 ( 6) hydrogen bonds : bond 0.04824 ( 370) hydrogen bonds : angle 3.98279 ( 1059) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.266 Fit side-chains REVERT: A 20 ARG cc_start: 0.8642 (tmm160) cc_final: 0.8044 (mtm110) REVERT: A 209 GLU cc_start: 0.8468 (mt-10) cc_final: 0.7728 (mt-10) REVERT: A 210 THR cc_start: 0.7455 (OUTLIER) cc_final: 0.6726 (p) REVERT: A 211 LYS cc_start: 0.9114 (mttm) cc_final: 0.8636 (mttm) REVERT: A 286 SER cc_start: 0.9283 (p) cc_final: 0.9062 (p) REVERT: A 293 LYS cc_start: 0.8090 (mmtt) cc_final: 0.7857 (mtpp) REVERT: B 175 GLN cc_start: 0.8368 (pp30) cc_final: 0.8083 (pp30) REVERT: B 273 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7675 (mp) REVERT: N 83 MET cc_start: 0.8254 (mtm) cc_final: 0.8044 (mtm) REVERT: S 5 GLN cc_start: 0.8542 (mp10) cc_final: 0.7982 (mp10) outliers start: 16 outliers final: 8 residues processed: 109 average time/residue: 0.0696 time to fit residues: 10.6626 Evaluate side-chains 102 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 266 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 60 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 78 optimal weight: 0.0570 chunk 7 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.118120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.097690 restraints weight = 13994.220| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.61 r_work: 0.3248 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7614 Z= 0.107 Angle : 0.501 6.188 10385 Z= 0.267 Chirality : 0.041 0.171 1210 Planarity : 0.003 0.038 1294 Dihedral : 4.034 31.089 1059 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.93 % Allowed : 14.88 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.27), residues: 958 helix: 1.89 (0.28), residues: 367 sheet: 0.77 (0.33), residues: 210 loop : -1.34 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 389 TYR 0.010 0.001 TYR N 95 PHE 0.021 0.001 PHE N 68 TRP 0.015 0.001 TRP B 169 HIS 0.002 0.000 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 7610) covalent geometry : angle 0.50020 (10379) SS BOND : bond 0.00244 ( 3) SS BOND : angle 1.47773 ( 6) hydrogen bonds : bond 0.04311 ( 370) hydrogen bonds : angle 3.86808 ( 1059) Misc. bond : bond 0.00030 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7680 (mt-10) REVERT: A 210 THR cc_start: 0.7388 (OUTLIER) cc_final: 0.6702 (p) REVERT: A 211 LYS cc_start: 0.9097 (mttm) cc_final: 0.8697 (mttp) REVERT: A 286 SER cc_start: 0.9264 (p) cc_final: 0.8966 (m) REVERT: A 293 LYS cc_start: 0.8074 (mmtt) cc_final: 0.7773 (mtpp) REVERT: B 175 GLN cc_start: 0.8319 (pp30) cc_final: 0.8080 (pp30) REVERT: B 176 GLN cc_start: 0.9047 (mt0) cc_final: 0.8794 (mt0) REVERT: B 273 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7636 (mp) REVERT: G 21 MET cc_start: 0.5391 (tmm) cc_final: 0.5097 (tmm) REVERT: G 41 CYS cc_start: 0.7244 (t) cc_final: 0.6442 (p) REVERT: S 5 GLN cc_start: 0.8570 (mp10) cc_final: 0.7949 (mp10) outliers start: 14 outliers final: 8 residues processed: 113 average time/residue: 0.0708 time to fit residues: 11.3501 Evaluate side-chains 105 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 201 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 84 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 24 optimal weight: 8.9990 chunk 17 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 285 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.117912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.097516 restraints weight = 13972.542| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 3.60 r_work: 0.3245 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7614 Z= 0.113 Angle : 0.504 6.707 10385 Z= 0.269 Chirality : 0.042 0.162 1210 Planarity : 0.003 0.038 1294 Dihedral : 3.984 31.398 1059 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.92 % Favored : 96.97 % Rotamer: Outliers : 1.79 % Allowed : 16.67 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.27), residues: 958 helix: 2.11 (0.28), residues: 361 sheet: 0.78 (0.33), residues: 210 loop : -1.27 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 389 TYR 0.010 0.001 TYR N 95 PHE 0.013 0.001 PHE R 264 TRP 0.013 0.001 TRP B 169 HIS 0.002 0.000 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 7610) covalent geometry : angle 0.50332 (10379) SS BOND : bond 0.00292 ( 3) SS BOND : angle 1.51598 ( 6) hydrogen bonds : bond 0.04395 ( 370) hydrogen bonds : angle 3.83058 ( 1059) Misc. bond : bond 0.00032 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8228 (mt-10) REVERT: A 210 THR cc_start: 0.7379 (OUTLIER) cc_final: 0.6737 (p) REVERT: A 286 SER cc_start: 0.9281 (p) cc_final: 0.9062 (p) REVERT: A 293 LYS cc_start: 0.8077 (mmtt) cc_final: 0.7768 (mtpp) REVERT: B 175 GLN cc_start: 0.8305 (pp30) cc_final: 0.8074 (pp30) REVERT: B 176 GLN cc_start: 0.9082 (mt0) cc_final: 0.8822 (mt0) REVERT: B 273 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7646 (mp) REVERT: G 41 CYS cc_start: 0.7301 (t) cc_final: 0.6441 (p) REVERT: S 5 GLN cc_start: 0.8546 (mp10) cc_final: 0.7984 (mp10) outliers start: 13 outliers final: 8 residues processed: 107 average time/residue: 0.0787 time to fit residues: 11.8205 Evaluate side-chains 109 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 201 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 17 optimal weight: 0.3980 chunk 43 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 123 GLN R 285 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.117015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.096844 restraints weight = 14057.813| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.59 r_work: 0.3250 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7614 Z= 0.110 Angle : 0.502 7.212 10385 Z= 0.266 Chirality : 0.041 0.168 1210 Planarity : 0.003 0.037 1294 Dihedral : 3.945 32.173 1059 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.34 % Favored : 96.56 % Rotamer: Outliers : 2.07 % Allowed : 16.80 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.27), residues: 958 helix: 2.19 (0.28), residues: 361 sheet: 0.85 (0.33), residues: 209 loop : -1.23 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 389 TYR 0.010 0.001 TYR N 95 PHE 0.015 0.001 PHE N 68 TRP 0.013 0.001 TRP B 169 HIS 0.002 0.000 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 7610) covalent geometry : angle 0.50061 (10379) SS BOND : bond 0.00281 ( 3) SS BOND : angle 1.54086 ( 6) hydrogen bonds : bond 0.04284 ( 370) hydrogen bonds : angle 3.82225 ( 1059) Misc. bond : bond 0.00033 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.189 Fit side-chains REVERT: A 20 ARG cc_start: 0.8553 (tmm160) cc_final: 0.8078 (mtm110) REVERT: A 209 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8215 (mt-10) REVERT: A 210 THR cc_start: 0.7365 (OUTLIER) cc_final: 0.6710 (p) REVERT: A 211 LYS cc_start: 0.9211 (mttp) cc_final: 0.8774 (mttm) REVERT: A 286 SER cc_start: 0.9286 (p) cc_final: 0.8992 (m) REVERT: A 293 LYS cc_start: 0.8077 (mmtt) cc_final: 0.7770 (mtpp) REVERT: B 175 GLN cc_start: 0.8292 (pp30) cc_final: 0.8066 (pp30) REVERT: B 176 GLN cc_start: 0.9071 (mt0) cc_final: 0.8712 (tt0) REVERT: B 273 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7607 (mp) REVERT: G 41 CYS cc_start: 0.7244 (t) cc_final: 0.6411 (p) REVERT: S 5 GLN cc_start: 0.8568 (mp10) cc_final: 0.7986 (mp10) outliers start: 15 outliers final: 10 residues processed: 113 average time/residue: 0.0693 time to fit residues: 11.0007 Evaluate side-chains 113 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 201 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 93 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 78 optimal weight: 0.0570 chunk 14 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 285 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.118986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.098772 restraints weight = 13840.279| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.58 r_work: 0.3275 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 7614 Z= 0.105 Angle : 0.509 7.433 10385 Z= 0.268 Chirality : 0.041 0.163 1210 Planarity : 0.003 0.037 1294 Dihedral : 3.894 33.131 1059 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.92 % Favored : 96.97 % Rotamer: Outliers : 1.79 % Allowed : 17.36 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.27), residues: 958 helix: 2.14 (0.28), residues: 367 sheet: 0.88 (0.33), residues: 209 loop : -1.21 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 389 TYR 0.009 0.001 TYR N 95 PHE 0.023 0.001 PHE N 68 TRP 0.013 0.001 TRP B 169 HIS 0.002 0.000 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 7610) covalent geometry : angle 0.50783 (10379) SS BOND : bond 0.00269 ( 3) SS BOND : angle 1.41756 ( 6) hydrogen bonds : bond 0.04013 ( 370) hydrogen bonds : angle 3.76196 ( 1059) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8144 (mt-10) REVERT: A 210 THR cc_start: 0.7258 (OUTLIER) cc_final: 0.6993 (t) REVERT: A 211 LYS cc_start: 0.9210 (mttp) cc_final: 0.8827 (mttm) REVERT: A 286 SER cc_start: 0.9282 (p) cc_final: 0.9004 (m) REVERT: A 293 LYS cc_start: 0.8055 (mmtt) cc_final: 0.7748 (mtpp) REVERT: B 175 GLN cc_start: 0.8274 (pp30) cc_final: 0.8054 (pp30) REVERT: B 176 GLN cc_start: 0.9049 (mt0) cc_final: 0.8666 (tt0) REVERT: B 273 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7630 (mp) REVERT: G 41 CYS cc_start: 0.7292 (t) cc_final: 0.6410 (p) REVERT: R 250 MET cc_start: 0.7942 (mtt) cc_final: 0.7628 (mtt) REVERT: S 5 GLN cc_start: 0.8580 (mp10) cc_final: 0.7984 (mp10) outliers start: 13 outliers final: 9 residues processed: 109 average time/residue: 0.0732 time to fit residues: 11.1760 Evaluate side-chains 113 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 92 optimal weight: 0.9980 chunk 57 optimal weight: 0.0570 chunk 93 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 123 GLN R 285 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.113609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.093217 restraints weight = 14381.514| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.54 r_work: 0.3199 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7614 Z= 0.113 Angle : 0.517 7.695 10385 Z= 0.273 Chirality : 0.041 0.170 1210 Planarity : 0.003 0.040 1294 Dihedral : 3.887 32.995 1059 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.13 % Favored : 96.76 % Rotamer: Outliers : 1.79 % Allowed : 17.77 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.27), residues: 958 helix: 2.13 (0.28), residues: 367 sheet: 0.94 (0.33), residues: 209 loop : -1.21 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 389 TYR 0.010 0.001 TYR N 95 PHE 0.016 0.001 PHE N 68 TRP 0.012 0.001 TRP B 169 HIS 0.002 0.000 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 7610) covalent geometry : angle 0.51570 (10379) SS BOND : bond 0.00293 ( 3) SS BOND : angle 1.47623 ( 6) hydrogen bonds : bond 0.04203 ( 370) hydrogen bonds : angle 3.77581 ( 1059) Misc. bond : bond 0.00031 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8162 (mt-10) REVERT: A 210 THR cc_start: 0.7536 (OUTLIER) cc_final: 0.7279 (t) REVERT: A 211 LYS cc_start: 0.9243 (mttp) cc_final: 0.8878 (mttm) REVERT: A 286 SER cc_start: 0.9310 (p) cc_final: 0.9076 (m) REVERT: A 293 LYS cc_start: 0.8216 (mmtt) cc_final: 0.7885 (mtpp) REVERT: B 175 GLN cc_start: 0.8344 (pp30) cc_final: 0.8108 (pp30) REVERT: B 176 GLN cc_start: 0.9145 (mt0) cc_final: 0.8763 (tt0) REVERT: B 273 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7727 (mp) REVERT: B 301 LYS cc_start: 0.7537 (mmmt) cc_final: 0.7311 (mmmm) REVERT: G 41 CYS cc_start: 0.7292 (t) cc_final: 0.6529 (p) REVERT: R 266 ILE cc_start: 0.8332 (mm) cc_final: 0.8121 (tt) REVERT: S 5 GLN cc_start: 0.8683 (mp10) cc_final: 0.8096 (mp10) outliers start: 13 outliers final: 9 residues processed: 108 average time/residue: 0.0773 time to fit residues: 11.7502 Evaluate side-chains 110 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 51 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 0.0970 chunk 70 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 285 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.111500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.091166 restraints weight = 14529.376| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.55 r_work: 0.3175 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7614 Z= 0.133 Angle : 0.541 7.605 10385 Z= 0.287 Chirality : 0.042 0.176 1210 Planarity : 0.003 0.042 1294 Dihedral : 3.998 32.303 1059 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.13 % Favored : 96.76 % Rotamer: Outliers : 1.79 % Allowed : 18.18 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.27), residues: 958 helix: 2.14 (0.28), residues: 367 sheet: 0.89 (0.33), residues: 210 loop : -1.20 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 389 TYR 0.010 0.001 TYR N 95 PHE 0.015 0.001 PHE R 264 TRP 0.011 0.001 TRP B 169 HIS 0.002 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 7610) covalent geometry : angle 0.54018 (10379) SS BOND : bond 0.00335 ( 3) SS BOND : angle 1.57846 ( 6) hydrogen bonds : bond 0.04713 ( 370) hydrogen bonds : angle 3.87170 ( 1059) Misc. bond : bond 0.00045 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1744.75 seconds wall clock time: 30 minutes 28.51 seconds (1828.51 seconds total)