Starting phenix.real_space_refine on Sat Jul 26 04:15:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rmh_24570/07_2025/7rmh_24570.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rmh_24570/07_2025/7rmh_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7rmh_24570/07_2025/7rmh_24570.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rmh_24570/07_2025/7rmh_24570.map" model { file = "/net/cci-nas-00/data/ceres_data/7rmh_24570/07_2025/7rmh_24570.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rmh_24570/07_2025/7rmh_24570.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 2, 'GLU:plan': 8, 'ASN:plan1': 4, 'ARG:plan': 4, 'ASP:plan': 9} 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, 'GLU:plan': 2, 'ARG:plan': 7, 'ASN:plan1': 5, 'ASP:plan': 13} 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: {'GLU:plan': 3, 'ARG:plan': 2, '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: {'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} 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: 5.24, per 1000 atoms: 0.70 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: 1.92 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.98 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: 2.32 Time building geometry restraints manager: 2.29 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: 2.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.700 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.220 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.021 0.002 TRP B 169 HIS 0.005 0.001 HIS A 220 PHE 0.019 0.002 PHE R 264 TYR 0.012 0.001 TYR N 95 ARG 0.004 0.000 ARG R 64 Details of bonding type rmsd hydrogen bonds : bond 0.13088 ( 370) hydrogen bonds : angle 5.55496 ( 1059) SS BOND : bond 0.00466 ( 3) SS BOND : angle 2.07929 ( 6) covalent geometry : bond 0.00372 ( 7610) covalent geometry : angle 0.74600 (10379) 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 : 0.814 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: 0.1946 time to fit residues: 37.9688 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 : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 29 optimal weight: 0.0070 chunk 45 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 87 optimal weight: 0.6980 overall best weight: 0.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.121649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.100229 restraints weight = 13526.600| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.69 r_work: 0.3255 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1466 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= 0.129 Angle : 0.540 7.623 10385 Z= 0.289 Chirality : 0.042 0.139 1210 Planarity : 0.004 0.034 1294 Dihedral : 4.274 25.923 1059 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.38 % Allowed : 8.95 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.26), residues: 958 helix: 0.71 (0.27), residues: 361 sheet: 0.83 (0.34), residues: 213 loop : -1.44 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 169 HIS 0.003 0.001 HIS R 265 PHE 0.013 0.001 PHE R 264 TYR 0.013 0.001 TYR N 95 ARG 0.005 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.05016 ( 370) hydrogen bonds : angle 4.10679 ( 1059) SS BOND : bond 0.00367 ( 3) SS BOND : angle 1.61661 ( 6) covalent geometry : bond 0.00290 ( 7610) covalent geometry : angle 0.53860 (10379) Misc. bond : bond 0.00037 ( 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 112 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 68 PHE cc_start: 0.7730 (m-80) cc_final: 0.7220 (m-80) REVERT: R 250 MET cc_start: 0.7795 (mtt) cc_final: 0.7593 (mtt) outliers start: 10 outliers final: 5 residues processed: 108 average time/residue: 0.1723 time to fit residues: 26.2279 Evaluate side-chains 96 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 SER 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 54 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 83 optimal weight: 0.0870 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 65 optimal weight: 0.0020 overall best weight: 0.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 73 ASN R 89 ASN R 285 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.122507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.101620 restraints weight = 13718.496| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.67 r_work: 0.3287 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7614 Z= 0.096 Angle : 0.492 7.006 10385 Z= 0.260 Chirality : 0.041 0.207 1210 Planarity : 0.003 0.031 1294 Dihedral : 4.017 28.259 1059 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.96 % Allowed : 11.02 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.27), residues: 958 helix: 1.32 (0.27), residues: 366 sheet: 0.90 (0.34), residues: 210 loop : -1.29 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.001 0.000 HIS A 357 PHE 0.011 0.001 PHE R 264 TYR 0.010 0.001 TYR N 95 ARG 0.005 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.04080 ( 370) hydrogen bonds : angle 3.85826 ( 1059) SS BOND : bond 0.00287 ( 3) SS BOND : angle 1.13696 ( 6) covalent geometry : bond 0.00208 ( 7610) covalent geometry : angle 0.49135 (10379) Misc. bond : bond 0.00021 ( 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 110 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7891 (mt-10) REVERT: B 175 GLN cc_start: 0.8251 (pp30) cc_final: 0.8050 (pp30) REVERT: N 68 PHE cc_start: 0.7555 (m-80) cc_final: 0.7188 (m-80) REVERT: R 250 MET cc_start: 0.7779 (mtt) cc_final: 0.7562 (mtt) outliers start: 7 outliers final: 4 residues processed: 107 average time/residue: 0.2209 time to fit residues: 33.8352 Evaluate side-chains 100 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 201 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 62 optimal weight: 4.9990 chunk 95 optimal weight: 0.2980 chunk 91 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.3623 r_free = 0.3623 target = 0.114696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.094261 restraints weight = 13983.456| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 3.60 r_work: 0.3188 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2174 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= 0.183 Angle : 0.569 6.587 10385 Z= 0.308 Chirality : 0.043 0.189 1210 Planarity : 0.003 0.038 1294 Dihedral : 4.179 25.959 1059 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.93 % Allowed : 11.85 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.27), residues: 958 helix: 1.47 (0.27), residues: 361 sheet: 0.79 (0.34), residues: 206 loop : -1.45 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS R 95 PHE 0.019 0.002 PHE R 264 TYR 0.013 0.001 TYR N 95 ARG 0.006 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.05666 ( 370) hydrogen bonds : angle 4.09939 ( 1059) SS BOND : bond 0.00468 ( 3) SS BOND : angle 1.67805 ( 6) covalent geometry : bond 0.00431 ( 7610) covalent geometry : angle 0.56819 (10379) Misc. bond : bond 0.00066 ( 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 113 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: A 286 SER cc_start: 0.9288 (p) cc_final: 0.9062 (p) REVERT: B 175 GLN cc_start: 0.8277 (pp30) cc_final: 0.7990 (pp30) REVERT: B 273 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7811 (mp) REVERT: S 5 GLN cc_start: 0.8543 (mp10) cc_final: 0.7981 (mp10) outliers start: 14 outliers final: 9 residues processed: 107 average time/residue: 0.1842 time to fit residues: 27.3604 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 : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 94 VAL 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 0 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 4 optimal weight: 0.4980 chunk 11 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 24 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 = 0.3649 r_free = 0.3649 target = 0.116622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.096181 restraints weight = 13854.259| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.58 r_work: 0.3218 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7614 Z= 0.124 Angle : 0.515 6.886 10385 Z= 0.276 Chirality : 0.042 0.183 1210 Planarity : 0.003 0.039 1294 Dihedral : 4.076 29.326 1059 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.20 % Allowed : 13.77 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.27), residues: 958 helix: 1.77 (0.28), residues: 361 sheet: 0.86 (0.34), residues: 205 loop : -1.36 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.002 0.001 HIS A 220 PHE 0.020 0.001 PHE N 68 TYR 0.011 0.001 TYR N 95 ARG 0.008 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.04783 ( 370) hydrogen bonds : angle 3.95100 ( 1059) SS BOND : bond 0.00377 ( 3) SS BOND : angle 1.33323 ( 6) covalent geometry : bond 0.00284 ( 7610) covalent geometry : angle 0.51426 (10379) Misc. bond : bond 0.00043 ( 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 : 0.922 Fit side-chains REVERT: A 209 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7846 (mt-10) REVERT: A 210 THR cc_start: 0.7015 (OUTLIER) cc_final: 0.6705 (t) REVERT: A 211 LYS cc_start: 0.9164 (mmtp) cc_final: 0.8863 (mmtm) REVERT: A 286 SER cc_start: 0.9283 (p) cc_final: 0.9064 (p) REVERT: A 293 LYS cc_start: 0.8105 (mmtt) cc_final: 0.7883 (mtpp) REVERT: B 175 GLN cc_start: 0.8290 (pp30) cc_final: 0.8062 (pp30) REVERT: N 83 MET cc_start: 0.8292 (mtm) cc_final: 0.8074 (mtm) REVERT: S 5 GLN cc_start: 0.8537 (mp10) cc_final: 0.7972 (mp10) outliers start: 16 outliers final: 7 residues processed: 111 average time/residue: 0.2562 time to fit residues: 40.9897 Evaluate side-chains 101 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 94 VAL 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 91 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 52 optimal weight: 8.9990 chunk 35 optimal weight: 0.0970 chunk 79 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 123 GLN R 24 GLN R 285 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.117186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.096857 restraints weight = 13961.857| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.60 r_work: 0.3225 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2410 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= 0.117 Angle : 0.520 6.977 10385 Z= 0.277 Chirality : 0.042 0.179 1210 Planarity : 0.003 0.035 1294 Dihedral : 4.131 30.397 1059 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.93 % Allowed : 14.74 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.27), residues: 958 helix: 1.95 (0.28), residues: 361 sheet: 0.85 (0.33), residues: 210 loop : -1.33 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.002 0.000 HIS A 357 PHE 0.024 0.001 PHE N 68 TYR 0.010 0.001 TYR N 95 ARG 0.008 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.04586 ( 370) hydrogen bonds : angle 3.90082 ( 1059) SS BOND : bond 0.00274 ( 3) SS BOND : angle 1.62898 ( 6) covalent geometry : bond 0.00267 ( 7610) covalent geometry : angle 0.51915 (10379) Misc. bond : bond 0.00036 ( 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 113 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.812 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7765 (mt-10) REVERT: A 210 THR cc_start: 0.6915 (OUTLIER) cc_final: 0.6179 (p) REVERT: A 211 LYS cc_start: 0.9166 (mmtp) cc_final: 0.8878 (mmtm) REVERT: A 286 SER cc_start: 0.9268 (p) cc_final: 0.9041 (p) REVERT: A 293 LYS cc_start: 0.8071 (mmtt) cc_final: 0.7853 (mtpp) REVERT: B 175 GLN cc_start: 0.8272 (pp30) cc_final: 0.8047 (pp30) REVERT: B 176 GLN cc_start: 0.9052 (mt0) cc_final: 0.8819 (mt0) REVERT: G 41 CYS cc_start: 0.7034 (t) cc_final: 0.6078 (p) REVERT: S 5 GLN cc_start: 0.8534 (mp10) cc_final: 0.7952 (mp10) outliers start: 14 outliers final: 9 residues processed: 109 average time/residue: 0.1737 time to fit residues: 26.4736 Evaluate side-chains 108 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 N residue 111 THR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 266 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 24 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 = 0.3613 r_free = 0.3613 target = 0.113694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.093500 restraints weight = 13908.915| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.54 r_work: 0.3208 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7614 Z= 0.160 Angle : 0.561 7.760 10385 Z= 0.300 Chirality : 0.043 0.184 1210 Planarity : 0.003 0.036 1294 Dihedral : 4.222 29.294 1059 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.55 % Favored : 96.35 % Rotamer: Outliers : 2.62 % Allowed : 15.29 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.27), residues: 958 helix: 1.89 (0.27), residues: 360 sheet: 0.80 (0.33), residues: 210 loop : -1.38 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS R 95 PHE 0.018 0.001 PHE R 264 TYR 0.012 0.001 TYR N 95 ARG 0.009 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.05369 ( 370) hydrogen bonds : angle 4.04946 ( 1059) SS BOND : bond 0.00368 ( 3) SS BOND : angle 1.80238 ( 6) covalent geometry : bond 0.00378 ( 7610) covalent geometry : angle 0.55953 (10379) Misc. bond : bond 0.00059 ( 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 113 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7795 (mt-10) REVERT: A 210 THR cc_start: 0.7152 (OUTLIER) cc_final: 0.6453 (p) REVERT: A 211 LYS cc_start: 0.9187 (mmtp) cc_final: 0.8977 (mmtm) REVERT: A 286 SER cc_start: 0.9308 (p) cc_final: 0.9088 (p) REVERT: A 293 LYS cc_start: 0.8106 (mmtt) cc_final: 0.7875 (mtpp) REVERT: B 175 GLN cc_start: 0.8289 (pp30) cc_final: 0.8068 (pp30) REVERT: G 41 CYS cc_start: 0.7128 (t) cc_final: 0.6237 (p) REVERT: S 5 GLN cc_start: 0.8617 (mp10) cc_final: 0.8009 (mp10) outliers start: 19 outliers final: 11 residues processed: 107 average time/residue: 0.1900 time to fit residues: 28.3329 Evaluate side-chains 104 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 369 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 266 ILE Chi-restraints excluded: chain R residue 309 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 22 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.107675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.087452 restraints weight = 14795.434| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.54 r_work: 0.3091 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7614 Z= 0.228 Angle : 0.629 8.651 10385 Z= 0.339 Chirality : 0.045 0.195 1210 Planarity : 0.004 0.037 1294 Dihedral : 4.544 30.200 1059 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.28 % Favored : 95.62 % Rotamer: Outliers : 2.07 % Allowed : 16.67 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.27), residues: 958 helix: 1.70 (0.27), residues: 360 sheet: 0.59 (0.33), residues: 211 loop : -1.52 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.004 0.001 HIS R 95 PHE 0.022 0.002 PHE N 68 TYR 0.015 0.002 TYR A 360 ARG 0.009 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.06439 ( 370) hydrogen bonds : angle 4.34037 ( 1059) SS BOND : bond 0.00487 ( 3) SS BOND : angle 2.08077 ( 6) covalent geometry : bond 0.00542 ( 7610) covalent geometry : angle 0.62719 (10379) Misc. bond : bond 0.00102 ( 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 107 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: A 210 THR cc_start: 0.7403 (OUTLIER) cc_final: 0.6760 (p) REVERT: A 293 LYS cc_start: 0.8348 (mmtt) cc_final: 0.8066 (mtpp) REVERT: B 175 GLN cc_start: 0.8387 (pp30) cc_final: 0.8128 (pp30) REVERT: S 5 GLN cc_start: 0.8747 (mp10) cc_final: 0.8255 (mp10) outliers start: 15 outliers final: 10 residues processed: 103 average time/residue: 0.1818 time to fit residues: 26.1641 Evaluate side-chains 101 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL 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 317 CYS Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 266 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 36 optimal weight: 1.9990 chunk 90 optimal weight: 0.3980 chunk 75 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 24 GLN R 239 GLN R 285 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.109231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.088899 restraints weight = 14615.646| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 3.55 r_work: 0.3124 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7614 Z= 0.140 Angle : 0.559 7.914 10385 Z= 0.299 Chirality : 0.043 0.184 1210 Planarity : 0.003 0.036 1294 Dihedral : 4.336 32.432 1059 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.55 % Favored : 96.35 % Rotamer: Outliers : 1.79 % Allowed : 18.04 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.27), residues: 958 helix: 1.84 (0.27), residues: 366 sheet: 0.62 (0.33), residues: 210 loop : -1.46 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.002 0.001 HIS A 362 PHE 0.017 0.001 PHE N 68 TYR 0.011 0.001 TYR N 95 ARG 0.008 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.05224 ( 370) hydrogen bonds : angle 4.08777 ( 1059) SS BOND : bond 0.00347 ( 3) SS BOND : angle 1.71291 ( 6) covalent geometry : bond 0.00324 ( 7610) covalent geometry : angle 0.55809 (10379) Misc. bond : bond 0.00051 ( 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 108 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7950 (mt-10) REVERT: A 210 THR cc_start: 0.7304 (OUTLIER) cc_final: 0.6609 (p) REVERT: A 211 LYS cc_start: 0.9221 (mmtp) cc_final: 0.9006 (mmtm) REVERT: A 293 LYS cc_start: 0.8295 (mmtt) cc_final: 0.8035 (mtpp) REVERT: B 175 GLN cc_start: 0.8387 (pp30) cc_final: 0.8133 (pp30) REVERT: S 5 GLN cc_start: 0.8723 (mp10) cc_final: 0.8121 (mp10) outliers start: 13 outliers final: 10 residues processed: 105 average time/residue: 0.1807 time to fit residues: 26.5777 Evaluate side-chains 102 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 317 CYS Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 266 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 32 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 85 optimal weight: 0.0980 chunk 78 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 13 optimal weight: 0.0670 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 239 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 = 0.3574 r_free = 0.3574 target = 0.112194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.091725 restraints weight = 14631.585| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 3.59 r_work: 0.3167 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7614 Z= 0.110 Angle : 0.527 7.478 10385 Z= 0.278 Chirality : 0.042 0.161 1210 Planarity : 0.003 0.037 1294 Dihedral : 4.126 33.597 1059 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.24 % Favored : 96.66 % Rotamer: Outliers : 1.52 % Allowed : 18.73 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.27), residues: 958 helix: 1.97 (0.28), residues: 373 sheet: 0.74 (0.33), residues: 210 loop : -1.32 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.002 0.000 HIS A 362 PHE 0.012 0.001 PHE R 264 TYR 0.009 0.001 TYR N 95 ARG 0.009 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.04365 ( 370) hydrogen bonds : angle 3.90714 ( 1059) SS BOND : bond 0.00265 ( 3) SS BOND : angle 1.51856 ( 6) covalent geometry : bond 0.00249 ( 7610) covalent geometry : angle 0.52570 (10379) Misc. bond : bond 0.00032 ( 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 105 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7875 (mt-10) REVERT: A 293 LYS cc_start: 0.8261 (mmtt) cc_final: 0.8004 (mtpp) REVERT: B 175 GLN cc_start: 0.8403 (pp30) cc_final: 0.8146 (pp30) REVERT: G 41 CYS cc_start: 0.7273 (t) cc_final: 0.6367 (p) REVERT: S 5 GLN cc_start: 0.8670 (mp10) cc_final: 0.8083 (mp10) outliers start: 11 outliers final: 9 residues processed: 103 average time/residue: 0.1953 time to fit residues: 28.0112 Evaluate side-chains 104 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 239 GLN Chi-restraints excluded: chain R residue 266 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 6 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 54 optimal weight: 0.3980 chunk 43 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 14 optimal weight: 0.0270 chunk 77 optimal weight: 0.5980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 60 HIS R 239 GLN R 285 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.112601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.092253 restraints weight = 14487.673| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.53 r_work: 0.3190 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7614 Z= 0.109 Angle : 0.524 7.673 10385 Z= 0.277 Chirality : 0.042 0.162 1210 Planarity : 0.003 0.041 1294 Dihedral : 4.074 33.559 1059 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.24 % Favored : 96.66 % Rotamer: Outliers : 1.38 % Allowed : 18.73 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.28), residues: 958 helix: 2.02 (0.28), residues: 373 sheet: 0.84 (0.33), residues: 210 loop : -1.28 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.008 0.001 HIS A 220 PHE 0.012 0.001 PHE R 264 TYR 0.009 0.001 TYR N 95 ARG 0.009 0.000 ARG A 389 Details of bonding type rmsd hydrogen bonds : bond 0.04268 ( 370) hydrogen bonds : angle 3.88770 ( 1059) SS BOND : bond 0.00253 ( 3) SS BOND : angle 1.48788 ( 6) covalent geometry : bond 0.00243 ( 7610) covalent geometry : angle 0.52302 (10379) Misc. bond : bond 0.00026 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3797.65 seconds wall clock time: 67 minutes 32.46 seconds (4052.46 seconds total)