Starting phenix.real_space_refine on Wed Mar 12 10:15:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gdb_29945/03_2025/8gdb_29945_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gdb_29945/03_2025/8gdb_29945.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/8gdb_29945/03_2025/8gdb_29945.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gdb_29945/03_2025/8gdb_29945.map" model { file = "/net/cci-nas-00/data/ceres_data/8gdb_29945/03_2025/8gdb_29945_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gdb_29945/03_2025/8gdb_29945_neut.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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 4856 2.51 5 N 1336 2.21 5 O 1374 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 7612 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1751 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 8, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 115 Chain: "B" Number of atoms: 2475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2475 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 166 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 2, 'ASP:plan': 11, 'ASN%COO:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 105 Chain: "G" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 381 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "N" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 904 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "R" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2076 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 12, 'TRANS': 270} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 64 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'P2E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.06, per 1000 atoms: 0.66 Number of scatterers: 7612 At special positions: 0 Unit cell: (99.36, 99.36, 124.2, 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 46 16.00 O 1374 8.00 N 1336 7.00 C 4856 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 1.1 seconds 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 11 sheets defined 40.3% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 11 through 39 removed outlier: 3.781A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 58 removed outlier: 3.672A pdb=" N LYS A 58 " --> pdb=" O ASN A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 removed outlier: 3.767A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.672A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 350 removed outlier: 3.536A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 389 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.605A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.907A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.760A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 44 removed outlier: 3.550A pdb=" N ALA R 38 " --> pdb=" O GLY R 34 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE R 39 " --> pdb=" O ASN R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 50 removed outlier: 3.681A pdb=" N LYS R 50 " --> pdb=" O LYS R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 54 through 82 Proline residue: R 74 - end of helix removed outlier: 3.633A pdb=" N ILE R 77 " --> pdb=" O SER R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 123 removed outlier: 4.002A pdb=" N LEU R 91 " --> pdb=" O GLY R 87 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS R 92 " --> pdb=" O GLY R 88 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU R 93 " --> pdb=" O GLN R 89 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR R 94 " --> pdb=" O PRO R 90 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS R 123 " --> pdb=" O LEU R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 131 Processing helix chain 'R' and resid 132 through 153 removed outlier: 3.673A pdb=" N ALA R 136 " --> pdb=" O ASP R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 221 Processing helix chain 'R' and resid 267 through 298 Proline residue: R 287 - end of helix Processing helix chain 'R' and resid 309 through 330 Proline residue: R 322 - end of helix Proline residue: R 326 - end of helix removed outlier: 3.984A pdb=" N TYR R 329 " --> pdb=" O ASP R 325 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 344 removed outlier: 4.385A pdb=" N LYS R 339 " --> pdb=" O THR R 335 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.832A pdb=" N ASP A 223 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.644A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.717A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.860A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.432A 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: 3.607A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.072A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.531A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.795A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.514A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.790A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 162 through 163 396 hydrogen bonds defined for protein. 1155 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: 2.19 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1419 1.33 - 1.45: 1969 1.45 - 1.57: 4314 1.57 - 1.69: 0 1.69 - 1.81: 62 Bond restraints: 7764 Sorted by residual: bond pdb=" C1 P2E R 501 " pdb=" O2 P2E R 501 " ideal model delta sigma weight residual 1.250 1.306 -0.056 2.00e-02 2.50e+03 7.70e+00 bond pdb=" C1 P2E R 501 " pdb=" C2 P2E R 501 " ideal model delta sigma weight residual 1.539 1.499 0.040 2.00e-02 2.50e+03 3.94e+00 bond pdb=" C1 P2E R 501 " pdb=" O1 P2E R 501 " ideal model delta sigma weight residual 1.247 1.211 0.036 2.00e-02 2.50e+03 3.29e+00 bond pdb=" C ILE R 286 " pdb=" N PRO R 287 " ideal model delta sigma weight residual 1.335 1.359 -0.023 1.36e-02 5.41e+03 2.89e+00 bond pdb=" N PRO R 24 " pdb=" CD PRO R 24 " ideal model delta sigma weight residual 1.473 1.495 -0.022 1.40e-02 5.10e+03 2.50e+00 ... (remaining 7759 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 10119 1.71 - 3.41: 381 3.41 - 5.12: 57 5.12 - 6.82: 20 6.82 - 8.53: 7 Bond angle restraints: 10584 Sorted by residual: angle pdb=" C TYR A 360 " pdb=" N PRO A 361 " pdb=" CA PRO A 361 " ideal model delta sigma weight residual 119.76 125.82 -6.06 1.00e+00 1.00e+00 3.68e+01 angle pdb=" N GLN R 84 " pdb=" CA GLN R 84 " pdb=" C GLN R 84 " ideal model delta sigma weight residual 109.59 116.44 -6.85 1.47e+00 4.63e-01 2.17e+01 angle pdb=" N VAL R 75 " pdb=" CA VAL R 75 " pdb=" C VAL R 75 " ideal model delta sigma weight residual 110.30 114.06 -3.76 9.70e-01 1.06e+00 1.50e+01 angle pdb=" C GLU A 327 " pdb=" N PRO A 328 " pdb=" CA PRO A 328 " ideal model delta sigma weight residual 118.97 115.28 3.69 1.04e+00 9.25e-01 1.26e+01 angle pdb=" N LEU R 71 " pdb=" CA LEU R 71 " pdb=" C LEU R 71 " ideal model delta sigma weight residual 111.40 115.64 -4.24 1.22e+00 6.72e-01 1.21e+01 ... (remaining 10579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.78: 4234 19.78 - 39.55: 279 39.55 - 59.33: 36 59.33 - 79.10: 15 79.10 - 98.88: 5 Dihedral angle restraints: 4569 sinusoidal: 1557 harmonic: 3012 Sorted by residual: dihedral pdb=" CA LYS N 33 " pdb=" C LYS N 33 " pdb=" N MET N 34 " pdb=" CA MET N 34 " ideal model delta harmonic sigma weight residual 180.00 150.11 29.89 0 5.00e+00 4.00e-02 3.57e+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 180.00 155.87 24.13 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA LEU R 331 " pdb=" C LEU R 331 " pdb=" N LEU R 332 " pdb=" CA LEU R 332 " ideal model delta harmonic sigma weight residual 180.00 159.56 20.44 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 4566 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 848 0.045 - 0.090: 280 0.090 - 0.136: 97 0.136 - 0.181: 17 0.181 - 0.226: 7 Chirality restraints: 1249 Sorted by residual: chirality pdb=" CB VAL R 320 " pdb=" CA VAL R 320 " pdb=" CG1 VAL R 320 " pdb=" CG2 VAL R 320 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C8 P2E R 501 " pdb=" C12 P2E R 501 " pdb=" C7 P2E R 501 " pdb=" C9 P2E R 501 " both_signs ideal model delta sigma weight residual False -2.53 -2.75 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA TYR B 59 " pdb=" N TYR B 59 " pdb=" C TYR B 59 " pdb=" CB TYR B 59 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1246 not shown) Planarity restraints: 1352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP R 325 " 0.043 5.00e-02 4.00e+02 6.42e-02 6.60e+00 pdb=" N PRO R 326 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO R 326 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 326 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE R 23 " -0.043 5.00e-02 4.00e+02 6.38e-02 6.51e+00 pdb=" N PRO R 24 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO R 24 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 24 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.041 5.00e-02 4.00e+02 6.25e-02 6.25e+00 pdb=" N PRO B 236 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.035 5.00e-02 4.00e+02 ... (remaining 1349 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1642 2.78 - 3.31: 6632 3.31 - 3.84: 12057 3.84 - 4.37: 13731 4.37 - 4.90: 25174 Nonbonded interactions: 59236 Sorted by model distance: nonbonded pdb=" OE2 GLU A 230 " pdb=" NH1 ARG A 232 " model vdw 2.255 3.120 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.288 3.040 nonbonded pdb=" OG1 THR R 64 " pdb=" OH TYR R 144 " model vdw 2.311 3.040 nonbonded pdb=" OD1 ASN A 292 " pdb=" OG1 THR A 364 " model vdw 2.316 3.040 nonbonded pdb=" O LEU R 67 " pdb=" CD1 LEU R 71 " model vdw 2.319 3.460 ... (remaining 59231 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.580 Find NCS groups from input model: 0.060 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: 0.010 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: 26.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7764 Z= 0.296 Angle : 0.796 8.527 10584 Z= 0.467 Chirality : 0.052 0.226 1249 Planarity : 0.006 0.064 1352 Dihedral : 14.282 98.876 2615 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.28 % Allowed : 1.11 % Favored : 98.61 % 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: -0.50 (0.25), residues: 1021 helix: 1.06 (0.26), residues: 379 sheet: -0.12 (0.35), residues: 229 loop : -1.79 (0.27), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 339 HIS 0.007 0.001 HIS A 357 PHE 0.017 0.002 PHE B 151 TYR 0.025 0.002 TYR N 60 ARG 0.010 0.001 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.824 Fit side-chains REVERT: A 320 THR cc_start: 0.8766 (t) cc_final: 0.8446 (m) outliers start: 2 outliers final: 2 residues processed: 132 average time/residue: 0.2660 time to fit residues: 46.1173 Evaluate side-chains 110 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain R residue 333 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 35 GLN A 218 ASN A 279 ASN A 294 GLN B 175 GLN R 216 GLN R 269 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.114857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.089213 restraints weight = 10714.322| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 2.04 r_work: 0.2804 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7764 Z= 0.251 Angle : 0.565 5.327 10584 Z= 0.304 Chirality : 0.044 0.142 1249 Planarity : 0.004 0.050 1352 Dihedral : 7.612 60.529 1150 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.11 % Allowed : 6.93 % Favored : 91.96 % 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: 0.28 (0.27), residues: 1021 helix: 2.12 (0.27), residues: 389 sheet: -0.23 (0.34), residues: 247 loop : -1.59 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 174 HIS 0.007 0.001 HIS A 357 PHE 0.016 0.001 PHE B 151 TYR 0.011 0.001 TYR R 130 ARG 0.004 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.857 Fit side-chains REVERT: B 78 LYS cc_start: 0.9060 (tppt) cc_final: 0.8562 (tptt) REVERT: R 116 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8566 (tm-30) outliers start: 8 outliers final: 5 residues processed: 120 average time/residue: 0.2777 time to fit residues: 43.0780 Evaluate side-chains 112 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 40 VAL Chi-restraints excluded: chain R residue 290 VAL Chi-restraints excluded: chain R residue 331 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 43 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 53 optimal weight: 0.0270 chunk 11 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 35 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.117292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.091391 restraints weight = 10844.289| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.07 r_work: 0.2853 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7764 Z= 0.170 Angle : 0.501 5.870 10584 Z= 0.267 Chirality : 0.042 0.136 1249 Planarity : 0.003 0.047 1352 Dihedral : 6.291 59.634 1145 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.39 % Allowed : 9.02 % Favored : 89.60 % 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: 0.63 (0.27), residues: 1021 helix: 2.54 (0.27), residues: 388 sheet: -0.07 (0.34), residues: 243 loop : -1.52 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 85 HIS 0.005 0.001 HIS A 357 PHE 0.011 0.001 PHE R 102 TYR 0.010 0.001 TYR R 130 ARG 0.003 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 1.643 Fit side-chains revert: symmetry clash REVERT: A 378 ASP cc_start: 0.8819 (m-30) cc_final: 0.8616 (m-30) REVERT: B 78 LYS cc_start: 0.9054 (tppt) cc_final: 0.8575 (tptt) REVERT: N 93 VAL cc_start: 0.8821 (t) cc_final: 0.8605 (t) REVERT: R 81 MET cc_start: 0.7953 (mmm) cc_final: 0.7726 (mtm) REVERT: R 116 GLU cc_start: 0.8977 (tm-30) cc_final: 0.8551 (tm-30) REVERT: R 219 ARG cc_start: 0.7525 (ttp80) cc_final: 0.7275 (ttp80) outliers start: 10 outliers final: 7 residues processed: 119 average time/residue: 0.3158 time to fit residues: 48.6901 Evaluate side-chains 119 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 43 CYS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 79 THR Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 331 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 60 optimal weight: 0.0570 chunk 47 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 43 optimal weight: 0.0000 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 overall best weight: 0.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 35 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.120005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.094544 restraints weight = 10617.595| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.02 r_work: 0.2866 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7764 Z= 0.145 Angle : 0.472 5.304 10584 Z= 0.253 Chirality : 0.041 0.135 1249 Planarity : 0.003 0.045 1352 Dihedral : 5.637 53.456 1145 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.97 % Allowed : 10.40 % Favored : 88.63 % 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: 0.87 (0.28), residues: 1021 helix: 2.79 (0.27), residues: 388 sheet: -0.04 (0.34), residues: 250 loop : -1.38 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 85 HIS 0.004 0.001 HIS A 357 PHE 0.011 0.001 PHE R 102 TYR 0.012 0.001 TYR N 60 ARG 0.003 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.812 Fit side-chains REVERT: B 78 LYS cc_start: 0.9055 (tppt) cc_final: 0.8612 (tptt) REVERT: N 93 VAL cc_start: 0.8804 (t) cc_final: 0.8592 (t) REVERT: R 116 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8649 (tm-30) outliers start: 7 outliers final: 6 residues processed: 124 average time/residue: 0.2385 time to fit residues: 38.0882 Evaluate side-chains 120 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 114 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 331 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 chunk 87 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 35 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.116931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.091028 restraints weight = 10760.684| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.07 r_work: 0.2851 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7764 Z= 0.178 Angle : 0.492 6.369 10584 Z= 0.262 Chirality : 0.042 0.134 1249 Planarity : 0.003 0.045 1352 Dihedral : 5.633 49.077 1145 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.39 % Allowed : 10.26 % Favored : 88.35 % 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: 1.00 (0.28), residues: 1021 helix: 2.85 (0.27), residues: 388 sheet: 0.11 (0.35), residues: 243 loop : -1.31 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 85 HIS 0.005 0.001 HIS A 357 PHE 0.014 0.001 PHE B 151 TYR 0.012 0.001 TYR N 60 ARG 0.005 0.000 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.877 Fit side-chains REVERT: B 78 LYS cc_start: 0.9070 (tppt) cc_final: 0.8641 (tptt) REVERT: N 93 VAL cc_start: 0.8801 (t) cc_final: 0.8586 (t) outliers start: 10 outliers final: 9 residues processed: 117 average time/residue: 0.2460 time to fit residues: 37.3187 Evaluate side-chains 116 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 331 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 16 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 35 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.121184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.095855 restraints weight = 10579.072| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.00 r_work: 0.2865 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7764 Z= 0.148 Angle : 0.467 5.367 10584 Z= 0.250 Chirality : 0.041 0.135 1249 Planarity : 0.003 0.044 1352 Dihedral : 5.539 51.608 1145 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.66 % Allowed : 10.96 % Favored : 87.38 % 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: 1.03 (0.28), residues: 1021 helix: 2.92 (0.27), residues: 388 sheet: 0.20 (0.35), residues: 230 loop : -1.36 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 85 HIS 0.004 0.001 HIS A 357 PHE 0.011 0.001 PHE R 102 TYR 0.013 0.001 TYR N 60 ARG 0.003 0.000 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.826 Fit side-chains REVERT: A 378 ASP cc_start: 0.8821 (m-30) cc_final: 0.8613 (m-30) REVERT: B 78 LYS cc_start: 0.9085 (tppt) cc_final: 0.8658 (tptt) REVERT: B 262 MET cc_start: 0.9100 (ttp) cc_final: 0.8855 (ttm) REVERT: N 93 VAL cc_start: 0.8816 (t) cc_final: 0.8614 (t) REVERT: R 219 ARG cc_start: 0.7641 (ttp80) cc_final: 0.7410 (ttp80) outliers start: 12 outliers final: 10 residues processed: 117 average time/residue: 0.2248 time to fit residues: 34.7883 Evaluate side-chains 118 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 43 CYS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 332 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 27 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.116832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.090952 restraints weight = 10740.299| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.07 r_work: 0.2843 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7764 Z= 0.175 Angle : 0.483 7.651 10584 Z= 0.259 Chirality : 0.041 0.134 1249 Planarity : 0.003 0.044 1352 Dihedral : 5.151 37.839 1145 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.08 % Allowed : 11.65 % Favored : 86.27 % 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: 1.03 (0.27), residues: 1021 helix: 2.93 (0.27), residues: 388 sheet: 0.38 (0.36), residues: 220 loop : -1.45 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 85 HIS 0.005 0.001 HIS A 357 PHE 0.013 0.001 PHE B 151 TYR 0.013 0.001 TYR N 60 ARG 0.002 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.840 Fit side-chains REVERT: A 378 ASP cc_start: 0.8845 (m-30) cc_final: 0.8624 (m-30) REVERT: B 78 LYS cc_start: 0.9071 (tppt) cc_final: 0.8648 (tptt) REVERT: B 262 MET cc_start: 0.9120 (ttp) cc_final: 0.8873 (ttm) REVERT: N 93 VAL cc_start: 0.8812 (t) cc_final: 0.8592 (t) REVERT: R 116 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8672 (tm-30) outliers start: 15 outliers final: 13 residues processed: 122 average time/residue: 0.2291 time to fit residues: 36.6035 Evaluate side-chains 125 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 43 CYS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 311 ASP Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 332 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 36 optimal weight: 0.4980 chunk 32 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 15 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.117926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.092246 restraints weight = 10758.190| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.03 r_work: 0.2847 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7764 Z= 0.173 Angle : 0.480 6.874 10584 Z= 0.258 Chirality : 0.041 0.134 1249 Planarity : 0.003 0.044 1352 Dihedral : 5.034 46.722 1145 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.80 % Allowed : 12.34 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.10 (0.27), residues: 1021 helix: 2.95 (0.27), residues: 388 sheet: 0.45 (0.36), residues: 218 loop : -1.39 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 85 HIS 0.005 0.001 HIS A 357 PHE 0.013 0.001 PHE B 151 TYR 0.012 0.001 TYR N 60 ARG 0.003 0.000 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 1.409 Fit side-chains REVERT: A 378 ASP cc_start: 0.8842 (m-30) cc_final: 0.8640 (m-30) REVERT: B 78 LYS cc_start: 0.9073 (tppt) cc_final: 0.8648 (tptt) REVERT: B 262 MET cc_start: 0.9096 (ttp) cc_final: 0.8857 (ttm) REVERT: N 93 VAL cc_start: 0.8840 (t) cc_final: 0.8631 (t) REVERT: R 116 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8671 (tm-30) outliers start: 13 outliers final: 11 residues processed: 124 average time/residue: 0.2846 time to fit residues: 46.1560 Evaluate side-chains 122 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain R residue 43 CYS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 311 ASP Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 332 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 56 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 33 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 0.0970 chunk 35 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 47 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 35 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.117995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.091981 restraints weight = 10969.758| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.10 r_work: 0.2857 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7764 Z= 0.142 Angle : 0.465 7.072 10584 Z= 0.250 Chirality : 0.041 0.173 1249 Planarity : 0.003 0.044 1352 Dihedral : 4.915 45.002 1145 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.53 % Allowed : 12.90 % Favored : 85.58 % 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: 1.13 (0.28), residues: 1021 helix: 2.98 (0.27), residues: 389 sheet: 0.31 (0.36), residues: 228 loop : -1.32 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 85 HIS 0.004 0.001 HIS A 357 PHE 0.010 0.001 PHE R 102 TYR 0.014 0.001 TYR N 60 ARG 0.003 0.000 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.910 Fit side-chains REVERT: A 378 ASP cc_start: 0.8884 (m-30) cc_final: 0.8618 (m-30) REVERT: B 78 LYS cc_start: 0.9070 (tppt) cc_final: 0.8645 (tptt) REVERT: B 262 MET cc_start: 0.9085 (ttp) cc_final: 0.8855 (ttm) REVERT: N 93 VAL cc_start: 0.8804 (t) cc_final: 0.8590 (t) REVERT: R 116 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8700 (tm-30) outliers start: 11 outliers final: 9 residues processed: 115 average time/residue: 0.2262 time to fit residues: 34.0104 Evaluate side-chains 116 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 311 ASP Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 332 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.8980 chunk 39 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 66 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.117282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.091306 restraints weight = 10864.195| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.08 r_work: 0.2851 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7764 Z= 0.153 Angle : 0.470 6.801 10584 Z= 0.253 Chirality : 0.041 0.163 1249 Planarity : 0.003 0.044 1352 Dihedral : 4.908 48.171 1145 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.80 % Allowed : 12.62 % Favored : 85.58 % 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: 1.14 (0.27), residues: 1021 helix: 2.99 (0.27), residues: 389 sheet: 0.47 (0.36), residues: 218 loop : -1.38 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 85 HIS 0.004 0.001 HIS A 357 PHE 0.011 0.001 PHE B 151 TYR 0.014 0.001 TYR N 60 ARG 0.006 0.000 ARG R 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.761 Fit side-chains REVERT: B 78 LYS cc_start: 0.9062 (tppt) cc_final: 0.8643 (tptt) REVERT: B 262 MET cc_start: 0.9106 (ttp) cc_final: 0.8880 (ttm) REVERT: N 93 VAL cc_start: 0.8809 (t) cc_final: 0.8593 (t) REVERT: R 116 GLU cc_start: 0.9068 (tm-30) cc_final: 0.8678 (tm-30) outliers start: 13 outliers final: 11 residues processed: 118 average time/residue: 0.2228 time to fit residues: 34.3354 Evaluate side-chains 119 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 174 TRP Chi-restraints excluded: chain R residue 311 ASP Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 331 LEU Chi-restraints excluded: chain R residue 332 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 86 optimal weight: 0.0980 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.124722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.099770 restraints weight = 10586.377| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.96 r_work: 0.2887 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7764 Z= 0.137 Angle : 0.456 6.567 10584 Z= 0.245 Chirality : 0.041 0.163 1249 Planarity : 0.003 0.044 1352 Dihedral : 4.882 54.257 1145 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.66 % Allowed : 12.76 % Favored : 85.58 % 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: 1.13 (0.28), residues: 1021 helix: 3.01 (0.27), residues: 389 sheet: 0.35 (0.36), residues: 222 loop : -1.34 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 85 HIS 0.004 0.001 HIS A 357 PHE 0.011 0.001 PHE R 102 TYR 0.014 0.001 TYR N 60 ARG 0.003 0.000 ARG R 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4762.29 seconds wall clock time: 85 minutes 18.63 seconds (5118.63 seconds total)