Starting phenix.real_space_refine on Thu Jul 2 19:52:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hk2_34842/07_2026/8hk2_34842.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hk2_34842/07_2026/8hk2_34842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8hk2_34842/07_2026/8hk2_34842.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hk2_34842/07_2026/8hk2_34842.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hk2_34842/07_2026/8hk2_34842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hk2_34842/07_2026/8hk2_34842.map" model { file = "/net/cci-nas-00/data/ceres_data/8hk2_34842/07_2026/8hk2_34842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hk2_34842/07_2026/8hk2_34842.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.050 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 517 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 76 5.16 5 C 6134 2.51 5 N 1609 2.21 5 O 1729 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9548 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2234 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 268} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1816 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "C" Number of atoms: 2580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2580 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 553 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 4, 'ASP:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 438 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 54} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 176 Unusual residues: {'CLR': 5, 'PLM': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 1.54, per 1000 atoms: 0.16 Number of scatterers: 9548 At special positions: 0 Unit cell: (107.12, 115.36, 150.792, 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 76 16.00 O 1729 8.00 N 1609 7.00 C 6134 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 95 " - pdb=" SG CYS A 172 " distance=1.69 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 149 " distance=2.09 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 49 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 56 " 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: 0.88 Conformation dependent library (CDL) restraints added in 228.5 milliseconds 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2268 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 14 sheets defined 40.7% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 20 through 51 Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 55 through 84 removed outlier: 3.623A pdb=" N ILE A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TRP A 60 " --> pdb=" O VAL A 56 " (cutoff:3.500A) Proline residue: A 76 - end of helix Processing helix chain 'A' and resid 93 through 126 Proline residue: A 99 - end of helix Processing helix chain 'A' and resid 126 through 134 removed outlier: 3.613A pdb=" N ASN A 132 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 154 Processing helix chain 'A' and resid 154 through 161 removed outlier: 3.726A pdb=" N PHE A 158 " --> pdb=" O CYS A 154 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 161 " --> pdb=" O VAL A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 345 removed outlier: 3.912A pdb=" N ILE A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 365 Processing helix chain 'A' and resid 373 through 402 Proline residue: A 392 - end of helix removed outlier: 3.511A pdb=" N LEU A 401 " --> pdb=" O GLY A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 436 removed outlier: 3.974A pdb=" N HIS A 418 " --> pdb=" O MET A 414 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) Proline residue: A 432 - end of helix Processing helix chain 'A' and resid 439 through 454 Processing helix chain 'B' and resid 6 through 32 Processing helix chain 'B' and resid 45 through 55 removed outlier: 3.785A pdb=" N LYS B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 removed outlier: 3.655A pdb=" N LYS B 210 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU B 216 " --> pdb=" O HIS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 Processing helix chain 'B' and resid 256 through 260 removed outlier: 4.195A pdb=" N THR B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 281 Processing helix chain 'B' and resid 282 through 286 removed outlier: 4.093A pdb=" N ILE B 285 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 309 Processing helix chain 'B' and resid 327 through 352 removed outlier: 3.990A pdb=" N ASN B 331 " --> pdb=" O THR B 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 26 Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'D' and resid 2 through 13 removed outlier: 4.461A pdb=" N GLY D 13 " --> pdb=" O MET D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 27 Processing helix chain 'D' and resid 36 through 41 Processing helix chain 'D' and resid 49 through 73 removed outlier: 3.600A pdb=" N HIS D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N HIS D 72 " --> pdb=" O ALA D 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'H' and resid 220 through 224 removed outlier: 3.700A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 162 through 166 removed outlier: 3.828A pdb=" N HIS A 169 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 185 through 190 removed outlier: 3.680A pdb=" N VAL B 185 " --> pdb=" O ASP B 200 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP B 200 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR B 187 " --> pdb=" O MET B 198 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET B 198 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE B 189 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B 34 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N PHE B 199 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU B 36 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYS B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE B 222 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU B 39 " --> pdb=" O CYS B 224 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N ALA B 226 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.686A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 7.046A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.718A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.464A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 4.085A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 276 through 278 removed outlier: 6.089A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.113A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.113A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 140 through 142 Processing sheet with id=AB5, first strand: chain 'H' and resid 146 through 148 removed outlier: 6.629A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1365 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.05 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1547 1.32 - 1.45: 2653 1.45 - 1.58: 5445 1.58 - 1.71: 0 1.71 - 1.83: 107 Bond restraints: 9752 Sorted by residual: bond pdb=" CA SER D 35 " pdb=" C SER D 35 " ideal model delta sigma weight residual 1.523 1.433 0.090 1.34e-02 5.57e+03 4.51e+01 bond pdb=" CA ASN D 30 " pdb=" C ASN D 30 " ideal model delta sigma weight residual 1.525 1.456 0.069 1.04e-02 9.25e+03 4.41e+01 bond pdb=" CA ARG B 21 " pdb=" C ARG B 21 " ideal model delta sigma weight residual 1.524 1.447 0.077 1.24e-02 6.50e+03 3.85e+01 bond pdb=" CA ARG D 64 " pdb=" C ARG D 64 " ideal model delta sigma weight residual 1.522 1.445 0.077 1.39e-02 5.18e+03 3.10e+01 bond pdb=" CA GLU D 29 " pdb=" C GLU D 29 " ideal model delta sigma weight residual 1.528 1.453 0.075 1.38e-02 5.25e+03 2.99e+01 ... (remaining 9747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 12826 2.74 - 5.48: 337 5.48 - 8.22: 48 8.22 - 10.95: 13 10.95 - 13.69: 2 Bond angle restraints: 13226 Sorted by residual: angle pdb=" N GLN D 3 " pdb=" CA GLN D 3 " pdb=" C GLN D 3 " ideal model delta sigma weight residual 112.54 98.85 13.69 1.22e+00 6.72e-01 1.26e+02 angle pdb=" N ARG D 64 " pdb=" CA ARG D 64 " pdb=" C ARG D 64 " ideal model delta sigma weight residual 112.89 102.64 10.25 1.24e+00 6.50e-01 6.83e+01 angle pdb=" N PRO D 31 " pdb=" CA PRO D 31 " pdb=" C PRO D 31 " ideal model delta sigma weight residual 113.57 103.08 10.49 1.31e+00 5.83e-01 6.41e+01 angle pdb=" N THR D 5 " pdb=" CA THR D 5 " pdb=" C THR D 5 " ideal model delta sigma weight residual 111.36 102.75 8.61 1.09e+00 8.42e-01 6.24e+01 angle pdb=" N CYS C 148 " pdb=" CA CYS C 148 " pdb=" C CYS C 148 " ideal model delta sigma weight residual 108.13 119.72 -11.59 1.72e+00 3.38e-01 4.54e+01 ... (remaining 13221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.33: 5574 18.33 - 36.66: 148 36.66 - 54.98: 30 54.98 - 73.31: 10 73.31 - 91.64: 2 Dihedral angle restraints: 5764 sinusoidal: 2258 harmonic: 3506 Sorted by residual: dihedral pdb=" C PHE D 34 " pdb=" N PHE D 34 " pdb=" CA PHE D 34 " pdb=" CB PHE D 34 " ideal model delta harmonic sigma weight residual -122.60 -143.57 20.97 0 2.50e+00 1.60e-01 7.03e+01 dihedral pdb=" N PHE D 34 " pdb=" C PHE D 34 " pdb=" CA PHE D 34 " pdb=" CB PHE D 34 " ideal model delta harmonic sigma weight residual 122.80 142.89 -20.09 0 2.50e+00 1.60e-01 6.46e+01 dihedral pdb=" CB CYS C 121 " pdb=" SG CYS C 121 " pdb=" SG CYS C 149 " pdb=" CB CYS C 149 " ideal model delta sinusoidal sigma weight residual 93.00 150.30 -57.30 1 1.00e+01 1.00e-02 4.41e+01 ... (remaining 5761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.190: 1493 0.190 - 0.380: 26 0.380 - 0.570: 4 0.570 - 0.761: 0 0.761 - 0.951: 2 Chirality restraints: 1525 Sorted by residual: chirality pdb=" CA PHE D 34 " pdb=" N PHE D 34 " pdb=" C PHE D 34 " pdb=" CB PHE D 34 " both_signs ideal model delta sigma weight residual False 2.51 1.56 0.95 2.00e-01 2.50e+01 2.26e+01 chirality pdb=" CA LEU D 63 " pdb=" N LEU D 63 " pdb=" C LEU D 63 " pdb=" CB LEU D 63 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.46e+01 chirality pdb=" CA CYS A 172 " pdb=" N CYS A 172 " pdb=" C CYS A 172 " pdb=" CB CYS A 172 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.25e+00 ... (remaining 1522 not shown) Planarity restraints: 1634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 94 " -0.023 2.00e-02 2.50e+03 4.78e-02 2.28e+01 pdb=" C LEU A 94 " 0.083 2.00e-02 2.50e+03 pdb=" O LEU A 94 " -0.031 2.00e-02 2.50e+03 pdb=" N CYS A 95 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 6 " -0.017 2.00e-02 2.50e+03 3.47e-02 1.21e+01 pdb=" C GLN C 6 " 0.060 2.00e-02 2.50e+03 pdb=" O GLN C 6 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU C 7 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET H 230 " -0.016 2.00e-02 2.50e+03 3.37e-02 1.13e+01 pdb=" C MET H 230 " 0.058 2.00e-02 2.50e+03 pdb=" O MET H 230 " -0.022 2.00e-02 2.50e+03 pdb=" N GLN H 231 " -0.020 2.00e-02 2.50e+03 ... (remaining 1631 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 165 2.67 - 3.23: 8329 3.23 - 3.79: 14560 3.79 - 4.34: 19417 4.34 - 4.90: 32653 Nonbonded interactions: 75124 Sorted by model distance: nonbonded pdb=" NZ LYS A 96 " pdb=" O ARG A 161 " model vdw 2.114 3.120 nonbonded pdb=" OG SER C 161 " pdb=" OD1 ASP C 163 " model vdw 2.235 3.040 nonbonded pdb=" OE2 GLU B 8 " pdb=" OH TYR H 175 " model vdw 2.242 3.040 nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.265 3.040 nonbonded pdb=" O THR A 165 " pdb=" OG1 THR A 165 " model vdw 2.272 3.040 ... (remaining 75119 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.260 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 : 0.008 0.341 9756 Z= 0.453 Angle : 1.118 36.524 13234 Z= 0.640 Chirality : 0.076 0.951 1525 Planarity : 0.007 0.055 1634 Dihedral : 9.666 91.640 3484 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.34 % Allowed : 2.52 % Favored : 97.14 % Rotamer: Outliers : 0.79 % Allowed : 2.87 % Favored : 96.34 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.24), residues: 1190 helix: 1.62 (0.24), residues: 465 sheet: 0.52 (0.29), residues: 306 loop : -1.35 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 67 TYR 0.016 0.002 TYR H 190 PHE 0.038 0.003 PHE A 396 TRP 0.039 0.003 TRP H 111 HIS 0.007 0.002 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00682 / 0.42 ( 9752) covalent geometry : angle 1.06047 / 0.62 (13226) SS BOND : bond 0.17336 / 9.10 ( 4) SS BOND : angle 14.40283 / 8.49 ( 8) hydrogen bonds : bond 0.13697 / 8.88 ( 481) hydrogen bonds : angle 6.12574 / 4.54 ( 1365) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 299 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8681 (tt) cc_final: 0.8471 (tm) REVERT: A 433 PHE cc_start: 0.8735 (m-80) cc_final: 0.8523 (m-80) REVERT: B 261 ASP cc_start: 0.6925 (t70) cc_final: 0.6698 (t0) REVERT: B 295 THR cc_start: 0.8142 (m) cc_final: 0.7932 (p) REVERT: C 74 SER cc_start: 0.7764 (p) cc_final: 0.7339 (p) REVERT: C 258 ASP cc_start: 0.7317 (t0) cc_final: 0.7072 (t0) REVERT: H 223 ASP cc_start: 0.8225 (m-30) cc_final: 0.7959 (m-30) REVERT: H 238 THR cc_start: 0.8876 (m) cc_final: 0.8635 (p) outliers start: 8 outliers final: 6 residues processed: 304 average time/residue: 0.4096 time to fit residues: 133.9872 Evaluate side-chains 231 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 225 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 1 SER Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 34 PHE Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 63 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.0010 chunk 51 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 213 HIS B 244 HIS B 269 ASN C 88 ASN C 142 HIS C 155 ASN C 176 GLN C 220 GLN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.110426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.097844 restraints weight = 16419.721| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.09 r_work: 0.3339 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9756 Z= 0.131 Angle : 0.578 8.930 13234 Z= 0.300 Chirality : 0.041 0.137 1525 Planarity : 0.005 0.050 1634 Dihedral : 5.617 59.097 1383 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.26 % Favored : 98.66 % Rotamer: Outliers : 3.07 % Allowed : 14.75 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.24), residues: 1190 helix: 2.43 (0.24), residues: 461 sheet: 0.71 (0.29), residues: 303 loop : -0.99 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 28 TYR 0.016 0.001 TYR H 190 PHE 0.016 0.002 PHE H 80 TRP 0.014 0.001 TRP H 111 HIS 0.005 0.001 HIS C 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 9752) covalent geometry : angle 0.57705 / 0.30 (13226) SS BOND : bond 0.00613 / 0.31 ( 4) SS BOND : angle 1.16538 / 0.74 ( 8) hydrogen bonds : bond 0.04117 / 2.69 ( 481) hydrogen bonds : angle 4.69987 / 3.53 ( 1365) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 236 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8273 (mm) REVERT: A 35 LEU cc_start: 0.8878 (mm) cc_final: 0.8606 (mm) REVERT: A 171 ARG cc_start: 0.7391 (mtt-85) cc_final: 0.7023 (mtt-85) REVERT: A 433 PHE cc_start: 0.9123 (m-80) cc_final: 0.8892 (m-80) REVERT: B 261 ASP cc_start: 0.7948 (t70) cc_final: 0.7618 (t0) REVERT: B 295 THR cc_start: 0.8214 (m) cc_final: 0.7799 (p) REVERT: C 74 SER cc_start: 0.8354 (p) cc_final: 0.8051 (p) REVERT: C 161 SER cc_start: 0.8568 (p) cc_final: 0.8352 (p) REVERT: D 18 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6520 (mp0) REVERT: D 63 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8473 (tm) outliers start: 31 outliers final: 9 residues processed: 245 average time/residue: 0.4229 time to fit residues: 111.2947 Evaluate side-chains 234 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 222 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 34 PHE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 220 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 5 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 0.0010 chunk 109 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 33 optimal weight: 0.0770 chunk 45 optimal weight: 2.9990 overall best weight: 0.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 176 GLN C 230 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.114061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.101265 restraints weight = 16312.569| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.18 r_work: 0.3318 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9756 Z= 0.118 Angle : 0.553 8.535 13234 Z= 0.279 Chirality : 0.040 0.132 1525 Planarity : 0.004 0.044 1634 Dihedral : 5.379 58.650 1380 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.51 % Favored : 98.40 % Rotamer: Outliers : 4.16 % Allowed : 15.15 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.24), residues: 1190 helix: 2.52 (0.24), residues: 468 sheet: 0.80 (0.29), residues: 301 loop : -0.96 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 28 TYR 0.014 0.001 TYR H 190 PHE 0.013 0.001 PHE H 80 TRP 0.018 0.001 TRP C 82 HIS 0.003 0.001 HIS A 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 9752) covalent geometry : angle 0.55093 / 0.28 (13226) SS BOND : bond 0.00874 / 0.42 ( 4) SS BOND : angle 1.84312 / 1.06 ( 8) hydrogen bonds : bond 0.03688 / 2.45 ( 481) hydrogen bonds : angle 4.36387 / 3.28 ( 1365) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 227 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 27 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.7986 (mpp) REVERT: A 367 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8300 (ttp-170) REVERT: A 433 PHE cc_start: 0.9125 (m-80) cc_final: 0.8858 (m-80) REVERT: B 198 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6476 (tpt) REVERT: B 261 ASP cc_start: 0.8012 (t70) cc_final: 0.7635 (t0) REVERT: B 295 THR cc_start: 0.8213 (m) cc_final: 0.7764 (p) REVERT: C 96 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8409 (mtp85) REVERT: C 254 ASP cc_start: 0.7858 (m-30) cc_final: 0.7649 (m-30) REVERT: D 18 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6435 (mp0) REVERT: D 63 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8467 (tm) REVERT: H 147 VAL cc_start: 0.8402 (OUTLIER) cc_final: 0.8095 (m) outliers start: 42 outliers final: 17 residues processed: 241 average time/residue: 0.4258 time to fit residues: 110.3603 Evaluate side-chains 245 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 221 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 34 PHE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 220 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 117 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 36 optimal weight: 0.0970 chunk 41 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 213 HIS C 176 GLN H 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.113048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.100432 restraints weight = 16335.881| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.11 r_work: 0.3306 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9756 Z= 0.122 Angle : 0.539 7.874 13234 Z= 0.274 Chirality : 0.039 0.130 1525 Planarity : 0.004 0.045 1634 Dihedral : 5.238 59.730 1380 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 4.75 % Allowed : 16.14 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.25), residues: 1190 helix: 2.49 (0.24), residues: 472 sheet: 0.90 (0.30), residues: 296 loop : -0.77 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 28 TYR 0.015 0.001 TYR H 190 PHE 0.016 0.001 PHE A 430 TRP 0.013 0.001 TRP C 82 HIS 0.004 0.001 HIS A 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 9752) covalent geometry : angle 0.53762 / 0.27 (13226) SS BOND : bond 0.00616 / 0.30 ( 4) SS BOND : angle 1.89984 / 1.06 ( 8) hydrogen bonds : bond 0.03548 / 2.35 ( 481) hydrogen bonds : angle 4.25855 / 3.21 ( 1365) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 225 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.7981 (mpp) REVERT: A 35 LEU cc_start: 0.8865 (mm) cc_final: 0.8595 (mm) REVERT: A 76 PRO cc_start: 0.8665 (Cg_exo) cc_final: 0.8419 (Cg_endo) REVERT: A 367 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8181 (ttp-170) REVERT: B 4 THR cc_start: 0.7927 (p) cc_final: 0.7699 (t) REVERT: B 261 ASP cc_start: 0.8036 (t70) cc_final: 0.7608 (t0) REVERT: B 273 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7662 (tt) REVERT: B 295 THR cc_start: 0.8205 (m) cc_final: 0.7739 (p) REVERT: C 96 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8414 (mtp85) REVERT: C 228 ASP cc_start: 0.8195 (m-30) cc_final: 0.7960 (p0) REVERT: D 18 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6407 (mp0) REVERT: D 28 ARG cc_start: 0.8171 (mmm160) cc_final: 0.7494 (mmt90) REVERT: H 91 THR cc_start: 0.8689 (OUTLIER) cc_final: 0.8462 (p) REVERT: H 147 VAL cc_start: 0.8422 (OUTLIER) cc_final: 0.8090 (m) outliers start: 48 outliers final: 18 residues processed: 245 average time/residue: 0.4365 time to fit residues: 114.6493 Evaluate side-chains 238 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 213 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 367 ARG Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 34 PHE Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 220 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 109 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 427 ASN C 17 GLN C 75 GLN C 176 GLN H 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.110448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.097743 restraints weight = 16350.287| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.09 r_work: 0.3261 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9756 Z= 0.161 Angle : 0.575 7.717 13234 Z= 0.292 Chirality : 0.041 0.131 1525 Planarity : 0.004 0.048 1634 Dihedral : 5.063 46.664 1378 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.86 % Allowed : 18.12 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.25), residues: 1190 helix: 2.43 (0.24), residues: 470 sheet: 0.77 (0.29), residues: 298 loop : -0.78 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 8 TYR 0.017 0.002 TYR H 190 PHE 0.020 0.002 PHE D 34 TRP 0.015 0.001 TRP C 82 HIS 0.005 0.001 HIS C 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 9752) covalent geometry : angle 0.57192 / 0.29 (13226) SS BOND : bond 0.00962 / 0.46 ( 4) SS BOND : angle 2.29377 / 1.28 ( 8) hydrogen bonds : bond 0.03847 / 2.57 ( 481) hydrogen bonds : angle 4.29053 / 3.24 ( 1365) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 227 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 27 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8243 (mpp) REVERT: A 35 LEU cc_start: 0.8884 (mm) cc_final: 0.8601 (mm) REVERT: A 377 ARG cc_start: 0.7697 (ttm110) cc_final: 0.7352 (mtp-110) REVERT: B 261 ASP cc_start: 0.8111 (t70) cc_final: 0.7672 (t0) REVERT: B 273 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7703 (tt) REVERT: B 295 THR cc_start: 0.8233 (m) cc_final: 0.7788 (p) REVERT: B 310 LEU cc_start: 0.8994 (mt) cc_final: 0.8694 (mp) REVERT: C 96 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8443 (mtp85) REVERT: C 228 ASP cc_start: 0.8193 (m-30) cc_final: 0.7872 (OUTLIER) REVERT: D 18 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6499 (mp0) REVERT: H 91 THR cc_start: 0.8815 (OUTLIER) cc_final: 0.8539 (p) REVERT: H 139 VAL cc_start: 0.9173 (p) cc_final: 0.8916 (m) REVERT: H 147 VAL cc_start: 0.8532 (OUTLIER) cc_final: 0.8181 (m) outliers start: 39 outliers final: 25 residues processed: 244 average time/residue: 0.4269 time to fit residues: 112.0813 Evaluate side-chains 248 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 218 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 34 PHE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 220 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 35 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN C 176 GLN H 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.110749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.098129 restraints weight = 16224.143| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.08 r_work: 0.3269 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9756 Z= 0.139 Angle : 0.568 8.301 13234 Z= 0.285 Chirality : 0.040 0.140 1525 Planarity : 0.004 0.048 1634 Dihedral : 4.940 39.086 1378 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.26 % Allowed : 18.32 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.25), residues: 1190 helix: 2.45 (0.24), residues: 471 sheet: 0.78 (0.29), residues: 297 loop : -0.78 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 8 TYR 0.014 0.001 TYR H 190 PHE 0.016 0.001 PHE D 34 TRP 0.017 0.001 TRP C 82 HIS 0.003 0.001 HIS A 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 9752) covalent geometry : angle 0.56605 / 0.28 (13226) SS BOND : bond 0.00779 / 0.38 ( 4) SS BOND : angle 1.97786 / 1.11 ( 8) hydrogen bonds : bond 0.03628 / 2.42 ( 481) hydrogen bonds : angle 4.23881 / 3.21 ( 1365) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 222 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 27 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7867 (mpp) REVERT: A 35 LEU cc_start: 0.8851 (mm) cc_final: 0.8549 (mm) REVERT: A 377 ARG cc_start: 0.7663 (ttm110) cc_final: 0.7332 (mtp-110) REVERT: B 240 MET cc_start: 0.6110 (ppp) cc_final: 0.5769 (pp-130) REVERT: B 261 ASP cc_start: 0.8126 (t70) cc_final: 0.7706 (t0) REVERT: B 273 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7746 (tt) REVERT: B 295 THR cc_start: 0.8299 (m) cc_final: 0.7840 (p) REVERT: B 310 LEU cc_start: 0.9039 (mt) cc_final: 0.8735 (mp) REVERT: C 96 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8442 (mtp85) REVERT: D 18 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6454 (mp0) REVERT: D 32 MET cc_start: 0.7326 (ppp) cc_final: 0.7117 (ppp) REVERT: D 66 GLN cc_start: 0.8220 (mt0) cc_final: 0.8016 (mt0) REVERT: H 91 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8523 (p) REVERT: H 139 VAL cc_start: 0.9153 (p) cc_final: 0.8874 (m) REVERT: H 147 VAL cc_start: 0.8565 (OUTLIER) cc_final: 0.8212 (m) outliers start: 43 outliers final: 23 residues processed: 244 average time/residue: 0.4648 time to fit residues: 121.6318 Evaluate side-chains 246 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 217 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 220 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 26 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN C 176 GLN H 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.110985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.098301 restraints weight = 16238.385| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.09 r_work: 0.3273 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9756 Z= 0.129 Angle : 0.562 9.085 13234 Z= 0.281 Chirality : 0.040 0.126 1525 Planarity : 0.004 0.048 1634 Dihedral : 4.695 29.077 1376 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.68 % Favored : 98.24 % Rotamer: Outliers : 4.06 % Allowed : 19.60 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.25), residues: 1190 helix: 2.50 (0.24), residues: 471 sheet: 0.70 (0.29), residues: 297 loop : -0.76 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 28 TYR 0.015 0.001 TYR H 190 PHE 0.018 0.001 PHE A 430 TRP 0.017 0.001 TRP C 82 HIS 0.003 0.001 HIS A 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 9752) covalent geometry : angle 0.56041 / 0.28 (13226) SS BOND : bond 0.00772 / 0.37 ( 4) SS BOND : angle 1.82002 / 1.03 ( 8) hydrogen bonds : bond 0.03530 / 2.36 ( 481) hydrogen bonds : angle 4.20854 / 3.19 ( 1365) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 227 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7883 (mpp) REVERT: A 35 LEU cc_start: 0.8853 (mm) cc_final: 0.8536 (mm) REVERT: A 377 ARG cc_start: 0.7657 (ttm110) cc_final: 0.7336 (mtp-110) REVERT: B 33 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8192 (mt-10) REVERT: B 261 ASP cc_start: 0.8144 (t70) cc_final: 0.7734 (t0) REVERT: B 273 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7719 (tt) REVERT: B 295 THR cc_start: 0.8301 (m) cc_final: 0.7841 (p) REVERT: B 310 LEU cc_start: 0.9036 (mt) cc_final: 0.8737 (mp) REVERT: C 96 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8436 (mtp85) REVERT: C 228 ASP cc_start: 0.8208 (m-30) cc_final: 0.7900 (OUTLIER) REVERT: D 18 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6406 (mp0) REVERT: D 19 LEU cc_start: 0.7849 (mp) cc_final: 0.7627 (tp) REVERT: D 28 ARG cc_start: 0.8356 (mmm160) cc_final: 0.7422 (mmt90) REVERT: D 32 MET cc_start: 0.7390 (ppp) cc_final: 0.7155 (ppp) REVERT: H 91 THR cc_start: 0.8841 (OUTLIER) cc_final: 0.8529 (p) REVERT: H 139 VAL cc_start: 0.9123 (p) cc_final: 0.8840 (m) REVERT: H 147 VAL cc_start: 0.8558 (OUTLIER) cc_final: 0.8201 (m) outliers start: 41 outliers final: 25 residues processed: 248 average time/residue: 0.4402 time to fit residues: 116.9904 Evaluate side-chains 250 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 220 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 220 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 3 optimal weight: 0.0370 chunk 77 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 GLN C 176 GLN H 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.112008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.099338 restraints weight = 16186.435| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.09 r_work: 0.3289 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9756 Z= 0.116 Angle : 0.569 9.481 13234 Z= 0.284 Chirality : 0.039 0.125 1525 Planarity : 0.004 0.048 1634 Dihedral : 4.630 29.918 1376 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.60 % Favored : 98.32 % Rotamer: Outliers : 3.56 % Allowed : 20.20 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.25), residues: 1190 helix: 2.61 (0.24), residues: 471 sheet: 0.63 (0.29), residues: 297 loop : -0.73 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 28 TYR 0.018 0.001 TYR H 190 PHE 0.015 0.001 PHE A 430 TRP 0.015 0.001 TRP C 82 HIS 0.003 0.001 HIS A 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 9752) covalent geometry : angle 0.56808 / 0.28 (13226) SS BOND : bond 0.00704 / 0.34 ( 4) SS BOND : angle 1.66141 / 0.95 ( 8) hydrogen bonds : bond 0.03394 / 2.26 ( 481) hydrogen bonds : angle 4.20951 / 3.20 ( 1365) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 220 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8147 (mpp) REVERT: A 35 LEU cc_start: 0.8833 (mm) cc_final: 0.8499 (mm) REVERT: A 171 ARG cc_start: 0.7364 (mtt-85) cc_final: 0.6564 (mmt180) REVERT: B 198 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.6682 (tpt) REVERT: B 261 ASP cc_start: 0.8167 (t70) cc_final: 0.7754 (t0) REVERT: B 273 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7652 (tt) REVERT: B 295 THR cc_start: 0.8261 (m) cc_final: 0.7785 (p) REVERT: B 310 LEU cc_start: 0.8999 (mt) cc_final: 0.8692 (mp) REVERT: C 96 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8442 (mtp85) REVERT: C 228 ASP cc_start: 0.8189 (m-30) cc_final: 0.7868 (p0) REVERT: D 18 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6416 (mp0) REVERT: D 19 LEU cc_start: 0.7814 (mp) cc_final: 0.7597 (tp) REVERT: D 28 ARG cc_start: 0.8320 (mmm160) cc_final: 0.7497 (mmt90) REVERT: D 32 MET cc_start: 0.7424 (ppp) cc_final: 0.6966 (ppp) REVERT: H 5 VAL cc_start: 0.8283 (t) cc_final: 0.7986 (p) REVERT: H 91 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8518 (p) REVERT: H 139 VAL cc_start: 0.9042 (OUTLIER) cc_final: 0.8754 (m) REVERT: H 140 MET cc_start: 0.8614 (mmt) cc_final: 0.8374 (mmt) outliers start: 36 outliers final: 21 residues processed: 237 average time/residue: 0.4523 time to fit residues: 115.2281 Evaluate side-chains 243 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 215 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 220 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 69 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 75 GLN C 176 GLN C 237 ASN H 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.110896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.098283 restraints weight = 16198.050| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.08 r_work: 0.3270 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9756 Z= 0.138 Angle : 0.595 9.915 13234 Z= 0.296 Chirality : 0.040 0.140 1525 Planarity : 0.004 0.057 1634 Dihedral : 4.696 32.100 1376 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.76 % Allowed : 20.40 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.25), residues: 1190 helix: 2.61 (0.24), residues: 471 sheet: 0.60 (0.29), residues: 296 loop : -0.69 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 8 TYR 0.015 0.001 TYR H 190 PHE 0.014 0.001 PHE H 239 TRP 0.014 0.001 TRP C 82 HIS 0.003 0.001 HIS A 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 9752) covalent geometry : angle 0.59303 / 0.30 (13226) SS BOND : bond 0.00796 / 0.38 ( 4) SS BOND : angle 1.89397 / 1.09 ( 8) hydrogen bonds : bond 0.03545 / 2.36 ( 481) hydrogen bonds : angle 4.24082 / 3.23 ( 1365) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 221 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8190 (mpp) REVERT: A 35 LEU cc_start: 0.8857 (mm) cc_final: 0.8509 (mm) REVERT: A 377 ARG cc_start: 0.7638 (ttm110) cc_final: 0.7316 (mtp-110) REVERT: B 261 ASP cc_start: 0.8153 (t70) cc_final: 0.7752 (t0) REVERT: B 273 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7732 (tt) REVERT: B 295 THR cc_start: 0.8299 (m) cc_final: 0.7821 (p) REVERT: B 310 LEU cc_start: 0.9025 (mt) cc_final: 0.8718 (mp) REVERT: C 96 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8263 (mtp85) REVERT: D 18 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6453 (mp0) REVERT: D 19 LEU cc_start: 0.7871 (mp) cc_final: 0.7659 (tp) REVERT: D 28 ARG cc_start: 0.8294 (mmm160) cc_final: 0.7506 (mmt90) REVERT: D 32 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.6991 (ppp) REVERT: H 5 VAL cc_start: 0.8332 (t) cc_final: 0.8044 (p) REVERT: H 43 LYS cc_start: 0.8875 (mmpt) cc_final: 0.8658 (mmpt) REVERT: H 91 THR cc_start: 0.8858 (OUTLIER) cc_final: 0.8543 (p) REVERT: H 139 VAL cc_start: 0.9056 (OUTLIER) cc_final: 0.8780 (m) outliers start: 38 outliers final: 23 residues processed: 239 average time/residue: 0.4243 time to fit residues: 109.0521 Evaluate side-chains 247 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 217 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 32 MET Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 155 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 78 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 HIS C 176 GLN C 230 ASN C 237 ASN H 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.110112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.097482 restraints weight = 16226.726| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.08 r_work: 0.3260 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9756 Z= 0.159 Angle : 0.631 10.159 13234 Z= 0.312 Chirality : 0.041 0.128 1525 Planarity : 0.004 0.055 1634 Dihedral : 4.810 34.074 1376 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.07 % Allowed : 21.78 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.25), residues: 1190 helix: 2.58 (0.24), residues: 471 sheet: 0.43 (0.29), residues: 292 loop : -0.69 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 28 TYR 0.016 0.001 TYR H 190 PHE 0.023 0.002 PHE H 239 TRP 0.016 0.002 TRP C 82 HIS 0.003 0.001 HIS A 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 ( 9752) covalent geometry : angle 0.62949 / 0.31 (13226) SS BOND : bond 0.00886 / 0.43 ( 4) SS BOND : angle 1.94973 / 1.11 ( 8) hydrogen bonds : bond 0.03674 / 2.45 ( 481) hydrogen bonds : angle 4.29539 / 3.28 ( 1365) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 222 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8181 (mpp) REVERT: A 35 LEU cc_start: 0.8881 (mm) cc_final: 0.8538 (mm) REVERT: A 82 LEU cc_start: 0.8911 (tt) cc_final: 0.8575 (tm) REVERT: A 377 ARG cc_start: 0.7676 (ttm110) cc_final: 0.7347 (mtp-110) REVERT: B 237 ASP cc_start: 0.8117 (t0) cc_final: 0.7836 (t0) REVERT: B 261 ASP cc_start: 0.8173 (t70) cc_final: 0.7776 (t0) REVERT: B 273 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7761 (tt) REVERT: B 295 THR cc_start: 0.8287 (m) cc_final: 0.7803 (p) REVERT: B 310 LEU cc_start: 0.9005 (mt) cc_final: 0.8627 (mp) REVERT: C 96 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8383 (mtp85) REVERT: C 138 GLU cc_start: 0.8298 (mm-30) cc_final: 0.8063 (mm-30) REVERT: C 214 ARG cc_start: 0.8618 (mtt180) cc_final: 0.8411 (mtt90) REVERT: D 18 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6484 (mp0) REVERT: D 19 LEU cc_start: 0.7941 (mp) cc_final: 0.7710 (tp) REVERT: D 28 ARG cc_start: 0.8320 (mmm160) cc_final: 0.7430 (mmt90) REVERT: D 32 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.6993 (ppp) REVERT: H 5 VAL cc_start: 0.8364 (t) cc_final: 0.8093 (p) REVERT: H 91 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8566 (p) REVERT: H 139 VAL cc_start: 0.8982 (OUTLIER) cc_final: 0.8705 (m) outliers start: 31 outliers final: 20 residues processed: 236 average time/residue: 0.4689 time to fit residues: 118.6172 Evaluate side-chains 248 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 221 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 6 GLU Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 32 MET Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 155 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 56 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 110 optimal weight: 0.0870 chunk 2 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 76 optimal weight: 0.0040 chunk 71 optimal weight: 0.8980 overall best weight: 0.4570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 75 GLN C 176 GLN C 237 ASN G 18 GLN H 82 GLN H 179 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.112605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.099937 restraints weight = 16128.663| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.08 r_work: 0.3354 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9756 Z= 0.113 Angle : 0.593 9.929 13234 Z= 0.293 Chirality : 0.039 0.161 1525 Planarity : 0.004 0.053 1634 Dihedral : 4.569 33.222 1376 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.87 % Allowed : 22.08 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.25), residues: 1190 helix: 2.57 (0.24), residues: 477 sheet: 0.50 (0.29), residues: 292 loop : -0.71 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 28 TYR 0.017 0.001 TYR H 190 PHE 0.026 0.001 PHE H 239 TRP 0.015 0.001 TRP C 82 HIS 0.003 0.001 HIS A 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 9752) covalent geometry : angle 0.59156 / 0.29 (13226) SS BOND : bond 0.00606 / 0.29 ( 4) SS BOND : angle 1.52925 / 0.87 ( 8) hydrogen bonds : bond 0.03240 / 2.15 ( 481) hydrogen bonds : angle 4.20863 / 3.21 ( 1365) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3245.77 seconds wall clock time: 55 minutes 58.98 seconds (3358.98 seconds total)