Starting phenix.real_space_refine on Sun Jun 8 22:32:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hk2_34842/06_2025/8hk2_34842.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hk2_34842/06_2025/8hk2_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hk2_34842/06_2025/8hk2_34842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hk2_34842/06_2025/8hk2_34842.map" model { file = "/net/cci-nas-00/data/ceres_data/8hk2_34842/06_2025/8hk2_34842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hk2_34842/06_2025/8hk2_34842.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} 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, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 4} 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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP: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: 6.02, per 1000 atoms: 0.63 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: 2.56 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.09 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: 3.06 Time building geometry restraints manager: 3.03 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: 5829 18.33 - 36.66: 173 36.66 - 54.98: 30 54.98 - 73.31: 10 73.31 - 91.64: 2 Dihedral angle restraints: 6044 sinusoidal: 2538 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 6041 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.330 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:13.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 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 : 9.701 91.640 3764 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.33 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (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 TRP 0.039 0.003 TRP H 111 HIS 0.007 0.002 HIS A 133 PHE 0.038 0.003 PHE A 396 TYR 0.016 0.002 TYR H 190 ARG 0.006 0.001 ARG H 67 Details of bonding type rmsd hydrogen bonds : bond 0.13697 ( 481) hydrogen bonds : angle 6.12574 ( 1365) SS BOND : bond 0.17336 ( 4) SS BOND : angle 14.40283 ( 8) covalent geometry : bond 0.00682 ( 9752) covalent geometry : angle 1.06047 (13226) *********************** 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 : 0.939 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: 1.1536 time to fit residues: 376.0800 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 : 0.998 ------------------------------------------------------------------------------- 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 99 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 244 HIS B 269 ASN C 88 ASN C 142 HIS C 155 ASN C 176 GLN H 77 ASN H 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.103590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.090699 restraints weight = 16261.833| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.14 r_work: 0.3216 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9756 Z= 0.269 Angle : 0.679 8.691 13234 Z= 0.356 Chirality : 0.045 0.157 1525 Planarity : 0.005 0.059 1634 Dihedral : 6.154 53.698 1663 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.68 % Favored : 98.24 % Rotamer: Outliers : 4.16 % Allowed : 13.37 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.24), residues: 1190 helix: 1.86 (0.24), residues: 474 sheet: 0.62 (0.29), residues: 303 loop : -1.22 (0.26), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 82 HIS 0.009 0.002 HIS C 142 PHE 0.021 0.003 PHE A 125 TYR 0.020 0.002 TYR H 190 ARG 0.007 0.001 ARG D 8 Details of bonding type rmsd hydrogen bonds : bond 0.04884 ( 481) hydrogen bonds : angle 4.85694 ( 1365) SS BOND : bond 0.01086 ( 4) SS BOND : angle 1.87953 ( 8) covalent geometry : bond 0.00638 ( 9752) covalent geometry : angle 0.67714 (13226) *********************** 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 291 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 249 time to evaluate : 1.432 Fit side-chains revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8904 (mm) cc_final: 0.8618 (mm) REVERT: A 76 PRO cc_start: 0.8733 (Cg_exo) cc_final: 0.8519 (Cg_endo) REVERT: A 171 ARG cc_start: 0.7529 (mtt-85) cc_final: 0.7074 (mtt-85) REVERT: A 340 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7328 (ttp-170) REVERT: A 377 ARG cc_start: 0.7867 (ttm110) cc_final: 0.7522 (mtp-110) REVERT: B 8 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7732 (mt-10) REVERT: B 240 MET cc_start: 0.5815 (pp-130) cc_final: 0.5331 (pp-130) REVERT: B 261 ASP cc_start: 0.8067 (t70) cc_final: 0.7639 (t0) REVERT: B 270 LYS cc_start: 0.8605 (mtmm) cc_final: 0.8371 (mtpp) REVERT: B 295 THR cc_start: 0.8285 (m) cc_final: 0.7854 (p) REVERT: C 25 CYS cc_start: 0.8580 (t) cc_final: 0.8359 (t) REVERT: D 32 MET cc_start: 0.7244 (ttm) cc_final: 0.6973 (tmm) REVERT: D 63 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8518 (tm) REVERT: H 147 VAL cc_start: 0.8414 (OUTLIER) cc_final: 0.8072 (m) REVERT: H 238 THR cc_start: 0.8995 (m) cc_final: 0.8714 (p) outliers start: 42 outliers final: 13 residues processed: 267 average time/residue: 1.2771 time to fit residues: 366.6803 Evaluate side-chains 245 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 229 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 278 ILE 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 34 PHE Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 164 SER 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 112 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 38 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 176 GLN C 220 GLN H 77 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 = 0.3586 r_free = 0.3586 target = 0.110294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.097538 restraints weight = 16263.075| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.16 r_work: 0.3251 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9756 Z= 0.136 Angle : 0.563 8.412 13234 Z= 0.288 Chirality : 0.041 0.132 1525 Planarity : 0.004 0.047 1634 Dihedral : 5.659 56.690 1660 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.60 % Favored : 98.32 % Rotamer: Outliers : 3.76 % Allowed : 16.93 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.24), residues: 1190 helix: 2.15 (0.24), residues: 474 sheet: 0.72 (0.29), residues: 303 loop : -1.02 (0.27), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.004 0.001 HIS A 63 PHE 0.023 0.002 PHE B 354 TYR 0.016 0.001 TYR H 190 ARG 0.008 0.000 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.03952 ( 481) hydrogen bonds : angle 4.47857 ( 1365) SS BOND : bond 0.01255 ( 4) SS BOND : angle 1.63514 ( 8) covalent geometry : bond 0.00311 ( 9752) covalent geometry : angle 0.56151 (13226) *********************** 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 266 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 228 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.7836 (mpp) REVERT: A 35 LEU cc_start: 0.8873 (mm) cc_final: 0.8566 (mm) REVERT: A 76 PRO cc_start: 0.8734 (Cg_exo) cc_final: 0.8496 (Cg_endo) REVERT: A 96 LYS cc_start: 0.8601 (mttt) cc_final: 0.8358 (mttm) REVERT: A 377 ARG cc_start: 0.7731 (ttm110) cc_final: 0.7393 (mtp-110) REVERT: B 4 THR cc_start: 0.7937 (p) cc_final: 0.7707 (t) REVERT: B 261 ASP cc_start: 0.8084 (t70) cc_final: 0.7654 (t0) REVERT: B 270 LYS cc_start: 0.8626 (mtmm) cc_final: 0.8386 (mtpp) REVERT: B 273 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7785 (tt) REVERT: B 295 THR cc_start: 0.8280 (m) cc_final: 0.7838 (p) REVERT: C 327 VAL cc_start: 0.8768 (OUTLIER) cc_final: 0.8566 (p) REVERT: D 63 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8469 (tm) REVERT: H 91 THR cc_start: 0.8726 (OUTLIER) cc_final: 0.8471 (p) REVERT: H 147 VAL cc_start: 0.8479 (OUTLIER) cc_final: 0.8126 (m) REVERT: H 238 THR cc_start: 0.9023 (m) cc_final: 0.8738 (p) outliers start: 38 outliers final: 12 residues processed: 243 average time/residue: 1.2249 time to fit residues: 318.0139 Evaluate side-chains 235 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 217 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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 334 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain B residue 34 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 C residue 270 ILE Chi-restraints excluded: chain C residue 327 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 102 optimal weight: 0.0870 chunk 6 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 80 optimal weight: 0.7980 chunk 86 optimal weight: 8.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3601 r_free = 0.3601 target = 0.111098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.098330 restraints weight = 16041.195| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.07 r_work: 0.3276 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2993 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= 0.117 Angle : 0.548 7.717 13234 Z= 0.279 Chirality : 0.040 0.129 1525 Planarity : 0.004 0.047 1634 Dihedral : 5.464 59.963 1660 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.56 % Allowed : 17.92 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.24), residues: 1190 helix: 2.37 (0.24), residues: 470 sheet: 0.87 (0.30), residues: 298 loop : -0.85 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.003 0.001 HIS A 63 PHE 0.026 0.001 PHE B 354 TYR 0.014 0.001 TYR H 190 ARG 0.011 0.001 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 481) hydrogen bonds : angle 4.29376 ( 1365) SS BOND : bond 0.00794 ( 4) SS BOND : angle 2.14602 ( 8) covalent geometry : bond 0.00265 ( 9752) covalent geometry : angle 0.54543 (13226) *********************** 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 260 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 224 time to evaluate : 1.585 Fit side-chains revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8854 (mm) cc_final: 0.8548 (mm) REVERT: A 76 PRO cc_start: 0.8713 (Cg_exo) cc_final: 0.8463 (Cg_endo) REVERT: A 377 ARG cc_start: 0.7672 (ttm110) cc_final: 0.7348 (mtp-110) REVERT: B 4 THR cc_start: 0.7977 (p) cc_final: 0.7737 (t) REVERT: B 261 ASP cc_start: 0.8080 (t70) cc_final: 0.7653 (t0) REVERT: B 273 LEU cc_start: 0.8151 (tt) cc_final: 0.7779 (tt) REVERT: B 295 THR cc_start: 0.8293 (m) cc_final: 0.7831 (p) REVERT: C 228 ASP cc_start: 0.8481 (p0) cc_final: 0.8262 (p0) REVERT: C 273 ILE cc_start: 0.8691 (mp) cc_final: 0.8474 (mt) REVERT: C 327 VAL cc_start: 0.8735 (OUTLIER) cc_final: 0.8529 (p) REVERT: H 91 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8472 (p) REVERT: H 139 VAL cc_start: 0.9167 (p) cc_final: 0.8920 (m) REVERT: H 147 VAL cc_start: 0.8506 (OUTLIER) cc_final: 0.8156 (m) REVERT: H 238 THR cc_start: 0.9013 (m) cc_final: 0.8751 (p) outliers start: 36 outliers final: 12 residues processed: 241 average time/residue: 1.5228 time to fit residues: 393.5097 Evaluate side-chains 230 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 215 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 334 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 285 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 327 VAL 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 57 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 HIS C 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.107832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.095216 restraints weight = 16067.879| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.05 r_work: 0.3230 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9756 Z= 0.197 Angle : 0.587 7.401 13234 Z= 0.303 Chirality : 0.042 0.137 1525 Planarity : 0.004 0.050 1634 Dihedral : 5.451 38.224 1658 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.96 % Allowed : 18.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.24), residues: 1190 helix: 2.30 (0.24), residues: 467 sheet: 0.76 (0.30), residues: 298 loop : -0.94 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 82 HIS 0.004 0.001 HIS B 213 PHE 0.031 0.002 PHE B 354 TYR 0.016 0.001 TYR H 190 ARG 0.014 0.001 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.04155 ( 481) hydrogen bonds : angle 4.40721 ( 1365) SS BOND : bond 0.01097 ( 4) SS BOND : angle 2.18734 ( 8) covalent geometry : bond 0.00468 ( 9752) covalent geometry : angle 0.58430 (13226) *********************** 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 267 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 227 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.7914 (mpp) REVERT: A 28 VAL cc_start: 0.8230 (m) cc_final: 0.8001 (p) REVERT: A 35 LEU cc_start: 0.8917 (mm) cc_final: 0.8581 (mm) REVERT: A 377 ARG cc_start: 0.7722 (ttm110) cc_final: 0.7386 (mtp-110) REVERT: B 240 MET cc_start: 0.5836 (pp-130) cc_final: 0.5609 (pp-130) REVERT: B 261 ASP cc_start: 0.8106 (t70) cc_final: 0.7680 (t0) REVERT: B 273 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7918 (tt) REVERT: B 295 THR cc_start: 0.8324 (m) cc_final: 0.7874 (p) REVERT: B 351 CYS cc_start: 0.8290 (m) cc_final: 0.8086 (m) REVERT: C 25 CYS cc_start: 0.8631 (t) cc_final: 0.8392 (t) REVERT: C 228 ASP cc_start: 0.8483 (p0) cc_final: 0.8265 (p0) REVERT: H 5 VAL cc_start: 0.8413 (t) cc_final: 0.8125 (p) REVERT: H 91 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8569 (p) REVERT: H 147 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8212 (m) outliers start: 40 outliers final: 17 residues processed: 246 average time/residue: 1.2076 time to fit residues: 318.7968 Evaluate side-chains 237 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 216 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 395 ILE 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 254 CYS 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 270 ILE Chi-restraints excluded: chain C residue 327 VAL 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 1 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 67 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 36 ASN C 75 GLN C 119 ASN C 176 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.109851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.097150 restraints weight = 16073.375| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.06 r_work: 0.3254 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9756 Z= 0.126 Angle : 0.553 7.789 13234 Z= 0.283 Chirality : 0.040 0.133 1525 Planarity : 0.004 0.053 1634 Dihedral : 5.118 34.489 1658 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.27 % Allowed : 19.80 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.24), residues: 1190 helix: 2.38 (0.24), residues: 469 sheet: 0.72 (0.29), residues: 297 loop : -0.87 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.002 0.001 HIS A 63 PHE 0.032 0.001 PHE B 354 TYR 0.014 0.001 TYR H 190 ARG 0.016 0.001 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 481) hydrogen bonds : angle 4.29330 ( 1365) SS BOND : bond 0.00743 ( 4) SS BOND : angle 1.50397 ( 8) covalent geometry : bond 0.00289 ( 9752) covalent geometry : angle 0.55151 (13226) *********************** 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 256 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 223 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 VAL cc_start: 0.8768 (t) cc_final: 0.8290 (t) REVERT: A 27 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7940 (mpp) REVERT: A 28 VAL cc_start: 0.8229 (m) cc_final: 0.8015 (p) REVERT: A 35 LEU cc_start: 0.8898 (mm) cc_final: 0.8579 (mm) REVERT: A 377 ARG cc_start: 0.7661 (ttm110) cc_final: 0.7341 (mtp-110) REVERT: B 240 MET cc_start: 0.5842 (pp-130) cc_final: 0.5462 (pp-130) REVERT: B 261 ASP cc_start: 0.8129 (t70) cc_final: 0.7704 (t0) REVERT: B 273 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7827 (tt) REVERT: B 295 THR cc_start: 0.8301 (m) cc_final: 0.7833 (p) REVERT: C 25 CYS cc_start: 0.8619 (t) cc_final: 0.8409 (t) REVERT: C 228 ASP cc_start: 0.8532 (p0) cc_final: 0.8314 (p0) REVERT: C 273 ILE cc_start: 0.8742 (mp) cc_final: 0.8499 (mt) REVERT: D 28 ARG cc_start: 0.8130 (mmm160) cc_final: 0.7510 (mmt90) REVERT: H 5 VAL cc_start: 0.8372 (t) cc_final: 0.8086 (p) REVERT: H 91 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8523 (p) REVERT: H 139 VAL cc_start: 0.9152 (p) cc_final: 0.8871 (m) REVERT: H 147 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8156 (m) REVERT: H 238 THR cc_start: 0.9068 (m) cc_final: 0.8699 (p) outliers start: 33 outliers final: 17 residues processed: 241 average time/residue: 1.2859 time to fit residues: 331.6374 Evaluate side-chains 241 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 220 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 MET 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 395 ILE 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 254 CYS Chi-restraints excluded: chain B residue 273 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 4 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.107157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.094310 restraints weight = 16194.614| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.14 r_work: 0.3212 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9756 Z= 0.213 Angle : 0.606 7.791 13234 Z= 0.311 Chirality : 0.042 0.161 1525 Planarity : 0.004 0.051 1634 Dihedral : 5.507 40.768 1658 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.96 % Allowed : 19.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.24), residues: 1190 helix: 2.26 (0.24), residues: 469 sheet: 0.58 (0.29), residues: 298 loop : -0.87 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 82 HIS 0.004 0.001 HIS B 213 PHE 0.034 0.002 PHE B 354 TYR 0.016 0.002 TYR H 190 ARG 0.008 0.001 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.04182 ( 481) hydrogen bonds : angle 4.39167 ( 1365) SS BOND : bond 0.01145 ( 4) SS BOND : angle 1.96445 ( 8) covalent geometry : bond 0.00505 ( 9752) covalent geometry : angle 0.60433 (13226) *********************** 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 257 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 217 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 VAL cc_start: 0.8812 (t) cc_final: 0.8316 (t) REVERT: A 27 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.7916 (mpp) REVERT: A 28 VAL cc_start: 0.8251 (m) cc_final: 0.8041 (p) REVERT: A 35 LEU cc_start: 0.8935 (mm) cc_final: 0.8626 (mm) REVERT: A 377 ARG cc_start: 0.7757 (ttm110) cc_final: 0.7427 (mtp-110) REVERT: B 240 MET cc_start: 0.5937 (pp-130) cc_final: 0.5527 (pp-130) REVERT: B 261 ASP cc_start: 0.8162 (t70) cc_final: 0.7751 (t0) REVERT: B 273 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7992 (tt) REVERT: C 25 CYS cc_start: 0.8625 (t) cc_final: 0.8380 (t) REVERT: C 273 ILE cc_start: 0.8782 (mp) cc_final: 0.8531 (mt) REVERT: D 28 ARG cc_start: 0.8083 (mmm160) cc_final: 0.7487 (mmt90) REVERT: H 5 VAL cc_start: 0.8433 (t) cc_final: 0.8158 (p) outliers start: 40 outliers final: 24 residues processed: 234 average time/residue: 1.1836 time to fit residues: 296.0578 Evaluate side-chains 236 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain A residue 52 MET 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 395 ILE Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 254 CYS 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 65 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 327 VAL 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 155 VAL Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 30 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 82 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 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 = 0.3578 r_free = 0.3578 target = 0.109363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.096499 restraints weight = 16199.132| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.15 r_work: 0.3235 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9756 Z= 0.131 Angle : 0.564 8.347 13234 Z= 0.287 Chirality : 0.040 0.135 1525 Planarity : 0.004 0.051 1634 Dihedral : 5.282 47.637 1658 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.87 % Allowed : 20.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.24), residues: 1190 helix: 2.38 (0.24), residues: 469 sheet: 0.62 (0.29), residues: 291 loop : -0.84 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.003 0.001 HIS B 213 PHE 0.031 0.001 PHE B 354 TYR 0.014 0.001 TYR H 190 ARG 0.008 0.001 ARG D 28 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 481) hydrogen bonds : angle 4.31764 ( 1365) SS BOND : bond 0.00797 ( 4) SS BOND : angle 1.49713 ( 8) covalent geometry : bond 0.00301 ( 9752) covalent geometry : angle 0.56249 (13226) *********************** 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 248 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 219 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 VAL cc_start: 0.8798 (t) cc_final: 0.8303 (t) REVERT: A 27 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.7942 (mpp) REVERT: A 28 VAL cc_start: 0.8242 (m) cc_final: 0.8036 (p) REVERT: A 35 LEU cc_start: 0.8914 (mm) cc_final: 0.8570 (mm) REVERT: A 377 ARG cc_start: 0.7693 (ttm110) cc_final: 0.7384 (mtp-110) REVERT: B 240 MET cc_start: 0.5921 (pp-130) cc_final: 0.5499 (pp-130) REVERT: B 261 ASP cc_start: 0.8158 (t70) cc_final: 0.7747 (t0) REVERT: B 262 THR cc_start: 0.8857 (OUTLIER) cc_final: 0.8562 (p) REVERT: B 273 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7916 (tt) REVERT: C 25 CYS cc_start: 0.8647 (t) cc_final: 0.8431 (t) REVERT: C 273 ILE cc_start: 0.8766 (mp) cc_final: 0.8514 (mt) REVERT: D 28 ARG cc_start: 0.7878 (mmm160) cc_final: 0.7600 (mmt90) REVERT: H 5 VAL cc_start: 0.8436 (t) cc_final: 0.8160 (p) REVERT: H 139 VAL cc_start: 0.9140 (p) cc_final: 0.8860 (m) outliers start: 29 outliers final: 19 residues processed: 232 average time/residue: 1.1435 time to fit residues: 284.3440 Evaluate side-chains 239 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 217 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain A residue 53 GLN 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 395 ILE Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 254 CYS 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 270 ILE Chi-restraints excluded: chain C residue 327 VAL 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 178 LEU Chi-restraints excluded: chain H residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 83 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 76 optimal weight: 0.3980 chunk 73 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 chunk 60 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 119 ASN C 176 GLN H 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.110079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.097219 restraints weight = 16116.374| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.13 r_work: 0.3249 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3650 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= 0.121 Angle : 0.554 8.377 13234 Z= 0.283 Chirality : 0.040 0.133 1525 Planarity : 0.004 0.050 1634 Dihedral : 5.163 50.758 1658 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.77 % Allowed : 21.09 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.24), residues: 1190 helix: 2.43 (0.24), residues: 469 sheet: 0.55 (0.29), residues: 293 loop : -0.77 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.004 0.001 HIS A 169 PHE 0.028 0.001 PHE B 354 TYR 0.014 0.001 TYR H 190 ARG 0.008 0.001 ARG H 18 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 481) hydrogen bonds : angle 4.28199 ( 1365) SS BOND : bond 0.00717 ( 4) SS BOND : angle 1.40734 ( 8) covalent geometry : bond 0.00276 ( 9752) covalent geometry : angle 0.55275 (13226) *********************** 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 251 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 223 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 VAL cc_start: 0.8750 (t) cc_final: 0.8220 (t) REVERT: A 27 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.7953 (mpp) REVERT: A 28 VAL cc_start: 0.8236 (m) cc_final: 0.8035 (p) REVERT: A 35 LEU cc_start: 0.8900 (mm) cc_final: 0.8579 (mm) REVERT: A 96 LYS cc_start: 0.8840 (mttt) cc_final: 0.8587 (mmtt) REVERT: A 377 ARG cc_start: 0.7671 (ttm110) cc_final: 0.7363 (mtp-110) REVERT: B 261 ASP cc_start: 0.8144 (t70) cc_final: 0.7740 (t0) REVERT: B 262 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8529 (p) REVERT: B 273 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7933 (tt) REVERT: C 228 ASP cc_start: 0.8507 (p0) cc_final: 0.8149 (p0) REVERT: C 273 ILE cc_start: 0.8759 (mp) cc_final: 0.8516 (mt) REVERT: D 28 ARG cc_start: 0.7789 (mmm160) cc_final: 0.7443 (mmt90) REVERT: H 5 VAL cc_start: 0.8406 (t) cc_final: 0.8127 (p) REVERT: H 139 VAL cc_start: 0.9114 (p) cc_final: 0.8821 (m) outliers start: 28 outliers final: 17 residues processed: 239 average time/residue: 1.1903 time to fit residues: 303.9997 Evaluate side-chains 238 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 218 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain A residue 53 GLN 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 395 ILE 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 254 CYS 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 270 ILE 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 155 VAL Chi-restraints excluded: chain H residue 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 61 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 83 optimal weight: 0.0970 chunk 70 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN C 32 GLN C 176 GLN D 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.109946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.097067 restraints weight = 16267.270| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.16 r_work: 0.3250 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9756 Z= 0.128 Angle : 0.588 8.619 13234 Z= 0.295 Chirality : 0.040 0.133 1525 Planarity : 0.004 0.051 1634 Dihedral : 5.161 52.717 1658 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.28 % Allowed : 21.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.24), residues: 1190 helix: 2.37 (0.24), residues: 475 sheet: 0.49 (0.29), residues: 293 loop : -0.79 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.002 0.001 HIS A 63 PHE 0.029 0.001 PHE B 354 TYR 0.014 0.001 TYR H 190 ARG 0.008 0.001 ARG H 18 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 481) hydrogen bonds : angle 4.27681 ( 1365) SS BOND : bond 0.00763 ( 4) SS BOND : angle 1.59587 ( 8) covalent geometry : bond 0.00297 ( 9752) covalent geometry : angle 0.58683 (13226) ********************** 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 245 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 222 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7979 (mpp) REVERT: A 35 LEU cc_start: 0.8895 (mm) cc_final: 0.8590 (mm) REVERT: A 96 LYS cc_start: 0.8843 (mttt) cc_final: 0.8581 (mmtt) REVERT: A 377 ARG cc_start: 0.7674 (ttm110) cc_final: 0.7364 (mtp-110) REVERT: B 197 LYS cc_start: 0.8207 (mmtp) cc_final: 0.7923 (mmtm) REVERT: B 261 ASP cc_start: 0.8174 (t70) cc_final: 0.7775 (t0) REVERT: B 273 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7959 (tt) REVERT: C 228 ASP cc_start: 0.8512 (p0) cc_final: 0.8162 (p0) REVERT: C 273 ILE cc_start: 0.8764 (mp) cc_final: 0.8520 (mt) REVERT: D 17 LYS cc_start: 0.6967 (tppp) cc_final: 0.6638 (tppt) REVERT: D 28 ARG cc_start: 0.7709 (mmm160) cc_final: 0.7313 (mmt90) REVERT: H 5 VAL cc_start: 0.8395 (t) cc_final: 0.8119 (p) REVERT: H 32 PHE cc_start: 0.8605 (m-10) cc_final: 0.8257 (m-80) REVERT: H 139 VAL cc_start: 0.9110 (p) cc_final: 0.8798 (m) outliers start: 23 outliers final: 20 residues processed: 233 average time/residue: 1.1920 time to fit residues: 297.1977 Evaluate side-chains 245 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 254 CYS 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 270 ILE 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 87 ARG Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 50 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 73 optimal weight: 0.0040 chunk 48 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 76 optimal weight: 0.0870 chunk 84 optimal weight: 0.0980 chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 overall best weight: 0.3370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 GLN C 75 GLN C 176 GLN C 237 ASN G 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.112192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.099495 restraints weight = 16177.539| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.06 r_work: 0.3323 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9756 Z= 0.105 Angle : 0.580 8.927 13234 Z= 0.287 Chirality : 0.039 0.188 1525 Planarity : 0.004 0.050 1634 Dihedral : 4.928 51.752 1658 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.08 % Allowed : 21.88 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.25), residues: 1190 helix: 2.48 (0.24), residues: 475 sheet: 0.55 (0.29), residues: 293 loop : -0.77 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 169 HIS 0.002 0.001 HIS A 133 PHE 0.025 0.001 PHE A 430 TYR 0.014 0.001 TYR H 190 ARG 0.008 0.001 ARG H 18 Details of bonding type rmsd hydrogen bonds : bond 0.03184 ( 481) hydrogen bonds : angle 4.18390 ( 1365) SS BOND : bond 0.00549 ( 4) SS BOND : angle 1.25314 ( 8) covalent geometry : bond 0.00232 ( 9752) covalent geometry : angle 0.57931 (13226) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8769.56 seconds wall clock time: 153 minutes 39.61 seconds (9219.61 seconds total)