Starting phenix.real_space_refine on Sun Dec 29 06:35:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hk2_34842/12_2024/8hk2_34842.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hk2_34842/12_2024/8hk2_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_34842/12_2024/8hk2_34842.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hk2_34842/12_2024/8hk2_34842.map" model { file = "/net/cci-nas-00/data/ceres_data/8hk2_34842/12_2024/8hk2_34842.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hk2_34842/12_2024/8hk2_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-5532/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: 5.71, per 1000 atoms: 0.60 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: 2.48 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: 1.07 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: 2.67 Time building geometry restraints manager: 2.85 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: 0.920 Set stop_for_unknowns flag: 0.010 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: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.340 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.200 ------------------------------------------------------------------------------- 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 : 0.007 0.097 9752 Z= 0.457 Angle : 1.060 13.693 13226 Z= 0.618 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 *********************** 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 : 1.113 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: 1.1547 time to fit residues: 376.1606 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 : 1.052 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 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 9752 Z= 0.416 Angle : 0.677 8.691 13226 Z= 0.355 Chirality : 0.045 0.157 1525 Planarity : 0.005 0.059 1634 Dihedral : 6.154 53.699 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 *********************** 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 : 1.076 Fit side-chains revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8743 (mm) cc_final: 0.8522 (mm) REVERT: A 171 ARG cc_start: 0.6951 (mtt-85) cc_final: 0.6681 (mtt-85) REVERT: A 340 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7112 (ttp-170) REVERT: A 433 PHE cc_start: 0.8798 (m-80) cc_final: 0.8582 (m-80) REVERT: B 8 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7354 (mt-10) REVERT: B 240 MET cc_start: 0.5900 (pp-130) cc_final: 0.5404 (pp-130) REVERT: B 261 ASP cc_start: 0.6998 (t70) cc_final: 0.6685 (t0) REVERT: B 295 THR cc_start: 0.8253 (m) cc_final: 0.7962 (p) REVERT: H 147 VAL cc_start: 0.8422 (OUTLIER) cc_final: 0.8092 (m) outliers start: 42 outliers final: 13 residues processed: 267 average time/residue: 1.2113 time to fit residues: 346.4278 Evaluate side-chains 242 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 227 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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 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 59 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9752 Z= 0.291 Angle : 0.597 8.271 13226 Z= 0.306 Chirality : 0.042 0.138 1525 Planarity : 0.004 0.048 1634 Dihedral : 5.664 45.853 1658 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.60 % Favored : 98.32 % Rotamer: Outliers : 4.75 % Allowed : 16.34 % Favored : 78.91 % 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: 0.97 (0.24), residues: 1190 helix: 2.06 (0.24), residues: 472 sheet: 0.70 (0.29), residues: 303 loop : -1.09 (0.27), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 82 HIS 0.004 0.001 HIS A 63 PHE 0.029 0.002 PHE B 354 TYR 0.017 0.002 TYR H 190 ARG 0.009 0.001 ARG D 28 *********************** 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 281 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 233 time to evaluate : 1.068 Fit side-chains revert: symmetry clash REVERT: A 27 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7186 (mpp) REVERT: A 35 LEU cc_start: 0.8731 (mm) cc_final: 0.8491 (mm) REVERT: A 96 LYS cc_start: 0.8685 (mttt) cc_final: 0.8474 (mttm) REVERT: B 240 MET cc_start: 0.5952 (pp-130) cc_final: 0.5407 (pp-130) REVERT: B 261 ASP cc_start: 0.6995 (t70) cc_final: 0.6693 (t0) REVERT: B 273 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7897 (tt) REVERT: B 295 THR cc_start: 0.8307 (m) cc_final: 0.7987 (p) REVERT: H 91 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8290 (p) REVERT: H 139 VAL cc_start: 0.8972 (OUTLIER) cc_final: 0.8750 (t) REVERT: H 147 VAL cc_start: 0.8564 (OUTLIER) cc_final: 0.8246 (m) outliers start: 48 outliers final: 15 residues processed: 253 average time/residue: 1.2542 time to fit residues: 338.8775 Evaluate side-chains 234 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 214 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 69 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain B residue 34 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 C residue 25 CYS 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 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 106 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 107 optimal weight: 0.0770 chunk 114 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- 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 77 ASN H 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9752 Z= 0.354 Angle : 0.611 8.002 13226 Z= 0.316 Chirality : 0.043 0.143 1525 Planarity : 0.004 0.049 1634 Dihedral : 5.745 46.782 1658 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.60 % Favored : 98.32 % Rotamer: Outliers : 4.06 % Allowed : 17.33 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.24), residues: 1190 helix: 2.02 (0.24), residues: 469 sheet: 0.70 (0.30), residues: 303 loop : -1.06 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 82 HIS 0.004 0.001 HIS B 213 PHE 0.034 0.002 PHE B 354 TYR 0.018 0.002 TYR H 190 ARG 0.010 0.001 ARG D 28 *********************** 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 266 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 225 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LEU cc_start: 0.8756 (mm) cc_final: 0.8513 (mm) REVERT: B 240 MET cc_start: 0.5962 (pp-130) cc_final: 0.5420 (pp-130) REVERT: B 261 ASP cc_start: 0.7057 (t70) cc_final: 0.6769 (t0) REVERT: B 273 LEU cc_start: 0.8361 (tt) cc_final: 0.8032 (tt) REVERT: H 5 VAL cc_start: 0.8451 (t) cc_final: 0.8230 (p) REVERT: H 139 VAL cc_start: 0.8983 (OUTLIER) cc_final: 0.8775 (t) REVERT: H 147 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8269 (m) REVERT: H 178 LEU cc_start: 0.8573 (tt) cc_final: 0.8143 (tp) outliers start: 41 outliers final: 22 residues processed: 245 average time/residue: 1.3177 time to fit residues: 344.3884 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 : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 364 GLN Chi-restraints excluded: chain A residue 388 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 254 CYS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 65 THR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.0870 chunk 97 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 36 ASN C 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9752 Z= 0.220 Angle : 0.555 7.892 13226 Z= 0.284 Chirality : 0.040 0.135 1525 Planarity : 0.004 0.049 1634 Dihedral : 5.383 44.195 1658 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.06 % Allowed : 18.42 % Favored : 77.52 % 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: 1.11 (0.24), residues: 1190 helix: 2.20 (0.24), residues: 469 sheet: 0.71 (0.30), residues: 295 loop : -0.93 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.003 0.001 HIS A 63 PHE 0.033 0.002 PHE B 354 TYR 0.015 0.001 TYR H 190 ARG 0.016 0.001 ARG D 28 *********************** 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 262 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 221 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7230 (mpp) REVERT: A 35 LEU cc_start: 0.8741 (mm) cc_final: 0.8480 (mm) REVERT: A 171 ARG cc_start: 0.6625 (mtt-85) cc_final: 0.6000 (mmt-90) REVERT: B 261 ASP cc_start: 0.6983 (t70) cc_final: 0.6700 (t0) REVERT: H 5 VAL cc_start: 0.8413 (t) cc_final: 0.8185 (p) REVERT: H 91 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8338 (p) REVERT: H 139 VAL cc_start: 0.8974 (OUTLIER) cc_final: 0.8761 (t) REVERT: H 147 VAL cc_start: 0.8622 (OUTLIER) cc_final: 0.8276 (m) REVERT: H 178 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8183 (tp) outliers start: 41 outliers final: 22 residues processed: 241 average time/residue: 1.2452 time to fit residues: 320.5321 Evaluate side-chains 241 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 MET Chi-restraints excluded: chain A residue 162 GLU 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 254 CYS 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 275 SER Chi-restraints excluded: chain C residue 279 SER 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 139 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 178 LEU 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 38 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 HIS C 75 GLN C 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9752 Z= 0.333 Angle : 0.601 7.778 13226 Z= 0.308 Chirality : 0.042 0.139 1525 Planarity : 0.004 0.056 1634 Dihedral : 5.664 50.169 1658 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.06 % Allowed : 18.91 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.88 (0.24), residues: 1190 helix: 2.01 (0.24), residues: 475 sheet: 0.55 (0.29), residues: 293 loop : -1.05 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 82 HIS 0.004 0.001 HIS B 213 PHE 0.033 0.002 PHE B 354 TYR 0.017 0.002 TYR H 190 ARG 0.015 0.001 ARG D 28 *********************** 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 255 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 214 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 VAL cc_start: 0.8747 (t) cc_final: 0.8177 (t) REVERT: A 27 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.7253 (mpp) REVERT: A 35 LEU cc_start: 0.8760 (mm) cc_final: 0.8522 (mm) REVERT: A 171 ARG cc_start: 0.6622 (mtt-85) cc_final: 0.5965 (mmt-90) REVERT: B 53 MET cc_start: 0.7369 (mmt) cc_final: 0.7108 (mmp) REVERT: B 240 MET cc_start: 0.5987 (pp-130) cc_final: 0.5513 (pp-130) REVERT: B 261 ASP cc_start: 0.6995 (t70) cc_final: 0.6699 (t0) REVERT: B 273 LEU cc_start: 0.8345 (tt) cc_final: 0.8029 (tt) REVERT: D 28 ARG cc_start: 0.7933 (mmm160) cc_final: 0.7470 (mmt90) REVERT: H 5 VAL cc_start: 0.8431 (t) cc_final: 0.8222 (p) REVERT: H 139 VAL cc_start: 0.8956 (OUTLIER) cc_final: 0.8753 (t) REVERT: H 147 VAL cc_start: 0.8670 (OUTLIER) cc_final: 0.8301 (m) REVERT: H 178 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8195 (tp) outliers start: 41 outliers final: 21 residues processed: 235 average time/residue: 1.2981 time to fit residues: 325.3529 Evaluate side-chains 233 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 208 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 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 254 CYS 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 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 139 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 178 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 65 optimal weight: 0.0970 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 96 optimal weight: 0.1980 chunk 63 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 176 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9752 Z= 0.223 Angle : 0.564 7.547 13226 Z= 0.287 Chirality : 0.041 0.134 1525 Planarity : 0.004 0.051 1634 Dihedral : 5.375 46.236 1658 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.17 % Allowed : 20.00 % Favored : 76.83 % 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: 0.98 (0.24), residues: 1190 helix: 2.14 (0.24), residues: 475 sheet: 0.54 (0.30), residues: 289 loop : -1.00 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 82 HIS 0.003 0.001 HIS A 63 PHE 0.034 0.002 PHE B 354 TYR 0.015 0.001 TYR H 190 ARG 0.010 0.001 ARG D 28 *********************** 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 247 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 215 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 VAL cc_start: 0.8735 (t) cc_final: 0.8140 (t) REVERT: A 27 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7256 (mpp) REVERT: A 35 LEU cc_start: 0.8744 (mm) cc_final: 0.8500 (mm) REVERT: B 240 MET cc_start: 0.6044 (pp-130) cc_final: 0.5598 (pp-130) REVERT: B 261 ASP cc_start: 0.6948 (t70) cc_final: 0.6652 (t0) REVERT: B 273 LEU cc_start: 0.8316 (tt) cc_final: 0.7986 (tt) REVERT: C 273 ILE cc_start: 0.8289 (mp) cc_final: 0.8088 (mt) REVERT: D 32 MET cc_start: 0.6734 (ppp) cc_final: 0.6485 (ppp) REVERT: H 5 VAL cc_start: 0.8362 (t) cc_final: 0.8157 (p) REVERT: H 139 VAL cc_start: 0.8931 (OUTLIER) cc_final: 0.8730 (t) outliers start: 32 outliers final: 17 residues processed: 232 average time/residue: 1.3260 time to fit residues: 328.4536 Evaluate side-chains 230 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 211 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 162 GLU 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 254 CYS 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 139 VAL Chi-restraints excluded: chain H residue 155 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.0270 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 overall best weight: 1.0642 ------------------------------------------------------------------------------- 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 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9752 Z= 0.240 Angle : 0.571 8.509 13226 Z= 0.290 Chirality : 0.041 0.134 1525 Planarity : 0.004 0.060 1634 Dihedral : 5.321 44.139 1658 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.37 % Allowed : 20.50 % 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: 0.92 (0.24), residues: 1190 helix: 2.10 (0.24), residues: 475 sheet: 0.42 (0.29), residues: 292 loop : -0.99 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 82 HIS 0.003 0.001 HIS A 63 PHE 0.034 0.001 PHE B 354 TYR 0.014 0.001 TYR H 190 ARG 0.017 0.001 ARG D 28 *********************** 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 242 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 VAL cc_start: 0.8741 (t) cc_final: 0.8156 (t) REVERT: A 27 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.7252 (mpp) REVERT: A 35 LEU cc_start: 0.8740 (mm) cc_final: 0.8490 (mm) REVERT: B 240 MET cc_start: 0.6096 (pp-130) cc_final: 0.5642 (pp-130) REVERT: B 261 ASP cc_start: 0.6998 (t70) cc_final: 0.6701 (t0) REVERT: B 273 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8023 (tt) REVERT: B 295 THR cc_start: 0.8553 (m) cc_final: 0.8165 (p) REVERT: D 28 ARG cc_start: 0.7710 (mmm160) cc_final: 0.7405 (mmt90) REVERT: D 32 MET cc_start: 0.6775 (ppp) cc_final: 0.6432 (ppp) REVERT: H 5 VAL cc_start: 0.8384 (t) cc_final: 0.8179 (p) REVERT: H 139 VAL cc_start: 0.8888 (OUTLIER) cc_final: 0.8683 (t) outliers start: 34 outliers final: 21 residues processed: 225 average time/residue: 1.3208 time to fit residues: 318.4074 Evaluate side-chains 231 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 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 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 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 87 ARG Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 178 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 0.0060 chunk 63 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 95 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN C 75 GLN C 119 ASN C 176 GLN C 259 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9752 Z= 0.219 Angle : 0.568 8.347 13226 Z= 0.288 Chirality : 0.040 0.133 1525 Planarity : 0.004 0.061 1634 Dihedral : 5.258 43.750 1658 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.07 % Allowed : 20.50 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.94 (0.24), residues: 1190 helix: 2.12 (0.24), residues: 475 sheet: 0.43 (0.29), residues: 291 loop : -0.99 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 82 HIS 0.004 0.001 HIS A 169 PHE 0.033 0.001 PHE B 354 TYR 0.014 0.001 TYR H 190 ARG 0.015 0.001 ARG D 28 *********************** 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 246 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 215 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 VAL cc_start: 0.8737 (t) cc_final: 0.8155 (t) REVERT: A 27 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7223 (mpp) REVERT: A 35 LEU cc_start: 0.8732 (mm) cc_final: 0.8486 (mm) REVERT: B 240 MET cc_start: 0.6063 (pp-130) cc_final: 0.5598 (pp-130) REVERT: B 261 ASP cc_start: 0.6974 (t70) cc_final: 0.6674 (t0) REVERT: B 273 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8025 (tt) REVERT: D 32 MET cc_start: 0.6813 (ppp) cc_final: 0.6518 (ppp) REVERT: H 5 VAL cc_start: 0.8372 (t) cc_final: 0.8169 (p) outliers start: 31 outliers final: 21 residues processed: 231 average time/residue: 1.2718 time to fit residues: 313.5868 Evaluate side-chains 232 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 209 time to evaluate : 1.161 ------------------------------------------------------------------------------- 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 162 GLU 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 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 87 ARG Chi-restraints excluded: chain H residue 91 THR 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 68 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN C 75 GLN C 119 ASN C 176 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9752 Z= 0.215 Angle : 0.582 8.910 13226 Z= 0.295 Chirality : 0.040 0.147 1525 Planarity : 0.004 0.051 1634 Dihedral : 5.227 44.836 1658 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.57 % Allowed : 21.78 % Favored : 75.64 % 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: 0.91 (0.24), residues: 1190 helix: 2.12 (0.24), residues: 475 sheet: 0.34 (0.29), residues: 293 loop : -0.96 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.003 0.001 HIS A 169 PHE 0.032 0.001 PHE B 354 TYR 0.014 0.001 TYR H 190 ARG 0.008 0.001 ARG H 18 ********************** 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 241 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 215 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 VAL cc_start: 0.8731 (t) cc_final: 0.8133 (t) REVERT: A 27 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7242 (mpp) REVERT: A 35 LEU cc_start: 0.8724 (mm) cc_final: 0.8497 (mm) REVERT: B 240 MET cc_start: 0.6026 (pp-130) cc_final: 0.5561 (pp-130) REVERT: B 261 ASP cc_start: 0.6975 (t70) cc_final: 0.6678 (t0) REVERT: B 273 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8032 (tt) REVERT: C 20 ASP cc_start: 0.7634 (m-30) cc_final: 0.7412 (m-30) REVERT: D 32 MET cc_start: 0.6824 (ppp) cc_final: 0.6448 (ppp) REVERT: H 5 VAL cc_start: 0.8364 (t) cc_final: 0.8159 (p) outliers start: 26 outliers final: 19 residues processed: 230 average time/residue: 1.2933 time to fit residues: 316.9680 Evaluate side-chains 232 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 211 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 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 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 279 SER 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 178 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 13 optimal weight: 0.0770 chunk 26 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 96 optimal weight: 0.0770 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 0.1980 chunk 82 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN 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 = 0.3598 r_free = 0.3598 target = 0.110896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.098383 restraints weight = 16021.807| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.04 r_work: 0.3278 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9752 Z= 0.165 Angle : 0.576 9.242 13226 Z= 0.290 Chirality : 0.040 0.131 1525 Planarity : 0.004 0.050 1634 Dihedral : 5.021 48.613 1658 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.78 % Allowed : 22.38 % 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 (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: 1.04 (0.24), residues: 1190 helix: 2.23 (0.24), residues: 475 sheet: 0.38 (0.29), residues: 293 loop : -0.88 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 169 HIS 0.003 0.001 HIS A 169 PHE 0.032 0.001 PHE A 430 TYR 0.012 0.001 TYR H 190 ARG 0.010 0.001 ARG D 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5088.84 seconds wall clock time: 91 minutes 23.77 seconds (5483.77 seconds total)