Starting phenix.real_space_refine on Fri Sep 11 12:48:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6xqn_22290/09_2026/6xqn_22290.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xqn_22290/09_2026/6xqn_22290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xqn_22290/09_2026/6xqn_22290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xqn_22290/09_2026/6xqn_22290.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6xqn_22290/09_2026/6xqn_22290.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6xqn_22290/09_2026/6xqn_22290.cif" model { file = "/net/cci-nas-00/data/ceres_data/6xqn_22290/09_2026/6xqn_22290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xqn_22290/09_2026/6xqn_22290.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 37 5.16 5 C 6170 2.51 5 N 1561 2.21 5 O 1664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9433 Number of models: 1 Model: "" Number of chains: 10 Chain: "E" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 223 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 29} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1166 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 3, 'GLN:plan1': 5, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 85 Chain: "B" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1128 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 3, 'GLN:plan1': 6, 'GLU:plan': 10, 'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 107 Chain: "G" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 174 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 23} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1156 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain breaks: 1 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 3, 'GLN:plan1': 5, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 94 Chain: "H" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 186 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 24} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1137 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain breaks: 1 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 3, 'GLN:plan1': 5, 'GLU:plan': 10, 'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 103 Chain: "I" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2243 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 6, 'TRANS': 300} Chain breaks: 3 Unresolved non-hydrogen bonds: 267 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 223 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 15, 'ARG:plan': 5, 'PHE:plan': 2, 'ASP:plan': 12, 'ASN:plan1': 2, 'GLN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 185 Chain: "J" Number of atoms: 2019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2019 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 4, 'TRANS': 286} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 418 Unresolved non-hydrogen angles: 501 Unresolved non-hydrogen dihedrals: 346 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ARG:plan': 13, 'GLN:plan1': 7, 'GLU:plan': 21, 'ASP:plan': 12, 'HIS:plan': 4, 'ASN:plan1': 5, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 254 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.18, per 1000 atoms: 0.23 Number of scatterers: 9433 At special positions: 0 Unit cell: (86.184, 112.784, 165.984, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 37 16.00 O 1664 8.00 N 1561 7.00 C 6170 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 357.1 milliseconds 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2458 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 2 sheets defined 80.6% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'E' and resid 65 through 95 removed outlier: 4.326A pdb=" N ARG E 69 " --> pdb=" O PHE E 65 " (cutoff:3.500A) Proline residue: E 76 - end of helix Processing helix chain 'A' and resid 179 through 190 Processing helix chain 'A' and resid 194 through 254 removed outlier: 3.788A pdb=" N GLN A 198 " --> pdb=" O GLU A 194 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) Proline residue: A 216 - end of helix removed outlier: 4.083A pdb=" N ARG A 231 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 286 removed outlier: 3.627A pdb=" N THR A 267 " --> pdb=" O MET A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 308 Processing helix chain 'A' and resid 313 through 336 Processing helix chain 'B' and resid 176 through 191 Processing helix chain 'B' and resid 194 through 256 removed outlier: 3.542A pdb=" N LYS B 199 " --> pdb=" O HIS B 195 " (cutoff:3.500A) Proline residue: B 216 - end of helix removed outlier: 4.426A pdb=" N ARG B 231 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 300 removed outlier: 3.514A pdb=" N THR B 267 " --> pdb=" O MET B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 336 removed outlier: 3.538A pdb=" N ASP B 336 " --> pdb=" O LYS B 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 92 Proline residue: G 76 - end of helix Processing helix chain 'C' and resid 179 through 190 Processing helix chain 'C' and resid 194 through 256 removed outlier: 3.734A pdb=" N GLN C 198 " --> pdb=" O GLU C 194 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU C 208 " --> pdb=" O THR C 204 " (cutoff:3.500A) Proline residue: C 216 - end of helix removed outlier: 3.765A pdb=" N ARG C 231 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 285 Processing helix chain 'C' and resid 293 through 308 Processing helix chain 'C' and resid 313 through 336 Processing helix chain 'H' and resid 68 through 92 Proline residue: H 76 - end of helix Processing helix chain 'D' and resid 176 through 192 Processing helix chain 'D' and resid 197 through 256 Proline residue: D 216 - end of helix removed outlier: 4.057A pdb=" N ARG D 231 " --> pdb=" O VAL D 227 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 300 removed outlier: 3.873A pdb=" N THR D 267 " --> pdb=" O MET D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 336 removed outlier: 3.541A pdb=" N TYR D 317 " --> pdb=" O ASP D 313 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 122 Processing helix chain 'I' and resid 125 through 132 Processing helix chain 'I' and resid 148 through 155 Processing helix chain 'I' and resid 193 through 199 removed outlier: 3.767A pdb=" N GLY I 199 " --> pdb=" O TYR I 196 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 218 removed outlier: 3.563A pdb=" N PHE I 211 " --> pdb=" O SER I 207 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER I 217 " --> pdb=" O THR I 213 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR I 218 " --> pdb=" O THR I 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 219 through 230 removed outlier: 3.638A pdb=" N PHE I 223 " --> pdb=" O PRO I 219 " (cutoff:3.500A) Processing helix chain 'I' and resid 239 through 253 Processing helix chain 'I' and resid 278 through 284 Processing helix chain 'I' and resid 292 through 314 Processing helix chain 'I' and resid 323 through 333 Processing helix chain 'I' and resid 339 through 351 Processing helix chain 'I' and resid 360 through 372 Processing helix chain 'I' and resid 373 through 388 removed outlier: 3.573A pdb=" N GLY I 388 " --> pdb=" O TYR I 384 " (cutoff:3.500A) Processing helix chain 'I' and resid 392 through 405 Processing helix chain 'I' and resid 409 through 419 removed outlier: 3.552A pdb=" N CYS I 413 " --> pdb=" O SER I 409 " (cutoff:3.500A) Processing helix chain 'I' and resid 429 through 442 Processing helix chain 'J' and resid 87 through 94 Processing helix chain 'J' and resid 105 through 115 Processing helix chain 'J' and resid 128 through 136 removed outlier: 3.941A pdb=" N LEU J 136 " --> pdb=" O ILE J 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 153 Processing helix chain 'J' and resid 159 through 172 Processing helix chain 'J' and resid 174 through 185 removed outlier: 3.517A pdb=" N HIS J 178 " --> pdb=" O HIS J 174 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP J 185 " --> pdb=" O PHE J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 205 Processing helix chain 'J' and resid 232 through 240 Processing helix chain 'J' and resid 248 through 273 removed outlier: 3.639A pdb=" N PHE J 252 " --> pdb=" O HIS J 248 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 289 Processing helix chain 'J' and resid 295 through 306 removed outlier: 3.809A pdb=" N TYR J 299 " --> pdb=" O ASN J 295 " (cutoff:3.500A) Processing helix chain 'J' and resid 314 through 327 Processing helix chain 'J' and resid 328 through 342 Processing helix chain 'J' and resid 346 through 359 Processing helix chain 'J' and resid 363 through 374 Processing helix chain 'J' and resid 383 through 397 Processing sheet with id=AA1, first strand: chain 'I' and resid 144 through 146 removed outlier: 6.318A pdb=" N LYS I 135 " --> pdb=" O LYS I 174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 101 through 103 786 hydrogen bonds defined for protein. 2337 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.32 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2989 1.34 - 1.46: 1831 1.46 - 1.58: 4722 1.58 - 1.69: 0 1.69 - 1.81: 69 Bond restraints: 9611 Sorted by residual: bond pdb=" N LYS A 308 " pdb=" CA LYS A 308 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.52e-02 4.33e+03 5.97e+00 bond pdb=" N LYS C 308 " pdb=" CA LYS C 308 " ideal model delta sigma weight residual 1.462 1.497 -0.035 1.46e-02 4.69e+03 5.87e+00 bond pdb=" C ALA A 307 " pdb=" N LYS A 308 " ideal model delta sigma weight residual 1.332 1.349 -0.017 1.40e-02 5.10e+03 1.50e+00 bond pdb=" C ALA C 307 " pdb=" N LYS C 308 " ideal model delta sigma weight residual 1.333 1.350 -0.017 1.45e-02 4.76e+03 1.37e+00 bond pdb=" CG LEU J 184 " pdb=" CD2 LEU J 184 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.18e+00 ... (remaining 9606 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 12825 1.85 - 3.69: 228 3.69 - 5.54: 35 5.54 - 7.39: 11 7.39 - 9.23: 4 Bond angle restraints: 13103 Sorted by residual: angle pdb=" N ARG I 129 " pdb=" CA ARG I 129 " pdb=" CB ARG I 129 " ideal model delta sigma weight residual 110.32 119.55 -9.23 1.70e+00 3.46e-01 2.95e+01 angle pdb=" N LEU J 328 " pdb=" CA LEU J 328 " pdb=" C LEU J 328 " ideal model delta sigma weight residual 112.34 118.26 -5.92 1.30e+00 5.92e-01 2.07e+01 angle pdb=" CA LEU G 92 " pdb=" CB LEU G 92 " pdb=" CG LEU G 92 " ideal model delta sigma weight residual 116.30 125.32 -9.02 3.50e+00 8.16e-02 6.64e+00 angle pdb=" CA LEU H 92 " pdb=" CB LEU H 92 " pdb=" CG LEU H 92 " ideal model delta sigma weight residual 116.30 125.15 -8.85 3.50e+00 8.16e-02 6.39e+00 angle pdb=" C THR D 254 " pdb=" N TRP D 255 " pdb=" CA TRP D 255 " ideal model delta sigma weight residual 122.26 118.46 3.80 1.59e+00 3.96e-01 5.71e+00 ... (remaining 13098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 4984 17.62 - 35.25: 485 35.25 - 52.87: 87 52.87 - 70.49: 12 70.49 - 88.12: 7 Dihedral angle restraints: 5575 sinusoidal: 1800 harmonic: 3775 Sorted by residual: dihedral pdb=" CA ALA A 307 " pdb=" C ALA A 307 " pdb=" N LYS A 308 " pdb=" CA LYS A 308 " ideal model delta harmonic sigma weight residual -180.00 -155.04 -24.96 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" N ARG I 129 " pdb=" C ARG I 129 " pdb=" CA ARG I 129 " pdb=" CB ARG I 129 " ideal model delta harmonic sigma weight residual 122.80 133.74 -10.94 0 2.50e+00 1.60e-01 1.91e+01 dihedral pdb=" CA HIS J 327 " pdb=" C HIS J 327 " pdb=" N LEU J 328 " pdb=" CA LEU J 328 " ideal model delta harmonic sigma weight residual -180.00 -159.87 -20.13 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 5572 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1440 0.069 - 0.137: 147 0.137 - 0.206: 5 0.206 - 0.274: 0 0.274 - 0.343: 1 Chirality restraints: 1593 Sorted by residual: chirality pdb=" CA ARG I 129 " pdb=" N ARG I 129 " pdb=" C ARG I 129 " pdb=" CB ARG I 129 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CB VAL I 416 " pdb=" CA VAL I 416 " pdb=" CG1 VAL I 416 " pdb=" CG2 VAL I 416 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CB ILE J 366 " pdb=" CA ILE J 366 " pdb=" CG1 ILE J 366 " pdb=" CG2 ILE J 366 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.10e-01 ... (remaining 1590 not shown) Planarity restraints: 1632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 196 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.13e+00 pdb=" C GLN B 196 " 0.052 2.00e-02 2.50e+03 pdb=" O GLN B 196 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU B 197 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 307 " 0.014 2.00e-02 2.50e+03 2.68e-02 7.20e+00 pdb=" C ALA C 307 " -0.046 2.00e-02 2.50e+03 pdb=" O ALA C 307 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS C 308 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 307 " 0.014 2.00e-02 2.50e+03 2.68e-02 7.17e+00 pdb=" C ALA A 307 " -0.046 2.00e-02 2.50e+03 pdb=" O ALA A 307 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS A 308 " 0.015 2.00e-02 2.50e+03 ... (remaining 1629 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 32 2.52 - 3.11: 7273 3.11 - 3.71: 14654 3.71 - 4.30: 18389 4.30 - 4.90: 31150 Nonbonded interactions: 71498 Sorted by model distance: nonbonded pdb=" OE2 GLU C 264 " pdb="CA CA B 401 " model vdw 1.922 2.510 nonbonded pdb=" OE2 GLU D 264 " pdb="CA CA B 401 " model vdw 1.978 2.510 nonbonded pdb=" OE2 GLU A 264 " pdb="CA CA B 401 " model vdw 2.132 2.510 nonbonded pdb=" OE2 GLU B 264 " pdb="CA CA B 401 " model vdw 2.139 2.510 nonbonded pdb=" OH TYR B 272 " pdb=" OE1 GLN C 246 " model vdw 2.229 3.040 ... (remaining 71493 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 178 through 194 or (resid 195 through 200 and (name N or n \ ame CA or name C or name O or name CB )) or resid 201 through 202 or (resid 203 \ and (name N or name CA or name C or name O or name CB )) or resid 204 through 20 \ 5 or (resid 206 and (name N or name CA or name C or name O or name CB )) or resi \ d 207 through 219 or (resid 220 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD )) or resid 221 through 251 or (resid 252 and (name \ N or name CA or name C or name O or name CB )) or resid 253 through 256 or (resi \ d 257 and (name N or name CA or name C or name O or name CB )) or resid 258 thro \ ugh 299 or (resid 300 and (name N or name CA or name C or name O or name CB )) o \ r resid 312 through 327 or (resid 328 and (name N or name CA or name C or name O \ or name CB )) or resid 329 through 336)) selection = (chain 'B' and (resid 178 through 251 or (resid 252 and (name N or name CA or na \ me C or name O or name CB )) or resid 253 through 256 or (resid 257 and (name N \ or name CA or name C or name O or name CB )) or resid 258 through 286 or resid 2 \ 92 through 336)) selection = (chain 'C' and (resid 178 through 194 or (resid 195 through 200 and (name N or n \ ame CA or name C or name O or name CB )) or resid 201 through 202 or (resid 203 \ and (name N or name CA or name C or name O or name CB )) or resid 204 through 20 \ 5 or (resid 206 and (name N or name CA or name C or name O or name CB )) or resi \ d 207 through 219 or (resid 220 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD )) or resid 221 through 299 or (resid 300 and (name \ N or name CA or name C or name O or name CB )) or resid 312 through 327 or (resi \ d 328 and (name N or name CA or name C or name O or name CB )) or resid 329 thro \ ugh 336)) selection = (chain 'D' and (resid 178 through 191 or (resid 192 through 200 and (name N or n \ ame CA or name C or name O or name CB )) or resid 201 through 202 or (resid 203 \ and (name N or name CA or name C or name O or name CB )) or resid 204 through 20 \ 5 or (resid 206 and (name N or name CA or name C or name O or name CB )) or resi \ d 207 through 251 or (resid 252 and (name N or name CA or name C or name O or na \ me CB )) or resid 253 through 256 or (resid 257 and (name N or name CA or name C \ or name O or name CB )) or resid 258 through 286 or resid 292 through 336)) } ncs_group { reference = chain 'G' selection = (chain 'H' and (resid 68 through 85 or (resid 86 and (name N or name CA or name \ C or name O or name CB )) or resid 87 through 92)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 9.490 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9611 Z= 0.221 Angle : 0.666 9.232 13103 Z= 0.369 Chirality : 0.041 0.343 1593 Planarity : 0.004 0.043 1632 Dihedral : 14.562 88.119 3117 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.87 % Allowed : 17.32 % Favored : 79.81 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.22), residues: 1256 helix: 0.79 (0.15), residues: 991 sheet: -4.08 (0.89), residues: 9 loop : -2.39 (0.30), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 154 TYR 0.010 0.001 TYR I 114 PHE 0.037 0.002 PHE I 282 TRP 0.020 0.002 TRP D 237 HIS 0.004 0.001 HIS J 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.22 ( 9611) covalent geometry : angle 0.66633 / 0.37 (13103) hydrogen bonds : bond 0.10533 / 7.47 ( 786) hydrogen bonds : angle 5.11210 / 3.70 ( 2337) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 265 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 LEU cc_start: 0.6666 (OUTLIER) cc_final: 0.6393 (mp) REVERT: A 220 LYS cc_start: 0.7349 (mmtt) cc_final: 0.7103 (mttp) REVERT: A 234 TRP cc_start: 0.7030 (t60) cc_final: 0.6527 (t60) REVERT: A 313 ASP cc_start: 0.6357 (t0) cc_final: 0.5872 (t0) REVERT: B 281 TYR cc_start: 0.6992 (t80) cc_final: 0.6015 (t80) REVERT: B 321 LYS cc_start: 0.7331 (mttt) cc_final: 0.7068 (mtpt) REVERT: B 322 ASP cc_start: 0.7702 (t70) cc_final: 0.7135 (m-30) REVERT: G 88 ILE cc_start: 0.6256 (OUTLIER) cc_final: 0.5851 (pt) REVERT: C 206 GLN cc_start: 0.7969 (tp40) cc_final: 0.7762 (tp40) REVERT: C 235 MET cc_start: 0.6664 (tpp) cc_final: 0.6415 (mtt) REVERT: C 262 ILE cc_start: 0.8536 (tp) cc_final: 0.8281 (tt) REVERT: C 324 ILE cc_start: 0.7169 (tt) cc_final: 0.6507 (pt) REVERT: H 80 ILE cc_start: 0.7026 (OUTLIER) cc_final: 0.6758 (mm) REVERT: D 286 ARG cc_start: 0.6907 (mmt90) cc_final: 0.6121 (ttp80) REVERT: D 332 LYS cc_start: 0.8338 (ttmt) cc_final: 0.7926 (tttt) REVERT: I 125 ASP cc_start: 0.8609 (t70) cc_final: 0.8401 (t0) REVERT: I 135 LYS cc_start: 0.8017 (tttt) cc_final: 0.7782 (tttp) REVERT: I 187 LYS cc_start: 0.8660 (mmtt) cc_final: 0.8329 (mttt) REVERT: I 201 CYS cc_start: 0.7100 (m) cc_final: 0.5902 (p) REVERT: I 247 GLN cc_start: 0.8227 (mt0) cc_final: 0.7298 (tp40) REVERT: I 309 LYS cc_start: 0.8088 (ttmt) cc_final: 0.7656 (ttpp) REVERT: J 112 SER cc_start: 0.8026 (OUTLIER) cc_final: 0.7818 (p) REVERT: J 160 TYR cc_start: 0.7066 (t80) cc_final: 0.6593 (t80) REVERT: J 201 GLN cc_start: 0.7781 (mt0) cc_final: 0.7377 (mt0) REVERT: J 300 TRP cc_start: 0.7051 (m100) cc_final: 0.6694 (m100) REVERT: J 318 PHE cc_start: 0.6230 (t80) cc_final: 0.5949 (t80) outliers start: 24 outliers final: 10 residues processed: 285 average time/residue: 0.1031 time to fit residues: 40.0051 Evaluate side-chains 201 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain J residue 112 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN C 315 ASN D 226 GLN D 315 ASN I 159 ASN J 323 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.185894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.137647 restraints weight = 14947.345| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.79 r_work: 0.3743 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9611 Z= 0.143 Angle : 0.562 8.007 13103 Z= 0.292 Chirality : 0.036 0.180 1593 Planarity : 0.004 0.035 1632 Dihedral : 4.810 50.702 1376 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.06 % Allowed : 21.27 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.23), residues: 1256 helix: 2.32 (0.16), residues: 1014 sheet: -3.75 (0.96), residues: 9 loop : -1.95 (0.32), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 333 TYR 0.011 0.001 TYR A 317 PHE 0.027 0.002 PHE J 90 TRP 0.010 0.001 TRP A 255 HIS 0.009 0.001 HIS J 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 9611) covalent geometry : angle 0.56156 / 0.29 (13103) hydrogen bonds : bond 0.04528 / 3.12 ( 786) hydrogen bonds : angle 3.94534 / 2.92 ( 2337) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 LYS cc_start: 0.7728 (mmtt) cc_final: 0.7403 (mttp) REVERT: B 322 ASP cc_start: 0.8231 (t70) cc_final: 0.7600 (m-30) REVERT: B 324 ILE cc_start: 0.7738 (tt) cc_final: 0.7491 (pt) REVERT: C 235 MET cc_start: 0.6746 (tpp) cc_final: 0.6476 (mtt) REVERT: C 326 LYS cc_start: 0.7634 (tptp) cc_final: 0.7143 (ttmm) REVERT: D 206 GLN cc_start: 0.8373 (tp40) cc_final: 0.8166 (tp40) REVERT: D 213 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7956 (tm-30) REVERT: D 226 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.7310 (pp30) REVERT: D 286 ARG cc_start: 0.6847 (mmt90) cc_final: 0.6121 (ttp80) REVERT: D 332 LYS cc_start: 0.8659 (ttmt) cc_final: 0.8134 (tttt) REVERT: I 135 LYS cc_start: 0.8385 (tttt) cc_final: 0.8141 (tttp) REVERT: I 187 LYS cc_start: 0.8703 (mmtt) cc_final: 0.8260 (mttt) REVERT: I 201 CYS cc_start: 0.7666 (m) cc_final: 0.6050 (p) REVERT: I 245 GLN cc_start: 0.7037 (mt0) cc_final: 0.6634 (mp10) REVERT: I 309 LYS cc_start: 0.8279 (ttmt) cc_final: 0.7972 (ttpp) REVERT: I 385 HIS cc_start: 0.7937 (t70) cc_final: 0.6737 (m-70) REVERT: J 300 TRP cc_start: 0.6922 (m100) cc_final: 0.6495 (m100) outliers start: 34 outliers final: 18 residues processed: 214 average time/residue: 0.0906 time to fit residues: 27.5989 Evaluate side-chains 186 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 315 ASN Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 169 ILE Chi-restraints excluded: chain J residue 266 MET Chi-restraints excluded: chain J residue 373 ILE Chi-restraints excluded: chain J residue 381 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 chunk 94 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 226 GLN D 246 GLN D 315 ASN I 159 ASN I 165 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.183483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.138432 restraints weight = 15050.434| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 3.17 r_work: 0.3677 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9611 Z= 0.150 Angle : 0.542 7.711 13103 Z= 0.280 Chirality : 0.036 0.280 1593 Planarity : 0.003 0.036 1632 Dihedral : 4.038 39.510 1359 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.06 % Allowed : 23.66 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.80 (0.23), residues: 1256 helix: 2.64 (0.16), residues: 1018 sheet: -1.13 (1.87), residues: 8 loop : -1.92 (0.32), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 333 TYR 0.013 0.001 TYR B 281 PHE 0.026 0.002 PHE J 90 TRP 0.008 0.001 TRP A 260 HIS 0.008 0.001 HIS I 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 9611) covalent geometry : angle 0.54201 / 0.28 (13103) hydrogen bonds : bond 0.04433 / 3.07 ( 786) hydrogen bonds : angle 3.74121 / 2.76 ( 2337) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 90 ASN cc_start: 0.7481 (t0) cc_final: 0.6843 (m-40) REVERT: A 217 LEU cc_start: 0.6598 (OUTLIER) cc_final: 0.6393 (mm) REVERT: A 220 LYS cc_start: 0.7788 (mmtt) cc_final: 0.7453 (mttp) REVERT: A 324 ILE cc_start: 0.8173 (mp) cc_final: 0.7947 (mp) REVERT: B 321 LYS cc_start: 0.7838 (mtpt) cc_final: 0.7609 (mtpt) REVERT: B 322 ASP cc_start: 0.8146 (t70) cc_final: 0.7517 (m-30) REVERT: B 324 ILE cc_start: 0.7822 (tt) cc_final: 0.7592 (pt) REVERT: C 235 MET cc_start: 0.6784 (tpp) cc_final: 0.6499 (mtt) REVERT: C 326 LYS cc_start: 0.7792 (tptp) cc_final: 0.7302 (ttmm) REVERT: D 213 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8269 (tm-30) REVERT: D 226 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7393 (pp30) REVERT: D 286 ARG cc_start: 0.6838 (mmt90) cc_final: 0.6139 (ttp80) REVERT: D 329 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7094 (tp) REVERT: D 332 LYS cc_start: 0.8724 (ttmt) cc_final: 0.8182 (ttpt) REVERT: I 135 LYS cc_start: 0.8487 (tttt) cc_final: 0.8211 (tttp) REVERT: I 187 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8121 (mtmt) REVERT: I 201 CYS cc_start: 0.7793 (m) cc_final: 0.6769 (t) REVERT: I 245 GLN cc_start: 0.6889 (mt0) cc_final: 0.6656 (mp10) REVERT: I 309 LYS cc_start: 0.8317 (ttmt) cc_final: 0.7977 (ttpp) REVERT: I 385 HIS cc_start: 0.8073 (t70) cc_final: 0.6840 (m-70) REVERT: J 300 TRP cc_start: 0.6868 (m100) cc_final: 0.6370 (m100) outliers start: 34 outliers final: 20 residues processed: 201 average time/residue: 0.0889 time to fit residues: 25.5903 Evaluate side-chains 187 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 169 ILE Chi-restraints excluded: chain J residue 266 MET Chi-restraints excluded: chain J residue 340 LEU Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 373 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 28 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 100 optimal weight: 0.2980 chunk 11 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 15 optimal weight: 20.0000 chunk 70 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 315 ASN C 316 GLN D 206 GLN D 226 GLN D 315 ASN I 159 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.192948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.147086 restraints weight = 15180.054| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 3.18 r_work: 0.3868 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9611 Z= 0.122 Angle : 0.510 8.103 13103 Z= 0.261 Chirality : 0.034 0.152 1593 Planarity : 0.003 0.036 1632 Dihedral : 3.805 28.025 1359 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.06 % Allowed : 25.57 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.10 (0.24), residues: 1256 helix: 2.86 (0.16), residues: 1019 sheet: None (None), residues: 0 loop : -1.87 (0.32), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 333 TYR 0.008 0.001 TYR A 317 PHE 0.026 0.001 PHE J 90 TRP 0.008 0.001 TRP A 260 HIS 0.002 0.000 HIS I 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 9611) covalent geometry : angle 0.50981 / 0.26 (13103) hydrogen bonds : bond 0.04093 / 2.83 ( 786) hydrogen bonds : angle 3.56578 / 2.62 ( 2337) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 90 ASN cc_start: 0.7537 (t0) cc_final: 0.6871 (m-40) REVERT: A 220 LYS cc_start: 0.7926 (mmtt) cc_final: 0.7639 (mttp) REVERT: A 235 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.6993 (mpp) REVERT: A 324 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.8015 (mp) REVERT: B 322 ASP cc_start: 0.8079 (t70) cc_final: 0.7547 (m-30) REVERT: C 206 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.7201 (tm-30) REVERT: C 235 MET cc_start: 0.6885 (tpp) cc_final: 0.6629 (mtt) REVERT: C 326 LYS cc_start: 0.7818 (tptp) cc_final: 0.7378 (ttmm) REVERT: D 213 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8193 (tm-30) REVERT: D 226 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7453 (pp30) REVERT: D 286 ARG cc_start: 0.6815 (mmt90) cc_final: 0.6356 (ttp-170) REVERT: D 320 LEU cc_start: 0.7909 (tp) cc_final: 0.7393 (tp) REVERT: D 332 LYS cc_start: 0.8773 (ttmt) cc_final: 0.8273 (tttt) REVERT: I 125 ASP cc_start: 0.8567 (t0) cc_final: 0.8287 (t0) REVERT: I 187 LYS cc_start: 0.8672 (mmtt) cc_final: 0.8387 (mtmt) REVERT: I 200 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7156 (mm-30) REVERT: I 309 LYS cc_start: 0.8420 (ttmt) cc_final: 0.8116 (ttpp) REVERT: I 385 HIS cc_start: 0.8061 (t70) cc_final: 0.6871 (m-70) REVERT: J 300 TRP cc_start: 0.6855 (m100) cc_final: 0.6338 (m100) outliers start: 34 outliers final: 22 residues processed: 197 average time/residue: 0.0906 time to fit residues: 25.2494 Evaluate side-chains 186 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 315 ASN Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 169 ILE Chi-restraints excluded: chain J residue 266 MET Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 373 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 22 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 6 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 206 GLN D 226 GLN ** D 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 ASN I 247 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.190660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.146838 restraints weight = 15165.871| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 3.12 r_work: 0.3833 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9611 Z= 0.137 Angle : 0.525 8.726 13103 Z= 0.269 Chirality : 0.035 0.155 1593 Planarity : 0.003 0.036 1632 Dihedral : 3.659 27.794 1357 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 5.97 % Allowed : 25.81 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.19 (0.24), residues: 1256 helix: 2.92 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -1.87 (0.33), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 333 TYR 0.008 0.001 TYR B 317 PHE 0.024 0.001 PHE J 90 TRP 0.010 0.001 TRP A 260 HIS 0.002 0.000 HIS I 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 9611) covalent geometry : angle 0.52514 / 0.27 (13103) hydrogen bonds : bond 0.04092 / 2.83 ( 786) hydrogen bonds : angle 3.53836 / 2.60 ( 2337) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 172 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 90 ASN cc_start: 0.7591 (t0) cc_final: 0.6837 (m-40) REVERT: A 213 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7578 (tm-30) REVERT: A 220 LYS cc_start: 0.7943 (mmtt) cc_final: 0.7645 (mttp) REVERT: A 235 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.6971 (mpp) REVERT: A 324 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.8071 (mp) REVERT: B 322 ASP cc_start: 0.8114 (t70) cc_final: 0.7597 (m-30) REVERT: B 327 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7368 (tp) REVERT: C 206 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.7138 (tm-30) REVERT: C 235 MET cc_start: 0.6945 (tpp) cc_final: 0.6663 (mtt) REVERT: C 326 LYS cc_start: 0.7888 (tptp) cc_final: 0.7478 (ttmm) REVERT: H 68 ILE cc_start: 0.6526 (OUTLIER) cc_final: 0.6314 (tp) REVERT: D 213 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8194 (tm-30) REVERT: D 286 ARG cc_start: 0.6830 (mmt90) cc_final: 0.6382 (ttp-170) REVERT: D 320 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7362 (tp) REVERT: D 329 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7273 (tp) REVERT: D 330 ASP cc_start: 0.9118 (t0) cc_final: 0.8760 (t0) REVERT: D 332 LYS cc_start: 0.8772 (ttmt) cc_final: 0.8276 (tttt) REVERT: I 125 ASP cc_start: 0.8567 (t0) cc_final: 0.8248 (t0) REVERT: I 187 LYS cc_start: 0.8661 (mmtt) cc_final: 0.8341 (mtmt) REVERT: I 200 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7257 (mm-30) REVERT: I 309 LYS cc_start: 0.8435 (ttmt) cc_final: 0.8126 (ttpp) REVERT: J 108 ASP cc_start: 0.8324 (m-30) cc_final: 0.7986 (m-30) REVERT: J 300 TRP cc_start: 0.6848 (m100) cc_final: 0.6278 (m100) outliers start: 50 outliers final: 24 residues processed: 211 average time/residue: 0.0808 time to fit residues: 24.7056 Evaluate side-chains 194 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 169 ILE Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 373 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 64 optimal weight: 3.9990 chunk 15 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 102 optimal weight: 0.0470 chunk 1 optimal weight: 1.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN ** D 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 ASN I 247 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.190506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.144123 restraints weight = 15073.205| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 3.00 r_work: 0.3849 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9611 Z= 0.129 Angle : 0.506 6.518 13103 Z= 0.262 Chirality : 0.035 0.156 1593 Planarity : 0.003 0.037 1632 Dihedral : 3.614 27.710 1357 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 5.50 % Allowed : 26.52 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.26 (0.24), residues: 1256 helix: 2.97 (0.16), residues: 1019 sheet: None (None), residues: 0 loop : -1.85 (0.33), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 333 TYR 0.019 0.001 TYR B 317 PHE 0.024 0.001 PHE J 90 TRP 0.010 0.001 TRP A 260 HIS 0.002 0.000 HIS J 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 9611) covalent geometry : angle 0.50567 / 0.26 (13103) hydrogen bonds : bond 0.03985 / 2.76 ( 786) hydrogen bonds : angle 3.49622 / 2.57 ( 2337) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 169 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7567 (tm-30) REVERT: A 220 LYS cc_start: 0.7981 (mmtt) cc_final: 0.7674 (mttp) REVERT: A 235 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.6934 (mpp) REVERT: A 324 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8155 (mp) REVERT: B 322 ASP cc_start: 0.8014 (t70) cc_final: 0.7572 (m-30) REVERT: B 327 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7355 (tp) REVERT: C 206 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.7078 (tm-30) REVERT: C 231 ARG cc_start: 0.7973 (ttm-80) cc_final: 0.7591 (mtm110) REVERT: C 235 MET cc_start: 0.6936 (tpp) cc_final: 0.6617 (mtt) REVERT: C 326 LYS cc_start: 0.7879 (tptp) cc_final: 0.7450 (ttmm) REVERT: H 68 ILE cc_start: 0.6528 (OUTLIER) cc_final: 0.6304 (tp) REVERT: D 206 GLN cc_start: 0.8228 (tp-100) cc_final: 0.7997 (tm-30) REVERT: D 213 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8187 (tm-30) REVERT: D 320 LEU cc_start: 0.7833 (tp) cc_final: 0.7282 (tp) REVERT: D 329 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7247 (tp) REVERT: D 330 ASP cc_start: 0.9086 (t0) cc_final: 0.8702 (t0) REVERT: D 332 LYS cc_start: 0.8780 (ttmt) cc_final: 0.8317 (tttt) REVERT: I 125 ASP cc_start: 0.8648 (t0) cc_final: 0.8354 (t0) REVERT: I 187 LYS cc_start: 0.8668 (mmtt) cc_final: 0.8359 (mtmt) REVERT: I 200 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7202 (mm-30) REVERT: I 309 LYS cc_start: 0.8429 (ttmt) cc_final: 0.8109 (ttpp) REVERT: I 437 MET cc_start: 0.6296 (mmp) cc_final: 0.5763 (mmp) REVERT: J 108 ASP cc_start: 0.8309 (m-30) cc_final: 0.8017 (m-30) REVERT: J 300 TRP cc_start: 0.6845 (m100) cc_final: 0.6228 (m100) outliers start: 46 outliers final: 29 residues processed: 202 average time/residue: 0.0820 time to fit residues: 24.1837 Evaluate side-chains 198 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 237 TRP Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 197 PHE Chi-restraints excluded: chain J residue 298 ILE Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 373 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 99 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 59 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 ASN I 159 ASN I 247 GLN J 178 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.190731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.144516 restraints weight = 15075.358| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 2.46 r_work: 0.3947 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3822 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9611 Z= 0.128 Angle : 0.516 6.890 13103 Z= 0.266 Chirality : 0.035 0.155 1593 Planarity : 0.003 0.036 1632 Dihedral : 3.603 27.504 1357 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 5.50 % Allowed : 27.12 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.22 (0.24), residues: 1256 helix: 2.94 (0.16), residues: 1018 sheet: None (None), residues: 0 loop : -1.79 (0.33), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 286 TYR 0.008 0.001 TYR A 317 PHE 0.022 0.001 PHE J 90 TRP 0.015 0.001 TRP B 234 HIS 0.001 0.000 HIS J 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 9611) covalent geometry : angle 0.51575 / 0.27 (13103) hydrogen bonds : bond 0.03954 / 2.75 ( 786) hydrogen bonds : angle 3.46678 / 2.55 ( 2337) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 169 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7717 (tm-30) REVERT: A 220 LYS cc_start: 0.8074 (mmtt) cc_final: 0.7749 (mttp) REVERT: A 235 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7256 (mpp) REVERT: B 234 TRP cc_start: 0.6903 (m100) cc_final: 0.6120 (m-10) REVERT: B 322 ASP cc_start: 0.8091 (t70) cc_final: 0.7660 (m-30) REVERT: B 327 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7446 (tp) REVERT: C 206 GLN cc_start: 0.7380 (OUTLIER) cc_final: 0.7022 (tm-30) REVERT: C 231 ARG cc_start: 0.8196 (ttm-80) cc_final: 0.7780 (mtm110) REVERT: C 235 MET cc_start: 0.7166 (tpp) cc_final: 0.6788 (mtt) REVERT: C 326 LYS cc_start: 0.7986 (tptp) cc_final: 0.7547 (ttmm) REVERT: H 68 ILE cc_start: 0.6548 (OUTLIER) cc_final: 0.6326 (tp) REVERT: D 320 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7561 (tp) REVERT: D 329 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7563 (tp) REVERT: D 330 ASP cc_start: 0.9112 (t0) cc_final: 0.8765 (t0) REVERT: D 332 LYS cc_start: 0.8816 (ttmt) cc_final: 0.8349 (tttt) REVERT: I 125 ASP cc_start: 0.8771 (t0) cc_final: 0.8450 (t0) REVERT: I 162 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.6909 (tm-30) REVERT: I 187 LYS cc_start: 0.8675 (mmtt) cc_final: 0.8318 (mtmt) REVERT: I 309 LYS cc_start: 0.8513 (ttmt) cc_final: 0.8213 (ttpp) REVERT: J 108 ASP cc_start: 0.8338 (m-30) cc_final: 0.8067 (m-30) REVERT: J 162 GLU cc_start: 0.5400 (tt0) cc_final: 0.5159 (tt0) REVERT: J 300 TRP cc_start: 0.6793 (m100) cc_final: 0.6127 (m100) outliers start: 46 outliers final: 28 residues processed: 204 average time/residue: 0.0823 time to fit residues: 24.5606 Evaluate side-chains 198 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 237 TRP Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 315 ASN Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 162 GLN Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 298 ILE Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 373 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 65 optimal weight: 0.5980 chunk 104 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 ASN I 159 ASN I 247 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.191330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.147955 restraints weight = 15137.742| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 2.77 r_work: 0.3855 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 9611 Z= 0.131 Angle : 0.538 7.421 13103 Z= 0.274 Chirality : 0.036 0.348 1593 Planarity : 0.003 0.036 1632 Dihedral : 3.601 27.457 1357 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.90 % Allowed : 27.60 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.23 (0.24), residues: 1256 helix: 2.94 (0.16), residues: 1018 sheet: -1.98 (1.96), residues: 8 loop : -1.71 (0.34), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 333 TYR 0.033 0.001 TYR B 317 PHE 0.020 0.001 PHE J 90 TRP 0.010 0.001 TRP A 260 HIS 0.002 0.000 HIS J 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 9611) covalent geometry : angle 0.53835 / 0.27 (13103) hydrogen bonds : bond 0.03934 / 2.74 ( 786) hydrogen bonds : angle 3.48579 / 2.57 ( 2337) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 167 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7639 (tm-30) REVERT: A 220 LYS cc_start: 0.7965 (mmtt) cc_final: 0.7661 (mttp) REVERT: A 235 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.6967 (mpp) REVERT: B 234 TRP cc_start: 0.6741 (m100) cc_final: 0.5919 (m-10) REVERT: B 322 ASP cc_start: 0.7981 (t70) cc_final: 0.7547 (m-30) REVERT: B 327 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7361 (tp) REVERT: C 206 GLN cc_start: 0.7315 (OUTLIER) cc_final: 0.6970 (tm-30) REVERT: C 231 ARG cc_start: 0.7994 (ttm-80) cc_final: 0.7603 (mtm110) REVERT: C 235 MET cc_start: 0.6962 (tpp) cc_final: 0.6633 (mtt) REVERT: C 326 LYS cc_start: 0.7861 (tptp) cc_final: 0.7428 (ttmm) REVERT: D 206 GLN cc_start: 0.7821 (tm-30) cc_final: 0.7535 (tm-30) REVERT: D 330 ASP cc_start: 0.8996 (t0) cc_final: 0.8650 (t0) REVERT: D 332 LYS cc_start: 0.8783 (ttmt) cc_final: 0.8358 (tttt) REVERT: I 125 ASP cc_start: 0.8664 (t0) cc_final: 0.8351 (t0) REVERT: I 162 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.6860 (tm-30) REVERT: I 187 LYS cc_start: 0.8620 (mmtt) cc_final: 0.8291 (mtmt) REVERT: I 309 LYS cc_start: 0.8425 (ttmt) cc_final: 0.8103 (ttpp) REVERT: J 108 ASP cc_start: 0.8334 (m-30) cc_final: 0.8067 (m-30) REVERT: J 162 GLU cc_start: 0.5374 (tt0) cc_final: 0.5114 (tt0) REVERT: J 300 TRP cc_start: 0.6775 (m100) cc_final: 0.6115 (m100) outliers start: 41 outliers final: 30 residues processed: 198 average time/residue: 0.0806 time to fit residues: 23.4912 Evaluate side-chains 195 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 195 HIS Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 237 TRP Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 315 ASN Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 162 GLN Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 298 ILE Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 373 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 99 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 315 ASN I 159 ASN I 247 GLN I 362 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.190850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.146393 restraints weight = 14937.425| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 3.04 r_work: 0.3844 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 9611 Z= 0.133 Angle : 0.554 9.729 13103 Z= 0.279 Chirality : 0.036 0.200 1593 Planarity : 0.003 0.036 1632 Dihedral : 3.609 27.529 1357 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.54 % Allowed : 28.43 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.23 (0.24), residues: 1256 helix: 2.92 (0.16), residues: 1018 sheet: -1.95 (1.49), residues: 13 loop : -1.62 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 333 TYR 0.009 0.001 TYR B 317 PHE 0.020 0.001 PHE J 90 TRP 0.010 0.001 TRP A 260 HIS 0.002 0.000 HIS J 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 9611) covalent geometry : angle 0.55389 / 0.28 (13103) hydrogen bonds : bond 0.03934 / 2.74 ( 786) hydrogen bonds : angle 3.50565 / 2.58 ( 2337) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7675 (tm-30) REVERT: A 220 LYS cc_start: 0.7969 (mmtt) cc_final: 0.7647 (mttp) REVERT: A 235 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7009 (mpp) REVERT: B 234 TRP cc_start: 0.6773 (m100) cc_final: 0.5940 (m-10) REVERT: B 322 ASP cc_start: 0.8008 (t70) cc_final: 0.7601 (m-30) REVERT: C 206 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.6970 (tm-30) REVERT: C 235 MET cc_start: 0.7004 (tpp) cc_final: 0.6659 (mtt) REVERT: C 326 LYS cc_start: 0.7880 (tptp) cc_final: 0.7434 (ttmm) REVERT: C 328 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8074 (mm-30) REVERT: D 206 GLN cc_start: 0.7888 (tm-30) cc_final: 0.7528 (tm-30) REVERT: D 330 ASP cc_start: 0.8998 (t0) cc_final: 0.8665 (t0) REVERT: D 332 LYS cc_start: 0.8684 (ttmt) cc_final: 0.8315 (tttt) REVERT: I 125 ASP cc_start: 0.8674 (t0) cc_final: 0.8360 (t0) REVERT: I 162 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.6864 (tm-30) REVERT: I 187 LYS cc_start: 0.8611 (mmtt) cc_final: 0.8315 (mtmt) REVERT: I 309 LYS cc_start: 0.8455 (ttmt) cc_final: 0.8163 (ttpp) REVERT: J 108 ASP cc_start: 0.8356 (m-30) cc_final: 0.8115 (m-30) REVERT: J 300 TRP cc_start: 0.6811 (m100) cc_final: 0.6117 (m100) outliers start: 38 outliers final: 32 residues processed: 195 average time/residue: 0.0836 time to fit residues: 23.6865 Evaluate side-chains 196 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 237 TRP Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 315 ASN Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 162 GLN Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain I residue 362 GLN Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 298 ILE Chi-restraints excluded: chain J residue 338 PHE Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 373 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 110 optimal weight: 0.0570 chunk 111 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 98 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 114 optimal weight: 0.0370 chunk 107 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 108 optimal weight: 6.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 ASN I 247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.190012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.149033 restraints weight = 15021.548| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 2.87 r_work: 0.3951 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 9611 Z= 0.114 Angle : 0.549 9.310 13103 Z= 0.274 Chirality : 0.035 0.197 1593 Planarity : 0.003 0.036 1632 Dihedral : 3.548 26.521 1357 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.75 % Allowed : 30.59 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.38 (0.24), residues: 1256 helix: 3.03 (0.16), residues: 1016 sheet: -1.68 (1.62), residues: 13 loop : -1.53 (0.36), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 333 TYR 0.011 0.001 TYR B 317 PHE 0.024 0.001 PHE I 361 TRP 0.011 0.001 TRP A 260 HIS 0.001 0.000 HIS I 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 9611) covalent geometry : angle 0.54886 / 0.27 (13103) hydrogen bonds : bond 0.03678 / 2.54 ( 786) hydrogen bonds : angle 3.47535 / 2.56 ( 2337) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2512 Ramachandran restraints generated. 1256 Oldfield, 0 Emsley, 1256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.6919 (mpp) REVERT: B 234 TRP cc_start: 0.6758 (m100) cc_final: 0.5969 (m-10) REVERT: B 322 ASP cc_start: 0.7875 (t70) cc_final: 0.7643 (m-30) REVERT: B 327 LEU cc_start: 0.7577 (tp) cc_final: 0.7333 (tp) REVERT: C 206 GLN cc_start: 0.7225 (OUTLIER) cc_final: 0.6963 (tm-30) REVERT: C 231 ARG cc_start: 0.8052 (ttm-80) cc_final: 0.7690 (mtm110) REVERT: C 235 MET cc_start: 0.7008 (tpp) cc_final: 0.6693 (mtt) REVERT: C 326 LYS cc_start: 0.7843 (tptp) cc_final: 0.7427 (ttmm) REVERT: C 328 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7991 (mm-30) REVERT: C 330 ASP cc_start: 0.8246 (t0) cc_final: 0.8039 (t0) REVERT: D 206 GLN cc_start: 0.7759 (tm-30) cc_final: 0.7411 (tm-30) REVERT: D 235 MET cc_start: 0.7321 (tpp) cc_final: 0.6885 (mmm) REVERT: D 330 ASP cc_start: 0.8939 (t0) cc_final: 0.8606 (t0) REVERT: D 332 LYS cc_start: 0.8648 (ttmt) cc_final: 0.8336 (tttt) REVERT: I 125 ASP cc_start: 0.8530 (t0) cc_final: 0.8235 (t0) REVERT: I 162 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.6825 (tm-30) REVERT: I 247 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7458 (tp40) REVERT: I 298 GLU cc_start: 0.7440 (tm-30) cc_final: 0.7075 (tt0) REVERT: I 309 LYS cc_start: 0.8472 (ttmt) cc_final: 0.8163 (ttpp) REVERT: J 108 ASP cc_start: 0.8401 (m-30) cc_final: 0.8153 (m-30) REVERT: J 300 TRP cc_start: 0.6682 (m100) cc_final: 0.6014 (m100) outliers start: 23 outliers final: 16 residues processed: 178 average time/residue: 0.0852 time to fit residues: 22.0509 Evaluate side-chains 180 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 255 TRP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 237 TRP Chi-restraints excluded: chain C residue 244 SER Chi-restraints excluded: chain C residue 329 LEU Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 162 GLN Chi-restraints excluded: chain I residue 247 GLN Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 298 ILE Chi-restraints excluded: chain J residue 373 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 49 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 78 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 247 GLN I 362 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.193680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.147697 restraints weight = 14992.829| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 2.38 r_work: 0.3987 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3860 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9611 Z= 0.136 Angle : 0.565 11.314 13103 Z= 0.283 Chirality : 0.036 0.191 1593 Planarity : 0.003 0.035 1632 Dihedral : 3.572 27.377 1357 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.58 % Allowed : 29.87 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.36 (0.24), residues: 1256 helix: 3.02 (0.16), residues: 1015 sheet: -1.65 (1.62), residues: 13 loop : -1.52 (0.36), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 333 TYR 0.011 0.001 TYR B 317 PHE 0.019 0.001 PHE J 90 TRP 0.010 0.001 TRP A 260 HIS 0.002 0.000 HIS J 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 9611) covalent geometry : angle 0.56490 / 0.28 (13103) hydrogen bonds : bond 0.03851 / 2.69 ( 786) hydrogen bonds : angle 3.51587 / 2.59 ( 2337) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2546.82 seconds wall clock time: 44 minutes 10.61 seconds (2650.61 seconds total)