Starting phenix.real_space_refine on Wed Mar 4 00:05:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xqn_22290/03_2026/6xqn_22290.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xqn_22290/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6xqn_22290/03_2026/6xqn_22290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xqn_22290/03_2026/6xqn_22290.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6xqn_22290/03_2026/6xqn_22290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xqn_22290/03_2026/6xqn_22290.map" } 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-dev-5986/lib/python3.9/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: 2.46, per 1000 atoms: 0.26 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: 0.64 Conformation dependent library (CDL) restraints added in 350.4 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: 0.25 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: 1.43 Time building geometry restraints manager: 0.87 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: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.900 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:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 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 covalent geometry : bond 0.00504 ( 9611) covalent geometry : angle 0.66633 (13103) hydrogen bonds : bond 0.10533 ( 786) hydrogen bonds : angle 5.11210 ( 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 : 0.399 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: 0.7817 (p) REVERT: J 160 TYR cc_start: 0.7066 (t80) cc_final: 0.6227 (t80) REVERT: J 201 GLN cc_start: 0.7781 (mt0) cc_final: 0.7376 (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: 0.0985 time to fit residues: 37.9068 Evaluate side-chains 199 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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: 0.9990 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... Flipped N/Q/H residues before XYZ refinement: A 226 GLN B 211 GLN C 315 ASN D 226 GLN D 315 ASN I 159 ASN I 165 HIS J 323 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.185872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.137585 restraints weight = 14946.635| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 2.80 r_work: 0.3741 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9611 Z= 0.144 Angle : 0.553 7.928 13103 Z= 0.289 Chirality : 0.036 0.177 1593 Planarity : 0.004 0.034 1632 Dihedral : 4.815 50.839 1376 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.18 % Allowed : 21.51 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1013 sheet: -3.77 (0.97), residues: 9 loop : -1.93 (0.32), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 333 TYR 0.012 0.001 TYR A 317 PHE 0.020 0.002 PHE J 338 TRP 0.011 0.001 TRP A 255 HIS 0.008 0.001 HIS J 323 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9611) covalent geometry : angle 0.55303 (13103) hydrogen bonds : bond 0.04540 ( 786) hydrogen bonds : angle 3.94302 ( 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: 35 poor density : 188 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 ASN cc_start: 0.7397 (t0) cc_final: 0.6648 (m-40) REVERT: A 220 LYS cc_start: 0.7670 (mmtt) cc_final: 0.7338 (mttp) REVERT: A 324 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7917 (mp) REVERT: B 322 ASP cc_start: 0.8177 (t70) cc_final: 0.7566 (m-30) REVERT: B 324 ILE cc_start: 0.7715 (tt) cc_final: 0.7478 (pt) REVERT: C 235 MET cc_start: 0.6707 (tpp) cc_final: 0.6434 (mtt) REVERT: C 326 LYS cc_start: 0.7608 (tptp) cc_final: 0.7105 (ttmm) REVERT: D 206 GLN cc_start: 0.8368 (tp40) cc_final: 0.8156 (tp40) REVERT: D 213 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7943 (tm-30) REVERT: D 226 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.7275 (pp30) REVERT: D 286 ARG cc_start: 0.6835 (mmt90) cc_final: 0.6096 (ttp80) REVERT: D 332 LYS cc_start: 0.8644 (ttmt) cc_final: 0.8116 (tttt) REVERT: I 135 LYS cc_start: 0.8452 (tttt) cc_final: 0.8189 (tttm) REVERT: I 187 LYS cc_start: 0.8703 (mmtt) cc_final: 0.8251 (mttt) REVERT: I 201 CYS cc_start: 0.7655 (m) cc_final: 0.6015 (p) REVERT: I 245 GLN cc_start: 0.6953 (mt0) cc_final: 0.6464 (mp10) REVERT: I 309 LYS cc_start: 0.8264 (ttmt) cc_final: 0.7935 (ttpp) REVERT: I 385 HIS cc_start: 0.7939 (t70) cc_final: 0.6740 (m-70) REVERT: J 300 TRP cc_start: 0.6924 (m100) cc_final: 0.6494 (m100) outliers start: 35 outliers final: 18 residues processed: 213 average time/residue: 0.0834 time to fit residues: 25.0793 Evaluate side-chains 187 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 167 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 ILE 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: 0.6980 chunk 75 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 316 GLN D 226 GLN D 246 GLN D 315 ASN I 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.182900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.138630 restraints weight = 15066.326| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 3.43 r_work: 0.3674 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9611 Z= 0.164 Angle : 0.559 7.486 13103 Z= 0.288 Chirality : 0.037 0.263 1593 Planarity : 0.004 0.038 1632 Dihedral : 4.112 41.006 1359 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.42 % Allowed : 24.13 % Favored : 71.45 % 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: 2.76 (0.23), residues: 1256 helix: 2.61 (0.16), residues: 1018 sheet: -1.19 (1.87), residues: 8 loop : -1.91 (0.32), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 333 TYR 0.012 0.001 TYR B 281 PHE 0.018 0.002 PHE I 282 TRP 0.008 0.001 TRP A 260 HIS 0.002 0.001 HIS I 165 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 9611) covalent geometry : angle 0.55871 (13103) hydrogen bonds : bond 0.04541 ( 786) hydrogen bonds : angle 3.76879 ( 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 213 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 176 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 90 ASN cc_start: 0.7516 (t0) cc_final: 0.6857 (m-40) REVERT: A 220 LYS cc_start: 0.7808 (mmtt) cc_final: 0.7468 (mttp) REVERT: A 324 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.8063 (mp) REVERT: B 317 TYR cc_start: 0.8774 (t80) cc_final: 0.8541 (t80) REVERT: B 321 LYS cc_start: 0.7781 (mtpt) cc_final: 0.7522 (mtpt) REVERT: B 322 ASP cc_start: 0.8174 (t70) cc_final: 0.7545 (m-30) REVERT: B 324 ILE cc_start: 0.7872 (tt) cc_final: 0.7669 (pt) REVERT: C 235 MET cc_start: 0.6893 (tpp) cc_final: 0.6563 (mtt) REVERT: C 326 LYS cc_start: 0.7830 (tptp) cc_final: 0.7325 (ttmm) REVERT: C 327 LEU cc_start: 0.7893 (mt) cc_final: 0.7647 (mt) REVERT: D 213 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8305 (tm-30) REVERT: D 226 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7356 (pp30) REVERT: D 286 ARG cc_start: 0.6839 (mmt90) cc_final: 0.6156 (ttp80) REVERT: D 332 LYS cc_start: 0.8726 (ttmt) cc_final: 0.8151 (ttpt) REVERT: I 135 LYS cc_start: 0.8498 (tttt) cc_final: 0.8224 (tttp) REVERT: I 187 LYS cc_start: 0.8683 (mmtt) cc_final: 0.8105 (mtmt) REVERT: I 201 CYS cc_start: 0.7872 (m) cc_final: 0.6825 (t) REVERT: I 309 LYS cc_start: 0.8324 (ttmt) cc_final: 0.8009 (ttpp) REVERT: I 385 HIS cc_start: 0.8104 (t70) cc_final: 0.6880 (m-70) REVERT: J 300 TRP cc_start: 0.6892 (m100) cc_final: 0.6376 (m100) outliers start: 37 outliers final: 21 residues processed: 204 average time/residue: 0.0836 time to fit residues: 24.1808 Evaluate side-chains 188 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain G residue 92 LEU 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 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 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 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: 0.9990 chunk 58 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 15 optimal weight: 20.0000 chunk 70 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN D 206 GLN D 226 GLN D 315 ASN I 159 ASN I 247 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.191969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.145931 restraints weight = 15209.838| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 3.12 r_work: 0.3870 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9611 Z= 0.128 Angle : 0.516 8.171 13103 Z= 0.266 Chirality : 0.035 0.154 1593 Planarity : 0.003 0.039 1632 Dihedral : 3.918 31.041 1359 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.54 % Allowed : 25.21 % Favored : 70.25 % 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: 3.06 (0.24), residues: 1256 helix: 2.83 (0.16), residues: 1018 sheet: None (None), residues: 0 loop : -1.86 (0.32), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 333 TYR 0.009 0.001 TYR A 317 PHE 0.013 0.001 PHE J 321 TRP 0.009 0.001 TRP A 260 HIS 0.002 0.000 HIS I 165 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9611) covalent geometry : angle 0.51612 (13103) hydrogen bonds : bond 0.04147 ( 786) hydrogen bonds : angle 3.60180 ( 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 210 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 172 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 90 ASN cc_start: 0.7560 (t0) cc_final: 0.6832 (m-40) REVERT: A 220 LYS cc_start: 0.7939 (mmtt) cc_final: 0.7641 (mttp) REVERT: A 235 MET cc_start: 0.7711 (OUTLIER) cc_final: 0.6962 (mpp) REVERT: A 324 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8134 (mp) REVERT: B 322 ASP cc_start: 0.8116 (t70) cc_final: 0.7569 (m-30) REVERT: B 324 ILE cc_start: 0.7934 (tt) cc_final: 0.7679 (pt) REVERT: C 206 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7204 (tm-30) REVERT: C 235 MET cc_start: 0.6891 (tpp) cc_final: 0.6641 (mtt) REVERT: C 326 LYS cc_start: 0.7821 (tptp) cc_final: 0.7398 (ttmm) REVERT: D 213 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8160 (tm-30) REVERT: D 286 ARG cc_start: 0.6816 (mmt90) cc_final: 0.6364 (ttp-170) REVERT: D 320 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7474 (tp) REVERT: D 332 LYS cc_start: 0.8760 (ttmt) cc_final: 0.8262 (tttt) REVERT: I 125 ASP cc_start: 0.8556 (t0) cc_final: 0.8268 (t0) REVERT: I 187 LYS cc_start: 0.8662 (mmtt) cc_final: 0.8376 (mtmt) REVERT: I 309 LYS cc_start: 0.8417 (ttmt) cc_final: 0.8124 (ttpp) REVERT: I 385 HIS cc_start: 0.8037 (t70) cc_final: 0.6851 (m-70) REVERT: J 278 MET cc_start: 0.5919 (ttm) cc_final: 0.5250 (ttm) REVERT: J 300 TRP cc_start: 0.6882 (m100) cc_final: 0.6336 (m100) outliers start: 38 outliers final: 22 residues processed: 200 average time/residue: 0.0849 time to fit residues: 24.0326 Evaluate side-chains 190 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU 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 334 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 206 GLN 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 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 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 280 THR Chi-restraints excluded: chain J residue 158 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: 0.0970 chunk 8 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 206 GLN D 315 ASN 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 = 0.4483 r_free = 0.4483 target = 0.189436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.142897 restraints weight = 15164.674| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.54 r_work: 0.3847 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9611 Z= 0.154 Angle : 0.540 7.520 13103 Z= 0.277 Chirality : 0.036 0.153 1593 Planarity : 0.003 0.037 1632 Dihedral : 3.843 28.693 1359 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 6.21 % Allowed : 26.05 % Favored : 67.74 % 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: 3.07 (0.24), residues: 1256 helix: 2.85 (0.16), residues: 1019 sheet: None (None), residues: 0 loop : -1.91 (0.33), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 333 TYR 0.010 0.001 TYR J 160 PHE 0.019 0.002 PHE I 243 TRP 0.010 0.001 TRP A 260 HIS 0.002 0.001 HIS J 323 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9611) covalent geometry : angle 0.53952 (13103) hydrogen bonds : bond 0.04230 ( 786) hydrogen bonds : angle 3.57387 ( 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 225 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 173 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7564 (tm-30) REVERT: A 220 LYS cc_start: 0.7935 (mmtt) cc_final: 0.7618 (mttp) REVERT: A 235 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.6883 (mpp) REVERT: B 322 ASP cc_start: 0.8112 (t70) cc_final: 0.7559 (m-30) REVERT: B 327 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7405 (tp) REVERT: C 206 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.7109 (tm-30) REVERT: C 235 MET cc_start: 0.6876 (tpp) cc_final: 0.6573 (mtt) REVERT: C 326 LYS cc_start: 0.7849 (tptp) cc_final: 0.7427 (ttmm) REVERT: H 68 ILE cc_start: 0.6604 (OUTLIER) cc_final: 0.6400 (tp) REVERT: D 213 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8218 (tm-30) REVERT: D 320 LEU cc_start: 0.7884 (tp) cc_final: 0.7324 (tp) REVERT: D 332 LYS cc_start: 0.8753 (ttmt) cc_final: 0.8260 (tttt) REVERT: I 125 ASP cc_start: 0.8679 (t0) cc_final: 0.8397 (t0) REVERT: I 187 LYS cc_start: 0.8601 (mmtt) cc_final: 0.8157 (mtmt) REVERT: I 201 CYS cc_start: 0.7790 (m) cc_final: 0.6894 (t) REVERT: I 245 GLN cc_start: 0.6937 (OUTLIER) cc_final: 0.6679 (pm20) REVERT: I 309 LYS cc_start: 0.8449 (ttmt) cc_final: 0.8173 (ttpp) REVERT: I 437 MET cc_start: 0.6269 (mmp) cc_final: 0.5915 (mmp) REVERT: J 278 MET cc_start: 0.6178 (ttm) cc_final: 0.5505 (ttm) REVERT: J 300 TRP cc_start: 0.6854 (m100) cc_final: 0.6255 (m100) outliers start: 52 outliers final: 31 residues processed: 215 average time/residue: 0.0768 time to fit residues: 23.6498 Evaluate side-chains 201 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU 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 285 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 327 LEU Chi-restraints excluded: chain C residue 203 LEU 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 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 329 LEU Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 245 GLN 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 233 THR 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: 4.9990 chunk 15 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 1 optimal weight: 0.0370 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 206 GLN ** D 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4488 r_free = 0.4488 target = 0.190555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.144219 restraints weight = 15120.052| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 3.01 r_work: 0.3864 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9611 Z= 0.125 Angle : 0.517 10.349 13103 Z= 0.264 Chirality : 0.035 0.158 1593 Planarity : 0.003 0.037 1632 Dihedral : 3.677 27.731 1357 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 5.14 % Allowed : 27.72 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.96 (0.16), residues: 1018 sheet: None (None), residues: 0 loop : -1.88 (0.33), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 333 TYR 0.008 0.001 TYR J 160 PHE 0.012 0.001 PHE J 321 TRP 0.010 0.001 TRP A 260 HIS 0.002 0.000 HIS I 165 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9611) covalent geometry : angle 0.51658 (13103) hydrogen bonds : bond 0.03967 ( 786) hydrogen bonds : angle 3.49097 ( 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 211 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7500 (tm-30) REVERT: A 220 LYS cc_start: 0.7999 (mmtt) cc_final: 0.7679 (mttp) REVERT: A 235 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.6948 (mpp) REVERT: B 234 TRP cc_start: 0.6261 (m-10) cc_final: 0.5907 (m100) REVERT: B 322 ASP cc_start: 0.8095 (t70) cc_final: 0.7579 (m-30) REVERT: B 327 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7360 (tp) REVERT: C 206 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.7071 (tm-30) REVERT: C 231 ARG cc_start: 0.7961 (ttm-80) cc_final: 0.7587 (mtm110) REVERT: C 235 MET cc_start: 0.6941 (tpp) cc_final: 0.6617 (mtt) REVERT: C 326 LYS cc_start: 0.7849 (tptp) cc_final: 0.7407 (ttmm) REVERT: H 68 ILE cc_start: 0.6550 (OUTLIER) cc_final: 0.6328 (tp) REVERT: D 206 GLN cc_start: 0.8261 (tp-100) cc_final: 0.8038 (tm-30) REVERT: D 320 LEU cc_start: 0.7852 (tp) cc_final: 0.7255 (tp) REVERT: D 332 LYS cc_start: 0.8738 (ttmt) cc_final: 0.8289 (tttt) REVERT: I 125 ASP cc_start: 0.8644 (t0) cc_final: 0.8347 (t0) REVERT: I 162 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.6886 (tm-30) REVERT: I 187 LYS cc_start: 0.8685 (mmtt) cc_final: 0.8352 (mtmt) REVERT: I 309 LYS cc_start: 0.8424 (ttmt) cc_final: 0.8111 (ttpp) REVERT: I 437 MET cc_start: 0.6348 (mmp) cc_final: 0.6021 (mmp) REVERT: J 108 ASP cc_start: 0.8336 (m-30) cc_final: 0.8029 (m-30) REVERT: J 278 MET cc_start: 0.6315 (ttm) cc_final: 0.5675 (ttm) REVERT: J 300 TRP cc_start: 0.6827 (m100) cc_final: 0.6175 (m100) outliers start: 43 outliers final: 31 residues processed: 199 average time/residue: 0.0800 time to fit residues: 23.0802 Evaluate side-chains 199 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain A residue 207 LEU 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 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 282 PHE 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 244 SER 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 99 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4475 r_free = 0.4475 target = 0.188638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.142206 restraints weight = 15145.564| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 3.00 r_work: 0.3828 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9611 Z= 0.164 Angle : 0.550 8.805 13103 Z= 0.284 Chirality : 0.036 0.153 1593 Planarity : 0.003 0.036 1632 Dihedral : 3.754 29.699 1357 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 5.97 % Allowed : 27.12 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.07 (0.24), residues: 1256 helix: 2.84 (0.16), residues: 1019 sheet: None (None), residues: 0 loop : -1.91 (0.33), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 333 TYR 0.010 0.001 TYR A 317 PHE 0.020 0.002 PHE I 243 TRP 0.010 0.001 TRP A 260 HIS 0.003 0.001 HIS J 323 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 9611) covalent geometry : angle 0.54956 (13103) hydrogen bonds : bond 0.04330 ( 786) hydrogen bonds : angle 3.56914 ( 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 218 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 168 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7501 (tm-30) REVERT: A 220 LYS cc_start: 0.7968 (mmtt) cc_final: 0.7616 (mttp) REVERT: A 235 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.6952 (mpp) REVERT: B 322 ASP cc_start: 0.7980 (t70) cc_final: 0.7593 (m-30) REVERT: B 327 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7426 (tp) REVERT: C 206 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.7139 (tm-30) REVERT: C 235 MET cc_start: 0.7006 (tpp) cc_final: 0.6659 (mtt) REVERT: C 326 LYS cc_start: 0.7873 (tptp) cc_final: 0.7410 (ttmm) REVERT: D 206 GLN cc_start: 0.8241 (tp-100) cc_final: 0.7968 (tm-30) REVERT: D 320 LEU cc_start: 0.7750 (tp) cc_final: 0.7381 (tp) REVERT: D 330 ASP cc_start: 0.9046 (t0) cc_final: 0.8656 (t0) REVERT: D 332 LYS cc_start: 0.8692 (ttmt) cc_final: 0.8278 (tttt) REVERT: I 125 ASP cc_start: 0.8693 (t0) cc_final: 0.8373 (t0) REVERT: I 162 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.6825 (tm-30) REVERT: I 187 LYS cc_start: 0.8665 (mmtt) cc_final: 0.8142 (mtmt) REVERT: I 201 CYS cc_start: 0.7751 (m) cc_final: 0.6814 (t) REVERT: I 309 LYS cc_start: 0.8364 (ttmt) cc_final: 0.8072 (ttpp) REVERT: I 437 MET cc_start: 0.6502 (mmp) cc_final: 0.6190 (mmp) REVERT: J 278 MET cc_start: 0.6303 (ttm) cc_final: 0.5638 (ttm) REVERT: J 300 TRP cc_start: 0.6728 (m100) cc_final: 0.6027 (m100) outliers start: 50 outliers final: 38 residues processed: 205 average time/residue: 0.0744 time to fit residues: 22.1531 Evaluate side-chains 207 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 165 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain A residue 207 LEU 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 285 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 324 ILE Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 195 HIS 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 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 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 197 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 65 optimal weight: 0.6980 chunk 104 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 60 optimal weight: 0.0770 chunk 55 optimal weight: 0.9990 chunk 57 optimal weight: 0.0770 chunk 11 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 315 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.191798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.146099 restraints weight = 15151.198| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.45 r_work: 0.3885 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9611 Z= 0.115 Angle : 0.526 8.695 13103 Z= 0.267 Chirality : 0.035 0.192 1593 Planarity : 0.003 0.036 1632 Dihedral : 3.610 27.887 1357 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.82 % Allowed : 28.43 % Favored : 67.74 % 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: 3.25 (0.24), residues: 1256 helix: 2.98 (0.16), residues: 1020 sheet: -2.04 (1.99), residues: 8 loop : -1.87 (0.33), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 333 TYR 0.009 0.001 TYR J 160 PHE 0.011 0.001 PHE J 268 TRP 0.011 0.001 TRP A 260 HIS 0.001 0.000 HIS I 165 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 9611) covalent geometry : angle 0.52602 (13103) hydrogen bonds : bond 0.03820 ( 786) hydrogen bonds : angle 3.42422 ( 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 202 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7562 (tm-30) REVERT: A 220 LYS cc_start: 0.7960 (mmtt) cc_final: 0.7606 (mttp) REVERT: A 235 MET cc_start: 0.7544 (OUTLIER) cc_final: 0.6858 (mpp) REVERT: B 322 ASP cc_start: 0.7884 (t70) cc_final: 0.7625 (m-30) REVERT: C 206 GLN cc_start: 0.7215 (OUTLIER) cc_final: 0.6937 (tm-30) REVERT: C 231 ARG cc_start: 0.7974 (ttm-80) cc_final: 0.7587 (mtm110) REVERT: C 235 MET cc_start: 0.6942 (tpp) cc_final: 0.6610 (mtt) REVERT: C 326 LYS cc_start: 0.7726 (tptp) cc_final: 0.7303 (ttmm) REVERT: D 206 GLN cc_start: 0.8159 (tp-100) cc_final: 0.7881 (tm-30) REVERT: D 235 MET cc_start: 0.7353 (tpp) cc_final: 0.6871 (mmm) REVERT: D 320 LEU cc_start: 0.7776 (tp) cc_final: 0.7516 (tp) REVERT: D 330 ASP cc_start: 0.9023 (t0) cc_final: 0.8649 (t0) REVERT: D 332 LYS cc_start: 0.8635 (ttmt) cc_final: 0.8279 (tttt) REVERT: I 125 ASP cc_start: 0.8608 (t0) cc_final: 0.8307 (t0) REVERT: I 162 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.6848 (tm-30) REVERT: I 187 LYS cc_start: 0.8586 (mmtt) cc_final: 0.8304 (mtmt) REVERT: I 309 LYS cc_start: 0.8395 (ttmt) cc_final: 0.8102 (ttpp) REVERT: J 108 ASP cc_start: 0.8369 (m-30) cc_final: 0.8106 (m-30) REVERT: J 278 MET cc_start: 0.6021 (ttm) cc_final: 0.5292 (ttm) REVERT: J 300 TRP cc_start: 0.6661 (m100) cc_final: 0.5993 (m100) outliers start: 32 outliers final: 25 residues processed: 195 average time/residue: 0.0681 time to fit residues: 19.5511 Evaluate side-chains 190 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 233 ASN Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 259 SER 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 244 SER Chi-restraints excluded: chain C residue 253 LEU 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 274 THR 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 J residue 158 ILE Chi-restraints excluded: chain J residue 266 MET Chi-restraints excluded: chain J residue 338 PHE 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: 0.8980 chunk 57 optimal weight: 0.5980 chunk 103 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 79 optimal weight: 0.3980 chunk 106 optimal weight: 2.9990 chunk 80 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 315 ASN I 362 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.193854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.148507 restraints weight = 15045.441| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 2.81 r_work: 0.3900 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.4159 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= 0.121 Angle : 0.538 8.244 13103 Z= 0.273 Chirality : 0.035 0.169 1593 Planarity : 0.003 0.036 1632 Dihedral : 3.575 27.454 1357 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.70 % Allowed : 29.15 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.30 (0.24), residues: 1256 helix: 3.01 (0.16), residues: 1020 sheet: -1.86 (2.10), residues: 8 loop : -1.87 (0.33), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 333 TYR 0.008 0.001 TYR J 160 PHE 0.012 0.001 PHE J 268 TRP 0.011 0.001 TRP A 260 HIS 0.001 0.000 HIS J 323 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 9611) covalent geometry : angle 0.53757 (13103) hydrogen bonds : bond 0.03830 ( 786) hydrogen bonds : angle 3.42871 ( 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 199 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7593 (tm-30) REVERT: A 220 LYS cc_start: 0.7994 (mmtt) cc_final: 0.7665 (mttp) REVERT: A 235 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.6934 (mpp) REVERT: B 322 ASP cc_start: 0.7858 (t70) cc_final: 0.7604 (m-30) REVERT: C 206 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6911 (tm-30) REVERT: C 231 ARG cc_start: 0.7991 (ttm-80) cc_final: 0.7609 (mtm110) REVERT: C 235 MET cc_start: 0.6965 (tpp) cc_final: 0.6663 (mtt) REVERT: C 326 LYS cc_start: 0.7851 (tptp) cc_final: 0.7416 (ttmm) REVERT: D 206 GLN cc_start: 0.8156 (tp-100) cc_final: 0.7891 (tm-30) REVERT: D 320 LEU cc_start: 0.7788 (tp) cc_final: 0.7461 (tp) REVERT: D 330 ASP cc_start: 0.9004 (t0) cc_final: 0.8630 (t0) REVERT: D 332 LYS cc_start: 0.8672 (ttmt) cc_final: 0.8334 (tttt) REVERT: I 125 ASP cc_start: 0.8643 (t0) cc_final: 0.8342 (t0) REVERT: I 162 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.6869 (tm-30) REVERT: I 187 LYS cc_start: 0.8555 (mmtt) cc_final: 0.8310 (mtmt) REVERT: I 309 LYS cc_start: 0.8458 (ttmt) cc_final: 0.8173 (ttpp) REVERT: J 108 ASP cc_start: 0.8361 (m-30) cc_final: 0.8112 (m-30) REVERT: J 278 MET cc_start: 0.6063 (ttm) cc_final: 0.5356 (ttm) REVERT: J 300 TRP cc_start: 0.6675 (m100) cc_final: 0.5988 (m100) outliers start: 31 outliers final: 25 residues processed: 190 average time/residue: 0.0759 time to fit residues: 21.0379 Evaluate side-chains 190 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 233 ASN Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 259 SER 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 244 SER Chi-restraints excluded: chain C residue 253 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 274 THR 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 362 GLN 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 373 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 110 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 108 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 362 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.192903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.147957 restraints weight = 15132.497| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.74 r_work: 0.3889 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9611 Z= 0.140 Angle : 0.571 9.580 13103 Z= 0.287 Chirality : 0.036 0.288 1593 Planarity : 0.003 0.036 1632 Dihedral : 3.601 28.125 1357 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.70 % Allowed : 29.27 % 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: 3.24 (0.24), residues: 1256 helix: 2.97 (0.16), residues: 1019 sheet: -1.69 (2.19), residues: 8 loop : -1.89 (0.32), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 333 TYR 0.012 0.001 TYR B 317 PHE 0.019 0.001 PHE I 361 TRP 0.009 0.001 TRP A 260 HIS 0.002 0.000 HIS J 323 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9611) covalent geometry : angle 0.57147 (13103) hydrogen bonds : bond 0.03961 ( 786) hydrogen bonds : angle 3.49454 ( 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 195 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7555 (tm-30) REVERT: A 220 LYS cc_start: 0.7986 (mmtt) cc_final: 0.7636 (mttp) REVERT: A 235 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.6932 (mpp) REVERT: B 322 ASP cc_start: 0.7856 (t70) cc_final: 0.7622 (m-30) REVERT: C 206 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.7068 (tm-30) REVERT: C 235 MET cc_start: 0.7010 (tpp) cc_final: 0.6707 (mtt) REVERT: C 326 LYS cc_start: 0.7873 (tptp) cc_final: 0.7446 (ttmm) REVERT: D 206 GLN cc_start: 0.8173 (tp-100) cc_final: 0.7902 (tm-30) REVERT: D 235 MET cc_start: 0.7433 (tpp) cc_final: 0.6950 (mmm) REVERT: D 320 LEU cc_start: 0.7850 (tp) cc_final: 0.7593 (tp) REVERT: D 330 ASP cc_start: 0.9002 (t0) cc_final: 0.8636 (t0) REVERT: D 332 LYS cc_start: 0.8653 (ttmt) cc_final: 0.8313 (tttt) REVERT: I 125 ASP cc_start: 0.8665 (t0) cc_final: 0.8357 (t0) REVERT: I 162 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.6870 (tm-30) REVERT: I 208 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.8043 (t0) REVERT: I 298 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7183 (tt0) REVERT: I 309 LYS cc_start: 0.8455 (ttmt) cc_final: 0.8169 (ttpp) REVERT: J 108 ASP cc_start: 0.8374 (m-30) cc_final: 0.8114 (m-30) REVERT: J 278 MET cc_start: 0.6061 (ttm) cc_final: 0.5345 (ttm) REVERT: J 300 TRP cc_start: 0.6696 (m100) cc_final: 0.5997 (m100) outliers start: 31 outliers final: 25 residues processed: 185 average time/residue: 0.0776 time to fit residues: 20.8282 Evaluate side-chains 191 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 233 ASN Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 259 SER 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 244 SER Chi-restraints excluded: chain C residue 253 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 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 208 ASP Chi-restraints excluded: chain I residue 215 VAL 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 335 MET Chi-restraints excluded: chain J residue 338 PHE 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: 0.0980 chunk 79 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 105 optimal weight: 0.0970 chunk 121 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 78 optimal weight: 0.2980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 362 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.194918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.149266 restraints weight = 15018.215| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 2.37 r_work: 0.3930 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3800 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.4323 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= 0.118 Angle : 0.549 8.064 13103 Z= 0.278 Chirality : 0.035 0.244 1593 Planarity : 0.003 0.036 1632 Dihedral : 3.549 27.442 1357 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.06 % Allowed : 29.39 % 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: 3.30 (0.24), residues: 1256 helix: 3.01 (0.16), residues: 1020 sheet: -1.88 (1.57), residues: 13 loop : -1.86 (0.33), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 333 TYR 0.015 0.001 TYR B 317 PHE 0.014 0.001 PHE I 361 TRP 0.010 0.001 TRP A 260 HIS 0.001 0.000 HIS J 323 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 9611) covalent geometry : angle 0.54946 (13103) hydrogen bonds : bond 0.03755 ( 786) hydrogen bonds : angle 3.45018 ( 2337) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2480.76 seconds wall clock time: 42 minutes 59.84 seconds (2579.84 seconds total)