Starting phenix.real_space_refine on Fri Mar 14 01:07:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xqn_22290/03_2025/6xqn_22290.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xqn_22290/03_2025/6xqn_22290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xqn_22290/03_2025/6xqn_22290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xqn_22290/03_2025/6xqn_22290.map" model { file = "/net/cci-nas-00/data/ceres_data/6xqn_22290/03_2025/6xqn_22290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xqn_22290/03_2025/6xqn_22290.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 5, 'GLU:plan': 7, 'ASN:plan1': 3, 'ARG:plan': 4, 'ASP:plan': 3} 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: {'GLN:plan1': 6, 'ASP:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 4} 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: {'GLN:plan1': 5, 'GLU:plan': 8, 'ASN:plan1': 3, 'ARG:plan': 5, 'ASP:plan': 3} 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: {'GLN:plan1': 5, 'ASP:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 4} 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: {'GLN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 5} 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: {'GLN:plan1': 7, 'ASP:plan': 12, 'ASN:plan1': 5, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 21, 'ARG:plan': 13} 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: 6.90, per 1000 atoms: 0.73 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: 3.36 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.25 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: 4.29 Time building geometry restraints manager: 3.90 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: 2.230 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 31.040 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:4.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.540 ------------------------------------------------------------------------------- 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= 0.328 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (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 TRP 0.020 0.002 TRP D 237 HIS 0.004 0.001 HIS J 98 PHE 0.037 0.002 PHE I 282 TYR 0.010 0.001 TYR I 114 ARG 0.007 0.001 ARG I 154 *********************** 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 : 0.982 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: 0.6416 (mtt) REVERT: C 262 ILE cc_start: 0.8536 (tp) cc_final: 0.8281 (tt) REVERT: C 324 ILE cc_start: 0.7169 (tt) cc_final: 0.6507 (pt) REVERT: H 80 ILE cc_start: 0.7026 (OUTLIER) cc_final: 0.6758 (mm) REVERT: D 286 ARG cc_start: 0.6907 (mmt90) cc_final: 0.6121 (ttp80) REVERT: D 332 LYS cc_start: 0.8338 (ttmt) cc_final: 0.7926 (tttt) REVERT: I 125 ASP cc_start: 0.8609 (t70) cc_final: 0.8401 (t0) REVERT: I 135 LYS cc_start: 0.8017 (tttt) cc_final: 0.7782 (tttp) REVERT: I 187 LYS cc_start: 0.8660 (mmtt) cc_final: 0.8329 (mttt) REVERT: I 201 CYS cc_start: 0.7100 (m) cc_final: 0.5902 (p) REVERT: I 247 GLN cc_start: 0.8227 (mt0) cc_final: 0.7298 (tp40) REVERT: I 309 LYS cc_start: 0.8088 (ttmt) cc_final: 0.7656 (ttpp) REVERT: J 112 SER cc_start: 0.8026 (OUTLIER) cc_final: 0.7818 (p) REVERT: J 160 TYR cc_start: 0.7066 (t80) cc_final: 0.6593 (t80) REVERT: J 201 GLN cc_start: 0.7781 (mt0) cc_final: 0.7377 (mt0) REVERT: J 300 TRP cc_start: 0.7051 (m100) cc_final: 0.6694 (m100) REVERT: J 318 PHE cc_start: 0.6230 (t80) cc_final: 0.5949 (t80) outliers start: 24 outliers final: 10 residues processed: 285 average time/residue: 0.2461 time to fit residues: 94.8929 Evaluate side-chains 201 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 106 optimal weight: 2.9990 chunk 95 optimal weight: 0.0070 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 0.2980 chunk 73 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN C 315 ASN D 226 GLN D 246 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 = 0.4434 r_free = 0.4434 target = 0.187271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.140695 restraints weight = 14862.754| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 3.46 r_work: 0.3722 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9611 Z= 0.181 Angle : 0.544 7.917 13103 Z= 0.282 Chirality : 0.036 0.178 1593 Planarity : 0.004 0.036 1632 Dihedral : 4.677 51.002 1376 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.23 % Allowed : 21.62 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.23), residues: 1256 helix: 2.38 (0.16), residues: 1014 sheet: -3.66 (0.98), residues: 9 loop : -1.90 (0.33), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 255 HIS 0.008 0.001 HIS J 323 PHE 0.028 0.002 PHE J 90 TYR 0.010 0.001 TYR A 317 ARG 0.005 0.001 ARG A 333 *********************** 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 220 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 ASN cc_start: 0.7389 (t0) cc_final: 0.6607 (m-40) REVERT: A 220 LYS cc_start: 0.7725 (mmtt) cc_final: 0.7394 (mttp) REVERT: B 322 ASP cc_start: 0.8263 (t70) cc_final: 0.7619 (m-30) REVERT: B 324 ILE cc_start: 0.7747 (tt) cc_final: 0.7498 (pt) REVERT: C 235 MET cc_start: 0.6802 (tpp) cc_final: 0.6509 (mtt) REVERT: C 326 LYS cc_start: 0.7706 (tptp) cc_final: 0.7187 (ttmm) REVERT: D 210 LEU cc_start: 0.8711 (mt) cc_final: 0.8504 (mt) REVERT: D 213 GLU cc_start: 0.8310 (tm-30) cc_final: 0.8002 (tm-30) REVERT: D 226 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7332 (pp30) REVERT: D 286 ARG cc_start: 0.6849 (mmt90) cc_final: 0.6127 (ttp80) REVERT: D 332 LYS cc_start: 0.8625 (ttmt) cc_final: 0.8107 (tttt) REVERT: I 135 LYS cc_start: 0.8403 (tttt) cc_final: 0.8160 (tttm) REVERT: I 187 LYS cc_start: 0.8715 (mmtt) cc_final: 0.8249 (mttt) REVERT: I 201 CYS cc_start: 0.7646 (m) cc_final: 0.5995 (p) REVERT: I 245 GLN cc_start: 0.7087 (mt0) cc_final: 0.6759 (mp10) REVERT: I 309 LYS cc_start: 0.8397 (ttmt) cc_final: 0.8085 (ttpp) REVERT: I 385 HIS cc_start: 0.8071 (t70) cc_final: 0.6822 (m-70) REVERT: J 256 MET cc_start: 0.6828 (tmm) cc_final: 0.6605 (tmm) REVERT: J 300 TRP cc_start: 0.7020 (m100) cc_final: 0.6569 (m100) outliers start: 27 outliers final: 14 residues processed: 210 average time/residue: 0.2115 time to fit residues: 61.7231 Evaluate side-chains 184 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 274 THR 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 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 30 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 16 optimal weight: 0.3980 chunk 51 optimal weight: 0.2980 chunk 116 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 67 optimal weight: 0.1980 chunk 32 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 206 GLN D 226 GLN D 315 ASN I 159 ASN I 165 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.186688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.138643 restraints weight = 15127.640| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.81 r_work: 0.3762 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9611 Z= 0.165 Angle : 0.503 7.375 13103 Z= 0.261 Chirality : 0.034 0.151 1593 Planarity : 0.003 0.038 1632 Dihedral : 3.895 32.243 1359 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.46 % Allowed : 22.82 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.24), residues: 1256 helix: 2.80 (0.16), residues: 1017 sheet: -1.85 (1.33), residues: 13 loop : -1.77 (0.33), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 260 HIS 0.008 0.001 HIS I 165 PHE 0.013 0.001 PHE J 321 TYR 0.013 0.001 TYR B 281 ARG 0.006 0.000 ARG A 333 *********************** 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 211 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 182 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 90 ASN cc_start: 0.7568 (t0) cc_final: 0.6822 (m-40) REVERT: A 220 LYS cc_start: 0.7684 (mmtt) cc_final: 0.7376 (mttp) REVERT: A 324 ILE cc_start: 0.8179 (mp) cc_final: 0.7973 (mp) REVERT: B 322 ASP cc_start: 0.7975 (t70) cc_final: 0.7410 (m-30) REVERT: B 324 ILE cc_start: 0.7776 (tt) cc_final: 0.7540 (pt) REVERT: C 235 MET cc_start: 0.6638 (tpp) cc_final: 0.6400 (mtt) REVERT: C 326 LYS cc_start: 0.7644 (tptp) cc_final: 0.7156 (ttmm) REVERT: D 210 LEU cc_start: 0.8761 (mt) cc_final: 0.8408 (mt) REVERT: D 213 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8220 (tm-30) REVERT: D 226 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7355 (pp30) REVERT: D 286 ARG cc_start: 0.6809 (mmt90) cc_final: 0.6176 (ttp-170) REVERT: D 332 LYS cc_start: 0.8673 (ttmt) cc_final: 0.8164 (tttt) REVERT: I 135 LYS cc_start: 0.8464 (tttt) cc_final: 0.8193 (tttp) REVERT: I 187 LYS cc_start: 0.8695 (mmtt) cc_final: 0.8353 (mtmt) REVERT: I 309 LYS cc_start: 0.8369 (ttmt) cc_final: 0.8021 (ttpp) REVERT: I 385 HIS cc_start: 0.8043 (t70) cc_final: 0.6807 (m-70) REVERT: J 300 TRP cc_start: 0.6811 (m100) cc_final: 0.6402 (m100) outliers start: 29 outliers final: 12 residues processed: 200 average time/residue: 0.2169 time to fit residues: 59.8314 Evaluate side-chains 179 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 78 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 320 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4494 r_free = 0.4494 target = 0.191018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.148736 restraints weight = 15154.687| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 3.06 r_work: 0.3876 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9611 Z= 0.201 Angle : 0.509 7.106 13103 Z= 0.265 Chirality : 0.035 0.155 1593 Planarity : 0.003 0.038 1632 Dihedral : 3.791 27.017 1359 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.42 % Allowed : 24.37 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.22 (0.24), residues: 1256 helix: 2.93 (0.16), residues: 1018 sheet: None (None), residues: 0 loop : -1.77 (0.33), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 260 HIS 0.002 0.000 HIS J 323 PHE 0.016 0.001 PHE I 282 TYR 0.012 0.001 TYR B 317 ARG 0.005 0.000 ARG A 333 *********************** 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 207 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 170 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 90 ASN cc_start: 0.7876 (t0) cc_final: 0.7248 (m-40) REVERT: A 213 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7562 (tm-30) REVERT: A 220 LYS cc_start: 0.7887 (mmtt) cc_final: 0.7620 (mttp) REVERT: A 324 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.8017 (mp) REVERT: B 322 ASP cc_start: 0.8145 (t70) cc_final: 0.7582 (m-30) REVERT: B 324 ILE cc_start: 0.7892 (tt) cc_final: 0.7606 (pt) REVERT: C 206 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.7212 (tm-30) REVERT: C 235 MET cc_start: 0.6899 (tpp) cc_final: 0.6657 (mtt) REVERT: C 326 LYS cc_start: 0.7832 (tptp) cc_final: 0.7419 (ttmm) REVERT: D 210 LEU cc_start: 0.8738 (mt) cc_final: 0.8501 (mt) REVERT: D 213 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8173 (tm-30) REVERT: D 226 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7526 (pp30) REVERT: D 286 ARG cc_start: 0.6880 (mmt90) cc_final: 0.6439 (ttp-170) REVERT: D 320 LEU cc_start: 0.7848 (tp) cc_final: 0.7493 (tp) REVERT: D 332 LYS cc_start: 0.8768 (ttmt) cc_final: 0.8287 (tttt) REVERT: I 135 LYS cc_start: 0.8571 (tttt) cc_final: 0.8366 (tttm) REVERT: I 187 LYS cc_start: 0.8686 (mmtt) cc_final: 0.8179 (mtmt) REVERT: I 201 CYS cc_start: 0.7907 (m) cc_final: 0.6990 (t) REVERT: I 309 LYS cc_start: 0.8463 (ttmt) cc_final: 0.8138 (ttpp) REVERT: I 385 HIS cc_start: 0.8043 (t70) cc_final: 0.6854 (m-70) REVERT: J 278 MET cc_start: 0.5974 (ttm) cc_final: 0.5155 (ttm) REVERT: J 300 TRP cc_start: 0.6824 (m100) cc_final: 0.6323 (m100) outliers start: 37 outliers final: 21 residues processed: 199 average time/residue: 0.2663 time to fit residues: 74.9214 Evaluate side-chains 189 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 225 GLU 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 D residue 182 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 291 LEU Chi-restraints excluded: chain D residue 315 ASN Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 169 ILE Chi-restraints excluded: chain J residue 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 71 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN C 316 GLN D 206 GLN D 226 GLN ** D 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 ASN I 247 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.190506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.145421 restraints weight = 15044.707| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 3.14 r_work: 0.3851 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9611 Z= 0.214 Angle : 0.524 7.515 13103 Z= 0.269 Chirality : 0.035 0.157 1593 Planarity : 0.003 0.037 1632 Dihedral : 3.708 28.345 1357 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 5.38 % Allowed : 25.21 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.27 (0.24), residues: 1256 helix: 2.97 (0.16), residues: 1018 sheet: None (None), residues: 0 loop : -1.75 (0.33), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 260 HIS 0.002 0.001 HIS I 165 PHE 0.016 0.001 PHE J 90 TYR 0.008 0.001 TYR A 317 ARG 0.006 0.000 ARG A 333 *********************** 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 220 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 90 ASN cc_start: 0.7676 (t0) cc_final: 0.7078 (m-40) REVERT: A 220 LYS cc_start: 0.7879 (mmtt) cc_final: 0.7580 (mttp) REVERT: B 322 ASP cc_start: 0.8143 (t70) cc_final: 0.7573 (m-30) REVERT: B 324 ILE cc_start: 0.7924 (tt) cc_final: 0.7634 (pt) REVERT: C 206 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.7123 (tm-30) REVERT: C 235 MET cc_start: 0.6888 (tpp) cc_final: 0.6588 (mtt) REVERT: C 326 LYS cc_start: 0.7850 (tptp) cc_final: 0.7404 (ttmm) REVERT: D 210 LEU cc_start: 0.8646 (mt) cc_final: 0.8436 (mt) REVERT: D 213 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8212 (tm-30) REVERT: D 286 ARG cc_start: 0.6801 (mmt90) cc_final: 0.6342 (ttp-170) REVERT: D 320 LEU cc_start: 0.7831 (tp) cc_final: 0.7452 (tp) REVERT: D 329 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7236 (tp) REVERT: D 332 LYS cc_start: 0.8779 (ttmt) cc_final: 0.8284 (tttt) REVERT: I 125 ASP cc_start: 0.8576 (t0) cc_final: 0.8262 (t0) REVERT: I 187 LYS cc_start: 0.8657 (mmtt) cc_final: 0.8342 (mtmt) REVERT: I 309 LYS cc_start: 0.8436 (ttmt) cc_final: 0.8128 (ttpp) REVERT: J 278 MET cc_start: 0.6083 (ttm) cc_final: 0.5425 (ttm) REVERT: J 300 TRP cc_start: 0.6882 (m100) cc_final: 0.6283 (m100) REVERT: J 318 PHE cc_start: 0.6091 (t80) cc_final: 0.5871 (t80) outliers start: 45 outliers final: 23 residues processed: 210 average time/residue: 0.1889 time to fit residues: 56.1970 Evaluate side-chains 191 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 206 GLN Chi-restraints excluded: chain C residue 225 GLU 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 D residue 182 LEU 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 321 LYS 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 169 ILE 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 12 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 108 optimal weight: 20.0000 chunk 68 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.191231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.144864 restraints weight = 15096.749| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 2.95 r_work: 0.3852 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9611 Z= 0.203 Angle : 0.535 10.184 13103 Z= 0.271 Chirality : 0.035 0.153 1593 Planarity : 0.003 0.039 1632 Dihedral : 3.692 28.067 1357 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.66 % Allowed : 26.28 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.28 (0.24), residues: 1256 helix: 2.98 (0.16), residues: 1017 sheet: None (None), residues: 0 loop : -1.75 (0.33), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 260 HIS 0.002 0.000 HIS J 323 PHE 0.018 0.001 PHE J 90 TYR 0.012 0.001 TYR J 160 ARG 0.007 0.000 ARG A 333 *********************** 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 214 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7327 (tm-30) REVERT: A 220 LYS cc_start: 0.7896 (mmtt) cc_final: 0.7590 (mttp) REVERT: B 322 ASP cc_start: 0.8129 (t70) cc_final: 0.7570 (m-30) REVERT: B 324 ILE cc_start: 0.7922 (tt) cc_final: 0.7607 (pt) REVERT: C 206 GLN cc_start: 0.7420 (OUTLIER) cc_final: 0.7100 (tm-30) REVERT: C 235 MET cc_start: 0.6928 (tpp) cc_final: 0.6609 (mtt) REVERT: C 326 LYS cc_start: 0.7833 (tptp) cc_final: 0.7380 (ttmm) REVERT: D 320 LEU cc_start: 0.7752 (tp) cc_final: 0.7134 (tp) REVERT: D 329 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7212 (tp) REVERT: D 330 ASP cc_start: 0.9050 (t0) cc_final: 0.8660 (t0) REVERT: D 332 LYS cc_start: 0.8770 (ttmt) cc_final: 0.8286 (tttt) REVERT: I 125 ASP cc_start: 0.8570 (t0) cc_final: 0.8239 (t0) REVERT: I 187 LYS cc_start: 0.8686 (mmtt) cc_final: 0.8355 (mtmt) REVERT: I 309 LYS cc_start: 0.8444 (ttmt) cc_final: 0.8132 (ttpp) REVERT: J 278 MET cc_start: 0.6371 (ttm) cc_final: 0.5783 (ttm) REVERT: J 300 TRP cc_start: 0.6861 (m100) cc_final: 0.6233 (m100) REVERT: J 318 PHE cc_start: 0.6064 (t80) cc_final: 0.5812 (t80) outliers start: 39 outliers final: 27 residues processed: 205 average time/residue: 0.2142 time to fit residues: 63.0784 Evaluate side-chains 192 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 259 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 237 TRP 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 182 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 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 197 PHE Chi-restraints excluded: chain J residue 298 ILE Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 373 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 112 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 124 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 48 optimal weight: 0.0870 chunk 36 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.9160 ------------------------------------------------------------------------------- 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 165 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.191036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.146285 restraints weight = 15178.477| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 3.19 r_work: 0.3833 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9611 Z= 0.219 Angle : 0.551 9.715 13103 Z= 0.281 Chirality : 0.036 0.160 1593 Planarity : 0.003 0.038 1632 Dihedral : 3.726 28.391 1357 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.66 % Allowed : 27.48 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.22 (0.24), residues: 1256 helix: 2.94 (0.16), residues: 1017 sheet: None (None), residues: 0 loop : -1.77 (0.33), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 234 HIS 0.007 0.001 HIS I 165 PHE 0.014 0.001 PHE I 243 TYR 0.014 0.001 TYR J 160 ARG 0.004 0.000 ARG A 333 *********************** 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 204 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 165 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7323 (tm-30) REVERT: A 220 LYS cc_start: 0.7985 (mmtt) cc_final: 0.7679 (mttp) REVERT: A 321 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7681 (ttpt) REVERT: B 234 TRP cc_start: 0.6757 (m100) cc_final: 0.5995 (m-10) REVERT: B 322 ASP cc_start: 0.8128 (t70) cc_final: 0.7589 (m-30) REVERT: C 206 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.7115 (tm-30) REVERT: C 235 MET cc_start: 0.7036 (tpp) cc_final: 0.6695 (mtt) REVERT: C 326 LYS cc_start: 0.7870 (tptp) cc_final: 0.7416 (ttmm) REVERT: D 206 GLN cc_start: 0.8273 (tp-100) cc_final: 0.8038 (tm-30) REVERT: D 320 LEU cc_start: 0.7750 (tp) cc_final: 0.7454 (tp) REVERT: D 329 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7405 (tp) REVERT: D 330 ASP cc_start: 0.9036 (t0) cc_final: 0.8671 (t0) REVERT: D 332 LYS cc_start: 0.8763 (ttmt) cc_final: 0.8287 (tttt) REVERT: I 125 ASP cc_start: 0.8610 (t0) cc_final: 0.8261 (t0) REVERT: I 162 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.6849 (tm-30) REVERT: I 187 LYS cc_start: 0.8639 (mmtt) cc_final: 0.8313 (mtmt) REVERT: I 309 LYS cc_start: 0.8464 (ttmt) cc_final: 0.8185 (ttpp) REVERT: I 437 MET cc_start: 0.6705 (mmp) cc_final: 0.6114 (mmp) REVERT: J 108 ASP cc_start: 0.8331 (m-30) cc_final: 0.8101 (m-30) REVERT: J 278 MET cc_start: 0.6393 (ttm) cc_final: 0.5749 (ttm) REVERT: J 300 TRP cc_start: 0.6807 (m100) cc_final: 0.6131 (m100) outliers start: 39 outliers final: 29 residues processed: 196 average time/residue: 0.1873 time to fit residues: 53.0018 Evaluate side-chains 194 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 321 LYS 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 203 LEU Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 237 TRP 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 182 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 329 LEU Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 162 GLN Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 298 ILE Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 373 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 109 optimal weight: 8.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 159 ASN J 178 HIS 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 = 0.193408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.148155 restraints weight = 15361.769| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 2.76 r_work: 0.3962 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3830 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.4039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9611 Z= 0.193 Angle : 0.539 8.679 13103 Z= 0.275 Chirality : 0.035 0.161 1593 Planarity : 0.003 0.036 1632 Dihedral : 3.699 27.839 1357 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.30 % Allowed : 27.72 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.30 (0.24), residues: 1256 helix: 2.99 (0.16), residues: 1019 sheet: -1.85 (2.01), residues: 8 loop : -1.75 (0.33), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 260 HIS 0.001 0.000 HIS A 304 PHE 0.012 0.001 PHE J 268 TYR 0.011 0.001 TYR J 160 ARG 0.004 0.000 ARG A 333 *********************** 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 207 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7446 (tm-30) REVERT: A 220 LYS cc_start: 0.8034 (mmtt) cc_final: 0.7692 (mttp) REVERT: B 234 TRP cc_start: 0.6928 (m100) cc_final: 0.6083 (m-10) REVERT: B 322 ASP cc_start: 0.8267 (t70) cc_final: 0.7699 (m-30) REVERT: B 327 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7466 (tp) REVERT: C 206 GLN cc_start: 0.7409 (OUTLIER) cc_final: 0.7066 (tm-30) REVERT: C 235 MET cc_start: 0.7214 (tpp) cc_final: 0.6841 (mtt) REVERT: C 326 LYS cc_start: 0.8001 (tptp) cc_final: 0.7517 (ttmm) REVERT: D 206 GLN cc_start: 0.8186 (tp-100) cc_final: 0.7925 (tm-30) REVERT: D 320 LEU cc_start: 0.7833 (tp) cc_final: 0.7389 (tp) REVERT: D 330 ASP cc_start: 0.9003 (t0) cc_final: 0.8649 (t0) REVERT: D 332 LYS cc_start: 0.8733 (ttmt) cc_final: 0.8303 (tttt) REVERT: I 125 ASP cc_start: 0.8861 (t0) cc_final: 0.8535 (t0) REVERT: I 162 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.6953 (tm-30) REVERT: I 187 LYS cc_start: 0.8657 (mmtt) cc_final: 0.8383 (mtmt) REVERT: I 247 GLN cc_start: 0.8496 (tt0) cc_final: 0.7625 (tp40) REVERT: I 309 LYS cc_start: 0.8557 (ttmt) cc_final: 0.8278 (ttpp) REVERT: I 437 MET cc_start: 0.7090 (mmp) cc_final: 0.6682 (mmp) REVERT: J 278 MET cc_start: 0.6577 (ttm) cc_final: 0.5883 (ttm) REVERT: J 300 TRP cc_start: 0.6840 (m100) cc_final: 0.6130 (m100) outliers start: 36 outliers final: 25 residues processed: 198 average time/residue: 0.1967 time to fit residues: 55.8194 Evaluate side-chains 193 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 237 TRP 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 182 LEU 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 I residue 118 ILE Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 162 GLN Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain J residue 158 ILE Chi-restraints excluded: chain J residue 298 ILE Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 373 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 97 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 80 optimal weight: 0.2980 chunk 83 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 159 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 = 0.4513 r_free = 0.4513 target = 0.192954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.147726 restraints weight = 15145.345| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 2.95 r_work: 0.3948 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9611 Z= 0.197 Angle : 0.549 8.556 13103 Z= 0.281 Chirality : 0.035 0.167 1593 Planarity : 0.003 0.035 1632 Dihedral : 3.694 28.014 1357 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.70 % Allowed : 28.67 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.27 (0.24), residues: 1256 helix: 2.97 (0.16), residues: 1019 sheet: -1.65 (2.12), residues: 8 loop : -1.78 (0.33), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 260 HIS 0.002 0.000 HIS J 323 PHE 0.012 0.001 PHE J 268 TYR 0.021 0.001 TYR A 317 ARG 0.005 0.000 ARG A 333 *********************** 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 197 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7295 (tm-30) REVERT: B 234 TRP cc_start: 0.6880 (m100) cc_final: 0.6067 (m-10) REVERT: B 322 ASP cc_start: 0.8154 (t70) cc_final: 0.7607 (m-30) REVERT: B 327 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7327 (tp) REVERT: C 206 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.7010 (tm-30) REVERT: C 235 MET cc_start: 0.7105 (tpp) cc_final: 0.6831 (mtt) REVERT: C 326 LYS cc_start: 0.7908 (tptp) cc_final: 0.7550 (ttmm) REVERT: D 206 GLN cc_start: 0.8137 (tp-100) cc_final: 0.7906 (tm-30) REVERT: D 235 MET cc_start: 0.7408 (tpp) cc_final: 0.6982 (mmm) REVERT: D 320 LEU cc_start: 0.7868 (tp) cc_final: 0.7558 (tp) REVERT: D 330 ASP cc_start: 0.8822 (t0) cc_final: 0.8475 (t0) REVERT: D 332 LYS cc_start: 0.8643 (ttmt) cc_final: 0.8377 (tttt) REVERT: I 125 ASP cc_start: 0.8528 (t0) cc_final: 0.8222 (t0) REVERT: I 162 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.6883 (tm-30) REVERT: I 247 GLN cc_start: 0.8256 (tt0) cc_final: 0.7678 (tp40) REVERT: I 309 LYS cc_start: 0.8462 (ttmt) cc_final: 0.8203 (ttpp) REVERT: I 393 LYS cc_start: 0.6787 (mtpt) cc_final: 0.6558 (mtpt) REVERT: I 437 MET cc_start: 0.6908 (mmp) cc_final: 0.6595 (mmp) REVERT: J 278 MET cc_start: 0.6396 (ttm) cc_final: 0.5698 (ttm) REVERT: J 300 TRP cc_start: 0.6657 (m100) cc_final: 0.5987 (m100) outliers start: 31 outliers final: 24 residues processed: 190 average time/residue: 0.2441 time to fit residues: 66.9575 Evaluate side-chains 188 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 237 TRP Chi-restraints excluded: chain C residue 319 VAL Chi-restraints excluded: chain D residue 182 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 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 338 PHE Chi-restraints excluded: chain J residue 354 VAL Chi-restraints excluded: chain J residue 373 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 67 optimal weight: 0.1980 chunk 10 optimal weight: 0.6980 chunk 109 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 54 optimal weight: 0.0970 chunk 100 optimal weight: 10.0000 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.194798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.150936 restraints weight = 15142.441| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 2.80 r_work: 0.3964 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9611 Z= 0.161 Angle : 0.544 8.946 13103 Z= 0.275 Chirality : 0.035 0.194 1593 Planarity : 0.003 0.039 1632 Dihedral : 3.636 26.525 1357 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.63 % Allowed : 30.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.42 (0.24), residues: 1256 helix: 3.13 (0.16), residues: 1008 sheet: -1.70 (1.61), residues: 13 loop : -1.75 (0.32), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 256 HIS 0.001 0.000 HIS J 323 PHE 0.014 0.001 PHE J 268 TYR 0.018 0.001 TYR A 317 ARG 0.006 0.000 ARG A 333 ********************** 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 185 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7353 (tm-30) REVERT: B 234 TRP cc_start: 0.6889 (m100) cc_final: 0.6087 (m-10) REVERT: B 322 ASP cc_start: 0.8141 (t70) cc_final: 0.7608 (m-30) REVERT: B 327 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7300 (tp) REVERT: C 206 GLN cc_start: 0.7088 (OUTLIER) cc_final: 0.6816 (tm-30) REVERT: C 235 MET cc_start: 0.7108 (tpp) cc_final: 0.6832 (mtt) REVERT: C 242 LEU cc_start: 0.7636 (mt) cc_final: 0.7413 (tt) REVERT: C 326 LYS cc_start: 0.7935 (tptp) cc_final: 0.7581 (ttmm) REVERT: C 328 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7955 (mm-30) REVERT: D 206 GLN cc_start: 0.8068 (tp-100) cc_final: 0.7487 (tm-30) REVERT: D 320 LEU cc_start: 0.7839 (tp) cc_final: 0.7484 (tp) REVERT: D 330 ASP cc_start: 0.8815 (t0) cc_final: 0.8471 (t0) REVERT: D 332 LYS cc_start: 0.8593 (ttmt) cc_final: 0.8358 (tttt) REVERT: I 125 ASP cc_start: 0.8466 (t0) cc_final: 0.8135 (t0) REVERT: I 162 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.6829 (tm-30) REVERT: I 247 GLN cc_start: 0.8176 (tt0) cc_final: 0.7671 (tp40) REVERT: I 298 GLU cc_start: 0.7435 (tm-30) cc_final: 0.7131 (tt0) REVERT: I 309 LYS cc_start: 0.8439 (ttmt) cc_final: 0.8166 (ttpp) REVERT: I 437 MET cc_start: 0.6911 (mmp) cc_final: 0.6618 (mmp) REVERT: J 278 MET cc_start: 0.6192 (ttm) cc_final: 0.5469 (ttm) REVERT: J 300 TRP cc_start: 0.6652 (m100) cc_final: 0.5981 (m100) outliers start: 22 outliers final: 17 residues processed: 179 average time/residue: 0.2426 time to fit residues: 63.0095 Evaluate side-chains 177 residues out of total 1153 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain B residue 233 ASN Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 237 TRP Chi-restraints excluded: chain D residue 182 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 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 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 119 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 123 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.195035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.150384 restraints weight = 15182.006| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 3.04 r_work: 0.3945 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.4432 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= 0.189 Angle : 0.560 9.674 13103 Z= 0.282 Chirality : 0.035 0.185 1593 Planarity : 0.003 0.039 1632 Dihedral : 3.600 27.356 1357 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.75 % Allowed : 29.99 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.38 (0.23), residues: 1256 helix: 3.09 (0.16), residues: 1015 sheet: -1.38 (2.31), residues: 8 loop : -1.85 (0.30), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 256 HIS 0.002 0.000 HIS J 323 PHE 0.013 0.001 PHE J 268 TYR 0.020 0.001 TYR A 317 ARG 0.005 0.000 ARG A 333 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5404.63 seconds wall clock time: 95 minutes 46.82 seconds (5746.82 seconds total)