Starting phenix.real_space_refine on Sat Dec 28 02:52:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8faz_28961/12_2024/8faz_28961.cif Found real_map, /net/cci-nas-00/data/ceres_data/8faz_28961/12_2024/8faz_28961.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8faz_28961/12_2024/8faz_28961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8faz_28961/12_2024/8faz_28961.map" model { file = "/net/cci-nas-00/data/ceres_data/8faz_28961/12_2024/8faz_28961.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8faz_28961/12_2024/8faz_28961.cif" } resolution = 2.3 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= 0.015 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 2 5.21 5 S 50 5.16 5 C 4619 2.51 5 N 1275 2.21 5 O 1377 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7331 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 570 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "C" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2470 Classifications: {'peptide': 314} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 301} Chain breaks: 2 Chain: "D" Number of atoms: 2288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2288 Classifications: {'peptide': 303} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 294} Chain breaks: 2 Chain: "X" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1912 Classifications: {'peptide': 236} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 229} Chain breaks: 3 Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.83, per 1000 atoms: 0.66 Number of scatterers: 7331 At special positions: 0 Unit cell: (68.73, 80.91, 111.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 50 16.00 P 8 15.00 Mg 2 11.99 O 1377 8.00 N 1275 7.00 C 4619 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: 1.82 Conformation dependent library (CDL) restraints added in 1.0 seconds 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1728 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 5 sheets defined 52.6% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'B' and resid 12 through 21 Processing helix chain 'B' and resid 26 through 33 removed outlier: 3.515A pdb=" N LEU B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 42 removed outlier: 4.061A pdb=" N LYS B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 58 Processing helix chain 'B' and resid 67 through 75 Processing helix chain 'C' and resid 13 through 17 Processing helix chain 'C' and resid 20 through 30 Processing helix chain 'C' and resid 34 through 40 removed outlier: 3.857A pdb=" N LEU C 38 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU C 40 " --> pdb=" O GLU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 53 through 67 Processing helix chain 'C' and resid 87 through 97 Processing helix chain 'C' and resid 104 through 110 Processing helix chain 'C' and resid 130 through 143 removed outlier: 3.536A pdb=" N VAL C 140 " --> pdb=" O MET C 136 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN C 143 " --> pdb=" O ALA C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 149 removed outlier: 6.100A pdb=" N CYS C 147 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 187 removed outlier: 3.883A pdb=" N GLU C 185 " --> pdb=" O GLN C 181 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N HIS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 196 removed outlier: 4.174A pdb=" N ARG C 193 " --> pdb=" O GLY C 189 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 207 Processing helix chain 'C' and resid 215 through 225 Processing helix chain 'C' and resid 225 through 233 Processing helix chain 'C' and resid 246 through 250 removed outlier: 3.749A pdb=" N HIS C 250 " --> pdb=" O PRO C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 277 Processing helix chain 'C' and resid 303 through 308 Processing helix chain 'D' and resid 13 through 23 removed outlier: 3.650A pdb=" N HIS D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 34 Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 46 through 62 Processing helix chain 'D' and resid 68 through 77 removed outlier: 3.536A pdb=" N THR D 77 " --> pdb=" O GLU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 removed outlier: 3.510A pdb=" N LYS D 91 " --> pdb=" O GLY D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 127 Processing helix chain 'D' and resid 142 through 154 Processing helix chain 'D' and resid 156 through 166 removed outlier: 3.553A pdb=" N ALA D 161 " --> pdb=" O GLU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 192 Processing helix chain 'D' and resid 207 through 216 removed outlier: 3.864A pdb=" N VAL D 211 " --> pdb=" O SER D 207 " (cutoff:3.500A) Proline residue: D 214 - end of helix Processing helix chain 'D' and resid 221 through 240 Processing helix chain 'D' and resid 267 through 271 removed outlier: 3.639A pdb=" N PHE D 270 " --> pdb=" O SER D 267 " (cutoff:3.500A) Processing helix chain 'X' and resid 23 through 28 Processing helix chain 'X' and resid 53 through 67 Processing helix chain 'X' and resid 88 through 100 Processing helix chain 'X' and resid 104 through 114 removed outlier: 3.683A pdb=" N ARG X 114 " --> pdb=" O TYR X 110 " (cutoff:3.500A) Processing helix chain 'X' and resid 122 through 140 removed outlier: 3.694A pdb=" N GLU X 134 " --> pdb=" O LEU X 130 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N SER X 135 " --> pdb=" O TYR X 131 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N MET X 136 " --> pdb=" O SER X 132 " (cutoff:3.500A) Processing helix chain 'X' and resid 154 through 162 Processing helix chain 'X' and resid 165 through 170 Processing helix chain 'X' and resid 170 through 188 Processing helix chain 'X' and resid 228 through 233 Processing sheet with id=AA1, first strand: chain 'B' and resid 65 through 66 removed outlier: 5.307A pdb=" N GLU C 154 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N THR C 120 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU C 313 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLU C 122 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N PHE C 315 " --> pdb=" O GLU C 122 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N CYS C 124 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N TRP C 317 " --> pdb=" O CYS C 124 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ARG C 312 " --> pdb=" O TYR C 327 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 85 through 86 removed outlier: 6.404A pdb=" N VAL D 132 " --> pdb=" O GLN D 168 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N VAL D 170 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N TYR D 134 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASN D 131 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL D 202 " --> pdb=" O ASN D 131 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LYS D 201 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL D 246 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL D 203 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N THR D 248 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL D 205 " --> pdb=" O THR D 248 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N HIS D 250 " --> pdb=" O VAL D 205 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 85 through 86 removed outlier: 6.404A pdb=" N VAL D 132 " --> pdb=" O GLN D 168 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N VAL D 170 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N TYR D 134 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASN D 131 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL D 202 " --> pdb=" O ASN D 131 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LYS D 201 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL D 246 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL D 203 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N THR D 248 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL D 205 " --> pdb=" O THR D 248 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N HIS D 250 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N THR D 103 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ASN D 249 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ILE D 105 " --> pdb=" O ASN D 249 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE D 251 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLY D 107 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 9.726A pdb=" N ARG D 253 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL D 102 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N ILE D 276 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLU D 104 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N LEU D 278 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL D 106 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N THR D 280 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ARG D 275 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 340 through 342 Processing sheet with id=AA5, first strand: chain 'D' and resid 66 through 67 removed outlier: 6.768A pdb=" N GLU X 77 " --> pdb=" O LEU X 145 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N ILE X 147 " --> pdb=" O GLU X 77 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU X 79 " --> pdb=" O ILE X 147 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASP X 42 " --> pdb=" O LEU X 191 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ALA X 193 " --> pdb=" O ASP X 42 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LEU X 44 " --> pdb=" O ALA X 193 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N THR X 195 " --> pdb=" O LEU X 44 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N PHE X 46 " --> pdb=" O THR X 195 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE X 43 " --> pdb=" O HIS X 237 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N MET X 239 " --> pdb=" O ILE X 43 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU X 45 " --> pdb=" O MET X 239 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N PHE X 241 " --> pdb=" O GLU X 45 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N HIS X 47 " --> pdb=" O PHE X 241 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N LYS X 243 " --> pdb=" O HIS X 47 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE X 269 " --> pdb=" O CYS X 280 " (cutoff:3.500A) 371 hydrogen bonds defined for protein. 1056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2410 1.34 - 1.46: 1539 1.46 - 1.58: 3409 1.58 - 1.69: 13 1.69 - 1.81: 72 Bond restraints: 7443 Sorted by residual: bond pdb=" O3A ANP D 401 " pdb=" PB ANP D 401 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.23e+01 bond pdb=" O3A ANP X 301 " pdb=" PB ANP X 301 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.10e+01 bond pdb=" N3B ANP X 301 " pdb=" PG ANP X 301 " ideal model delta sigma weight residual 1.795 1.690 0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" N3B ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.73e+01 bond pdb=" O5' ANP D 401 " pdb=" PA ANP D 401 " ideal model delta sigma weight residual 1.655 1.579 0.076 2.00e-02 2.50e+03 1.43e+01 ... (remaining 7438 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.47: 10005 3.47 - 6.95: 44 6.95 - 10.42: 4 10.42 - 13.89: 2 13.89 - 17.36: 2 Bond angle restraints: 10057 Sorted by residual: angle pdb=" PB ANP X 301 " pdb=" N3B ANP X 301 " pdb=" PG ANP X 301 " ideal model delta sigma weight residual 126.95 109.59 17.36 3.00e+00 1.11e-01 3.35e+01 angle pdb=" PB ANP D 401 " pdb=" N3B ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sigma weight residual 126.95 109.85 17.10 3.00e+00 1.11e-01 3.25e+01 angle pdb=" N ILE C 183 " pdb=" CA ILE C 183 " pdb=" C ILE C 183 " ideal model delta sigma weight residual 112.80 108.50 4.30 1.15e+00 7.56e-01 1.40e+01 angle pdb=" O1B ANP D 401 " pdb=" PB ANP D 401 " pdb=" O2B ANP D 401 " ideal model delta sigma weight residual 120.08 109.22 10.86 3.00e+00 1.11e-01 1.31e+01 angle pdb=" O1B ANP X 301 " pdb=" PB ANP X 301 " pdb=" O2B ANP X 301 " ideal model delta sigma weight residual 120.08 109.40 10.68 3.00e+00 1.11e-01 1.27e+01 ... (remaining 10052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.63: 4424 26.63 - 53.26: 106 53.26 - 79.90: 8 79.90 - 106.53: 3 106.53 - 133.16: 1 Dihedral angle restraints: 4542 sinusoidal: 1879 harmonic: 2663 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 73.16 -133.16 1 2.00e+01 2.50e-03 4.04e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 -147.03 87.03 1 2.00e+01 2.50e-03 2.28e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 -0.52 -59.48 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 4539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1038 0.056 - 0.112: 129 0.112 - 0.167: 8 0.167 - 0.223: 0 0.223 - 0.279: 2 Chirality restraints: 1177 Sorted by residual: chirality pdb=" C3' ANP X 301 " pdb=" C2' ANP X 301 " pdb=" C4' ANP X 301 " pdb=" O3' ANP X 301 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C3' ANP D 401 " pdb=" C2' ANP D 401 " pdb=" C4' ANP D 401 " pdb=" O3' ANP D 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA ILE C 144 " pdb=" N ILE C 144 " pdb=" C ILE C 144 " pdb=" CB ILE C 144 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 1174 not shown) Planarity restraints: 1258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY X 48 " -0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO X 49 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO X 49 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO X 49 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 342 " 0.018 5.00e-02 4.00e+02 2.68e-02 1.15e+00 pdb=" N PRO C 343 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO C 343 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 343 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 42 " 0.017 5.00e-02 4.00e+02 2.50e-02 9.98e-01 pdb=" N PRO C 43 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO C 43 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 43 " 0.014 5.00e-02 4.00e+02 ... (remaining 1255 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 82 2.57 - 3.15: 5991 3.15 - 3.73: 12089 3.73 - 4.32: 17103 4.32 - 4.90: 27967 Nonbonded interactions: 63232 Sorted by model distance: nonbonded pdb=" OG1 THR X 55 " pdb="MG MG X 302 " model vdw 1.986 2.170 nonbonded pdb=" O3G ANP D 401 " pdb="MG MG D 402 " model vdw 1.992 2.170 nonbonded pdb=" O1G ANP X 301 " pdb="MG MG X 302 " model vdw 2.013 2.170 nonbonded pdb=" OG1 THR D 114 " pdb="MG MG D 402 " model vdw 2.013 2.170 nonbonded pdb=" O1B ANP X 301 " pdb="MG MG X 302 " model vdw 2.027 2.170 ... (remaining 63227 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.260 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 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 : 0.004 0.145 7443 Z= 0.289 Angle : 0.616 17.364 10057 Z= 0.269 Chirality : 0.039 0.279 1177 Planarity : 0.003 0.028 1258 Dihedral : 11.246 133.159 2814 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.50 % Allowed : 2.74 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: 0.35 (0.28), residues: 904 helix: 0.68 (0.25), residues: 417 sheet: 0.30 (0.45), residues: 151 loop : -0.19 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP X 231 HIS 0.002 0.001 HIS X 40 PHE 0.007 0.001 PHE D 173 TYR 0.011 0.001 TYR C 210 ARG 0.002 0.000 ARG D 275 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 190 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: B 13 GLN cc_start: 0.7078 (mm-40) cc_final: 0.6856 (mm-40) REVERT: B 46 TYR cc_start: 0.7941 (t80) cc_final: 0.7361 (t80) REVERT: C 181 GLN cc_start: 0.7027 (tt0) cc_final: 0.6563 (tm-30) REVERT: D 36 LEU cc_start: 0.7396 (mt) cc_final: 0.7161 (mm) REVERT: D 174 ASP cc_start: 0.7860 (m-30) cc_final: 0.7649 (m-30) REVERT: D 292 MET cc_start: 0.8468 (mmm) cc_final: 0.8043 (mmp) REVERT: X 26 GLU cc_start: 0.7634 (tt0) cc_final: 0.6915 (tp30) REVERT: X 64 ARG cc_start: 0.8202 (mtp85) cc_final: 0.7911 (mmm160) REVERT: X 224 ARG cc_start: 0.8649 (ttt-90) cc_final: 0.8192 (ttt-90) outliers start: 4 outliers final: 2 residues processed: 193 average time/residue: 1.1930 time to fit residues: 243.2302 Evaluate side-chains 149 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 147 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 208 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 0.1980 chunk 38 optimal weight: 5.9990 chunk 23 optimal weight: 0.0070 chunk 46 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 65 GLN C 267 GLN D 60 GLN D 301 GLN X 252 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7443 Z= 0.194 Angle : 0.570 6.541 10057 Z= 0.280 Chirality : 0.042 0.149 1177 Planarity : 0.004 0.048 1258 Dihedral : 8.150 103.238 1067 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.24 % Allowed : 11.07 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: 0.44 (0.28), residues: 904 helix: 0.88 (0.24), residues: 439 sheet: 0.04 (0.45), residues: 146 loop : -0.24 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP X 231 HIS 0.004 0.001 HIS X 60 PHE 0.011 0.001 PHE C 164 TYR 0.014 0.001 TYR X 131 ARG 0.009 0.000 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: C 181 GLN cc_start: 0.7145 (tt0) cc_final: 0.6668 (tm-30) REVERT: C 205 LEU cc_start: 0.7726 (mt) cc_final: 0.7516 (mp) REVERT: D 36 LEU cc_start: 0.7425 (mt) cc_final: 0.7196 (mm) REVERT: D 259 ARG cc_start: 0.7359 (pmm-80) cc_final: 0.7059 (pmm-80) REVERT: X 25 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.6713 (pmmt) REVERT: X 26 GLU cc_start: 0.7641 (tt0) cc_final: 0.6972 (tp30) REVERT: X 88 ASP cc_start: 0.7893 (t70) cc_final: 0.7467 (t70) outliers start: 18 outliers final: 9 residues processed: 188 average time/residue: 1.2239 time to fit residues: 244.5911 Evaluate side-chains 165 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 83 THR Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 171 SER Chi-restraints excluded: chain X residue 182 LYS Chi-restraints excluded: chain X residue 239 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 GLN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN ** X 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 169 GLN X 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7443 Z= 0.241 Angle : 0.570 6.874 10057 Z= 0.279 Chirality : 0.042 0.150 1177 Planarity : 0.004 0.052 1258 Dihedral : 7.352 78.427 1067 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.36 % Allowed : 15.05 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: 0.34 (0.28), residues: 904 helix: 0.82 (0.24), residues: 438 sheet: -0.23 (0.43), residues: 151 loop : -0.19 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 314 HIS 0.006 0.001 HIS X 40 PHE 0.010 0.001 PHE C 346 TYR 0.015 0.002 TYR X 131 ARG 0.009 0.001 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.879 Fit side-chains REVERT: C 103 PHE cc_start: 0.7499 (t80) cc_final: 0.7192 (t80) REVERT: C 181 GLN cc_start: 0.7141 (tt0) cc_final: 0.6594 (tm-30) REVERT: D 259 ARG cc_start: 0.7424 (pmm-80) cc_final: 0.7179 (pmm-80) REVERT: X 26 GLU cc_start: 0.7657 (tt0) cc_final: 0.7060 (tp30) REVERT: X 199 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7839 (mtp) outliers start: 19 outliers final: 9 residues processed: 174 average time/residue: 1.2515 time to fit residues: 229.8700 Evaluate side-chains 164 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain X residue 27 ILE Chi-restraints excluded: chain X residue 83 THR Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 182 LYS Chi-restraints excluded: chain X residue 194 THR Chi-restraints excluded: chain X residue 199 MET Chi-restraints excluded: chain X residue 239 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 169 GLN X 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7443 Z= 0.263 Angle : 0.598 6.883 10057 Z= 0.290 Chirality : 0.043 0.149 1177 Planarity : 0.004 0.058 1258 Dihedral : 6.754 75.379 1067 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.23 % Allowed : 15.80 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: 0.46 (0.28), residues: 904 helix: 0.92 (0.25), residues: 427 sheet: -0.40 (0.43), residues: 153 loop : 0.05 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 314 HIS 0.008 0.001 HIS X 40 PHE 0.018 0.002 PHE C 248 TYR 0.015 0.002 TYR X 131 ARG 0.012 0.001 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 103 PHE cc_start: 0.7471 (t80) cc_final: 0.7199 (t80) REVERT: C 181 GLN cc_start: 0.7163 (tt0) cc_final: 0.6635 (tm-30) REVERT: D 16 MET cc_start: 0.6266 (ptp) cc_final: 0.5949 (ptm) REVERT: D 259 ARG cc_start: 0.7400 (pmm-80) cc_final: 0.7087 (pmm-80) REVERT: X 26 GLU cc_start: 0.7684 (tt0) cc_final: 0.7071 (tp30) REVERT: X 45 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6988 (tp30) outliers start: 26 outliers final: 12 residues processed: 165 average time/residue: 1.2922 time to fit residues: 224.4259 Evaluate side-chains 156 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 83 THR Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 182 LYS Chi-restraints excluded: chain X residue 194 THR Chi-restraints excluded: chain X residue 239 MET Chi-restraints excluded: chain X residue 280 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN C 11 GLN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN ** X 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 169 GLN X 252 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 7443 Z= 0.296 Angle : 0.607 7.174 10057 Z= 0.297 Chirality : 0.043 0.189 1177 Planarity : 0.004 0.058 1258 Dihedral : 6.546 72.923 1066 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.49 % Allowed : 17.04 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: 0.40 (0.28), residues: 904 helix: 0.91 (0.25), residues: 426 sheet: -0.49 (0.42), residues: 152 loop : -0.02 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 314 HIS 0.008 0.001 HIS X 40 PHE 0.013 0.002 PHE C 248 TYR 0.015 0.002 TYR C 210 ARG 0.014 0.001 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.841 Fit side-chains REVERT: B 45 SER cc_start: 0.8553 (p) cc_final: 0.8298 (p) REVERT: B 55 MET cc_start: 0.7505 (tpp) cc_final: 0.7280 (tpt) REVERT: C 144 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8150 (mp) REVERT: C 181 GLN cc_start: 0.7158 (tt0) cc_final: 0.6612 (tm-30) REVERT: D 259 ARG cc_start: 0.7401 (pmm-80) cc_final: 0.7108 (pmm-80) REVERT: X 26 GLU cc_start: 0.7704 (tt0) cc_final: 0.7035 (tp30) REVERT: X 45 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.6992 (tp30) REVERT: X 243 LYS cc_start: 0.8362 (ttpp) cc_final: 0.8149 (ttmt) outliers start: 20 outliers final: 10 residues processed: 149 average time/residue: 1.1555 time to fit residues: 182.4048 Evaluate side-chains 153 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 182 LYS Chi-restraints excluded: chain X residue 194 THR Chi-restraints excluded: chain X residue 239 MET Chi-restraints excluded: chain X residue 266 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 73 optimal weight: 0.0170 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.0030 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 0.0020 chunk 84 optimal weight: 3.9990 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN C 97 GLN C 133 GLN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 169 GLN X 252 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7443 Z= 0.166 Angle : 0.579 7.409 10057 Z= 0.280 Chirality : 0.041 0.212 1177 Planarity : 0.004 0.051 1258 Dihedral : 6.172 62.365 1066 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.99 % Allowed : 18.28 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: 0.50 (0.28), residues: 904 helix: 1.06 (0.25), residues: 432 sheet: -0.42 (0.42), residues: 152 loop : -0.11 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 314 HIS 0.008 0.001 HIS X 40 PHE 0.012 0.001 PHE C 148 TYR 0.012 0.001 TYR C 210 ARG 0.016 0.001 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.886 Fit side-chains REVERT: C 103 PHE cc_start: 0.7307 (t80) cc_final: 0.6971 (t80) REVERT: C 181 GLN cc_start: 0.7132 (tt0) cc_final: 0.6617 (tm-30) REVERT: C 260 ARG cc_start: 0.7637 (mtm110) cc_final: 0.7412 (ptt90) REVERT: D 16 MET cc_start: 0.6067 (ptp) cc_final: 0.5775 (ptm) REVERT: D 113 LYS cc_start: 0.8192 (mtmm) cc_final: 0.7736 (mtmm) REVERT: D 259 ARG cc_start: 0.7415 (pmm-80) cc_final: 0.7114 (pmm-80) REVERT: X 26 GLU cc_start: 0.7697 (tt0) cc_final: 0.6948 (tp30) REVERT: X 45 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7007 (tp30) outliers start: 16 outliers final: 7 residues processed: 157 average time/residue: 1.0901 time to fit residues: 181.7638 Evaluate side-chains 137 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 239 MET Chi-restraints excluded: chain X residue 266 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 GLN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 HIS D 301 GLN ** X 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 169 GLN X 252 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7443 Z= 0.267 Angle : 0.628 9.529 10057 Z= 0.303 Chirality : 0.044 0.302 1177 Planarity : 0.004 0.046 1258 Dihedral : 6.369 61.148 1066 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.11 % Allowed : 18.41 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: 0.54 (0.28), residues: 904 helix: 1.04 (0.25), residues: 427 sheet: -0.48 (0.42), residues: 152 loop : 0.08 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 314 HIS 0.008 0.001 HIS X 40 PHE 0.010 0.001 PHE C 248 TYR 0.016 0.002 TYR X 131 ARG 0.010 0.001 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.836 Fit side-chains REVERT: B 45 SER cc_start: 0.8447 (p) cc_final: 0.8212 (p) REVERT: C 181 GLN cc_start: 0.7107 (tt0) cc_final: 0.6589 (tm-30) REVERT: C 260 ARG cc_start: 0.7644 (mtm110) cc_final: 0.7399 (ptt90) REVERT: D 259 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.7114 (pmm-80) REVERT: X 26 GLU cc_start: 0.7696 (tt0) cc_final: 0.7034 (tp30) REVERT: X 45 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6956 (tp30) outliers start: 17 outliers final: 10 residues processed: 150 average time/residue: 1.1320 time to fit residues: 180.1464 Evaluate side-chains 146 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 182 LYS Chi-restraints excluded: chain X residue 194 THR Chi-restraints excluded: chain X residue 239 MET Chi-restraints excluded: chain X residue 266 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 55 optimal weight: 0.0470 chunk 59 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 68 optimal weight: 0.0070 chunk 79 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN ** X 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 169 GLN X 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7443 Z= 0.188 Angle : 0.636 9.874 10057 Z= 0.304 Chirality : 0.042 0.241 1177 Planarity : 0.004 0.046 1258 Dihedral : 6.166 57.555 1066 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.87 % Allowed : 19.53 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: 0.54 (0.28), residues: 904 helix: 1.13 (0.25), residues: 428 sheet: -0.47 (0.42), residues: 152 loop : -0.08 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 314 HIS 0.008 0.001 HIS X 40 PHE 0.010 0.001 PHE C 148 TYR 0.012 0.001 TYR X 131 ARG 0.011 0.001 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.860 Fit side-chains REVERT: C 181 GLN cc_start: 0.7053 (tt0) cc_final: 0.6550 (tm-30) REVERT: D 259 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.7112 (pmm-80) REVERT: X 26 GLU cc_start: 0.7693 (tt0) cc_final: 0.6986 (tp30) REVERT: X 45 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7008 (tp30) outliers start: 15 outliers final: 10 residues processed: 143 average time/residue: 1.1678 time to fit residues: 177.3108 Evaluate side-chains 137 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 182 LYS Chi-restraints excluded: chain X residue 194 THR Chi-restraints excluded: chain X residue 239 MET Chi-restraints excluded: chain X residue 266 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 GLN C 97 GLN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN ** X 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7443 Z= 0.280 Angle : 0.662 10.497 10057 Z= 0.320 Chirality : 0.044 0.272 1177 Planarity : 0.004 0.054 1258 Dihedral : 6.335 57.418 1066 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.62 % Allowed : 20.90 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: 0.46 (0.28), residues: 904 helix: 0.99 (0.25), residues: 428 sheet: -0.49 (0.43), residues: 152 loop : -0.01 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP D 314 HIS 0.008 0.001 HIS B 50 PHE 0.009 0.001 PHE C 211 TYR 0.018 0.002 TYR X 131 ARG 0.013 0.001 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.862 Fit side-chains REVERT: B 45 SER cc_start: 0.8481 (p) cc_final: 0.8255 (p) REVERT: C 181 GLN cc_start: 0.7100 (tt0) cc_final: 0.6585 (tm-30) REVERT: D 259 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7132 (pmm-80) REVERT: X 26 GLU cc_start: 0.7701 (tt0) cc_final: 0.7018 (tp30) REVERT: X 45 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7016 (tp30) outliers start: 13 outliers final: 13 residues processed: 136 average time/residue: 1.2485 time to fit residues: 179.9508 Evaluate side-chains 147 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 182 LYS Chi-restraints excluded: chain X residue 194 THR Chi-restraints excluded: chain X residue 236 LYS Chi-restraints excluded: chain X residue 239 MET Chi-restraints excluded: chain X residue 266 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 57 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN ** X 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 252 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7443 Z= 0.230 Angle : 0.694 11.231 10057 Z= 0.331 Chirality : 0.044 0.261 1177 Planarity : 0.004 0.057 1258 Dihedral : 6.264 57.343 1066 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.87 % Allowed : 20.90 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: 0.43 (0.28), residues: 904 helix: 1.02 (0.25), residues: 427 sheet: -0.52 (0.43), residues: 152 loop : -0.12 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 314 HIS 0.007 0.001 HIS X 40 PHE 0.008 0.001 PHE C 148 TYR 0.019 0.002 TYR X 131 ARG 0.014 0.001 ARG B 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.842 Fit side-chains REVERT: B 45 SER cc_start: 0.8438 (p) cc_final: 0.8204 (p) REVERT: C 181 GLN cc_start: 0.7086 (tt0) cc_final: 0.6585 (tm-30) REVERT: C 321 GLN cc_start: 0.7913 (tm-30) cc_final: 0.7649 (tm130) REVERT: D 259 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7068 (pmm-80) REVERT: X 26 GLU cc_start: 0.7694 (tt0) cc_final: 0.7014 (tp30) REVERT: X 45 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6995 (tp30) REVERT: X 199 MET cc_start: 0.7961 (mtp) cc_final: 0.7735 (mtp) outliers start: 15 outliers final: 13 residues processed: 140 average time/residue: 1.2757 time to fit residues: 188.4913 Evaluate side-chains 144 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain X residue 45 GLU Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 83 THR Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 182 LYS Chi-restraints excluded: chain X residue 194 THR Chi-restraints excluded: chain X residue 236 LYS Chi-restraints excluded: chain X residue 239 MET Chi-restraints excluded: chain X residue 266 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 63 optimal weight: 0.0670 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 GLN C 97 GLN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN ** X 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.130731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.119268 restraints weight = 11918.243| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.08 r_work: 0.3884 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3751 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7443 Z= 0.226 Angle : 0.675 11.389 10057 Z= 0.324 Chirality : 0.045 0.434 1177 Planarity : 0.004 0.058 1258 Dihedral : 6.279 56.900 1066 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.87 % Allowed : 21.27 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % 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: 0.43 (0.28), residues: 904 helix: 1.04 (0.25), residues: 427 sheet: -0.50 (0.43), residues: 152 loop : -0.14 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 314 HIS 0.007 0.001 HIS X 40 PHE 0.008 0.001 PHE C 346 TYR 0.021 0.002 TYR X 131 ARG 0.014 0.001 ARG B 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3570.69 seconds wall clock time: 65 minutes 3.82 seconds (3903.82 seconds total)