Starting phenix.real_space_refine on Thu Jul 2 07:15:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8faz_28961/07_2026/8faz_28961.cif Found real_map, /net/cci-nas-00/data/ceres_data/8faz_28961/07_2026/8faz_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8faz_28961/07_2026/8faz_28961.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8faz_28961/07_2026/8faz_28961.cif" model { file = "/net/cci-nas-00/data/ceres_data/8faz_28961/07_2026/8faz_28961.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8faz_28961/07_2026/8faz_28961.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8faz_28961/07_2026/8faz_28961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8faz_28961/07_2026/8faz_28961.map" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 1.48, per 1000 atoms: 0.20 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: 0.44 Conformation dependent library (CDL) restraints added in 347.1 milliseconds 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: 0.15 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: 0.73 Time building geometry restraints manager: 0.56 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: 4384 26.63 - 53.26: 91 53.26 - 79.90: 8 79.90 - 106.53: 2 106.53 - 133.16: 1 Dihedral angle restraints: 4486 sinusoidal: 1823 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 4483 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: 0.920 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: 0.020 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.510 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 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= 0.218 Angle : 0.616 17.364 10057 Z= 0.269 Chirality : 0.039 0.279 1177 Planarity : 0.003 0.028 1258 Dihedral : 10.771 133.159 2758 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (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 ARG 0.002 0.000 ARG D 275 TYR 0.011 0.001 TYR C 210 PHE 0.007 0.001 PHE D 173 TRP 0.008 0.001 TRP X 231 HIS 0.002 0.001 HIS X 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.22 ( 7443) covalent geometry : angle 0.61589 / 0.27 (10057) hydrogen bonds : bond 0.23531 / 15.65 ( 365) hydrogen bonds : angle 7.52025 / 5.39 ( 1056) *********************** 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 : 0.173 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: 0.3803 time to fit residues: 77.6907 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 : 0.232 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 65 GLN C 263 ASN C 267 GLN D 60 GLN D 301 GLN X 252 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.128024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.116626 restraints weight = 12088.132| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.09 r_work: 0.3848 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3708 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 7443 Z= 0.272 Angle : 0.641 7.202 10057 Z= 0.318 Chirality : 0.045 0.158 1177 Planarity : 0.005 0.057 1258 Dihedral : 7.281 104.034 1011 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.74 % Allowed : 11.19 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.27), residues: 904 helix: 0.65 (0.24), residues: 433 sheet: -0.38 (0.45), residues: 139 loop : -0.25 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 18 TYR 0.015 0.002 TYR X 131 PHE 0.011 0.002 PHE C 346 TRP 0.009 0.002 TRP X 231 HIS 0.007 0.001 HIS X 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.27 ( 7443) covalent geometry : angle 0.64080 / 0.32 (10057) hydrogen bonds : bond 0.04785 / 3.16 ( 365) hydrogen bonds : angle 5.23670 / 3.70 ( 1056) *********************** 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 185 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 163 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: C 181 GLN cc_start: 0.7555 (tt0) cc_final: 0.7024 (tm-30) REVERT: C 205 LEU cc_start: 0.7879 (mt) cc_final: 0.7622 (mp) REVERT: D 36 LEU cc_start: 0.7430 (mt) cc_final: 0.7147 (mm) REVERT: D 259 ARG cc_start: 0.7746 (pmm-80) cc_final: 0.7425 (pmm-80) REVERT: X 26 GLU cc_start: 0.7992 (tt0) cc_final: 0.7364 (tp30) REVERT: X 259 CYS cc_start: 0.7864 (t) cc_final: 0.7641 (t) outliers start: 22 outliers final: 10 residues processed: 176 average time/residue: 0.4752 time to fit residues: 88.3059 Evaluate side-chains 155 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain X residue 76 VAL 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 194 THR 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 8 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.129812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.118127 restraints weight = 11908.744| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 2.10 r_work: 0.3870 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3733 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7443 Z= 0.149 Angle : 0.569 6.852 10057 Z= 0.279 Chirality : 0.042 0.222 1177 Planarity : 0.004 0.050 1258 Dihedral : 6.768 90.236 1009 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.86 % Allowed : 14.18 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.28), residues: 904 helix: 0.80 (0.24), residues: 438 sheet: -0.39 (0.43), residues: 151 loop : -0.28 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 18 TYR 0.013 0.001 TYR X 131 PHE 0.010 0.001 PHE D 173 TRP 0.007 0.001 TRP X 231 HIS 0.007 0.001 HIS X 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 7443) covalent geometry : angle 0.56904 / 0.28 (10057) hydrogen bonds : bond 0.03653 / 2.43 ( 365) hydrogen bonds : angle 4.86755 / 3.43 ( 1056) *********************** 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 189 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 55 MET cc_start: 0.7620 (tpp) cc_final: 0.7378 (tpt) REVERT: C 103 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.7313 (t80) REVERT: C 144 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8174 (mp) REVERT: C 181 GLN cc_start: 0.7520 (tt0) cc_final: 0.6992 (tm-30) REVERT: C 205 LEU cc_start: 0.7735 (mt) cc_final: 0.7489 (mp) REVERT: D 259 ARG cc_start: 0.7760 (pmm-80) cc_final: 0.7492 (pmm-80) REVERT: X 26 GLU cc_start: 0.7937 (tt0) cc_final: 0.7223 (tp30) outliers start: 23 outliers final: 11 residues processed: 179 average time/residue: 0.4198 time to fit residues: 79.6287 Evaluate side-chains 162 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain C residue 103 PHE Chi-restraints excluded: chain C residue 144 ILE 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 D residue 299 SER Chi-restraints excluded: chain X residue 27 ILE 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 194 THR 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 82 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 88 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 13 GLN C 97 GLN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 ASN D 249 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.129725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.118099 restraints weight = 12089.836| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 2.10 r_work: 0.3871 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3735 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7443 Z= 0.148 Angle : 0.572 7.320 10057 Z= 0.277 Chirality : 0.042 0.176 1177 Planarity : 0.004 0.055 1258 Dihedral : 6.204 83.976 1009 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.61 % Allowed : 16.29 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.28), residues: 904 helix: 1.02 (0.25), residues: 426 sheet: -0.39 (0.43), residues: 151 loop : -0.04 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 18 TYR 0.014 0.001 TYR X 131 PHE 0.019 0.001 PHE C 248 TRP 0.008 0.001 TRP X 231 HIS 0.008 0.001 HIS X 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 7443) covalent geometry : angle 0.57246 / 0.28 (10057) hydrogen bonds : bond 0.03311 / 2.20 ( 365) hydrogen bonds : angle 4.67639 / 3.29 ( 1056) *********************** 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 181 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: B 33 LEU cc_start: 0.9320 (mt) cc_final: 0.9035 (mt) REVERT: B 55 MET cc_start: 0.7769 (tpp) cc_final: 0.7492 (tpt) REVERT: C 103 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.7320 (t80) REVERT: C 181 GLN cc_start: 0.7520 (tt0) cc_final: 0.7007 (tm-30) REVERT: C 205 LEU cc_start: 0.7700 (mt) cc_final: 0.7484 (mp) REVERT: D 259 ARG cc_start: 0.7815 (pmm-80) cc_final: 0.7565 (pmm-80) REVERT: X 26 GLU cc_start: 0.7948 (tt0) cc_final: 0.7241 (tp30) REVERT: X 64 ARG cc_start: 0.8206 (mmm160) cc_final: 0.7941 (mmm160) outliers start: 21 outliers final: 10 residues processed: 171 average time/residue: 0.4175 time to fit residues: 75.4625 Evaluate side-chains 147 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain C residue 103 PHE 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 27 ILE 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 280 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.128781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.116956 restraints weight = 12080.827| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 2.12 r_work: 0.3852 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3714 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7443 Z= 0.190 Angle : 0.608 6.837 10057 Z= 0.298 Chirality : 0.043 0.189 1177 Planarity : 0.004 0.037 1258 Dihedral : 5.960 77.959 1008 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.23 % Allowed : 16.54 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.28), residues: 904 helix: 1.01 (0.25), residues: 426 sheet: -0.48 (0.43), residues: 152 loop : -0.00 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 18 TYR 0.014 0.002 TYR X 131 PHE 0.015 0.002 PHE C 248 TRP 0.011 0.002 TRP D 314 HIS 0.008 0.001 HIS X 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 ( 7443) covalent geometry : angle 0.60829 / 0.30 (10057) hydrogen bonds : bond 0.03456 / 2.30 ( 365) hydrogen bonds : angle 4.64114 / 3.25 ( 1056) *********************** 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 176 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: B 55 MET cc_start: 0.7922 (tpp) cc_final: 0.7674 (tpt) REVERT: C 103 PHE cc_start: 0.7690 (OUTLIER) cc_final: 0.7348 (t80) REVERT: C 181 GLN cc_start: 0.7554 (tt0) cc_final: 0.7072 (tm-30) REVERT: C 205 LEU cc_start: 0.7744 (mt) cc_final: 0.7521 (mp) REVERT: D 259 ARG cc_start: 0.7785 (pmm-80) cc_final: 0.7498 (pmm-80) REVERT: X 26 GLU cc_start: 0.8016 (tt0) cc_final: 0.7287 (tp30) REVERT: X 64 ARG cc_start: 0.8274 (mmm160) cc_final: 0.8050 (mmm160) outliers start: 26 outliers final: 12 residues processed: 162 average time/residue: 0.4644 time to fit residues: 79.3232 Evaluate side-chains 151 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 D residue 157 GLU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain X residue 27 ILE 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 280 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 80 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 29 optimal weight: 0.0270 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 0.3980 chunk 32 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.130750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.119166 restraints weight = 11999.608| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.10 r_work: 0.3886 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7443 Z= 0.124 Angle : 0.578 7.583 10057 Z= 0.284 Chirality : 0.041 0.184 1177 Planarity : 0.003 0.033 1258 Dihedral : 5.622 69.717 1008 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.11 % Allowed : 18.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.28), residues: 904 helix: 1.15 (0.25), residues: 426 sheet: -0.39 (0.43), residues: 150 loop : 0.05 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 18 TYR 0.012 0.001 TYR C 210 PHE 0.011 0.001 PHE C 248 TRP 0.017 0.002 TRP D 314 HIS 0.009 0.001 HIS X 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 7443) covalent geometry : angle 0.57848 / 0.28 (10057) hydrogen bonds : bond 0.03071 / 2.04 ( 365) hydrogen bonds : angle 4.52360 / 3.16 ( 1056) *********************** 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 174 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.252 Fit side-chains REVERT: B 55 MET cc_start: 0.7793 (tpp) cc_final: 0.7549 (tpt) REVERT: C 103 PHE cc_start: 0.7627 (OUTLIER) cc_final: 0.7247 (t80) REVERT: C 181 GLN cc_start: 0.7504 (tt0) cc_final: 0.7029 (tm-30) REVERT: C 260 ARG cc_start: 0.7566 (mtm110) cc_final: 0.7318 (ptt90) REVERT: D 113 LYS cc_start: 0.8232 (mtmm) cc_final: 0.7716 (mtmm) REVERT: D 259 ARG cc_start: 0.7804 (pmm-80) cc_final: 0.7502 (pmm-80) REVERT: X 26 GLU cc_start: 0.7969 (tt0) cc_final: 0.7249 (tp30) outliers start: 17 outliers final: 10 residues processed: 165 average time/residue: 0.4202 time to fit residues: 73.4744 Evaluate side-chains 146 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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 D residue 277 LEU 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 194 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 88 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 19 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 29 optimal weight: 0.0030 chunk 32 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 13 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.131204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.119433 restraints weight = 12088.455| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 2.12 r_work: 0.3884 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3747 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7443 Z= 0.131 Angle : 0.611 9.629 10057 Z= 0.293 Chirality : 0.042 0.266 1177 Planarity : 0.004 0.042 1258 Dihedral : 5.421 64.066 1008 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.36 % Allowed : 19.53 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.28), residues: 904 helix: 1.15 (0.25), residues: 433 sheet: -0.45 (0.43), residues: 152 loop : -0.03 (0.36), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 18 TYR 0.015 0.001 TYR X 131 PHE 0.010 0.001 PHE X 87 TRP 0.021 0.002 TRP D 314 HIS 0.009 0.001 HIS X 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 7443) covalent geometry : angle 0.61146 / 0.29 (10057) hydrogen bonds : bond 0.03049 / 2.02 ( 365) hydrogen bonds : angle 4.49516 / 3.14 ( 1056) *********************** 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 168 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.293 Fit side-chains REVERT: B 15 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7887 (tp) REVERT: B 55 MET cc_start: 0.7882 (tpp) cc_final: 0.7640 (tpt) REVERT: C 10 MET cc_start: 0.7315 (ptt) cc_final: 0.7051 (ptt) REVERT: C 103 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.7200 (t80) REVERT: C 181 GLN cc_start: 0.7516 (tt0) cc_final: 0.7030 (tm-30) REVERT: D 259 ARG cc_start: 0.7793 (pmm-80) cc_final: 0.7483 (pmm-80) REVERT: X 26 GLU cc_start: 0.7997 (tt0) cc_final: 0.7258 (tp30) outliers start: 19 outliers final: 7 residues processed: 157 average time/residue: 0.4423 time to fit residues: 73.8645 Evaluate side-chains 137 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 15 LEU 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 D residue 277 LEU Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 194 THR Chi-restraints excluded: chain X residue 239 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 51 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 chunk 63 optimal weight: 0.0770 chunk 57 optimal weight: 3.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 13 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.130608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.119100 restraints weight = 12128.960| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 2.10 r_work: 0.3882 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7443 Z= 0.150 Angle : 0.625 9.874 10057 Z= 0.304 Chirality : 0.042 0.170 1177 Planarity : 0.004 0.045 1258 Dihedral : 5.289 58.274 1008 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.99 % Allowed : 21.02 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.28), residues: 904 helix: 1.18 (0.25), residues: 427 sheet: -0.45 (0.44), residues: 152 loop : 0.03 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 18 TYR 0.016 0.001 TYR X 131 PHE 0.010 0.001 PHE X 80 TRP 0.029 0.002 TRP D 314 HIS 0.008 0.001 HIS X 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 7443) covalent geometry : angle 0.62528 / 0.30 (10057) hydrogen bonds : bond 0.03099 / 2.06 ( 365) hydrogen bonds : angle 4.50045 / 3.13 ( 1056) *********************** 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 161 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.174 Fit side-chains REVERT: B 55 MET cc_start: 0.7906 (tpp) cc_final: 0.7673 (tpt) REVERT: C 103 PHE cc_start: 0.7583 (OUTLIER) cc_final: 0.7220 (t80) REVERT: C 181 GLN cc_start: 0.7488 (tt0) cc_final: 0.7023 (tm-30) REVERT: C 260 ARG cc_start: 0.7594 (mtm110) cc_final: 0.7368 (ptt90) REVERT: D 113 LYS cc_start: 0.8209 (mtmm) cc_final: 0.7625 (mtmm) REVERT: D 259 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7461 (pmm-80) REVERT: X 26 GLU cc_start: 0.7986 (tt0) cc_final: 0.7245 (tp30) outliers start: 16 outliers final: 9 residues processed: 149 average time/residue: 0.4068 time to fit residues: 64.1990 Evaluate side-chains 142 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 D residue 259 ARG Chi-restraints excluded: chain D residue 277 LEU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 54 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 76 optimal weight: 0.0570 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 13 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.131057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.119501 restraints weight = 11999.818| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 2.10 r_work: 0.3887 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3752 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7443 Z= 0.140 Angle : 0.631 11.206 10057 Z= 0.303 Chirality : 0.042 0.159 1177 Planarity : 0.004 0.050 1258 Dihedral : 5.245 55.854 1008 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.11 % Allowed : 21.14 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.28), residues: 904 helix: 1.19 (0.25), residues: 427 sheet: -0.43 (0.44), residues: 152 loop : -0.01 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 18 TYR 0.016 0.002 TYR X 131 PHE 0.011 0.001 PHE X 80 TRP 0.034 0.002 TRP D 314 HIS 0.008 0.001 HIS X 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 7443) covalent geometry : angle 0.63140 / 0.30 (10057) hydrogen bonds : bond 0.03066 / 2.02 ( 365) hydrogen bonds : angle 4.49416 / 3.12 ( 1056) *********************** 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 158 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.284 Fit side-chains REVERT: B 55 MET cc_start: 0.7885 (tpp) cc_final: 0.7625 (tpt) REVERT: C 103 PHE cc_start: 0.7577 (OUTLIER) cc_final: 0.7233 (t80) REVERT: C 181 GLN cc_start: 0.7471 (tt0) cc_final: 0.6985 (tm-30) REVERT: D 113 LYS cc_start: 0.8185 (mtmm) cc_final: 0.7624 (mtmm) REVERT: D 259 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7476 (pmm-80) REVERT: X 26 GLU cc_start: 0.8027 (tt0) cc_final: 0.7288 (tp30) outliers start: 17 outliers final: 11 residues processed: 148 average time/residue: 0.4288 time to fit residues: 67.1363 Evaluate side-chains 146 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.196 ------------------------------------------------------------------------------- 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 D residue 128 LEU Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 277 LEU 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 199 MET Chi-restraints excluded: chain X residue 239 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 51 optimal weight: 0.1980 chunk 58 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 23 optimal weight: 0.0980 chunk 83 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 0.2980 chunk 62 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.132873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.121242 restraints weight = 12045.419| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 2.13 r_work: 0.3904 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3769 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7443 Z= 0.127 Angle : 0.659 15.894 10057 Z= 0.316 Chirality : 0.043 0.234 1177 Planarity : 0.004 0.052 1258 Dihedral : 4.949 49.861 1008 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.62 % Allowed : 21.39 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.28), residues: 904 helix: 1.24 (0.25), residues: 427 sheet: -0.41 (0.43), residues: 152 loop : -0.00 (0.36), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 18 TYR 0.019 0.002 TYR X 131 PHE 0.011 0.001 PHE X 80 TRP 0.034 0.002 TRP D 314 HIS 0.008 0.001 HIS X 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 7443) covalent geometry : angle 0.65927 / 0.32 (10057) hydrogen bonds : bond 0.02978 / 1.96 ( 365) hydrogen bonds : angle 4.46076 / 3.09 ( 1056) ********************** 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 151 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.255 Fit side-chains REVERT: C 181 GLN cc_start: 0.7487 (tt0) cc_final: 0.6975 (tm-30) REVERT: C 321 GLN cc_start: 0.7605 (tm-30) cc_final: 0.7359 (tm130) REVERT: D 259 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7530 (pmm-80) outliers start: 13 outliers final: 11 residues processed: 143 average time/residue: 0.3685 time to fit residues: 55.9953 Evaluate side-chains 140 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.194 ------------------------------------------------------------------------------- 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 318 ASP Chi-restraints excluded: chain D residue 259 ARG Chi-restraints excluded: chain D residue 277 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 1 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 33 optimal weight: 0.0980 chunk 14 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 13 GLN C 11 GLN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.130522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.118899 restraints weight = 12095.904| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 2.11 r_work: 0.3878 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3743 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7443 Z= 0.171 Angle : 0.680 15.702 10057 Z= 0.326 Chirality : 0.043 0.176 1177 Planarity : 0.004 0.057 1258 Dihedral : 5.081 54.176 1008 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.12 % Allowed : 22.89 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.28), residues: 904 helix: 1.16 (0.25), residues: 427 sheet: -0.44 (0.44), residues: 152 loop : -0.05 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 18 TYR 0.021 0.002 TYR X 131 PHE 0.009 0.001 PHE X 80 TRP 0.036 0.002 TRP D 314 HIS 0.008 0.001 HIS X 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 7443) covalent geometry : angle 0.68017 / 0.33 (10057) hydrogen bonds : bond 0.03208 / 2.12 ( 365) hydrogen bonds : angle 4.54057 / 3.15 ( 1056) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2665.45 seconds wall clock time: 46 minutes 4.43 seconds (2764.43 seconds total)