Starting phenix.real_space_refine on Sun Aug 24 03:21:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tmo_41396/08_2025/8tmo_41396.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tmo_41396/08_2025/8tmo_41396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tmo_41396/08_2025/8tmo_41396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tmo_41396/08_2025/8tmo_41396.map" model { file = "/net/cci-nas-00/data/ceres_data/8tmo_41396/08_2025/8tmo_41396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tmo_41396/08_2025/8tmo_41396.cif" } resolution = 3.1 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= 0.014 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 793 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 3 5.21 5 S 58 5.16 5 C 10437 2.51 5 N 2613 2.21 5 O 2948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16059 Number of models: 1 Model: "" Number of chains: 9 Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 803 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "H" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 969 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "A" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2805 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain: "B" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2917 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 15, 'TRANS': 334} Chain: "C" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2812 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 13, 'TRANS': 322} Chain: "D" Number of atoms: 2860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2860 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 15, 'TRANS': 327} Chain: "E" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2890 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 15, 'TRANS': 331} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.36, per 1000 atoms: 0.27 Number of scatterers: 16059 At special positions: 0 Unit cell: (124.371, 142.442, 139.253, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 Mg 3 11.99 O 2948 8.00 N 2613 7.00 C 10437 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 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: 1.40 Conformation dependent library (CDL) restraints added in 719.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3726 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 11 sheets defined 52.0% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 removed outlier: 4.067A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 55 removed outlier: 3.772A pdb=" N ARG A 54 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 81 removed outlier: 3.525A pdb=" N VAL A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 removed outlier: 3.641A pdb=" N LEU A 87 " --> pdb=" O HIS A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 157 Processing helix chain 'A' and resid 165 through 202 removed outlier: 3.604A pdb=" N LEU A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 238 Proline residue: A 227 - end of helix Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 247 through 280 removed outlier: 3.602A pdb=" N PHE A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 311 removed outlier: 3.850A pdb=" N LYS A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASN A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) Proline residue: A 303 - end of helix Processing helix chain 'A' and resid 325 through 348 Processing helix chain 'B' and resid 47 through 54 Proline residue: B 52 - end of helix Processing helix chain 'B' and resid 69 through 81 Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 147 through 157 Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 165 through 202 removed outlier: 3.531A pdb=" N LEU B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE B 182 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 238 removed outlier: 3.577A pdb=" N VAL B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) Proline residue: B 227 - end of helix Processing helix chain 'B' and resid 247 through 311 removed outlier: 3.529A pdb=" N PHE B 251 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP B 270 " --> pdb=" O GLU B 266 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ILE B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 3.552A pdb=" N ILE B 307 " --> pdb=" O PRO B 303 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 348 Processing helix chain 'C' and resid 70 through 80 Processing helix chain 'C' and resid 83 through 86 Processing helix chain 'C' and resid 87 through 92 removed outlier: 4.033A pdb=" N ASN C 92 " --> pdb=" O GLU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 157 Processing helix chain 'C' and resid 167 through 202 Processing helix chain 'C' and resid 205 through 238 removed outlier: 4.300A pdb=" N GLN C 209 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Proline residue: C 227 - end of helix removed outlier: 3.754A pdb=" N ASP C 238 " --> pdb=" O SER C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 311 Proline residue: C 303 - end of helix Processing helix chain 'C' and resid 325 through 348 Processing helix chain 'D' and resid 46 through 51 removed outlier: 3.566A pdb=" N SER D 49 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 81 removed outlier: 4.198A pdb=" N VAL D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 90 Processing helix chain 'D' and resid 147 through 157 Processing helix chain 'D' and resid 165 through 202 removed outlier: 3.936A pdb=" N ASP D 180 " --> pdb=" O ALA D 176 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N TYR D 181 " --> pdb=" O LEU D 177 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE D 182 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL D 183 " --> pdb=" O ASP D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 238 Proline residue: D 227 - end of helix removed outlier: 3.644A pdb=" N LEU D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP D 238 " --> pdb=" O SER D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 312 removed outlier: 3.914A pdb=" N LEU D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP D 277 " --> pdb=" O SER D 273 " (cutoff:3.500A) Proline residue: D 303 - end of helix Processing helix chain 'D' and resid 325 through 348 removed outlier: 3.704A pdb=" N VAL D 329 " --> pdb=" O TRP D 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 56 removed outlier: 3.589A pdb=" N SER E 56 " --> pdb=" O PHE E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 81 removed outlier: 4.092A pdb=" N VAL E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 92 Processing helix chain 'E' and resid 147 through 156 Processing helix chain 'E' and resid 165 through 202 Processing helix chain 'E' and resid 204 through 238 Proline residue: E 227 - end of helix removed outlier: 3.730A pdb=" N GLU E 230 " --> pdb=" O TRP E 226 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP E 238 " --> pdb=" O SER E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 312 removed outlier: 4.161A pdb=" N LEU E 276 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASP E 277 " --> pdb=" O SER E 273 " (cutoff:3.500A) Proline residue: E 303 - end of helix Processing helix chain 'E' and resid 325 through 348 Processing sheet with id=AA1, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AA2, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.358A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.358A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.692A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER H 52 " --> pdb=" O SER H 57 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER H 57 " --> pdb=" O SER H 52 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.855A pdb=" N TYR H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N TYR H 100 " --> pdb=" O MET H 113 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N MET H 113 " --> pdb=" O TYR H 100 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TYR H 102 " --> pdb=" O ASN H 111 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ASN H 111 " --> pdb=" O TYR H 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 39 through 44 removed outlier: 3.542A pdb=" N CYS A 135 " --> pdb=" O THR A 132 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 39 through 44 removed outlier: 4.283A pdb=" N GLU B 121 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP B 116 " --> pdb=" O GLU B 121 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 39 through 44 removed outlier: 3.524A pdb=" N VAL C 136 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET C 138 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU C 123 " --> pdb=" O THR C 114 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR C 114 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 39 through 44 removed outlier: 3.732A pdb=" N GLU D 123 " --> pdb=" O THR D 114 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 39 through 44 1019 hydrogen bonds defined for protein. 2925 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: 2.55 Time building geometry restraints manager: 1.84 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: 5055 1.34 - 1.46: 3005 1.46 - 1.57: 8256 1.57 - 1.69: 0 1.69 - 1.81: 107 Bond restraints: 16423 Sorted by residual: bond pdb=" CG LEU B 304 " pdb=" CD2 LEU B 304 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.13e+00 bond pdb=" CG1 ILE C 192 " pdb=" CD1 ILE C 192 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.66e+00 bond pdb=" N ASN C 134 " pdb=" CA ASN C 134 " ideal model delta sigma weight residual 1.457 1.472 -0.014 1.29e-02 6.01e+03 1.23e+00 bond pdb=" C PRO D 240 " pdb=" N PRO D 241 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.21e+00 bond pdb=" CG LEU B 173 " pdb=" CD1 LEU B 173 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.20e+00 ... (remaining 16418 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 21989 2.36 - 4.72: 247 4.72 - 7.08: 30 7.08 - 9.44: 5 9.44 - 11.80: 1 Bond angle restraints: 22272 Sorted by residual: angle pdb=" CA MET A 291 " pdb=" CB MET A 291 " pdb=" CG MET A 291 " ideal model delta sigma weight residual 114.10 122.19 -8.09 2.00e+00 2.50e-01 1.63e+01 angle pdb=" C LEU A 235 " pdb=" N TYR A 236 " pdb=" CA TYR A 236 " ideal model delta sigma weight residual 122.53 115.31 7.22 1.92e+00 2.71e-01 1.41e+01 angle pdb=" N THR D 45 " pdb=" CA THR D 45 " pdb=" C THR D 45 " ideal model delta sigma weight residual 114.56 109.88 4.68 1.27e+00 6.20e-01 1.36e+01 angle pdb=" C LEU B 235 " pdb=" N TYR B 236 " pdb=" CA TYR B 236 " ideal model delta sigma weight residual 122.54 116.50 6.04 1.65e+00 3.67e-01 1.34e+01 angle pdb=" CA LEU B 304 " pdb=" CB LEU B 304 " pdb=" CG LEU B 304 " ideal model delta sigma weight residual 116.30 128.10 -11.80 3.50e+00 8.16e-02 1.14e+01 ... (remaining 22267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 8743 18.00 - 35.99: 908 35.99 - 53.99: 169 53.99 - 71.99: 30 71.99 - 89.99: 17 Dihedral angle restraints: 9867 sinusoidal: 4102 harmonic: 5765 Sorted by residual: dihedral pdb=" CB CYS L 24 " pdb=" SG CYS L 24 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 146.36 -53.36 1 1.00e+01 1.00e-02 3.87e+01 dihedral pdb=" CA PRO D 240 " pdb=" C PRO D 240 " pdb=" N PRO D 241 " pdb=" CA PRO D 241 " ideal model delta harmonic sigma weight residual 180.00 -159.92 -20.08 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA ILE E 300 " pdb=" C ILE E 300 " pdb=" N PHE E 301 " pdb=" CA PHE E 301 " ideal model delta harmonic sigma weight residual -180.00 -161.10 -18.90 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 9864 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1884 0.045 - 0.091: 503 0.091 - 0.136: 136 0.136 - 0.181: 9 0.181 - 0.226: 1 Chirality restraints: 2533 Sorted by residual: chirality pdb=" CG LEU B 304 " pdb=" CB LEU B 304 " pdb=" CD1 LEU B 304 " pdb=" CD2 LEU B 304 " both_signs ideal model delta sigma weight residual False -2.59 -2.82 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB VAL D 239 " pdb=" CA VAL D 239 " pdb=" CG1 VAL D 239 " pdb=" CG2 VAL D 239 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.16e-01 chirality pdb=" CA HIS C 212 " pdb=" N HIS C 212 " pdb=" C HIS C 212 " pdb=" CB HIS C 212 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.70e-01 ... (remaining 2530 not shown) Planarity restraints: 2785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 240 " -0.040 5.00e-02 4.00e+02 6.01e-02 5.77e+00 pdb=" N PRO C 241 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO C 241 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 241 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 240 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO D 241 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 241 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 241 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 212 " -0.017 2.00e-02 2.50e+03 1.51e-02 3.44e+00 pdb=" CG HIS C 212 " 0.030 2.00e-02 2.50e+03 pdb=" ND1 HIS C 212 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 HIS C 212 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 HIS C 212 " -0.012 2.00e-02 2.50e+03 pdb=" NE2 HIS C 212 " 0.001 2.00e-02 2.50e+03 ... (remaining 2782 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 263 2.69 - 3.24: 16170 3.24 - 3.79: 25567 3.79 - 4.35: 32810 4.35 - 4.90: 54151 Nonbonded interactions: 128961 Sorted by model distance: nonbonded pdb=" NE2 GLN D 260 " pdb=" O HIS E 94 " model vdw 2.133 3.120 nonbonded pdb=" O TYR B 34 " pdb=" OG1 THR B 58 " model vdw 2.189 3.040 nonbonded pdb=" OH TYR B 23 " pdb=" OE2 GLU B 123 " model vdw 2.196 3.040 nonbonded pdb=" O LYS A 111 " pdb=" OH TYR A 181 " model vdw 2.210 3.040 nonbonded pdb=" O GLU A 204 " pdb=" OG1 THR A 207 " model vdw 2.215 3.040 ... (remaining 128956 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 17 through 350) selection = (chain 'B' and resid 17 through 350) selection = (chain 'C' and resid 17 through 350) selection = (chain 'D' and resid 17 through 350) selection = (chain 'E' and resid 17 through 350) } 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=0.49 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: 3.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.870 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 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 : 0.003 0.050 16425 Z= 0.153 Angle : 0.627 11.797 22276 Z= 0.332 Chirality : 0.043 0.226 2533 Planarity : 0.005 0.060 2785 Dihedral : 15.055 89.987 6135 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.82 % Favored : 95.08 % Rotamer: Outliers : 0.06 % Allowed : 0.55 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.20), residues: 1930 helix: 1.72 (0.17), residues: 963 sheet: 0.60 (0.27), residues: 359 loop : -1.72 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 202 TYR 0.021 0.001 TYR B 279 PHE 0.019 0.001 PHE E 27 TRP 0.009 0.001 TRP H 47 HIS 0.013 0.001 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.00335 (16423) covalent geometry : angle 0.62630 (22272) SS BOND : bond 0.00261 ( 2) SS BOND : angle 1.46112 ( 4) hydrogen bonds : bond 0.12282 ( 1003) hydrogen bonds : angle 6.02423 ( 2925) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 363 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: H 13 GLN cc_start: 0.8219 (mm-40) cc_final: 0.7984 (mm110) REVERT: H 123 THR cc_start: 0.8072 (p) cc_final: 0.7816 (p) REVERT: H 124 VAL cc_start: 0.8382 (t) cc_final: 0.8019 (m) REVERT: A 89 ASP cc_start: 0.6842 (m-30) cc_final: 0.6625 (m-30) REVERT: A 125 GLU cc_start: 0.8007 (tt0) cc_final: 0.7209 (tt0) REVERT: A 193 ASP cc_start: 0.6942 (t70) cc_final: 0.6701 (t70) REVERT: A 197 GLU cc_start: 0.6303 (mm-30) cc_final: 0.5816 (mp0) REVERT: A 272 VAL cc_start: 0.8491 (t) cc_final: 0.8148 (m) REVERT: A 331 LEU cc_start: 0.6093 (tt) cc_final: 0.5877 (tt) REVERT: C 260 GLN cc_start: 0.6720 (mm110) cc_final: 0.6505 (mm-40) REVERT: D 29 ILE cc_start: 0.8360 (mt) cc_final: 0.8134 (mt) REVERT: D 45 THR cc_start: 0.7013 (p) cc_final: 0.6057 (p) REVERT: D 112 MET cc_start: 0.7131 (ttp) cc_final: 0.6894 (mtp) REVERT: E 291 MET cc_start: 0.7510 (ttm) cc_final: 0.7154 (ttp) REVERT: E 314 ASN cc_start: 0.5372 (m-40) cc_final: 0.5160 (m110) outliers start: 1 outliers final: 0 residues processed: 363 average time/residue: 0.1229 time to fit residues: 67.2829 Evaluate side-chains 307 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.0970 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN A 217 ASN B 104 ASN C 33 ASN C 63 ASN C 68 HIS C 74 GLN C 140 GLN D 94 HIS D 260 GLN E 140 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.166443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.136438 restraints weight = 28920.273| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.70 r_work: 0.3619 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3620 r_free = 0.3620 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16425 Z= 0.174 Angle : 0.618 8.590 22276 Z= 0.330 Chirality : 0.044 0.187 2533 Planarity : 0.005 0.058 2785 Dihedral : 4.375 20.038 2155 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.30 % Favored : 95.60 % Rotamer: Outliers : 1.99 % Allowed : 10.67 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.20), residues: 1930 helix: 1.97 (0.16), residues: 974 sheet: 0.67 (0.28), residues: 348 loop : -1.73 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 40 TYR 0.025 0.001 TYR B 279 PHE 0.037 0.002 PHE C 53 TRP 0.009 0.001 TRP H 47 HIS 0.007 0.001 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.00393 (16423) covalent geometry : angle 0.61815 (22272) SS BOND : bond 0.00625 ( 2) SS BOND : angle 1.60958 ( 4) hydrogen bonds : bond 0.05611 ( 1003) hydrogen bonds : angle 4.82942 ( 2925) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 327 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 76 LYS cc_start: 0.8098 (ptmm) cc_final: 0.7851 (ptmm) REVERT: H 123 THR cc_start: 0.8104 (p) cc_final: 0.7847 (p) REVERT: H 124 VAL cc_start: 0.8616 (t) cc_final: 0.8251 (m) REVERT: A 89 ASP cc_start: 0.7142 (m-30) cc_final: 0.6902 (m-30) REVERT: A 197 GLU cc_start: 0.6444 (mm-30) cc_final: 0.5911 (mp0) REVERT: A 270 ASP cc_start: 0.7702 (m-30) cc_final: 0.7426 (m-30) REVERT: A 289 GLU cc_start: 0.6793 (mt-10) cc_final: 0.6576 (mt-10) REVERT: A 291 MET cc_start: 0.6952 (mmp) cc_final: 0.6587 (mmt) REVERT: B 74 GLN cc_start: 0.8496 (tt0) cc_final: 0.8190 (tt0) REVERT: C 260 GLN cc_start: 0.7084 (mm110) cc_final: 0.6727 (mm-40) REVERT: D 260 GLN cc_start: 0.8279 (tt0) cc_final: 0.8072 (tt0) REVERT: E 263 ASP cc_start: 0.7194 (m-30) cc_final: 0.6969 (m-30) REVERT: E 314 ASN cc_start: 0.5520 (m-40) cc_final: 0.5257 (m110) outliers start: 36 outliers final: 25 residues processed: 341 average time/residue: 0.1245 time to fit residues: 63.8724 Evaluate side-chains 327 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 302 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 313 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 108 optimal weight: 4.9990 chunk 188 optimal weight: 0.8980 chunk 161 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 186 optimal weight: 0.4980 chunk 123 optimal weight: 4.9990 chunk 135 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN B 104 ASN D 94 HIS D 209 GLN E 140 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.163724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.133102 restraints weight = 29330.303| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.37 r_work: 0.3616 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16425 Z= 0.188 Angle : 0.611 8.696 22276 Z= 0.326 Chirality : 0.044 0.187 2533 Planarity : 0.005 0.058 2785 Dihedral : 4.379 19.548 2155 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.61 % Favored : 95.28 % Rotamer: Outliers : 3.15 % Allowed : 14.38 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.19), residues: 1930 helix: 1.94 (0.16), residues: 975 sheet: 0.66 (0.28), residues: 346 loop : -1.78 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 165 TYR 0.020 0.001 TYR H 103 PHE 0.032 0.002 PHE C 53 TRP 0.010 0.001 TRP H 47 HIS 0.006 0.001 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.00430 (16423) covalent geometry : angle 0.61078 (22272) SS BOND : bond 0.00937 ( 2) SS BOND : angle 1.17936 ( 4) hydrogen bonds : bond 0.05532 ( 1003) hydrogen bonds : angle 4.72524 ( 2925) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 311 time to evaluate : 0.579 Fit side-chains revert: symmetry clash REVERT: H 76 LYS cc_start: 0.8094 (ptmm) cc_final: 0.7860 (ptmm) REVERT: H 123 THR cc_start: 0.8093 (p) cc_final: 0.7843 (p) REVERT: H 124 VAL cc_start: 0.8609 (t) cc_final: 0.8262 (m) REVERT: A 89 ASP cc_start: 0.7283 (m-30) cc_final: 0.6991 (m-30) REVERT: A 113 PHE cc_start: 0.8771 (m-80) cc_final: 0.8522 (m-80) REVERT: A 134 ASN cc_start: 0.6821 (t0) cc_final: 0.6564 (t0) REVERT: A 163 LYS cc_start: 0.8492 (mtmt) cc_final: 0.8153 (mtmt) REVERT: A 270 ASP cc_start: 0.7630 (m-30) cc_final: 0.7375 (m-30) REVERT: A 289 GLU cc_start: 0.6871 (mt-10) cc_final: 0.6627 (mt-10) REVERT: A 291 MET cc_start: 0.6988 (mmp) cc_final: 0.6754 (mmt) REVERT: A 315 PHE cc_start: 0.7042 (m-80) cc_final: 0.6811 (m-80) REVERT: B 74 GLN cc_start: 0.8424 (tt0) cc_final: 0.8119 (tt0) REVERT: B 261 ILE cc_start: 0.8280 (mm) cc_final: 0.8073 (mt) REVERT: C 260 GLN cc_start: 0.7067 (mm110) cc_final: 0.6700 (mm-40) REVERT: D 95 GLN cc_start: 0.8003 (tm-30) cc_final: 0.7750 (tm-30) REVERT: D 126 GLN cc_start: 0.7594 (tp-100) cc_final: 0.7352 (tp-100) REVERT: E 69 ARG cc_start: 0.7729 (mtp-110) cc_final: 0.7519 (ptm160) REVERT: E 256 ASP cc_start: 0.7181 (m-30) cc_final: 0.6981 (m-30) REVERT: E 263 ASP cc_start: 0.7134 (m-30) cc_final: 0.6914 (m-30) REVERT: E 314 ASN cc_start: 0.5606 (m-40) cc_final: 0.5365 (m110) outliers start: 57 outliers final: 45 residues processed: 339 average time/residue: 0.1192 time to fit residues: 61.3511 Evaluate side-chains 342 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 297 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 94 HIS Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 156 TYR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 313 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN B 104 ASN D 94 HIS D 209 GLN ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.166169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.136585 restraints weight = 29153.282| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.43 r_work: 0.3604 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16425 Z= 0.188 Angle : 0.614 8.780 22276 Z= 0.326 Chirality : 0.044 0.166 2533 Planarity : 0.005 0.058 2785 Dihedral : 4.393 19.433 2155 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.61 % Favored : 95.28 % Rotamer: Outliers : 3.87 % Allowed : 16.04 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.19), residues: 1930 helix: 1.94 (0.16), residues: 970 sheet: 0.54 (0.27), residues: 348 loop : -1.78 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 210 TYR 0.020 0.001 TYR H 103 PHE 0.030 0.002 PHE C 53 TRP 0.010 0.001 TRP H 47 HIS 0.006 0.001 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.00432 (16423) covalent geometry : angle 0.61365 (22272) SS BOND : bond 0.00099 ( 2) SS BOND : angle 1.23505 ( 4) hydrogen bonds : bond 0.05460 ( 1003) hydrogen bonds : angle 4.67673 ( 2925) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 314 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: L 79 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8194 (mp) REVERT: H 76 LYS cc_start: 0.8088 (ptmm) cc_final: 0.7844 (ptmm) REVERT: H 123 THR cc_start: 0.8094 (p) cc_final: 0.7860 (p) REVERT: H 124 VAL cc_start: 0.8622 (t) cc_final: 0.8298 (m) REVERT: A 89 ASP cc_start: 0.7157 (m-30) cc_final: 0.6883 (m-30) REVERT: A 134 ASN cc_start: 0.6819 (t0) cc_final: 0.6532 (t0) REVERT: A 163 LYS cc_start: 0.8506 (mtmt) cc_final: 0.8167 (mtmt) REVERT: A 289 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6709 (mt-10) REVERT: A 315 PHE cc_start: 0.7084 (m-80) cc_final: 0.6879 (m-80) REVERT: B 74 GLN cc_start: 0.8434 (tt0) cc_final: 0.8135 (tt0) REVERT: B 261 ILE cc_start: 0.8266 (mm) cc_final: 0.8058 (mt) REVERT: C 260 GLN cc_start: 0.7058 (mm110) cc_final: 0.6704 (mm-40) REVERT: C 318 MET cc_start: 0.5006 (mtm) cc_final: 0.4160 (ptp) REVERT: D 95 GLN cc_start: 0.8034 (tm-30) cc_final: 0.7767 (tm-30) REVERT: D 126 GLN cc_start: 0.7586 (tp-100) cc_final: 0.7336 (tp-100) REVERT: D 207 THR cc_start: 0.7873 (OUTLIER) cc_final: 0.7597 (t) REVERT: E 23 TYR cc_start: 0.6882 (m-10) cc_final: 0.6649 (m-80) REVERT: E 263 ASP cc_start: 0.7133 (m-30) cc_final: 0.6923 (m-30) REVERT: E 291 MET cc_start: 0.8079 (ttp) cc_final: 0.7864 (ttt) REVERT: E 314 ASN cc_start: 0.5605 (m-40) cc_final: 0.5373 (m110) outliers start: 70 outliers final: 50 residues processed: 357 average time/residue: 0.1067 time to fit residues: 57.7027 Evaluate side-chains 341 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 289 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 156 TYR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 313 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 42 optimal weight: 0.6980 chunk 156 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 188 optimal weight: 0.3980 chunk 165 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN B 104 ASN D 94 HIS ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.164736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.135344 restraints weight = 29607.197| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.47 r_work: 0.3597 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16425 Z= 0.189 Angle : 0.621 8.771 22276 Z= 0.329 Chirality : 0.044 0.211 2533 Planarity : 0.005 0.057 2785 Dihedral : 4.404 19.056 2155 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.61 % Favored : 95.28 % Rotamer: Outliers : 4.15 % Allowed : 18.36 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.19), residues: 1930 helix: 1.94 (0.16), residues: 970 sheet: 0.51 (0.27), residues: 350 loop : -1.79 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 24 TYR 0.020 0.001 TYR H 103 PHE 0.030 0.002 PHE C 53 TRP 0.010 0.001 TRP H 47 HIS 0.006 0.001 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.00434 (16423) covalent geometry : angle 0.62136 (22272) SS BOND : bond 0.00165 ( 2) SS BOND : angle 1.12511 ( 4) hydrogen bonds : bond 0.05424 ( 1003) hydrogen bonds : angle 4.65001 ( 2925) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 305 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: L 79 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8194 (mp) REVERT: H 76 LYS cc_start: 0.8062 (ptmm) cc_final: 0.7852 (ptmm) REVERT: H 123 THR cc_start: 0.8094 (p) cc_final: 0.7823 (p) REVERT: H 124 VAL cc_start: 0.8639 (t) cc_final: 0.8306 (m) REVERT: A 89 ASP cc_start: 0.7141 (m-30) cc_final: 0.6862 (m-30) REVERT: A 134 ASN cc_start: 0.6827 (t0) cc_final: 0.6521 (t0) REVERT: A 163 LYS cc_start: 0.8498 (mtmt) cc_final: 0.8233 (mtmt) REVERT: A 246 GLU cc_start: 0.7607 (pp20) cc_final: 0.7330 (pp20) REVERT: A 289 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6657 (mt-10) REVERT: A 291 MET cc_start: 0.7251 (mmt) cc_final: 0.6831 (mmt) REVERT: B 74 GLN cc_start: 0.8450 (tt0) cc_final: 0.8144 (tt0) REVERT: B 121 GLU cc_start: 0.6399 (mm-30) cc_final: 0.6149 (mm-30) REVERT: B 261 ILE cc_start: 0.8252 (mm) cc_final: 0.8036 (mt) REVERT: C 260 GLN cc_start: 0.6959 (mm110) cc_final: 0.6588 (mm-40) REVERT: C 318 MET cc_start: 0.5065 (mtm) cc_final: 0.4331 (ptp) REVERT: D 95 GLN cc_start: 0.7992 (tm-30) cc_final: 0.7774 (tm-30) REVERT: D 126 GLN cc_start: 0.7600 (tp-100) cc_final: 0.7389 (tp-100) REVERT: D 207 THR cc_start: 0.7881 (OUTLIER) cc_final: 0.7654 (t) REVERT: D 311 TYR cc_start: 0.7317 (m-80) cc_final: 0.6922 (m-80) outliers start: 75 outliers final: 55 residues processed: 352 average time/residue: 0.1076 time to fit residues: 58.1906 Evaluate side-chains 351 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 294 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 156 TYR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 313 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 26 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 184 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 25 optimal weight: 0.0770 chunk 66 optimal weight: 0.9990 chunk 168 optimal weight: 0.4980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 13 GLN A 217 ASN B 104 ASN C 74 GLN D 94 HIS ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.158543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.128556 restraints weight = 29643.648| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.34 r_work: 0.3624 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16425 Z= 0.153 Angle : 0.608 8.192 22276 Z= 0.320 Chirality : 0.044 0.226 2533 Planarity : 0.004 0.058 2785 Dihedral : 4.322 19.017 2155 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.30 % Favored : 95.60 % Rotamer: Outliers : 3.82 % Allowed : 19.03 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.20), residues: 1930 helix: 2.13 (0.16), residues: 969 sheet: 0.62 (0.28), residues: 332 loop : -1.75 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 40 TYR 0.017 0.001 TYR H 103 PHE 0.030 0.001 PHE C 53 TRP 0.008 0.001 TRP D 226 HIS 0.008 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00339 (16423) covalent geometry : angle 0.60756 (22272) SS BOND : bond 0.00167 ( 2) SS BOND : angle 0.80244 ( 4) hydrogen bonds : bond 0.05147 ( 1003) hydrogen bonds : angle 4.52664 ( 2925) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 315 time to evaluate : 0.663 Fit side-chains REVERT: L 79 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8155 (mp) REVERT: H 76 LYS cc_start: 0.8036 (ptmm) cc_final: 0.7824 (ptmm) REVERT: H 123 THR cc_start: 0.8042 (p) cc_final: 0.7811 (p) REVERT: H 124 VAL cc_start: 0.8610 (t) cc_final: 0.8281 (m) REVERT: A 89 ASP cc_start: 0.7031 (m-30) cc_final: 0.6778 (m-30) REVERT: A 134 ASN cc_start: 0.6769 (t0) cc_final: 0.6475 (t0) REVERT: A 163 LYS cc_start: 0.8482 (mtmt) cc_final: 0.8263 (mtmt) REVERT: A 246 GLU cc_start: 0.7488 (pp20) cc_final: 0.7185 (pp20) REVERT: A 270 ASP cc_start: 0.7550 (m-30) cc_final: 0.7202 (m-30) REVERT: A 289 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6743 (mt-10) REVERT: A 291 MET cc_start: 0.7110 (mmt) cc_final: 0.6738 (mmt) REVERT: B 74 GLN cc_start: 0.8383 (tt0) cc_final: 0.8066 (tt0) REVERT: B 121 GLU cc_start: 0.6484 (mm-30) cc_final: 0.6168 (mm-30) REVERT: B 134 ASN cc_start: 0.7916 (m-40) cc_final: 0.7653 (m-40) REVERT: B 261 ILE cc_start: 0.8249 (mm) cc_final: 0.8026 (mt) REVERT: C 260 GLN cc_start: 0.6907 (mm110) cc_final: 0.6453 (mm-40) REVERT: C 318 MET cc_start: 0.5089 (mtm) cc_final: 0.4126 (ptp) REVERT: D 95 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7748 (tm-30) REVERT: D 311 TYR cc_start: 0.7295 (m-80) cc_final: 0.6698 (m-80) outliers start: 69 outliers final: 55 residues processed: 356 average time/residue: 0.1124 time to fit residues: 61.5969 Evaluate side-chains 356 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 300 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 156 TYR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 156 TYR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 313 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 144 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 176 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 151 optimal weight: 0.5980 chunk 21 optimal weight: 0.2980 chunk 171 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN B 104 ASN C 74 GLN D 94 HIS D 126 GLN D 209 GLN ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.162554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.130164 restraints weight = 29317.126| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.47 r_work: 0.3613 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16425 Z= 0.161 Angle : 0.616 8.551 22276 Z= 0.324 Chirality : 0.043 0.178 2533 Planarity : 0.004 0.058 2785 Dihedral : 4.287 18.761 2155 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.56 % Favored : 95.34 % Rotamer: Outliers : 4.20 % Allowed : 19.91 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.19), residues: 1930 helix: 2.17 (0.16), residues: 968 sheet: 0.76 (0.28), residues: 336 loop : -1.80 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 165 TYR 0.017 0.001 TYR H 103 PHE 0.031 0.001 PHE C 53 TRP 0.008 0.001 TRP D 226 HIS 0.006 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00364 (16423) covalent geometry : angle 0.61550 (22272) SS BOND : bond 0.00146 ( 2) SS BOND : angle 0.78432 ( 4) hydrogen bonds : bond 0.05106 ( 1003) hydrogen bonds : angle 4.52422 ( 2925) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 302 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: L 79 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8215 (mp) REVERT: H 76 LYS cc_start: 0.8026 (ptmm) cc_final: 0.7818 (ptmm) REVERT: H 123 THR cc_start: 0.8075 (p) cc_final: 0.7809 (p) REVERT: H 124 VAL cc_start: 0.8631 (t) cc_final: 0.8313 (m) REVERT: A 89 ASP cc_start: 0.7052 (m-30) cc_final: 0.6798 (m-30) REVERT: A 134 ASN cc_start: 0.6792 (t0) cc_final: 0.6498 (t0) REVERT: A 163 LYS cc_start: 0.8518 (mtmt) cc_final: 0.8293 (mtmt) REVERT: A 246 GLU cc_start: 0.7442 (pp20) cc_final: 0.7115 (pp20) REVERT: A 270 ASP cc_start: 0.7564 (m-30) cc_final: 0.7197 (m-30) REVERT: A 289 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6738 (mt-10) REVERT: A 291 MET cc_start: 0.7070 (mmt) cc_final: 0.6803 (mmt) REVERT: A 302 MET cc_start: 0.7756 (mmm) cc_final: 0.7402 (mtm) REVERT: B 74 GLN cc_start: 0.8403 (tt0) cc_final: 0.8111 (tt0) REVERT: B 121 GLU cc_start: 0.6605 (mm-30) cc_final: 0.6264 (mm-30) REVERT: B 134 ASN cc_start: 0.7919 (m-40) cc_final: 0.7674 (m-40) REVERT: B 261 ILE cc_start: 0.8216 (mm) cc_final: 0.8012 (mt) REVERT: C 260 GLN cc_start: 0.6956 (mm110) cc_final: 0.6516 (mm-40) REVERT: C 318 MET cc_start: 0.4957 (mtm) cc_final: 0.3928 (ptp) REVERT: C 346 LYS cc_start: 0.8892 (tppt) cc_final: 0.8493 (mtmm) REVERT: D 130 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7684 (mm) REVERT: D 311 TYR cc_start: 0.7446 (m-80) cc_final: 0.6863 (m-80) outliers start: 76 outliers final: 60 residues processed: 347 average time/residue: 0.1191 time to fit residues: 63.3770 Evaluate side-chains 357 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 295 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 156 TYR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 156 TYR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 313 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 187 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 0 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 178 optimal weight: 0.4980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN B 104 ASN C 74 GLN D 94 HIS D 209 GLN ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.164790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.132660 restraints weight = 29637.797| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.46 r_work: 0.3601 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16425 Z= 0.190 Angle : 0.638 9.069 22276 Z= 0.335 Chirality : 0.045 0.235 2533 Planarity : 0.005 0.059 2785 Dihedral : 4.332 18.911 2155 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.66 % Favored : 95.23 % Rotamer: Outliers : 4.31 % Allowed : 20.63 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.19), residues: 1930 helix: 2.09 (0.16), residues: 967 sheet: 0.73 (0.28), residues: 336 loop : -1.82 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 162 TYR 0.020 0.001 TYR H 103 PHE 0.031 0.002 PHE A 306 TRP 0.009 0.001 TRP H 47 HIS 0.006 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00441 (16423) covalent geometry : angle 0.63774 (22272) SS BOND : bond 0.00129 ( 2) SS BOND : angle 0.98002 ( 4) hydrogen bonds : bond 0.05244 ( 1003) hydrogen bonds : angle 4.58095 ( 2925) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 305 time to evaluate : 0.673 Fit side-chains REVERT: L 79 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8226 (mp) REVERT: H 76 LYS cc_start: 0.8050 (ptmm) cc_final: 0.7829 (ptmm) REVERT: H 81 LEU cc_start: 0.8151 (tp) cc_final: 0.7939 (tp) REVERT: H 123 THR cc_start: 0.8065 (p) cc_final: 0.7813 (p) REVERT: H 124 VAL cc_start: 0.8638 (t) cc_final: 0.8316 (m) REVERT: A 65 THR cc_start: 0.5767 (OUTLIER) cc_final: 0.5534 (p) REVERT: A 89 ASP cc_start: 0.7054 (m-30) cc_final: 0.6797 (m-30) REVERT: A 134 ASN cc_start: 0.6785 (t0) cc_final: 0.6479 (t0) REVERT: A 163 LYS cc_start: 0.8511 (mtmt) cc_final: 0.8279 (mtmt) REVERT: A 246 GLU cc_start: 0.7467 (pp20) cc_final: 0.7129 (pp20) REVERT: A 270 ASP cc_start: 0.7566 (m-30) cc_final: 0.7185 (m-30) REVERT: A 289 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6788 (mt-10) REVERT: A 291 MET cc_start: 0.7142 (mmt) cc_final: 0.6856 (mmt) REVERT: A 302 MET cc_start: 0.7672 (mmm) cc_final: 0.7397 (mtm) REVERT: B 74 GLN cc_start: 0.8405 (tt0) cc_final: 0.8096 (tt0) REVERT: C 74 GLN cc_start: 0.6763 (mm110) cc_final: 0.6498 (mm-40) REVERT: C 111 LYS cc_start: 0.7613 (tptt) cc_final: 0.7286 (tptp) REVERT: C 260 GLN cc_start: 0.6974 (mm110) cc_final: 0.6500 (mm-40) REVERT: D 95 GLN cc_start: 0.7925 (tm-30) cc_final: 0.7550 (tm-30) REVERT: D 130 ILE cc_start: 0.7946 (OUTLIER) cc_final: 0.7696 (mm) REVERT: D 311 TYR cc_start: 0.7455 (m-80) cc_final: 0.6883 (m-80) REVERT: E 85 LEU cc_start: 0.8046 (mm) cc_final: 0.7827 (mt) REVERT: E 302 MET cc_start: 0.7337 (mtm) cc_final: 0.7064 (mtp) REVERT: E 344 TYR cc_start: 0.5194 (OUTLIER) cc_final: 0.4132 (p90) outliers start: 78 outliers final: 61 residues processed: 351 average time/residue: 0.1157 time to fit residues: 62.6522 Evaluate side-chains 364 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 299 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 156 TYR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 156 TYR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 313 MET Chi-restraints excluded: chain E residue 334 MET Chi-restraints excluded: chain E residue 344 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 119 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 183 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 78 optimal weight: 0.3980 chunk 187 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN B 104 ASN C 63 ASN D 94 HIS D 209 GLN ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.161007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.128736 restraints weight = 29617.532| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.46 r_work: 0.3606 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16425 Z= 0.181 Angle : 0.643 9.891 22276 Z= 0.338 Chirality : 0.044 0.214 2533 Planarity : 0.005 0.059 2785 Dihedral : 4.358 18.550 2155 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.51 % Favored : 95.39 % Rotamer: Outliers : 4.26 % Allowed : 20.91 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.19), residues: 1930 helix: 2.09 (0.16), residues: 967 sheet: 0.69 (0.28), residues: 338 loop : -1.82 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 162 TYR 0.019 0.001 TYR H 103 PHE 0.029 0.002 PHE C 53 TRP 0.009 0.001 TRP H 47 HIS 0.007 0.001 HIS E 68 Details of bonding type rmsd covalent geometry : bond 0.00417 (16423) covalent geometry : angle 0.64307 (22272) SS BOND : bond 0.00129 ( 2) SS BOND : angle 0.87234 ( 4) hydrogen bonds : bond 0.05241 ( 1003) hydrogen bonds : angle 4.57867 ( 2925) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 308 time to evaluate : 0.625 Fit side-chains REVERT: L 79 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8237 (mp) REVERT: H 76 LYS cc_start: 0.8018 (ptmm) cc_final: 0.7810 (ptmm) REVERT: H 123 THR cc_start: 0.8080 (p) cc_final: 0.7830 (p) REVERT: H 124 VAL cc_start: 0.8648 (t) cc_final: 0.8329 (m) REVERT: A 89 ASP cc_start: 0.7066 (m-30) cc_final: 0.6812 (m-30) REVERT: A 134 ASN cc_start: 0.6785 (t0) cc_final: 0.6488 (t0) REVERT: A 163 LYS cc_start: 0.8537 (mtmt) cc_final: 0.8298 (mtmt) REVERT: A 246 GLU cc_start: 0.7408 (pp20) cc_final: 0.7064 (pp20) REVERT: A 270 ASP cc_start: 0.7586 (m-30) cc_final: 0.7214 (m-30) REVERT: A 289 GLU cc_start: 0.7075 (mt-10) cc_final: 0.6761 (mt-10) REVERT: A 302 MET cc_start: 0.7770 (mmm) cc_final: 0.7428 (mtm) REVERT: B 74 GLN cc_start: 0.8427 (tt0) cc_final: 0.8128 (tt0) REVERT: C 260 GLN cc_start: 0.6948 (mm110) cc_final: 0.6506 (mm-40) REVERT: D 130 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7689 (mm) REVERT: D 311 TYR cc_start: 0.7504 (m-80) cc_final: 0.6928 (m-80) REVERT: E 85 LEU cc_start: 0.8026 (mm) cc_final: 0.7815 (mt) REVERT: E 302 MET cc_start: 0.6943 (mtm) cc_final: 0.6725 (mtp) REVERT: E 344 TYR cc_start: 0.5141 (OUTLIER) cc_final: 0.4167 (p90) outliers start: 77 outliers final: 66 residues processed: 353 average time/residue: 0.1164 time to fit residues: 63.2268 Evaluate side-chains 368 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 299 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 156 TYR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 140 GLN Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 156 TYR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 313 MET Chi-restraints excluded: chain E residue 334 MET Chi-restraints excluded: chain E residue 344 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 30 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 150 optimal weight: 0.5980 chunk 134 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 188 optimal weight: 0.2980 chunk 74 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN B 104 ASN C 74 GLN D 94 HIS ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.164461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.133326 restraints weight = 29397.929| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.62 r_work: 0.3587 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16425 Z= 0.215 Angle : 0.684 13.839 22276 Z= 0.357 Chirality : 0.045 0.224 2533 Planarity : 0.005 0.059 2785 Dihedral : 4.426 18.756 2155 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.61 % Favored : 95.28 % Rotamer: Outliers : 4.31 % Allowed : 20.69 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.19), residues: 1930 helix: 2.04 (0.16), residues: 959 sheet: 0.49 (0.28), residues: 351 loop : -1.89 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 162 TYR 0.021 0.002 TYR H 103 PHE 0.032 0.002 PHE A 306 TRP 0.010 0.001 TRP H 47 HIS 0.006 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00502 (16423) covalent geometry : angle 0.68385 (22272) SS BOND : bond 0.00123 ( 2) SS BOND : angle 1.03927 ( 4) hydrogen bonds : bond 0.05449 ( 1003) hydrogen bonds : angle 4.66886 ( 2925) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 297 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: L 79 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8281 (mp) REVERT: H 76 LYS cc_start: 0.8068 (ptmm) cc_final: 0.7843 (ptmm) REVERT: H 81 LEU cc_start: 0.8132 (tp) cc_final: 0.7928 (tp) REVERT: H 123 THR cc_start: 0.8081 (p) cc_final: 0.7824 (p) REVERT: H 124 VAL cc_start: 0.8678 (t) cc_final: 0.8328 (m) REVERT: A 89 ASP cc_start: 0.7113 (m-30) cc_final: 0.6861 (m-30) REVERT: A 134 ASN cc_start: 0.6817 (t0) cc_final: 0.6493 (t0) REVERT: A 246 GLU cc_start: 0.7456 (pp20) cc_final: 0.7120 (pp20) REVERT: A 270 ASP cc_start: 0.7594 (m-30) cc_final: 0.7214 (m-30) REVERT: A 289 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6666 (mt-10) REVERT: A 302 MET cc_start: 0.7659 (mmm) cc_final: 0.7403 (mtm) REVERT: B 74 GLN cc_start: 0.8439 (tt0) cc_final: 0.8124 (tt0) REVERT: C 111 LYS cc_start: 0.7639 (tptt) cc_final: 0.7381 (tptp) REVERT: C 260 GLN cc_start: 0.6975 (mm110) cc_final: 0.6496 (mm-40) REVERT: C 318 MET cc_start: 0.4995 (mtm) cc_final: 0.4759 (ttm) REVERT: D 130 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7701 (mm) REVERT: D 140 GLN cc_start: 0.6221 (pt0) cc_final: 0.5987 (pt0) REVERT: D 311 TYR cc_start: 0.7520 (m-80) cc_final: 0.6938 (m-80) REVERT: E 85 LEU cc_start: 0.8078 (mm) cc_final: 0.7862 (mt) outliers start: 78 outliers final: 67 residues processed: 343 average time/residue: 0.1223 time to fit residues: 64.3274 Evaluate side-chains 361 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 292 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 334 MET Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 83 HIS Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 156 TYR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 34 TYR Chi-restraints excluded: chain D residue 130 ILE Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 156 TYR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 313 MET Chi-restraints excluded: chain E residue 344 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 67 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 180 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN B 104 ASN D 94 HIS ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 314 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.156527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.126838 restraints weight = 29473.976| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.42 r_work: 0.3602 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.247 16425 Z= 0.285 Angle : 0.880 59.184 22276 Z= 0.487 Chirality : 0.045 0.325 2533 Planarity : 0.005 0.059 2785 Dihedral : 4.441 19.136 2155 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.66 % Favored : 95.23 % Rotamer: Outliers : 4.15 % Allowed : 21.02 % Favored : 74.83 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.19), residues: 1930 helix: 2.03 (0.16), residues: 959 sheet: 0.47 (0.27), residues: 352 loop : -1.88 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 162 TYR 0.021 0.001 TYR H 103 PHE 0.030 0.002 PHE A 306 TRP 0.011 0.001 TRP H 47 HIS 0.005 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00635 (16423) covalent geometry : angle 0.88016 (22272) SS BOND : bond 0.00107 ( 2) SS BOND : angle 1.00086 ( 4) hydrogen bonds : bond 0.05444 ( 1003) hydrogen bonds : angle 4.66952 ( 2925) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4376.28 seconds wall clock time: 75 minutes 45.48 seconds (4545.48 seconds total)