Starting phenix.real_space_refine on Sat Jun 14 23:05:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tmo_41396/06_2025/8tmo_41396.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tmo_41396/06_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_41396/06_2025/8tmo_41396.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tmo_41396/06_2025/8tmo_41396.map" model { file = "/net/cci-nas-00/data/ceres_data/8tmo_41396/06_2025/8tmo_41396.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tmo_41396/06_2025/8tmo_41396.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.71, per 1000 atoms: 0.67 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: 4.05 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.63 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: 5.78 Time building geometry restraints manager: 4.81 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: 17.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.040 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 39.680 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.100 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (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 TRP 0.009 0.001 TRP H 47 HIS 0.013 0.001 HIS C 212 PHE 0.019 0.001 PHE E 27 TYR 0.021 0.001 TYR B 279 ARG 0.003 0.000 ARG D 202 Details of bonding type rmsd hydrogen bonds : bond 0.12282 ( 1003) hydrogen bonds : angle 6.02423 ( 2925) SS BOND : bond 0.00261 ( 2) SS BOND : angle 1.46112 ( 4) covalent geometry : bond 0.00335 (16423) covalent geometry : angle 0.62630 (22272) *********************** 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 : 1.699 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: 0.2714 time to fit residues: 148.3114 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 : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 8.9990 chunk 77 optimal weight: 0.6980 chunk 149 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 chunk 173 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN A 217 ASN B 104 ASN C 33 ASN C 63 ASN ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 HIS D 260 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.166074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.135508 restraints weight = 28862.923| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.53 r_work: 0.3621 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 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 = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16425 Z= 0.195 Angle : 0.629 8.811 22276 Z= 0.336 Chirality : 0.044 0.186 2533 Planarity : 0.005 0.058 2785 Dihedral : 4.405 20.113 2155 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.40 % Favored : 95.49 % Rotamer: Outliers : 2.05 % Allowed : 10.51 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.19), residues: 1930 helix: 1.91 (0.16), residues: 973 sheet: 0.72 (0.28), residues: 344 loop : -1.77 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.007 0.001 HIS C 212 PHE 0.034 0.002 PHE C 53 TYR 0.026 0.002 TYR B 279 ARG 0.005 0.000 ARG C 40 Details of bonding type rmsd hydrogen bonds : bond 0.05814 ( 1003) hydrogen bonds : angle 4.91236 ( 2925) SS BOND : bond 0.00233 ( 2) SS BOND : angle 1.71572 ( 4) covalent geometry : bond 0.00447 (16423) covalent geometry : angle 0.62871 (22272) *********************** 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 365 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 328 time to evaluate : 1.877 Fit side-chains revert: symmetry clash REVERT: H 76 LYS cc_start: 0.8082 (ptmm) cc_final: 0.7838 (ptmm) REVERT: H 123 THR cc_start: 0.8125 (p) cc_final: 0.7888 (p) REVERT: H 124 VAL cc_start: 0.8621 (t) cc_final: 0.8264 (m) REVERT: A 89 ASP cc_start: 0.7116 (m-30) cc_final: 0.6877 (m-30) REVERT: A 197 GLU cc_start: 0.6469 (mm-30) cc_final: 0.5974 (mp0) REVERT: A 270 ASP cc_start: 0.7710 (m-30) cc_final: 0.7446 (m-30) REVERT: A 289 GLU cc_start: 0.6780 (mt-10) cc_final: 0.6569 (mt-10) REVERT: A 291 MET cc_start: 0.6908 (mmp) cc_final: 0.6581 (mmt) REVERT: A 318 MET cc_start: 0.6901 (ppp) cc_final: 0.6698 (ppp) REVERT: B 74 GLN cc_start: 0.8503 (tt0) cc_final: 0.8221 (tt0) REVERT: C 260 GLN cc_start: 0.7078 (mm110) cc_final: 0.6744 (mm-40) REVERT: D 260 GLN cc_start: 0.8251 (tt0) cc_final: 0.8022 (tt0) REVERT: E 263 ASP cc_start: 0.7158 (m-30) cc_final: 0.6948 (m-30) REVERT: E 314 ASN cc_start: 0.5583 (m-40) cc_final: 0.5329 (m110) outliers start: 37 outliers final: 25 residues processed: 342 average time/residue: 0.2740 time to fit residues: 140.7478 Evaluate side-chains 326 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 301 time to evaluate : 2.002 ------------------------------------------------------------------------------- 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 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 150 VAL 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 4 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 157 optimal weight: 0.0040 chunk 185 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 13 GLN A 95 GLN A 217 ASN B 104 ASN ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 HIS D 209 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.164167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.134639 restraints weight = 28965.621| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.32 r_work: 0.3623 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3627 r_free = 0.3627 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3627 r_free = 0.3627 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16425 Z= 0.170 Angle : 0.604 8.581 22276 Z= 0.321 Chirality : 0.044 0.170 2533 Planarity : 0.005 0.056 2785 Dihedral : 4.359 19.404 2155 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.40 % Favored : 95.49 % Rotamer: Outliers : 3.15 % Allowed : 14.21 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.19), residues: 1930 helix: 1.97 (0.16), residues: 975 sheet: 0.65 (0.28), residues: 348 loop : -1.76 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.007 0.001 HIS C 212 PHE 0.032 0.001 PHE C 53 TYR 0.019 0.001 TYR B 279 ARG 0.003 0.000 ARG C 165 Details of bonding type rmsd hydrogen bonds : bond 0.05444 ( 1003) hydrogen bonds : angle 4.70182 ( 2925) SS BOND : bond 0.00499 ( 2) SS BOND : angle 1.13080 ( 4) covalent geometry : bond 0.00384 (16423) covalent geometry : angle 0.60434 (22272) *********************** 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 369 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 312 time to evaluate : 1.822 Fit side-chains revert: symmetry clash REVERT: H 76 LYS cc_start: 0.8074 (ptmm) cc_final: 0.7861 (ptmm) REVERT: H 123 THR cc_start: 0.8084 (p) cc_final: 0.7836 (p) REVERT: H 124 VAL cc_start: 0.8606 (t) cc_final: 0.8281 (m) REVERT: A 89 ASP cc_start: 0.7222 (m-30) cc_final: 0.6976 (m-30) REVERT: A 134 ASN cc_start: 0.6840 (t0) cc_final: 0.6586 (t0) REVERT: A 197 GLU cc_start: 0.6439 (mm-30) cc_final: 0.5958 (mp0) REVERT: A 270 ASP cc_start: 0.7630 (m-30) cc_final: 0.7410 (m-30) REVERT: A 289 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6661 (mt-10) REVERT: B 74 GLN cc_start: 0.8418 (tt0) cc_final: 0.8121 (tt0) REVERT: B 261 ILE cc_start: 0.8254 (mm) cc_final: 0.8054 (mt) REVERT: B 288 ASN cc_start: 0.7685 (OUTLIER) cc_final: 0.7479 (t0) REVERT: C 116 ASP cc_start: 0.8042 (t0) cc_final: 0.7823 (t0) REVERT: C 260 GLN cc_start: 0.7079 (mm110) cc_final: 0.6707 (mm-40) REVERT: D 79 PHE cc_start: 0.7387 (t80) cc_final: 0.6971 (t80) REVERT: D 95 GLN cc_start: 0.8002 (tm-30) cc_final: 0.7742 (tm-30) REVERT: D 126 GLN cc_start: 0.7628 (tp-100) cc_final: 0.7384 (tp-100) REVERT: E 256 ASP cc_start: 0.7252 (m-30) cc_final: 0.7028 (m-30) REVERT: E 263 ASP cc_start: 0.7124 (m-30) cc_final: 0.6907 (m-30) REVERT: E 314 ASN cc_start: 0.5146 (m-40) cc_final: 0.4932 (m110) outliers start: 57 outliers final: 44 residues processed: 340 average time/residue: 0.2675 time to fit residues: 137.2713 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 : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 86 THR Chi-restraints excluded: chain H residue 2 VAL 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 A residue 235 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 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 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 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 94 HIS Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 156 TYR 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 27 optimal weight: 3.9990 chunk 174 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 167 optimal weight: 0.0870 chunk 89 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 217 ASN B 104 ASN ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.163741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.132063 restraints weight = 29178.162| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.87 r_work: 0.3564 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16425 Z= 0.201 Angle : 0.623 8.922 22276 Z= 0.331 Chirality : 0.044 0.168 2533 Planarity : 0.005 0.058 2785 Dihedral : 4.398 19.419 2155 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.51 % Favored : 95.39 % Rotamer: Outliers : 3.93 % Allowed : 16.37 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.19), residues: 1930 helix: 1.90 (0.16), residues: 970 sheet: 0.57 (0.27), residues: 345 loop : -1.81 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.006 0.001 HIS C 212 PHE 0.031 0.002 PHE C 53 TYR 0.021 0.001 TYR H 103 ARG 0.004 0.000 ARG D 210 Details of bonding type rmsd hydrogen bonds : bond 0.05519 ( 1003) hydrogen bonds : angle 4.70929 ( 2925) SS BOND : bond 0.00534 ( 2) SS BOND : angle 1.21220 ( 4) covalent geometry : bond 0.00465 (16423) covalent geometry : angle 0.62268 (22272) *********************** 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 387 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 316 time to evaluate : 1.726 Fit side-chains revert: symmetry clash REVERT: L 79 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8206 (mp) REVERT: H 76 LYS cc_start: 0.8123 (ptmm) cc_final: 0.7878 (ptmm) REVERT: H 123 THR cc_start: 0.8122 (p) cc_final: 0.7854 (p) REVERT: H 124 VAL cc_start: 0.8676 (t) cc_final: 0.8327 (m) REVERT: A 89 ASP cc_start: 0.7163 (m-30) cc_final: 0.6896 (m-30) REVERT: A 134 ASN cc_start: 0.6815 (t0) cc_final: 0.6511 (t0) REVERT: A 163 LYS cc_start: 0.8505 (mtmt) cc_final: 0.8162 (mtmt) REVERT: A 197 GLU cc_start: 0.6484 (mm-30) cc_final: 0.5951 (mp0) REVERT: A 289 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6738 (mt-10) REVERT: A 315 PHE cc_start: 0.7066 (m-80) cc_final: 0.6776 (m-80) REVERT: B 74 GLN cc_start: 0.8494 (tt0) cc_final: 0.8191 (tt0) REVERT: B 121 GLU cc_start: 0.6580 (mm-30) cc_final: 0.6231 (mm-30) REVERT: B 261 ILE cc_start: 0.8317 (mm) cc_final: 0.8097 (mt) REVERT: C 116 ASP cc_start: 0.8109 (t0) cc_final: 0.7811 (t0) REVERT: C 260 GLN cc_start: 0.7088 (mm110) cc_final: 0.6735 (mm-40) REVERT: C 318 MET cc_start: 0.5031 (mtm) cc_final: 0.4228 (ptp) REVERT: D 95 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7777 (tm-30) REVERT: D 126 GLN cc_start: 0.7625 (tp-100) cc_final: 0.7377 (tp-100) REVERT: D 207 THR cc_start: 0.7971 (OUTLIER) cc_final: 0.7686 (t) REVERT: E 263 ASP cc_start: 0.7299 (m-30) cc_final: 0.7053 (m-30) REVERT: E 314 ASN cc_start: 0.5688 (m-40) cc_final: 0.5451 (m110) outliers start: 71 outliers final: 52 residues processed: 359 average time/residue: 0.2579 time to fit residues: 139.9210 Evaluate side-chains 353 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 299 time to evaluate : 1.666 ------------------------------------------------------------------------------- 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 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 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 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 82 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 158 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 HIS D 209 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.163050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.134134 restraints weight = 29728.996| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.50 r_work: 0.3591 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1729 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= 0.194 Angle : 0.623 8.921 22276 Z= 0.330 Chirality : 0.044 0.189 2533 Planarity : 0.005 0.058 2785 Dihedral : 4.413 19.131 2155 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.51 % Favored : 95.39 % Rotamer: Outliers : 4.04 % Allowed : 18.20 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.19), residues: 1930 helix: 1.92 (0.16), residues: 970 sheet: 0.49 (0.27), residues: 351 loop : -1.81 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.006 0.001 HIS C 212 PHE 0.031 0.002 PHE C 53 TYR 0.021 0.002 TYR H 103 ARG 0.004 0.000 ARG C 40 Details of bonding type rmsd hydrogen bonds : bond 0.05480 ( 1003) hydrogen bonds : angle 4.67669 ( 2925) SS BOND : bond 0.00148 ( 2) SS BOND : angle 1.15422 ( 4) covalent geometry : bond 0.00446 (16423) covalent geometry : angle 0.62330 (22272) *********************** 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 387 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 314 time to evaluate : 1.709 Fit side-chains revert: symmetry clash REVERT: L 79 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8190 (mp) REVERT: H 76 LYS cc_start: 0.8080 (ptmm) cc_final: 0.7824 (ptmm) REVERT: H 123 THR cc_start: 0.8078 (p) cc_final: 0.7829 (p) REVERT: H 124 VAL cc_start: 0.8653 (t) cc_final: 0.8318 (m) REVERT: A 89 ASP cc_start: 0.7125 (m-30) cc_final: 0.6843 (m-30) REVERT: A 134 ASN cc_start: 0.6803 (t0) cc_final: 0.6528 (t0) REVERT: A 163 LYS cc_start: 0.8497 (mtmt) cc_final: 0.8157 (mtmt) REVERT: A 197 GLU cc_start: 0.6474 (mm-30) cc_final: 0.5943 (mp0) REVERT: A 246 GLU cc_start: 0.7585 (pp20) cc_final: 0.7340 (pp20) REVERT: A 289 GLU cc_start: 0.7010 (mt-10) cc_final: 0.6749 (mt-10) REVERT: A 291 MET cc_start: 0.7265 (mmt) cc_final: 0.6902 (mmt) REVERT: A 315 PHE cc_start: 0.7004 (m-80) cc_final: 0.6744 (m-80) REVERT: B 74 GLN cc_start: 0.8430 (tt0) cc_final: 0.8111 (tt0) REVERT: B 121 GLU cc_start: 0.6670 (mm-30) cc_final: 0.6265 (mm-30) REVERT: B 261 ILE cc_start: 0.8280 (mm) cc_final: 0.8049 (mt) REVERT: C 116 ASP cc_start: 0.8135 (t0) cc_final: 0.7815 (t0) REVERT: C 260 GLN cc_start: 0.7064 (mm110) cc_final: 0.6683 (mm-40) REVERT: C 318 MET cc_start: 0.5067 (mtm) cc_final: 0.4314 (ptp) REVERT: D 95 GLN cc_start: 0.8028 (tm-30) cc_final: 0.7789 (tm-30) REVERT: D 126 GLN cc_start: 0.7624 (tp-100) cc_final: 0.7389 (tp-100) REVERT: D 311 TYR cc_start: 0.7301 (m-80) cc_final: 0.6911 (m-80) REVERT: E 263 ASP cc_start: 0.7253 (m-30) cc_final: 0.7026 (m-30) REVERT: E 314 ASN cc_start: 0.5587 (m-40) cc_final: 0.5340 (m110) outliers start: 73 outliers final: 55 residues processed: 357 average time/residue: 0.2523 time to fit residues: 136.9380 Evaluate side-chains 355 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 299 time to evaluate : 1.694 ------------------------------------------------------------------------------- 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 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 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 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 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 105 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 166 optimal weight: 0.5980 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN D 94 HIS D 209 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.156759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.126771 restraints weight = 29637.178| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.33 r_work: 0.3592 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 16425 Z= 0.198 Angle : 0.631 8.887 22276 Z= 0.334 Chirality : 0.044 0.175 2533 Planarity : 0.005 0.058 2785 Dihedral : 4.422 19.158 2155 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.77 % Favored : 95.13 % Rotamer: Outliers : 4.09 % Allowed : 19.25 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.19), residues: 1930 helix: 1.94 (0.16), residues: 968 sheet: 0.46 (0.27), residues: 351 loop : -1.84 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.008 0.001 HIS D 94 PHE 0.032 0.002 PHE C 53 TYR 0.021 0.002 TYR H 103 ARG 0.004 0.000 ARG C 40 Details of bonding type rmsd hydrogen bonds : bond 0.05451 ( 1003) hydrogen bonds : angle 4.66880 ( 2925) SS BOND : bond 0.00169 ( 2) SS BOND : angle 1.15606 ( 4) covalent geometry : bond 0.00457 (16423) covalent geometry : angle 0.63106 (22272) *********************** 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 379 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 305 time to evaluate : 1.795 Fit side-chains REVERT: L 79 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8237 (mp) REVERT: H 76 LYS cc_start: 0.8064 (ptmm) cc_final: 0.7860 (ptmm) REVERT: H 123 THR cc_start: 0.8098 (p) cc_final: 0.7848 (p) REVERT: H 124 VAL cc_start: 0.8662 (t) cc_final: 0.8337 (m) REVERT: A 89 ASP cc_start: 0.7117 (m-30) cc_final: 0.6836 (m-30) REVERT: A 134 ASN cc_start: 0.6816 (t0) cc_final: 0.6504 (t0) REVERT: A 163 LYS cc_start: 0.8508 (mtmt) cc_final: 0.8240 (mtmt) REVERT: A 246 GLU cc_start: 0.7495 (pp20) cc_final: 0.7228 (pp20) REVERT: A 270 ASP cc_start: 0.7590 (m-30) cc_final: 0.7262 (m-30) REVERT: A 289 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6623 (mt-10) REVERT: A 291 MET cc_start: 0.7311 (mmt) cc_final: 0.6918 (mmt) REVERT: A 302 MET cc_start: 0.7750 (mmm) cc_final: 0.7408 (mtm) REVERT: A 313 MET cc_start: 0.6527 (mpp) cc_final: 0.6319 (mtp) REVERT: A 315 PHE cc_start: 0.7099 (m-80) cc_final: 0.6736 (m-80) REVERT: B 74 GLN cc_start: 0.8439 (tt0) cc_final: 0.8135 (tt0) REVERT: B 121 GLU cc_start: 0.6702 (mm-30) cc_final: 0.6311 (mm-30) REVERT: C 116 ASP cc_start: 0.8147 (t0) cc_final: 0.7852 (t0) REVERT: C 260 GLN cc_start: 0.7064 (mm110) cc_final: 0.6651 (mm-40) REVERT: C 318 MET cc_start: 0.5138 (mtm) cc_final: 0.4243 (ptp) REVERT: D 95 GLN cc_start: 0.7958 (tm-30) cc_final: 0.7736 (tm-30) REVERT: D 130 ILE cc_start: 0.7936 (OUTLIER) cc_final: 0.7694 (mm) REVERT: D 311 TYR cc_start: 0.7402 (m-80) cc_final: 0.6977 (m-80) REVERT: E 263 ASP cc_start: 0.7131 (m-30) cc_final: 0.6924 (m-30) REVERT: E 314 ASN cc_start: 0.5629 (m-40) cc_final: 0.5425 (m110) outliers start: 74 outliers final: 58 residues processed: 347 average time/residue: 0.2638 time to fit residues: 139.0513 Evaluate side-chains 355 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 295 time to evaluate : 1.712 ------------------------------------------------------------------------------- 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 83 MET 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 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 60 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN D 94 HIS D 126 GLN D 209 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.162521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.132147 restraints weight = 29431.757| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.60 r_work: 0.3582 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 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 : 0.005 0.041 16425 Z= 0.201 Angle : 0.640 10.658 22276 Z= 0.337 Chirality : 0.045 0.179 2533 Planarity : 0.005 0.059 2785 Dihedral : 4.431 19.014 2155 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.56 % Favored : 95.34 % Rotamer: Outliers : 4.42 % Allowed : 20.02 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.19), residues: 1930 helix: 1.93 (0.16), residues: 968 sheet: 0.47 (0.28), residues: 350 loop : -1.87 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.006 0.001 HIS D 94 PHE 0.032 0.002 PHE C 53 TYR 0.021 0.001 TYR H 103 ARG 0.004 0.000 ARG C 40 Details of bonding type rmsd hydrogen bonds : bond 0.05468 ( 1003) hydrogen bonds : angle 4.67588 ( 2925) SS BOND : bond 0.00121 ( 2) SS BOND : angle 1.04512 ( 4) covalent geometry : bond 0.00465 (16423) covalent geometry : angle 0.64008 (22272) *********************** 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 374 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 294 time to evaluate : 2.937 Fit side-chains REVERT: L 79 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8299 (mp) REVERT: H 76 LYS cc_start: 0.8064 (ptmm) cc_final: 0.7850 (ptmm) REVERT: H 123 THR cc_start: 0.8117 (p) cc_final: 0.7870 (p) REVERT: H 124 VAL cc_start: 0.8665 (t) cc_final: 0.8338 (m) REVERT: A 65 THR cc_start: 0.5752 (OUTLIER) cc_final: 0.5515 (p) REVERT: A 89 ASP cc_start: 0.7144 (m-30) cc_final: 0.6872 (m-30) REVERT: A 134 ASN cc_start: 0.6831 (t0) cc_final: 0.6523 (t0) REVERT: A 246 GLU cc_start: 0.7477 (pp20) cc_final: 0.7188 (pp20) REVERT: A 270 ASP cc_start: 0.7599 (m-30) cc_final: 0.7251 (m-30) REVERT: A 289 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6678 (mt-10) REVERT: A 291 MET cc_start: 0.7261 (mmt) cc_final: 0.6922 (mmt) REVERT: A 302 MET cc_start: 0.7715 (mmm) cc_final: 0.7390 (mtm) REVERT: A 315 PHE cc_start: 0.7073 (m-80) cc_final: 0.6729 (m-80) REVERT: B 74 GLN cc_start: 0.8456 (tt0) cc_final: 0.8150 (tt0) REVERT: B 121 GLU cc_start: 0.6742 (mm-30) cc_final: 0.6339 (mm-30) REVERT: C 116 ASP cc_start: 0.8156 (t0) cc_final: 0.7864 (t0) REVERT: C 260 GLN cc_start: 0.6993 (mm110) cc_final: 0.6613 (mm-40) REVERT: C 318 MET cc_start: 0.5090 (mtm) cc_final: 0.4126 (ptp) REVERT: D 95 GLN cc_start: 0.7926 (tm-30) cc_final: 0.7698 (tm-30) REVERT: D 130 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7686 (mm) REVERT: D 311 TYR cc_start: 0.7491 (m-80) cc_final: 0.7027 (m-80) REVERT: E 314 ASN cc_start: 0.5593 (m-40) cc_final: 0.5385 (m110) outliers start: 80 outliers final: 60 residues processed: 339 average time/residue: 0.3236 time to fit residues: 169.2933 Evaluate side-chains 352 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 289 time to evaluate : 4.199 ------------------------------------------------------------------------------- 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 83 MET 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 127 VAL Chi-restraints excluded: chain A residue 128 SER 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 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 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 251 PHE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 69 optimal weight: 0.9980 chunk 155 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 139 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN B 104 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN D 94 HIS D 209 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.157242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.126871 restraints weight = 29476.680| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.41 r_work: 0.3609 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16425 Z= 0.175 Angle : 0.641 12.691 22276 Z= 0.336 Chirality : 0.044 0.174 2533 Planarity : 0.005 0.059 2785 Dihedral : 4.395 18.821 2155 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.56 % Favored : 95.34 % Rotamer: Outliers : 4.04 % Allowed : 20.69 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.19), residues: 1930 helix: 2.01 (0.16), residues: 968 sheet: 0.44 (0.27), residues: 353 loop : -1.84 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.006 0.001 HIS D 94 PHE 0.032 0.002 PHE C 53 TYR 0.019 0.001 TYR H 103 ARG 0.006 0.000 ARG D 162 Details of bonding type rmsd hydrogen bonds : bond 0.05331 ( 1003) hydrogen bonds : angle 4.60925 ( 2925) SS BOND : bond 0.00239 ( 2) SS BOND : angle 0.95501 ( 4) covalent geometry : bond 0.00398 (16423) covalent geometry : angle 0.64083 (22272) *********************** 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 379 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 306 time to evaluate : 2.232 Fit side-chains REVERT: L 79 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8276 (mp) REVERT: H 76 LYS cc_start: 0.8052 (ptmm) cc_final: 0.7839 (ptmm) REVERT: H 123 THR cc_start: 0.8062 (p) cc_final: 0.7810 (p) REVERT: H 124 VAL cc_start: 0.8651 (t) cc_final: 0.8315 (m) REVERT: A 65 THR cc_start: 0.5812 (OUTLIER) cc_final: 0.5585 (p) REVERT: A 89 ASP cc_start: 0.7161 (m-30) cc_final: 0.6895 (m-30) REVERT: A 134 ASN cc_start: 0.6812 (t0) cc_final: 0.6502 (t0) REVERT: A 163 LYS cc_start: 0.8507 (mtmt) cc_final: 0.8265 (mtmt) REVERT: A 246 GLU cc_start: 0.7436 (pp20) cc_final: 0.7130 (pp20) REVERT: A 270 ASP cc_start: 0.7567 (m-30) cc_final: 0.7195 (m-30) REVERT: A 289 GLU cc_start: 0.6977 (mt-10) cc_final: 0.6634 (mt-10) REVERT: A 291 MET cc_start: 0.7319 (mmt) cc_final: 0.6930 (mmt) REVERT: A 302 MET cc_start: 0.7694 (mmm) cc_final: 0.7353 (mtm) REVERT: A 313 MET cc_start: 0.6829 (mtp) cc_final: 0.6449 (mpp) REVERT: B 74 GLN cc_start: 0.8416 (tt0) cc_final: 0.8110 (tt0) REVERT: B 121 GLU cc_start: 0.6733 (mm-30) cc_final: 0.6294 (mm-30) REVERT: C 116 ASP cc_start: 0.8176 (t0) cc_final: 0.7872 (t0) REVERT: C 260 GLN cc_start: 0.6976 (mm110) cc_final: 0.6519 (mm-40) REVERT: C 318 MET cc_start: 0.5055 (mtm) cc_final: 0.4053 (ptp) REVERT: D 130 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7678 (mm) REVERT: D 311 TYR cc_start: 0.7473 (m-80) cc_final: 0.6982 (m-80) REVERT: E 85 LEU cc_start: 0.8057 (mm) cc_final: 0.7840 (mt) outliers start: 73 outliers final: 61 residues processed: 348 average time/residue: 0.2920 time to fit residues: 154.1516 Evaluate side-chains 362 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 298 time to evaluate : 1.992 ------------------------------------------------------------------------------- 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 83 MET 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 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 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 251 PHE 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 156 TYR Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 313 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 28 optimal weight: 0.0370 chunk 110 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 81 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 69 optimal weight: 0.0770 overall best weight: 0.4416 ------------------------------------------------------------------------------- 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 ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN D 94 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.164616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.133305 restraints weight = 29286.933| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.62 r_work: 0.3615 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16425 Z= 0.150 Angle : 0.631 13.899 22276 Z= 0.329 Chirality : 0.043 0.174 2533 Planarity : 0.005 0.059 2785 Dihedral : 4.321 18.494 2155 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.40 % Favored : 95.49 % Rotamer: Outliers : 3.71 % Allowed : 21.40 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.20), residues: 1930 helix: 2.15 (0.16), residues: 968 sheet: 0.66 (0.28), residues: 338 loop : -1.81 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 226 HIS 0.006 0.001 HIS D 94 PHE 0.031 0.002 PHE C 53 TYR 0.016 0.001 TYR H 103 ARG 0.009 0.000 ARG D 162 Details of bonding type rmsd hydrogen bonds : bond 0.05066 ( 1003) hydrogen bonds : angle 4.51106 ( 2925) SS BOND : bond 0.00177 ( 2) SS BOND : angle 0.75052 ( 4) covalent geometry : bond 0.00332 (16423) covalent geometry : angle 0.63056 (22272) *********************** 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 383 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 316 time to evaluate : 1.780 Fit side-chains revert: symmetry clash REVERT: L 79 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8207 (mp) REVERT: H 76 LYS cc_start: 0.8009 (ptmm) cc_final: 0.7801 (ptmm) REVERT: H 123 THR cc_start: 0.8063 (p) cc_final: 0.7809 (p) REVERT: H 124 VAL cc_start: 0.8638 (t) cc_final: 0.8311 (m) REVERT: A 89 ASP cc_start: 0.7047 (m-30) cc_final: 0.6795 (m-30) REVERT: A 113 PHE cc_start: 0.8780 (m-80) cc_final: 0.8483 (m-80) REVERT: A 134 ASN cc_start: 0.6783 (t0) cc_final: 0.6491 (t0) REVERT: A 163 LYS cc_start: 0.8490 (mtmt) cc_final: 0.8277 (mtmt) REVERT: A 246 GLU cc_start: 0.7434 (pp20) cc_final: 0.7120 (pp20) REVERT: A 270 ASP cc_start: 0.7557 (m-30) cc_final: 0.7182 (m-30) REVERT: A 289 GLU cc_start: 0.6985 (mt-10) cc_final: 0.6675 (mt-10) REVERT: A 302 MET cc_start: 0.7634 (mmm) cc_final: 0.7310 (mtm) REVERT: B 74 GLN cc_start: 0.8400 (tt0) cc_final: 0.8099 (tt0) REVERT: B 121 GLU cc_start: 0.6713 (mm-30) cc_final: 0.6273 (mm-30) REVERT: B 134 ASN cc_start: 0.7905 (m-40) cc_final: 0.7652 (m-40) REVERT: C 111 LYS cc_start: 0.7611 (tptt) cc_final: 0.7346 (tptp) REVERT: C 116 ASP cc_start: 0.8184 (t0) cc_final: 0.7876 (t0) REVERT: C 260 GLN cc_start: 0.6930 (mm110) cc_final: 0.6490 (mm-40) REVERT: C 318 MET cc_start: 0.5060 (mtm) cc_final: 0.3929 (ptp) REVERT: D 95 GLN cc_start: 0.7958 (tm-30) cc_final: 0.7638 (tm-30) REVERT: D 130 ILE cc_start: 0.7946 (OUTLIER) cc_final: 0.7696 (mm) REVERT: D 311 TYR cc_start: 0.7423 (m-80) cc_final: 0.6729 (m-80) REVERT: E 85 LEU cc_start: 0.8055 (mm) cc_final: 0.7846 (mt) REVERT: E 344 TYR cc_start: 0.5135 (OUTLIER) cc_final: 0.4128 (p90) outliers start: 67 outliers final: 54 residues processed: 356 average time/residue: 0.2751 time to fit residues: 150.7656 Evaluate side-chains 357 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 300 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 79 LEU 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 65 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 128 SER 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 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 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 251 PHE 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 225 ILE Chi-restraints excluded: chain D residue 248 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 109 VAL Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 156 TYR 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 85 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 16 optimal weight: 0.1980 chunk 109 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 182 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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 ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 HIS D 209 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.162581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.130615 restraints weight = 29669.702| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.71 r_work: 0.3596 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2034 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= 0.177 Angle : 0.655 15.490 22276 Z= 0.341 Chirality : 0.044 0.187 2533 Planarity : 0.005 0.059 2785 Dihedral : 4.358 18.655 2155 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.66 % Favored : 95.23 % Rotamer: Outliers : 3.87 % Allowed : 21.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.19), residues: 1930 helix: 2.05 (0.16), residues: 969 sheet: 0.65 (0.28), residues: 339 loop : -1.83 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.006 0.001 HIS D 94 PHE 0.032 0.002 PHE C 53 TYR 0.030 0.001 TYR A 279 ARG 0.009 0.000 ARG D 162 Details of bonding type rmsd hydrogen bonds : bond 0.05197 ( 1003) hydrogen bonds : angle 4.56597 ( 2925) SS BOND : bond 0.00101 ( 2) SS BOND : angle 0.93680 ( 4) covalent geometry : bond 0.00407 (16423) covalent geometry : angle 0.65524 (22272) ********************** 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 378 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 308 time to evaluate : 1.932 Fit side-chains revert: symmetry clash REVERT: L 79 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8240 (mp) REVERT: H 76 LYS cc_start: 0.8032 (ptmm) cc_final: 0.7816 (ptmm) REVERT: H 123 THR cc_start: 0.8077 (p) cc_final: 0.7827 (p) REVERT: H 124 VAL cc_start: 0.8658 (t) cc_final: 0.8318 (m) REVERT: A 65 THR cc_start: 0.5787 (OUTLIER) cc_final: 0.5541 (p) REVERT: A 89 ASP cc_start: 0.7105 (m-30) cc_final: 0.6872 (m-30) REVERT: A 134 ASN cc_start: 0.6797 (t0) cc_final: 0.6499 (t0) REVERT: A 246 GLU cc_start: 0.7462 (pp20) cc_final: 0.7123 (pp20) REVERT: A 270 ASP cc_start: 0.7566 (m-30) cc_final: 0.7198 (m-30) REVERT: A 289 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6769 (mt-10) REVERT: A 302 MET cc_start: 0.7584 (mmm) cc_final: 0.7249 (mtm) REVERT: B 74 GLN cc_start: 0.8411 (tt0) cc_final: 0.8106 (tt0) REVERT: B 121 GLU cc_start: 0.6745 (mm-30) cc_final: 0.6283 (mm-30) REVERT: C 74 GLN cc_start: 0.6967 (mm-40) cc_final: 0.6503 (mm-40) REVERT: C 111 LYS cc_start: 0.7612 (tptt) cc_final: 0.7321 (tptp) REVERT: C 116 ASP cc_start: 0.8211 (t0) cc_final: 0.7902 (t0) REVERT: C 260 GLN cc_start: 0.6966 (mm110) cc_final: 0.6501 (mm-40) REVERT: C 318 MET cc_start: 0.5049 (mtm) cc_final: 0.3961 (ptp) REVERT: D 95 GLN cc_start: 0.7979 (tm-30) cc_final: 0.7633 (tm-30) REVERT: D 130 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7713 (mm) REVERT: D 311 TYR cc_start: 0.7435 (m-80) cc_final: 0.6814 (m-80) REVERT: E 85 LEU cc_start: 0.8083 (mm) cc_final: 0.7869 (mt) REVERT: E 344 TYR cc_start: 0.5166 (OUTLIER) cc_final: 0.4083 (p90) outliers start: 70 outliers final: 58 residues processed: 346 average time/residue: 0.3303 time to fit residues: 176.1937 Evaluate side-chains 366 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 304 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 6 GLU Chi-restraints excluded: chain H residue 12 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 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 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 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 251 PHE 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 225 ILE Chi-restraints excluded: chain D residue 248 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 156 TYR 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 127 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 chunk 93 optimal weight: 0.0870 chunk 165 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 142 optimal weight: 0.0570 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 HIS D 209 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.161885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.129604 restraints weight = 29428.416| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.45 r_work: 0.3617 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16425 Z= 0.161 Angle : 0.653 14.563 22276 Z= 0.339 Chirality : 0.044 0.188 2533 Planarity : 0.005 0.059 2785 Dihedral : 4.334 18.444 2155 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.25 % Favored : 95.65 % Rotamer: Outliers : 3.76 % Allowed : 21.29 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.19), residues: 1930 helix: 2.11 (0.16), residues: 969 sheet: 0.67 (0.28), residues: 338 loop : -1.79 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 226 HIS 0.007 0.001 HIS D 94 PHE 0.033 0.002 PHE C 53 TYR 0.025 0.001 TYR A 279 ARG 0.010 0.000 ARG D 162 Details of bonding type rmsd hydrogen bonds : bond 0.05119 ( 1003) hydrogen bonds : angle 4.52912 ( 2925) SS BOND : bond 0.00131 ( 2) SS BOND : angle 0.80868 ( 4) covalent geometry : bond 0.00363 (16423) covalent geometry : angle 0.65306 (22272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10167.87 seconds wall clock time: 179 minutes 5.96 seconds (10745.96 seconds total)