Starting phenix.real_space_refine on Wed Aug 5 12:55:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m1s_63581/08_2026/9m1s_63581.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m1s_63581/08_2026/9m1s_63581.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m1s_63581/08_2026/9m1s_63581.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m1s_63581/08_2026/9m1s_63581.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m1s_63581/08_2026/9m1s_63581.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m1s_63581/08_2026/9m1s_63581.map" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.088 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 6242 2.51 5 N 1692 2.21 5 O 1841 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9840 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1863 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2542 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'ASP:plan': 4, 'TYR:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 49 Chain: "G" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 430 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 955 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "S" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1743 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2298 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 275} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'ITN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.84, per 1000 atoms: 0.19 Number of scatterers: 9840 At special positions: 0 Unit cell: (86.92, 123.82, 132.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 1841 8.00 N 1692 7.00 C 6242 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 183 " 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: 0.92 Conformation dependent library (CDL) restraints added in 350.1 milliseconds 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2370 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 16 sheets defined 36.1% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 15 through 40 removed outlier: 3.504A pdb=" N ALA A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.683A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.540A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.678A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.818A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 62 removed outlier: 3.517A pdb=" N HIS R 34 " --> pdb=" O PRO R 30 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU R 36 " --> pdb=" O LYS R 32 " (cutoff:3.500A) Proline residue: R 37 - end of helix Proline residue: R 49 - end of helix removed outlier: 3.681A pdb=" N MET R 62 " --> pdb=" O TYR R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 85 removed outlier: 4.008A pdb=" N ILE R 71 " --> pdb=" O SER R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 95 removed outlier: 3.985A pdb=" N LEU R 89 " --> pdb=" O SER R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 146 through 172 removed outlier: 3.682A pdb=" N ALA R 150 " --> pdb=" O LYS R 146 " (cutoff:3.500A) Proline residue: R 167 - end of helix removed outlier: 4.161A pdb=" N PHE R 170 " --> pdb=" O ILE R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 207 removed outlier: 3.720A pdb=" N TRP R 197 " --> pdb=" O ASN R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 227 Processing helix chain 'R' and resid 233 through 270 Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 273 through 293 Proline residue: R 289 - end of helix Processing helix chain 'R' and resid 293 through 302 Processing helix chain 'R' and resid 306 through 313 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.540A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.615A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.658A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.218A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.623A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.686A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.646A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.711A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.113A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.756A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.269A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB6, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.513A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'R' and resid 173 through 176 removed outlier: 3.943A pdb=" N THR R 173 " --> pdb=" O LEU R 184 " (cutoff:3.500A) 530 hydrogen bonds defined for protein. 1458 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: 1.56 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2642 1.33 - 1.45: 1833 1.45 - 1.57: 5475 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 10040 Sorted by residual: bond pdb=" N LYS B 301 " pdb=" CA LYS B 301 " ideal model delta sigma weight residual 1.455 1.478 -0.024 1.38e-02 5.25e+03 2.91e+00 bond pdb=" C TYR A 391 " pdb=" O TYR A 391 " ideal model delta sigma weight residual 1.235 1.213 0.022 1.34e-02 5.57e+03 2.64e+00 bond pdb=" C2 ITN R 401 " pdb=" C3 ITN R 401 " ideal model delta sigma weight residual 1.495 1.527 -0.032 2.00e-02 2.50e+03 2.58e+00 bond pdb=" CA TYR A 391 " pdb=" C TYR A 391 " ideal model delta sigma weight residual 1.523 1.500 0.023 1.48e-02 4.57e+03 2.40e+00 bond pdb=" C GLU A 390 " pdb=" O GLU A 390 " ideal model delta sigma weight residual 1.237 1.222 0.015 1.17e-02 7.31e+03 1.56e+00 ... (remaining 10035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 13379 1.96 - 3.91: 199 3.91 - 5.87: 28 5.87 - 7.83: 6 7.83 - 9.78: 3 Bond angle restraints: 13615 Sorted by residual: angle pdb=" N TYR A 391 " pdb=" CA TYR A 391 " pdb=" C TYR A 391 " ideal model delta sigma weight residual 112.92 117.54 -4.62 1.23e+00 6.61e-01 1.41e+01 angle pdb=" CA LYS G 20 " pdb=" CB LYS G 20 " pdb=" CG LYS G 20 " ideal model delta sigma weight residual 114.10 121.11 -7.01 2.00e+00 2.50e-01 1.23e+01 angle pdb=" C ASP S 73 " pdb=" N ASP S 74 " pdb=" CA ASP S 74 " ideal model delta sigma weight residual 119.78 123.62 -3.84 1.24e+00 6.50e-01 9.58e+00 angle pdb=" N LYS G 20 " pdb=" CA LYS G 20 " pdb=" CB LYS G 20 " ideal model delta sigma weight residual 110.12 114.35 -4.23 1.47e+00 4.63e-01 8.27e+00 angle pdb=" C ILE R 135 " pdb=" CA ILE R 135 " pdb=" CB ILE R 135 " ideal model delta sigma weight residual 111.80 108.43 3.37 1.18e+00 7.18e-01 8.17e+00 ... (remaining 13610 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 5269 17.88 - 35.75: 496 35.75 - 53.63: 152 53.63 - 71.51: 32 71.51 - 89.38: 11 Dihedral angle restraints: 5960 sinusoidal: 2290 harmonic: 3670 Sorted by residual: dihedral pdb=" CA ARG S 191 " pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta harmonic sigma weight residual 180.00 160.88 19.12 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 161.78 18.22 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 162.08 17.92 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 5957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1431 0.074 - 0.148: 125 0.148 - 0.222: 2 0.222 - 0.296: 0 0.296 - 0.370: 1 Chirality restraints: 1559 Sorted by residual: chirality pdb=" CA TYR A 391 " pdb=" N TYR A 391 " pdb=" C TYR A 391 " pdb=" CB TYR A 391 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CA LEU R 235 " pdb=" N LEU R 235 " pdb=" C LEU R 235 " pdb=" CB LEU R 235 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.93e-01 chirality pdb=" CG LEU R 269 " pdb=" CB LEU R 269 " pdb=" CD1 LEU R 269 " pdb=" CD2 LEU R 269 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.34e-01 ... (remaining 1556 not shown) Planarity restraints: 1728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG R 63 " -0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO R 64 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO R 64 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 64 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO A 332 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.026 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO S 75 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.022 5.00e-02 4.00e+02 ... (remaining 1725 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2477 2.80 - 3.32: 9078 3.32 - 3.85: 16664 3.85 - 4.37: 20080 4.37 - 4.90: 35136 Nonbonded interactions: 83435 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.272 3.040 nonbonded pdb=" O ASP S 74 " pdb=" ND2 ASN S 77 " model vdw 2.303 3.120 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.307 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.309 3.040 nonbonded pdb=" NE2 GLN A 59 " pdb=" O SER A 366 " model vdw 2.337 3.120 ... (remaining 83430 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.970 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 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 0.032 10041 Z= 0.142 Angle : 0.605 9.783 13617 Z= 0.336 Chirality : 0.042 0.370 1559 Planarity : 0.004 0.050 1728 Dihedral : 16.047 89.382 3587 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.19 % Allowed : 20.07 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.24), residues: 1244 helix: 2.39 (0.25), residues: 396 sheet: 0.18 (0.28), residues: 321 loop : 0.40 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 333 TYR 0.023 0.001 TYR A 391 PHE 0.019 0.001 PHE R 170 TRP 0.017 0.001 TRP B 82 HIS 0.007 0.001 HIS R 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (10040) covalent geometry : angle 0.60544 / 0.34 (13615) SS BOND : bond 0.00223 / 0.12 ( 1) SS BOND : angle 0.49511 / 0.28 ( 2) hydrogen bonds : bond 0.14229 / 9.54 ( 523) hydrogen bonds : angle 5.45179 / 3.90 ( 1458) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 247 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7334 (mt-10) REVERT: A 58 LYS cc_start: 0.8106 (mtpp) cc_final: 0.7733 (mttt) REVERT: A 223 ASP cc_start: 0.8395 (t0) cc_final: 0.8193 (t70) REVERT: A 252 ASP cc_start: 0.7078 (t0) cc_final: 0.6668 (t70) REVERT: A 342 ARG cc_start: 0.8393 (ttm110) cc_final: 0.7977 (ttm170) REVERT: A 347 ASP cc_start: 0.8137 (m-30) cc_final: 0.7928 (m-30) REVERT: A 370 GLU cc_start: 0.7760 (pt0) cc_final: 0.7520 (mm-30) REVERT: A 380 LYS cc_start: 0.8192 (tttt) cc_final: 0.7905 (tttt) REVERT: A 392 ASN cc_start: 0.8602 (m-40) cc_final: 0.8398 (m110) REVERT: B 44 GLN cc_start: 0.7992 (mt0) cc_final: 0.7758 (mt0) REVERT: B 46 ARG cc_start: 0.7741 (mtp85) cc_final: 0.7213 (mtp85) REVERT: B 195 ASP cc_start: 0.8424 (p0) cc_final: 0.8059 (p0) REVERT: B 303 ASP cc_start: 0.7807 (m-30) cc_final: 0.7581 (m-30) REVERT: G 38 MET cc_start: 0.8226 (ttp) cc_final: 0.7990 (ttp) REVERT: G 47 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7907 (mt-10) REVERT: N 46 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7792 (tt0) REVERT: N 91 THR cc_start: 0.8799 (t) cc_final: 0.8498 (m) REVERT: S 18 ARG cc_start: 0.8069 (tpt-90) cc_final: 0.7498 (tpp80) REVERT: S 87 ARG cc_start: 0.7011 (mtm-85) cc_final: 0.6763 (mtt180) REVERT: S 158 SER cc_start: 0.8033 (p) cc_final: 0.7773 (t) REVERT: S 160 ARG cc_start: 0.7084 (mtm180) cc_final: 0.6860 (mpp-170) REVERT: S 186 GLN cc_start: 0.7996 (tt0) cc_final: 0.7791 (tt0) REVERT: R 42 ILE cc_start: 0.7632 (mt) cc_final: 0.7353 (mt) REVERT: R 206 THR cc_start: 0.8388 (m) cc_final: 0.8109 (m) REVERT: R 269 LEU cc_start: 0.8312 (mt) cc_final: 0.7990 (mt) outliers start: 2 outliers final: 0 residues processed: 249 average time/residue: 0.5565 time to fit residues: 147.9795 Evaluate side-chains 184 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 GLN A 294 GLN B 32 GLN B 88 ASN B 237 ASN G 24 ASN N 77 ASN S 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.143981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.100264 restraints weight = 12025.006| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.24 r_work: 0.3123 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10041 Z= 0.195 Angle : 0.591 7.565 13617 Z= 0.313 Chirality : 0.044 0.141 1559 Planarity : 0.004 0.054 1728 Dihedral : 5.060 74.412 1374 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.64 % Allowed : 18.95 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.24), residues: 1244 helix: 2.51 (0.25), residues: 407 sheet: 0.25 (0.28), residues: 338 loop : 0.44 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 218 TYR 0.018 0.002 TYR R 92 PHE 0.015 0.002 PHE B 235 TRP 0.014 0.002 TRP A 234 HIS 0.008 0.002 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 (10040) covalent geometry : angle 0.59129 / 0.31 (13615) SS BOND : bond 0.00487 / 0.26 ( 1) SS BOND : angle 0.41643 / 0.24 ( 2) hydrogen bonds : bond 0.04139 / 2.68 ( 523) hydrogen bonds : angle 4.62374 / 3.30 ( 1458) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 211 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7261 (mt-10) REVERT: A 38 ARG cc_start: 0.8517 (mtp-110) cc_final: 0.7609 (ttp-110) REVERT: A 58 LYS cc_start: 0.8030 (mtpp) cc_final: 0.7669 (mtmm) REVERT: A 370 GLU cc_start: 0.7956 (pt0) cc_final: 0.7328 (mm-30) REVERT: B 44 GLN cc_start: 0.8347 (mt0) cc_final: 0.8086 (mt0) REVERT: B 46 ARG cc_start: 0.8196 (mtp85) cc_final: 0.7534 (mtp85) REVERT: B 195 ASP cc_start: 0.8270 (p0) cc_final: 0.8067 (p0) REVERT: B 303 ASP cc_start: 0.8069 (m-30) cc_final: 0.7839 (m-30) REVERT: B 327 VAL cc_start: 0.8898 (OUTLIER) cc_final: 0.8667 (p) REVERT: G 38 MET cc_start: 0.8427 (ttp) cc_final: 0.8148 (ttp) REVERT: G 47 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8137 (mt-10) REVERT: N 43 LYS cc_start: 0.7521 (mmtt) cc_final: 0.7266 (mtpp) REVERT: N 46 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8126 (tt0) REVERT: N 53 GLN cc_start: 0.8358 (mp10) cc_final: 0.8085 (mp10) REVERT: N 91 THR cc_start: 0.8697 (t) cc_final: 0.8352 (m) REVERT: S 19 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.8026 (tptp) REVERT: S 46 GLU cc_start: 0.8389 (tt0) cc_final: 0.8168 (tt0) REVERT: S 183 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.8068 (mt0) REVERT: S 186 GLN cc_start: 0.8176 (tt0) cc_final: 0.7821 (pt0) REVERT: R 35 TYR cc_start: 0.7982 (t80) cc_final: 0.7711 (t80) REVERT: R 59 ILE cc_start: 0.8286 (pt) cc_final: 0.8065 (pt) REVERT: R 60 PHE cc_start: 0.7700 (m-80) cc_final: 0.7331 (m-10) REVERT: R 74 ASN cc_start: 0.8143 (m-40) cc_final: 0.7939 (m-40) REVERT: R 235 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7165 (tp) REVERT: R 237 GLN cc_start: 0.7645 (mt0) cc_final: 0.7385 (mm110) outliers start: 39 outliers final: 17 residues processed: 233 average time/residue: 0.5361 time to fit residues: 134.1088 Evaluate side-chains 209 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 196 LYS Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 300 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 54 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 GLN A 294 GLN B 237 ASN G 24 ASN R 310 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.143166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.098931 restraints weight = 11846.795| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.26 r_work: 0.3037 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10041 Z= 0.171 Angle : 0.564 11.035 13617 Z= 0.295 Chirality : 0.042 0.138 1559 Planarity : 0.004 0.048 1728 Dihedral : 4.918 70.041 1374 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.55 % Allowed : 19.98 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.24), residues: 1244 helix: 2.51 (0.25), residues: 406 sheet: 0.27 (0.28), residues: 338 loop : 0.37 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.016 0.001 TYR S 190 PHE 0.015 0.002 PHE R 113 TRP 0.017 0.002 TRP A 234 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (10040) covalent geometry : angle 0.56422 / 0.30 (13615) SS BOND : bond 0.00400 / 0.21 ( 1) SS BOND : angle 0.51471 / 0.30 ( 2) hydrogen bonds : bond 0.03897 / 2.53 ( 523) hydrogen bonds : angle 4.50605 / 3.22 ( 1458) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 202 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7179 (mt-10) REVERT: A 38 ARG cc_start: 0.8489 (mtp-110) cc_final: 0.7555 (ttp-110) REVERT: A 50 ASN cc_start: 0.8688 (p0) cc_final: 0.8462 (p0) REVERT: A 58 LYS cc_start: 0.7928 (mtpp) cc_final: 0.7571 (mtmm) REVERT: A 370 GLU cc_start: 0.7976 (pt0) cc_final: 0.7317 (mm-30) REVERT: B 44 GLN cc_start: 0.8324 (mt0) cc_final: 0.8067 (mt0) REVERT: B 46 ARG cc_start: 0.8170 (mtp85) cc_final: 0.7436 (mtp85) REVERT: B 186 ASP cc_start: 0.7913 (m-30) cc_final: 0.7544 (m-30) REVERT: B 314 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8508 (ttt180) REVERT: G 38 MET cc_start: 0.8353 (ttp) cc_final: 0.8047 (ttp) REVERT: G 46 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8016 (mptm) REVERT: G 47 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8137 (mt-10) REVERT: N 46 GLU cc_start: 0.8379 (tm-30) cc_final: 0.7772 (tt0) REVERT: N 53 GLN cc_start: 0.8325 (mp10) cc_final: 0.8047 (mp10) REVERT: N 111 THR cc_start: 0.8854 (t) cc_final: 0.8510 (m) REVERT: S 19 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7766 (tptp) REVERT: S 186 GLN cc_start: 0.8144 (tt0) cc_final: 0.7775 (pt0) REVERT: S 202 ARG cc_start: 0.6492 (ptp90) cc_final: 0.6225 (ptp90) REVERT: R 42 ILE cc_start: 0.7957 (mt) cc_final: 0.7740 (mt) REVERT: R 60 PHE cc_start: 0.7601 (m-80) cc_final: 0.7208 (m-10) REVERT: R 74 ASN cc_start: 0.8211 (m-40) cc_final: 0.7967 (m110) REVERT: R 235 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.7046 (tt) REVERT: R 237 GLN cc_start: 0.7614 (mt0) cc_final: 0.7229 (mm110) REVERT: R 288 ARG cc_start: 0.8068 (mtm-85) cc_final: 0.7528 (mtm-85) outliers start: 38 outliers final: 22 residues processed: 227 average time/residue: 0.5727 time to fit residues: 139.5147 Evaluate side-chains 214 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 305 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 65 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 chunk 15 optimal weight: 0.0170 chunk 23 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.2022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 GLN A 292 ASN A 294 GLN A 392 ASN G 24 ASN R 310 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.143878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.099215 restraints weight = 11931.596| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.32 r_work: 0.3058 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10041 Z= 0.137 Angle : 0.527 8.877 13617 Z= 0.277 Chirality : 0.041 0.134 1559 Planarity : 0.004 0.052 1728 Dihedral : 4.715 65.420 1374 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.73 % Allowed : 20.17 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.24), residues: 1244 helix: 2.57 (0.25), residues: 407 sheet: 0.32 (0.28), residues: 333 loop : 0.30 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 134 TYR 0.015 0.001 TYR S 190 PHE 0.013 0.001 PHE B 199 TRP 0.015 0.001 TRP A 234 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (10040) covalent geometry : angle 0.52719 / 0.28 (13615) SS BOND : bond 0.00303 / 0.16 ( 1) SS BOND : angle 0.50261 / 0.29 ( 2) hydrogen bonds : bond 0.03556 / 2.31 ( 523) hydrogen bonds : angle 4.37623 / 3.13 ( 1458) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7103 (mt-10) REVERT: A 38 ARG cc_start: 0.8485 (mtp-110) cc_final: 0.7548 (ttp-110) REVERT: A 58 LYS cc_start: 0.7877 (mtpp) cc_final: 0.7512 (mttt) REVERT: A 370 GLU cc_start: 0.7996 (pt0) cc_final: 0.7242 (mm-30) REVERT: B 44 GLN cc_start: 0.8285 (mt0) cc_final: 0.8027 (mt0) REVERT: B 46 ARG cc_start: 0.8187 (mtp85) cc_final: 0.7427 (mtp85) REVERT: B 186 ASP cc_start: 0.7768 (m-30) cc_final: 0.7361 (m-30) REVERT: B 314 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8482 (ttt180) REVERT: B 327 VAL cc_start: 0.8791 (OUTLIER) cc_final: 0.8567 (p) REVERT: G 38 MET cc_start: 0.8199 (ttp) cc_final: 0.7881 (ttp) REVERT: G 47 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8131 (mt-10) REVERT: N 46 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7764 (tt0) REVERT: N 53 GLN cc_start: 0.8262 (mp10) cc_final: 0.7975 (mp10) REVERT: N 111 THR cc_start: 0.8773 (t) cc_final: 0.8466 (m) REVERT: S 19 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7614 (tptp) REVERT: S 186 GLN cc_start: 0.8113 (tt0) cc_final: 0.7786 (pt0) REVERT: S 202 ARG cc_start: 0.6413 (ptp90) cc_final: 0.6048 (ptp90) REVERT: R 42 ILE cc_start: 0.7853 (mt) cc_final: 0.7647 (mt) REVERT: R 60 PHE cc_start: 0.7592 (m-80) cc_final: 0.7211 (m-10) REVERT: R 74 ASN cc_start: 0.8146 (m-40) cc_final: 0.7945 (m110) REVERT: R 235 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.7004 (tt) REVERT: R 237 GLN cc_start: 0.7579 (mt0) cc_final: 0.7134 (mm110) REVERT: R 268 ARG cc_start: 0.7700 (ttt-90) cc_final: 0.7306 (ttt-90) outliers start: 40 outliers final: 27 residues processed: 218 average time/residue: 0.4902 time to fit residues: 114.7668 Evaluate side-chains 222 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 235 LEU Chi-restraints excluded: chain R residue 248 LEU Chi-restraints excluded: chain R residue 300 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 77 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 GLN A 292 ASN A 294 GLN A 392 ASN B 237 ASN G 24 ASN N 77 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.141377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.098117 restraints weight = 12152.837| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.20 r_work: 0.3061 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 10041 Z= 0.265 Angle : 0.623 8.621 13617 Z= 0.327 Chirality : 0.045 0.140 1559 Planarity : 0.004 0.051 1728 Dihedral : 5.109 62.005 1374 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 5.04 % Allowed : 19.23 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.24), residues: 1244 helix: 2.34 (0.25), residues: 406 sheet: 0.24 (0.28), residues: 335 loop : 0.24 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 134 TYR 0.017 0.002 TYR R 118 PHE 0.015 0.002 PHE R 115 TRP 0.020 0.002 TRP A 234 HIS 0.007 0.002 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.27 (10040) covalent geometry : angle 0.62336 / 0.33 (13615) SS BOND : bond 0.00345 / 0.18 ( 1) SS BOND : angle 0.33312 / 0.19 ( 2) hydrogen bonds : bond 0.04339 / 2.81 ( 523) hydrogen bonds : angle 4.69658 / 3.37 ( 1458) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 181 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7361 (mt-10) REVERT: A 38 ARG cc_start: 0.8562 (mtp-110) cc_final: 0.7692 (ttm110) REVERT: A 58 LYS cc_start: 0.7939 (mtpp) cc_final: 0.7561 (mttt) REVERT: A 370 GLU cc_start: 0.8073 (pt0) cc_final: 0.7392 (mm-30) REVERT: B 44 GLN cc_start: 0.8348 (mt0) cc_final: 0.8103 (mt0) REVERT: B 46 ARG cc_start: 0.8260 (mtp85) cc_final: 0.7558 (mtp85) REVERT: B 57 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8936 (pttp) REVERT: B 327 VAL cc_start: 0.8883 (OUTLIER) cc_final: 0.8636 (p) REVERT: G 38 MET cc_start: 0.8493 (ttp) cc_final: 0.8259 (ttp) REVERT: N 46 GLU cc_start: 0.8398 (tm-30) cc_final: 0.7836 (tt0) REVERT: S 87 ARG cc_start: 0.6576 (OUTLIER) cc_final: 0.6234 (mtt180) REVERT: S 99 SER cc_start: 0.9403 (p) cc_final: 0.9167 (p) REVERT: S 186 GLN cc_start: 0.8218 (tt0) cc_final: 0.7794 (pt0) REVERT: S 202 ARG cc_start: 0.6574 (ptp90) cc_final: 0.6246 (ptp90) REVERT: R 60 PHE cc_start: 0.7590 (m-80) cc_final: 0.7281 (m-10) REVERT: R 84 THR cc_start: 0.7979 (OUTLIER) cc_final: 0.7779 (t) REVERT: R 159 ILE cc_start: 0.7604 (OUTLIER) cc_final: 0.7366 (mt) REVERT: R 268 ARG cc_start: 0.7712 (ttt-90) cc_final: 0.7364 (ttt-90) REVERT: R 288 ARG cc_start: 0.8236 (mtm-85) cc_final: 0.7581 (mtm-85) outliers start: 54 outliers final: 32 residues processed: 220 average time/residue: 0.4669 time to fit residues: 110.1022 Evaluate side-chains 213 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 176 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 169 THR Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 195 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 85 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 24 ASN R 237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.143708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.099416 restraints weight = 11860.408| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.31 r_work: 0.3055 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10041 Z= 0.119 Angle : 0.521 8.139 13617 Z= 0.273 Chirality : 0.041 0.134 1559 Planarity : 0.004 0.049 1728 Dihedral : 4.618 57.957 1374 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.45 % Allowed : 21.38 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.24), residues: 1244 helix: 2.58 (0.25), residues: 408 sheet: 0.41 (0.28), residues: 328 loop : 0.24 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 129 TYR 0.021 0.001 TYR R 92 PHE 0.012 0.001 PHE R 113 TRP 0.015 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (10040) covalent geometry : angle 0.52128 / 0.27 (13615) SS BOND : bond 0.00308 / 0.16 ( 1) SS BOND : angle 0.49773 / 0.29 ( 2) hydrogen bonds : bond 0.03420 / 2.22 ( 523) hydrogen bonds : angle 4.36949 / 3.11 ( 1458) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 191 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7108 (mt-10) REVERT: A 38 ARG cc_start: 0.8504 (mtp-110) cc_final: 0.7595 (ttp-110) REVERT: A 58 LYS cc_start: 0.7845 (mtpp) cc_final: 0.7445 (mtmm) REVERT: A 370 GLU cc_start: 0.8006 (pt0) cc_final: 0.7249 (mm-30) REVERT: B 44 GLN cc_start: 0.8315 (mt0) cc_final: 0.8071 (mt0) REVERT: B 46 ARG cc_start: 0.8221 (mtp85) cc_final: 0.7445 (mtp85) REVERT: B 134 ARG cc_start: 0.7805 (ptt90) cc_final: 0.7237 (ptm-80) REVERT: B 186 ASP cc_start: 0.7662 (m-30) cc_final: 0.7254 (m-30) REVERT: B 327 VAL cc_start: 0.8801 (OUTLIER) cc_final: 0.8589 (p) REVERT: G 38 MET cc_start: 0.8254 (ttp) cc_final: 0.7982 (ttp) REVERT: N 46 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7792 (tt0) REVERT: N 117 TYR cc_start: 0.9123 (m-80) cc_final: 0.8896 (m-80) REVERT: S 11 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7512 (tm) REVERT: S 19 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7660 (tptp) REVERT: S 186 GLN cc_start: 0.8154 (tt0) cc_final: 0.7832 (pt0) REVERT: S 202 ARG cc_start: 0.6499 (ptp90) cc_final: 0.6135 (ptp90) REVERT: R 60 PHE cc_start: 0.7539 (m-80) cc_final: 0.7243 (m-10) REVERT: R 237 GLN cc_start: 0.7488 (mt0) cc_final: 0.7055 (mm110) REVERT: R 268 ARG cc_start: 0.7678 (ttt-90) cc_final: 0.7312 (ttt-90) outliers start: 37 outliers final: 22 residues processed: 218 average time/residue: 0.4526 time to fit residues: 106.4647 Evaluate side-chains 208 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 85 SER Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 169 THR Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 195 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 ASN G 24 ASN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.142825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.098333 restraints weight = 11842.782| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.31 r_work: 0.3049 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10041 Z= 0.142 Angle : 0.540 8.060 13617 Z= 0.282 Chirality : 0.041 0.141 1559 Planarity : 0.004 0.052 1728 Dihedral : 4.693 60.974 1374 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 4.39 % Allowed : 20.82 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.24), residues: 1244 helix: 2.60 (0.25), residues: 408 sheet: 0.34 (0.28), residues: 335 loop : 0.34 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 129 TYR 0.016 0.001 TYR A 311 PHE 0.013 0.001 PHE R 113 TRP 0.014 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (10040) covalent geometry : angle 0.53993 / 0.28 (13615) SS BOND : bond 0.00267 / 0.14 ( 1) SS BOND : angle 0.51375 / 0.30 ( 2) hydrogen bonds : bond 0.03555 / 2.31 ( 523) hydrogen bonds : angle 4.38743 / 3.13 ( 1458) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 185 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7108 (mt-10) REVERT: A 38 ARG cc_start: 0.8507 (mtp-110) cc_final: 0.7601 (ttp-170) REVERT: A 58 LYS cc_start: 0.7822 (mtpp) cc_final: 0.7422 (mtmm) REVERT: A 370 GLU cc_start: 0.8013 (pt0) cc_final: 0.7273 (mm-30) REVERT: B 44 GLN cc_start: 0.8316 (mt0) cc_final: 0.8079 (mt0) REVERT: B 46 ARG cc_start: 0.8207 (mtp85) cc_final: 0.7461 (mtp85) REVERT: B 134 ARG cc_start: 0.7797 (ptt90) cc_final: 0.7237 (ptm-80) REVERT: B 186 ASP cc_start: 0.7715 (m-30) cc_final: 0.7297 (m-30) REVERT: B 327 VAL cc_start: 0.8829 (OUTLIER) cc_final: 0.8595 (p) REVERT: G 38 MET cc_start: 0.8285 (ttp) cc_final: 0.8027 (ttp) REVERT: N 46 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7835 (tt0) REVERT: S 11 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7605 (tm) REVERT: S 19 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7699 (tptp) REVERT: S 183 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8027 (mt0) REVERT: S 186 GLN cc_start: 0.8146 (tt0) cc_final: 0.7841 (pt0) REVERT: S 202 ARG cc_start: 0.6557 (ptp90) cc_final: 0.6190 (ptp90) REVERT: R 60 PHE cc_start: 0.7439 (m-80) cc_final: 0.7137 (m-10) REVERT: R 237 GLN cc_start: 0.7515 (mt0) cc_final: 0.7069 (mm110) REVERT: R 268 ARG cc_start: 0.7718 (ttt-90) cc_final: 0.7341 (ttt-90) REVERT: R 300 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7505 (mp) outliers start: 47 outliers final: 27 residues processed: 217 average time/residue: 0.5476 time to fit residues: 127.6839 Evaluate side-chains 215 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 300 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 121 optimal weight: 6.9990 chunk 28 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.143731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.099594 restraints weight = 11783.703| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.30 r_work: 0.3047 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10041 Z= 0.125 Angle : 0.534 8.925 13617 Z= 0.276 Chirality : 0.041 0.139 1559 Planarity : 0.004 0.050 1728 Dihedral : 4.514 51.872 1374 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.73 % Allowed : 21.76 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.24), residues: 1244 helix: 2.64 (0.25), residues: 409 sheet: 0.46 (0.28), residues: 328 loop : 0.31 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 129 TYR 0.017 0.001 TYR A 311 PHE 0.012 0.001 PHE R 113 TRP 0.014 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (10040) covalent geometry : angle 0.53354 / 0.28 (13615) SS BOND : bond 0.00250 / 0.13 ( 1) SS BOND : angle 0.55966 / 0.32 ( 2) hydrogen bonds : bond 0.03394 / 2.21 ( 523) hydrogen bonds : angle 4.31721 / 3.07 ( 1458) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7014 (mt-10) REVERT: A 38 ARG cc_start: 0.8481 (mtp-110) cc_final: 0.7559 (ttp-170) REVERT: A 58 LYS cc_start: 0.7738 (mtpp) cc_final: 0.7337 (mtmm) REVERT: A 370 GLU cc_start: 0.7964 (pt0) cc_final: 0.7180 (mm-30) REVERT: B 44 GLN cc_start: 0.8307 (mt0) cc_final: 0.8068 (mt0) REVERT: B 46 ARG cc_start: 0.8185 (mtp85) cc_final: 0.7418 (mtp85) REVERT: B 57 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8841 (pttp) REVERT: B 134 ARG cc_start: 0.7758 (ptt90) cc_final: 0.7144 (ptm-80) REVERT: B 186 ASP cc_start: 0.7597 (m-30) cc_final: 0.7212 (m-30) REVERT: B 327 VAL cc_start: 0.8785 (OUTLIER) cc_final: 0.8555 (p) REVERT: G 38 MET cc_start: 0.8158 (ttp) cc_final: 0.7906 (ttp) REVERT: N 46 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7787 (tt0) REVERT: S 11 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7539 (tm) REVERT: S 19 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7704 (tptp) REVERT: S 186 GLN cc_start: 0.8094 (tt0) cc_final: 0.7793 (pt0) REVERT: S 202 ARG cc_start: 0.6455 (ptp90) cc_final: 0.6071 (ptp90) REVERT: R 42 ILE cc_start: 0.7958 (tt) cc_final: 0.7714 (pp) REVERT: R 60 PHE cc_start: 0.7404 (m-80) cc_final: 0.7096 (m-10) REVERT: R 237 GLN cc_start: 0.7424 (mt0) cc_final: 0.6984 (mm110) REVERT: R 268 ARG cc_start: 0.7691 (ttt-90) cc_final: 0.7327 (ttt-90) REVERT: R 300 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7430 (mp) outliers start: 40 outliers final: 29 residues processed: 215 average time/residue: 0.5588 time to fit residues: 129.0436 Evaluate side-chains 211 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 300 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 3 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 ASN B 237 ASN N 77 ASN S 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.139826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.096686 restraints weight = 12175.286| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.18 r_work: 0.3060 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 10041 Z= 0.353 Angle : 0.694 8.840 13617 Z= 0.361 Chirality : 0.048 0.155 1559 Planarity : 0.005 0.056 1728 Dihedral : 5.187 53.814 1374 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.39 % Allowed : 21.20 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.24), residues: 1244 helix: 2.14 (0.25), residues: 407 sheet: 0.27 (0.27), residues: 337 loop : 0.19 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 129 TYR 0.022 0.002 TYR R 118 PHE 0.023 0.002 PHE A 212 TRP 0.023 0.002 TRP A 234 HIS 0.009 0.002 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00841 / 0.35 (10040) covalent geometry : angle 0.69440 / 0.36 (13615) SS BOND : bond 0.00392 / 0.21 ( 1) SS BOND : angle 0.16017 / 0.09 ( 2) hydrogen bonds : bond 0.04660 / 3.04 ( 523) hydrogen bonds : angle 4.78712 / 3.45 ( 1458) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 173 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7435 (mt-10) REVERT: A 38 ARG cc_start: 0.8614 (mtp-110) cc_final: 0.7762 (ttm110) REVERT: A 58 LYS cc_start: 0.7809 (mtpp) cc_final: 0.7424 (mttt) REVERT: A 370 GLU cc_start: 0.8129 (pt0) cc_final: 0.7401 (mm-30) REVERT: B 44 GLN cc_start: 0.8438 (mt0) cc_final: 0.8226 (mt0) REVERT: B 46 ARG cc_start: 0.8293 (mtp85) cc_final: 0.7589 (mtp85) REVERT: B 57 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8965 (pttp) REVERT: B 314 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8467 (ttt180) REVERT: B 327 VAL cc_start: 0.8908 (OUTLIER) cc_final: 0.8664 (p) REVERT: G 38 MET cc_start: 0.8526 (ttp) cc_final: 0.8308 (ttp) REVERT: N 46 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8013 (tt0) REVERT: S 11 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7634 (tm) REVERT: S 183 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8092 (mt0) REVERT: S 186 GLN cc_start: 0.8325 (tt0) cc_final: 0.7898 (pt0) REVERT: S 202 ARG cc_start: 0.6612 (ptp90) cc_final: 0.6228 (ptp90) REVERT: R 42 ILE cc_start: 0.8130 (tt) cc_final: 0.7864 (pp) REVERT: R 60 PHE cc_start: 0.7426 (m-80) cc_final: 0.7146 (m-10) REVERT: R 268 ARG cc_start: 0.7699 (ttt-90) cc_final: 0.7353 (ttt-90) outliers start: 47 outliers final: 32 residues processed: 205 average time/residue: 0.5865 time to fit residues: 128.7632 Evaluate side-chains 210 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain R residue 169 THR Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 195 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 28 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 66 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 13 GLN B 237 ASN G 24 ASN S 82 GLN R 237 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.146726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105110 restraints weight = 11926.795| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.15 r_work: 0.3163 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10041 Z= 0.113 Angle : 0.555 10.713 13617 Z= 0.283 Chirality : 0.041 0.141 1559 Planarity : 0.004 0.047 1728 Dihedral : 4.566 49.586 1374 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.99 % Allowed : 22.69 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.24), residues: 1244 helix: 2.52 (0.25), residues: 408 sheet: 0.43 (0.28), residues: 328 loop : 0.22 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 129 TYR 0.018 0.001 TYR S 190 PHE 0.015 0.001 PHE A 212 TRP 0.013 0.001 TRP A 234 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (10040) covalent geometry : angle 0.55525 / 0.28 (13615) SS BOND : bond 0.00291 / 0.15 ( 1) SS BOND : angle 0.66850 / 0.38 ( 2) hydrogen bonds : bond 0.03355 / 2.20 ( 523) hydrogen bonds : angle 4.36420 / 3.12 ( 1458) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7282 (mt-10) REVERT: A 38 ARG cc_start: 0.8572 (mtp-110) cc_final: 0.7714 (ttm110) REVERT: A 58 LYS cc_start: 0.7867 (mtpp) cc_final: 0.7493 (mttt) REVERT: A 370 GLU cc_start: 0.8096 (pt0) cc_final: 0.7376 (mm-30) REVERT: B 44 GLN cc_start: 0.8383 (mt0) cc_final: 0.8146 (mt0) REVERT: B 46 ARG cc_start: 0.8273 (mtp85) cc_final: 0.7555 (mtp85) REVERT: B 134 ARG cc_start: 0.7866 (ptt90) cc_final: 0.7330 (ptm-80) REVERT: B 186 ASP cc_start: 0.7762 (m-30) cc_final: 0.7407 (m-30) REVERT: B 327 VAL cc_start: 0.8873 (OUTLIER) cc_final: 0.8643 (p) REVERT: G 38 MET cc_start: 0.8392 (ttp) cc_final: 0.8154 (ttp) REVERT: N 46 GLU cc_start: 0.8333 (tm-30) cc_final: 0.7834 (tt0) REVERT: N 53 GLN cc_start: 0.8385 (mp10) cc_final: 0.8109 (mp10) REVERT: S 11 LEU cc_start: 0.8154 (mm) cc_final: 0.7664 (tm) REVERT: S 166 LEU cc_start: 0.8907 (tt) cc_final: 0.8573 (tp) REVERT: S 183 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8087 (mt0) REVERT: S 186 GLN cc_start: 0.8211 (tt0) cc_final: 0.7927 (pt0) REVERT: S 202 ARG cc_start: 0.6662 (ptp90) cc_final: 0.6326 (ptp90) REVERT: R 42 ILE cc_start: 0.8140 (tt) cc_final: 0.7901 (pp) REVERT: R 60 PHE cc_start: 0.7476 (m-80) cc_final: 0.7180 (m-10) REVERT: R 237 GLN cc_start: 0.7629 (mt0) cc_final: 0.7192 (mm110) REVERT: R 268 ARG cc_start: 0.7817 (ttt-90) cc_final: 0.7459 (ttt-90) REVERT: R 300 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7612 (mp) outliers start: 32 outliers final: 24 residues processed: 210 average time/residue: 0.5462 time to fit residues: 123.0769 Evaluate side-chains 210 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 141 THR Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 162 SER Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 300 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 30 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 ASN N 77 ASN S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.145887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.103395 restraints weight = 12045.996| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.20 r_work: 0.3146 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10041 Z= 0.123 Angle : 0.571 12.590 13617 Z= 0.290 Chirality : 0.041 0.151 1559 Planarity : 0.004 0.052 1728 Dihedral : 4.549 48.574 1374 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.61 % Allowed : 22.88 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.24), residues: 1244 helix: 2.60 (0.25), residues: 408 sheet: 0.41 (0.28), residues: 324 loop : 0.20 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 129 TYR 0.017 0.001 TYR A 311 PHE 0.016 0.001 PHE R 88 TRP 0.013 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (10040) covalent geometry : angle 0.57080 / 0.29 (13615) SS BOND : bond 0.00210 / 0.11 ( 1) SS BOND : angle 0.82098 / 0.47 ( 2) hydrogen bonds : bond 0.03411 / 2.23 ( 523) hydrogen bonds : angle 4.31376 / 3.08 ( 1458) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4100.55 seconds wall clock time: 70 minutes 31.55 seconds (4231.55 seconds total)