Starting phenix.real_space_refine on Wed Feb 4 05:26:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p94_71398/02_2026/9p94_71398.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p94_71398/02_2026/9p94_71398.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9p94_71398/02_2026/9p94_71398.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p94_71398/02_2026/9p94_71398.map" model { file = "/net/cci-nas-00/data/ceres_data/9p94_71398/02_2026/9p94_71398.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p94_71398/02_2026/9p94_71398.cif" } resolution = 3.0 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= 0.016 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 57 5.16 5 C 5553 2.51 5 N 1519 2.21 5 O 1604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8733 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 221 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "R" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2640 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 13, 'TRANS': 331} Chain breaks: 4 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 8, 'GLN:plan1': 3, 'ARG:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 128 Chain: "A" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1887 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Time building chain proxies: 2.30, per 1000 atoms: 0.26 Number of scatterers: 8733 At special positions: 0 Unit cell: (78.26, 99.76, 165.12, 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 57 16.00 O 1604 8.00 N 1519 7.00 C 5553 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 34 " - pdb=" SG CYS R 63 " distance=2.03 Simple disulfide: pdb=" SG CYS R 54 " - pdb=" SG CYS R 118 " distance=2.03 Simple disulfide: pdb=" SG CYS R 77 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " 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: 0.66 Conformation dependent library (CDL) restraints added in 258.8 milliseconds 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 11 sheets defined 42.2% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.504A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 25 removed outlier: 4.046A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 43 Processing helix chain 'N' and resid 28 through 32 removed outlier: 4.014A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.042A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 27 Processing helix chain 'R' and resid 28 through 43 removed outlier: 3.662A pdb=" N ALA R 32 " --> pdb=" O LYS R 28 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU R 36 " --> pdb=" O ALA R 32 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS R 37 " --> pdb=" O MET R 33 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU R 43 " --> pdb=" O GLN R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 82 Processing helix chain 'R' and resid 129 through 135 removed outlier: 3.909A pdb=" N GLY R 135 " --> pdb=" O PHE R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 178 removed outlier: 3.588A pdb=" N PHE R 178 " --> pdb=" O ILE R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 211 Processing helix chain 'R' and resid 223 through 257 removed outlier: 3.507A pdb=" N LYS R 227 " --> pdb=" O THR R 223 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY R 248 " --> pdb=" O LEU R 244 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 291 Proline residue: R 277 - end of helix Processing helix chain 'R' and resid 302 through 336 removed outlier: 3.836A pdb=" N ILE R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 347 through 363 Proline residue: R 360 - end of helix Processing helix chain 'R' and resid 364 through 368 removed outlier: 3.522A pdb=" N VAL R 368 " --> pdb=" O HIS R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 388 Processing helix chain 'R' and resid 391 through 401 Processing helix chain 'R' and resid 404 through 418 Processing helix chain 'A' and resid 13 through 40 removed outlier: 3.754A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.564A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) 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 312 through 318 removed outlier: 3.627A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.564A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.641A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 61 removed outlier: 4.074A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.455A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN B 125 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.428A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.700A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.581A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.656A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 3 through 8 Processing sheet with id=AA9, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.622A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 72 through 75 removed outlier: 3.792A pdb=" N GLY R 122 " --> pdb=" O THR R 119 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 208 through 213 removed outlier: 3.542A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) 451 hydrogen bonds defined for protein. 1278 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: 1.43 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2849 1.34 - 1.46: 2161 1.46 - 1.58: 3831 1.58 - 1.70: 0 1.70 - 1.82: 78 Bond restraints: 8919 Sorted by residual: bond pdb=" N ASN R 42 " pdb=" CA ASN R 42 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.20e-02 6.94e+03 6.96e+00 bond pdb=" N GLU R 43 " pdb=" CA GLU R 43 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.36e+00 bond pdb=" C GLU R 43 " pdb=" O GLU R 43 " ideal model delta sigma weight residual 1.231 1.247 -0.016 2.00e-02 2.50e+03 6.49e-01 bond pdb=" CA THR N 114 " pdb=" CB THR N 114 " ideal model delta sigma weight residual 1.530 1.542 -0.012 1.69e-02 3.50e+03 4.87e-01 bond pdb=" CA ARG R 264 " pdb=" CB ARG R 264 " ideal model delta sigma weight residual 1.529 1.540 -0.011 1.62e-02 3.81e+03 4.56e-01 ... (remaining 8914 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 11759 1.14 - 2.29: 268 2.29 - 3.43: 38 3.43 - 4.58: 13 4.58 - 5.72: 5 Bond angle restraints: 12083 Sorted by residual: angle pdb=" N ILE B 33 " pdb=" CA ILE B 33 " pdb=" C ILE B 33 " ideal model delta sigma weight residual 113.42 109.41 4.01 1.17e+00 7.31e-01 1.18e+01 angle pdb=" CA TYR R 157 " pdb=" CB TYR R 157 " pdb=" CG TYR R 157 " ideal model delta sigma weight residual 113.90 119.62 -5.72 1.80e+00 3.09e-01 1.01e+01 angle pdb=" C LEU R 156 " pdb=" N TYR R 157 " pdb=" CA TYR R 157 " ideal model delta sigma weight residual 121.14 116.01 5.13 1.75e+00 3.27e-01 8.60e+00 angle pdb=" CA ASN R 42 " pdb=" C ASN R 42 " pdb=" O ASN R 42 " ideal model delta sigma weight residual 120.90 118.26 2.64 1.07e+00 8.73e-01 6.09e+00 angle pdb=" CA TYR R 267 " pdb=" CB TYR R 267 " pdb=" CG TYR R 267 " ideal model delta sigma weight residual 113.90 118.11 -4.21 1.80e+00 3.09e-01 5.48e+00 ... (remaining 12078 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 4962 17.43 - 34.86: 260 34.86 - 52.29: 36 52.29 - 69.72: 6 69.72 - 87.15: 4 Dihedral angle restraints: 5268 sinusoidal: 2019 harmonic: 3249 Sorted by residual: dihedral pdb=" CB CYS R 226 " pdb=" SG CYS R 226 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual 93.00 154.08 -61.08 1 1.00e+01 1.00e-02 4.96e+01 dihedral pdb=" CB CYS R 54 " pdb=" SG CYS R 54 " pdb=" SG CYS R 118 " pdb=" CB CYS R 118 " ideal model delta sinusoidal sigma weight residual 93.00 44.07 48.93 1 1.00e+01 1.00e-02 3.29e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 58.95 34.05 1 1.00e+01 1.00e-02 1.65e+01 ... (remaining 5265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 785 0.027 - 0.053: 354 0.053 - 0.080: 132 0.080 - 0.107: 53 0.107 - 0.133: 23 Chirality restraints: 1347 Sorted by residual: chirality pdb=" CA VAL G 54 " pdb=" N VAL G 54 " pdb=" C VAL G 54 " pdb=" CB VAL G 54 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA TYR R 157 " pdb=" N TYR R 157 " pdb=" C TYR R 157 " pdb=" CB TYR R 157 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.91e-01 ... (remaining 1344 not shown) Planarity restraints: 1539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 52 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO G 53 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 267 " 0.011 2.00e-02 2.50e+03 7.76e-03 1.21e+00 pdb=" CG TYR R 267 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR R 267 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR R 267 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR R 267 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR R 267 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR R 267 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR R 267 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 234 " -0.008 2.00e-02 2.50e+03 6.62e-03 1.09e+00 pdb=" CG TRP A 234 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP A 234 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 234 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 234 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 234 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 234 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 234 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 234 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 234 " 0.001 2.00e-02 2.50e+03 ... (remaining 1536 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 134 2.68 - 3.23: 8318 3.23 - 3.79: 13389 3.79 - 4.34: 18202 4.34 - 4.90: 30892 Nonbonded interactions: 70935 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.120 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.194 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.215 3.040 nonbonded pdb=" O ALA A 48 " pdb=" OG SER A 51 " model vdw 2.253 3.040 nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.258 3.120 ... (remaining 70930 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.520 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 8925 Z= 0.124 Angle : 0.448 5.724 12095 Z= 0.250 Chirality : 0.039 0.133 1347 Planarity : 0.002 0.032 1539 Dihedral : 10.846 87.147 3150 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: 1.77 (0.26), residues: 1095 helix: 2.63 (0.25), residues: 421 sheet: 0.64 (0.34), residues: 240 loop : 0.09 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 185 TYR 0.018 0.001 TYR R 267 PHE 0.018 0.001 PHE R 196 TRP 0.018 0.001 TRP A 234 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8919) covalent geometry : angle 0.44614 (12083) SS BOND : bond 0.00246 ( 6) SS BOND : angle 1.27218 ( 12) hydrogen bonds : bond 0.16684 ( 451) hydrogen bonds : angle 6.02429 ( 1278) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8015 (m-80) cc_final: 0.7757 (m-80) REVERT: B 172 GLU cc_start: 0.9094 (tp30) cc_final: 0.8743 (tp30) REVERT: N 90 ASP cc_start: 0.7777 (m-30) cc_final: 0.7434 (m-30) REVERT: P 15 LYS cc_start: 0.8945 (ttmm) cc_final: 0.8720 (ttmm) REVERT: P 16 GLN cc_start: 0.8121 (mt0) cc_final: 0.7381 (mm-40) REVERT: R 60 ASN cc_start: 0.7326 (m110) cc_final: 0.6610 (m-40) REVERT: R 85 ASN cc_start: 0.8867 (m110) cc_final: 0.8425 (t0) REVERT: R 267 TYR cc_start: 0.6794 (t80) cc_final: 0.6539 (t80) REVERT: R 292 ASP cc_start: 0.8444 (t0) cc_final: 0.7979 (t0) REVERT: R 299 MET cc_start: 0.9139 (mtm) cc_final: 0.8699 (mtp) REVERT: R 379 ARG cc_start: 0.7224 (ttt-90) cc_final: 0.6981 (ttp80) REVERT: R 380 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7182 (mp0) REVERT: R 406 GLU cc_start: 0.8496 (mp0) cc_final: 0.8261 (mp0) REVERT: A 333 ARG cc_start: 0.8903 (mtp85) cc_final: 0.8672 (mmp80) outliers start: 0 outliers final: 1 residues processed: 156 average time/residue: 0.6094 time to fit residues: 100.3293 Evaluate side-chains 118 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 301 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN N 31 ASN N 123 GLN A 12 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.101173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.072673 restraints weight = 16941.726| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.10 r_work: 0.2881 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8925 Z= 0.269 Angle : 0.596 6.371 12095 Z= 0.323 Chirality : 0.043 0.173 1347 Planarity : 0.004 0.045 1539 Dihedral : 4.874 87.790 1218 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.54 % Allowed : 10.11 % Favored : 88.35 % 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: 1.48 (0.26), residues: 1095 helix: 2.39 (0.24), residues: 430 sheet: 0.52 (0.33), residues: 236 loop : -0.16 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 96 TYR 0.039 0.002 TYR R 157 PHE 0.020 0.002 PHE R 196 TRP 0.017 0.002 TRP R 243 HIS 0.011 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00637 ( 8919) covalent geometry : angle 0.59526 (12083) SS BOND : bond 0.00434 ( 6) SS BOND : angle 1.12392 ( 12) hydrogen bonds : bond 0.05145 ( 451) hydrogen bonds : angle 4.62902 ( 1278) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 172 GLU cc_start: 0.9276 (tp30) cc_final: 0.8872 (tp30) REVERT: B 260 GLU cc_start: 0.8790 (tt0) cc_final: 0.8568 (tt0) REVERT: G 36 ASP cc_start: 0.7705 (m-30) cc_final: 0.7316 (m-30) REVERT: G 47 GLU cc_start: 0.8581 (mm-30) cc_final: 0.7965 (mt-10) REVERT: G 58 GLU cc_start: 0.8889 (tp30) cc_final: 0.8557 (tm-30) REVERT: N 39 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8545 (tt0) REVERT: N 89 GLU cc_start: 0.7944 (pp20) cc_final: 0.7737 (pp20) REVERT: P 16 GLN cc_start: 0.8056 (mt0) cc_final: 0.7385 (mm110) REVERT: R 85 ASN cc_start: 0.8876 (m110) cc_final: 0.8427 (t0) REVERT: R 146 GLN cc_start: 0.6803 (mm-40) cc_final: 0.6536 (mm-40) REVERT: R 257 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7229 (mm-30) REVERT: R 380 GLU cc_start: 0.7994 (mm-30) cc_final: 0.6998 (mp0) REVERT: R 406 GLU cc_start: 0.8436 (mp0) cc_final: 0.8144 (mp0) REVERT: A 333 ARG cc_start: 0.8967 (mtp85) cc_final: 0.8586 (mmp80) outliers start: 14 outliers final: 12 residues processed: 118 average time/residue: 0.6146 time to fit residues: 76.8181 Evaluate side-chains 118 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 26 VAL Chi-restraints excluded: chain R residue 132 ASP Chi-restraints excluded: chain R residue 301 ASP Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 325 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 55 optimal weight: 0.6980 chunk 58 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 53 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN N 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.103476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.074936 restraints weight = 16643.969| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 3.12 r_work: 0.2923 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8925 Z= 0.131 Angle : 0.488 5.214 12095 Z= 0.266 Chirality : 0.039 0.156 1347 Planarity : 0.003 0.032 1539 Dihedral : 4.714 89.110 1218 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.65 % Allowed : 12.31 % Favored : 86.04 % 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: 1.70 (0.26), residues: 1095 helix: 2.80 (0.24), residues: 424 sheet: 0.51 (0.33), residues: 231 loop : -0.16 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 38 TYR 0.029 0.001 TYR R 157 PHE 0.012 0.001 PHE B 292 TRP 0.015 0.001 TRP R 243 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8919) covalent geometry : angle 0.48760 (12083) SS BOND : bond 0.00347 ( 6) SS BOND : angle 1.05210 ( 12) hydrogen bonds : bond 0.04328 ( 451) hydrogen bonds : angle 4.28410 ( 1278) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8962 (OUTLIER) cc_final: 0.8576 (m-80) REVERT: B 172 GLU cc_start: 0.9262 (tp30) cc_final: 0.8915 (tp30) REVERT: B 215 GLU cc_start: 0.8584 (pt0) cc_final: 0.7936 (pp20) REVERT: B 260 GLU cc_start: 0.8750 (tt0) cc_final: 0.8541 (tt0) REVERT: G 36 ASP cc_start: 0.7646 (m-30) cc_final: 0.7209 (m-30) REVERT: G 58 GLU cc_start: 0.8943 (tp30) cc_final: 0.8520 (tm-30) REVERT: N 38 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7709 (ttm170) REVERT: N 39 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8530 (tt0) REVERT: P 15 LYS cc_start: 0.8906 (ttmm) cc_final: 0.8677 (ttmm) REVERT: P 16 GLN cc_start: 0.7954 (mt0) cc_final: 0.7299 (mm110) REVERT: R 85 ASN cc_start: 0.8850 (m110) cc_final: 0.8453 (t0) REVERT: R 257 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7223 (mm-30) REVERT: R 299 MET cc_start: 0.8927 (mtm) cc_final: 0.8643 (mtm) REVERT: R 379 ARG cc_start: 0.7147 (ttt-90) cc_final: 0.6826 (ttt-90) REVERT: R 380 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7085 (mp0) REVERT: R 406 GLU cc_start: 0.8473 (mp0) cc_final: 0.8198 (mp0) REVERT: A 333 ARG cc_start: 0.8972 (mtp85) cc_final: 0.8581 (mmp80) outliers start: 15 outliers final: 8 residues processed: 121 average time/residue: 0.5522 time to fit residues: 70.9407 Evaluate side-chains 120 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain R residue 301 ASP Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 248 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 44 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 59 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 50.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 123 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.103880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.075400 restraints weight = 16972.597| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.16 r_work: 0.2936 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8925 Z= 0.122 Angle : 0.477 5.436 12095 Z= 0.259 Chirality : 0.039 0.191 1347 Planarity : 0.003 0.042 1539 Dihedral : 4.529 84.138 1218 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.87 % Allowed : 13.41 % Favored : 84.73 % 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: 1.74 (0.26), residues: 1095 helix: 2.89 (0.24), residues: 428 sheet: 0.43 (0.33), residues: 232 loop : -0.20 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 38 TYR 0.027 0.001 TYR R 157 PHE 0.011 0.001 PHE A 376 TRP 0.013 0.001 TRP R 243 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 8919) covalent geometry : angle 0.47595 (12083) SS BOND : bond 0.00322 ( 6) SS BOND : angle 0.89615 ( 12) hydrogen bonds : bond 0.03987 ( 451) hydrogen bonds : angle 4.08619 ( 1278) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8944 (OUTLIER) cc_final: 0.8609 (m-80) REVERT: B 172 GLU cc_start: 0.9270 (tp30) cc_final: 0.8927 (tp30) REVERT: G 36 ASP cc_start: 0.7679 (m-30) cc_final: 0.7235 (m-30) REVERT: G 47 GLU cc_start: 0.8636 (mm-30) cc_final: 0.7957 (mt-10) REVERT: G 58 GLU cc_start: 0.8981 (tp30) cc_final: 0.8457 (tm-30) REVERT: N 38 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.7721 (ttm170) REVERT: N 87 LYS cc_start: 0.7770 (ttmm) cc_final: 0.7443 (mtpm) REVERT: N 89 GLU cc_start: 0.7751 (pm20) cc_final: 0.7244 (pm20) REVERT: P 16 GLN cc_start: 0.7954 (mt0) cc_final: 0.7266 (mm110) REVERT: R 85 ASN cc_start: 0.8864 (m110) cc_final: 0.8445 (t0) REVERT: R 257 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7185 (mm-30) REVERT: R 271 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7909 (mp) REVERT: R 299 MET cc_start: 0.8892 (mtm) cc_final: 0.8629 (mtm) REVERT: R 374 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8295 (mt-10) REVERT: R 379 ARG cc_start: 0.7256 (ttt-90) cc_final: 0.7022 (ttt-90) REVERT: R 380 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7059 (mp0) REVERT: R 406 GLU cc_start: 0.8493 (mp0) cc_final: 0.8237 (mp0) REVERT: A 333 ARG cc_start: 0.8976 (mtp85) cc_final: 0.8566 (mmp80) outliers start: 17 outliers final: 11 residues processed: 126 average time/residue: 0.5466 time to fit residues: 73.2869 Evaluate side-chains 119 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain P residue 23 LEU Chi-restraints excluded: chain R residue 271 ILE Chi-restraints excluded: chain R residue 301 ASP Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain A residue 248 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 66 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.103498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.075051 restraints weight = 16916.882| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.14 r_work: 0.2928 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8925 Z= 0.136 Angle : 0.477 5.287 12095 Z= 0.259 Chirality : 0.039 0.230 1347 Planarity : 0.003 0.028 1539 Dihedral : 4.617 90.448 1218 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.76 % Allowed : 14.29 % Favored : 83.96 % 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: 1.78 (0.26), residues: 1095 helix: 2.95 (0.24), residues: 428 sheet: 0.48 (0.33), residues: 233 loop : -0.21 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 379 TYR 0.027 0.001 TYR R 157 PHE 0.011 0.001 PHE A 376 TRP 0.013 0.001 TRP R 243 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8919) covalent geometry : angle 0.47608 (12083) SS BOND : bond 0.00328 ( 6) SS BOND : angle 0.85960 ( 12) hydrogen bonds : bond 0.03978 ( 451) hydrogen bonds : angle 4.05121 ( 1278) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7395 (ttp-110) cc_final: 0.7176 (ttp-110) REVERT: B 59 TYR cc_start: 0.8964 (OUTLIER) cc_final: 0.8719 (m-80) REVERT: B 172 GLU cc_start: 0.9241 (tp30) cc_final: 0.8849 (tp30) REVERT: G 36 ASP cc_start: 0.7691 (m-30) cc_final: 0.7250 (m-30) REVERT: G 58 GLU cc_start: 0.9024 (tp30) cc_final: 0.8540 (tm-30) REVERT: N 38 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7741 (ttm170) REVERT: N 39 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8551 (tt0) REVERT: N 53 GLN cc_start: 0.8091 (mp10) cc_final: 0.7541 (mp10) REVERT: N 105 ARG cc_start: 0.8599 (mtp180) cc_final: 0.8241 (mtp-110) REVERT: P 16 GLN cc_start: 0.7964 (mt0) cc_final: 0.7277 (mm110) REVERT: R 85 ASN cc_start: 0.8882 (m110) cc_final: 0.8422 (t0) REVERT: R 257 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7197 (mm-30) REVERT: R 271 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7894 (mp) REVERT: R 299 MET cc_start: 0.8867 (mtm) cc_final: 0.8659 (mtm) REVERT: R 374 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8301 (mt-10) REVERT: R 379 ARG cc_start: 0.7259 (ttt-90) cc_final: 0.7005 (ttt-90) REVERT: R 380 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7091 (mp0) REVERT: R 406 GLU cc_start: 0.8501 (mp0) cc_final: 0.8231 (mp0) REVERT: A 333 ARG cc_start: 0.8980 (mtp85) cc_final: 0.8564 (mmp80) outliers start: 16 outliers final: 11 residues processed: 126 average time/residue: 0.5880 time to fit residues: 78.5857 Evaluate side-chains 125 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain R residue 271 ILE Chi-restraints excluded: chain R residue 301 ASP Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain A residue 248 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN N 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.103402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.074776 restraints weight = 16846.852| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.16 r_work: 0.2952 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8925 Z= 0.117 Angle : 0.483 6.344 12095 Z= 0.261 Chirality : 0.039 0.218 1347 Planarity : 0.003 0.050 1539 Dihedral : 4.482 85.128 1218 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.09 % Allowed : 14.40 % Favored : 83.52 % 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: 1.91 (0.26), residues: 1095 helix: 3.10 (0.24), residues: 422 sheet: 0.56 (0.33), residues: 233 loop : -0.16 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 38 TYR 0.025 0.001 TYR R 157 PHE 0.011 0.001 PHE A 376 TRP 0.013 0.001 TRP R 243 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8919) covalent geometry : angle 0.48237 (12083) SS BOND : bond 0.00294 ( 6) SS BOND : angle 0.83857 ( 12) hydrogen bonds : bond 0.03759 ( 451) hydrogen bonds : angle 3.95106 ( 1278) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7499 (ttp-110) cc_final: 0.7274 (ttp-110) REVERT: B 172 GLU cc_start: 0.9242 (tp30) cc_final: 0.8860 (tp30) REVERT: B 215 GLU cc_start: 0.8637 (pt0) cc_final: 0.8012 (pp20) REVERT: G 36 ASP cc_start: 0.7801 (m-30) cc_final: 0.7364 (m-30) REVERT: G 58 GLU cc_start: 0.9034 (tp30) cc_final: 0.8551 (tm-30) REVERT: N 38 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.7852 (ttm170) REVERT: N 53 GLN cc_start: 0.8267 (mp10) cc_final: 0.7753 (mp10) REVERT: P 15 LYS cc_start: 0.9013 (ttmm) cc_final: 0.8428 (ttpp) REVERT: P 16 GLN cc_start: 0.8093 (mt0) cc_final: 0.7360 (mm110) REVERT: R 85 ASN cc_start: 0.8811 (m110) cc_final: 0.8384 (t0) REVERT: R 257 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7200 (mm-30) REVERT: R 271 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7838 (mp) REVERT: R 374 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8317 (mt-10) REVERT: R 380 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7150 (mp0) REVERT: R 406 GLU cc_start: 0.8481 (mp0) cc_final: 0.8164 (pm20) REVERT: R 412 LYS cc_start: 0.7350 (mptt) cc_final: 0.6695 (ptpt) REVERT: A 333 ARG cc_start: 0.8966 (mtp85) cc_final: 0.8597 (mmp80) outliers start: 19 outliers final: 12 residues processed: 131 average time/residue: 0.6011 time to fit residues: 83.5156 Evaluate side-chains 124 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain R residue 271 ILE Chi-restraints excluded: chain R residue 301 ASP Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain A residue 248 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 1 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 74 optimal weight: 0.0370 chunk 9 optimal weight: 0.4980 chunk 87 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN N 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.103289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.074878 restraints weight = 16906.065| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.14 r_work: 0.2951 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8925 Z= 0.121 Angle : 0.484 5.569 12095 Z= 0.262 Chirality : 0.039 0.153 1347 Planarity : 0.003 0.033 1539 Dihedral : 4.595 93.544 1218 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.43 % Allowed : 16.37 % Favored : 82.20 % 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: 1.86 (0.26), residues: 1095 helix: 2.97 (0.24), residues: 429 sheet: 0.50 (0.33), residues: 238 loop : -0.12 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 379 TYR 0.025 0.001 TYR R 157 PHE 0.011 0.001 PHE A 376 TRP 0.013 0.001 TRP R 243 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8919) covalent geometry : angle 0.48375 (12083) SS BOND : bond 0.00294 ( 6) SS BOND : angle 0.82374 ( 12) hydrogen bonds : bond 0.03730 ( 451) hydrogen bonds : angle 3.93655 ( 1278) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7457 (ttp-110) cc_final: 0.7227 (ttp-110) REVERT: B 172 GLU cc_start: 0.9227 (tp30) cc_final: 0.8849 (tp30) REVERT: G 36 ASP cc_start: 0.7823 (m-30) cc_final: 0.7424 (m-30) REVERT: G 58 GLU cc_start: 0.9035 (tp30) cc_final: 0.8565 (tm-30) REVERT: N 38 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.7857 (ttm170) REVERT: N 53 GLN cc_start: 0.8302 (mp10) cc_final: 0.7775 (mp10) REVERT: P 15 LYS cc_start: 0.8981 (ttmm) cc_final: 0.8380 (ttpp) REVERT: P 16 GLN cc_start: 0.8050 (mt0) cc_final: 0.7299 (mm110) REVERT: R 85 ASN cc_start: 0.8844 (m110) cc_final: 0.8438 (t0) REVERT: R 257 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7186 (mm-30) REVERT: R 271 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7843 (mp) REVERT: R 374 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8307 (mt-10) REVERT: R 380 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7122 (mp0) REVERT: R 406 GLU cc_start: 0.8437 (mp0) cc_final: 0.8150 (pm20) REVERT: R 412 LYS cc_start: 0.7410 (mptt) cc_final: 0.6730 (ptpt) REVERT: A 333 ARG cc_start: 0.8945 (mtp85) cc_final: 0.8590 (mmp80) outliers start: 13 outliers final: 11 residues processed: 123 average time/residue: 0.5910 time to fit residues: 77.1976 Evaluate side-chains 124 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain R residue 271 ILE Chi-restraints excluded: chain R residue 301 ASP Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain A residue 248 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 52 optimal weight: 40.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.102826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.074059 restraints weight = 16950.830| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.16 r_work: 0.2941 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8925 Z= 0.139 Angle : 0.508 6.877 12095 Z= 0.272 Chirality : 0.039 0.157 1347 Planarity : 0.003 0.056 1539 Dihedral : 4.431 80.780 1218 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.87 % Allowed : 16.15 % Favored : 81.98 % 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: 1.90 (0.26), residues: 1095 helix: 3.05 (0.24), residues: 422 sheet: 0.51 (0.33), residues: 238 loop : -0.09 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 38 TYR 0.025 0.001 TYR R 157 PHE 0.013 0.001 PHE N 103 TRP 0.013 0.001 TRP R 243 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8919) covalent geometry : angle 0.50739 (12083) SS BOND : bond 0.00304 ( 6) SS BOND : angle 0.80304 ( 12) hydrogen bonds : bond 0.03844 ( 451) hydrogen bonds : angle 3.95458 ( 1278) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7464 (ttp-110) cc_final: 0.7232 (ttp-110) REVERT: B 172 GLU cc_start: 0.9236 (tp30) cc_final: 0.8875 (tp30) REVERT: B 292 PHE cc_start: 0.9128 (m-80) cc_final: 0.8864 (m-80) REVERT: G 36 ASP cc_start: 0.7831 (m-30) cc_final: 0.7520 (m-30) REVERT: G 58 GLU cc_start: 0.9081 (tp30) cc_final: 0.8601 (tm-30) REVERT: N 38 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.7885 (ttm170) REVERT: N 53 GLN cc_start: 0.8296 (mp10) cc_final: 0.7705 (mp10) REVERT: P 15 LYS cc_start: 0.8989 (ttmm) cc_final: 0.8442 (ttpp) REVERT: P 16 GLN cc_start: 0.8063 (mt0) cc_final: 0.7314 (mm110) REVERT: R 85 ASN cc_start: 0.8854 (m110) cc_final: 0.8376 (t0) REVERT: R 257 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7221 (mm-30) REVERT: R 271 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7828 (mp) REVERT: R 292 ASP cc_start: 0.8486 (t0) cc_final: 0.7518 (t70) REVERT: R 374 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8291 (mt-10) REVERT: R 380 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7143 (mp0) REVERT: R 406 GLU cc_start: 0.8454 (mp0) cc_final: 0.8190 (pm20) REVERT: R 412 LYS cc_start: 0.7417 (mptt) cc_final: 0.6741 (ptpt) REVERT: A 333 ARG cc_start: 0.8945 (mtp85) cc_final: 0.8579 (mmp80) outliers start: 17 outliers final: 12 residues processed: 124 average time/residue: 0.6334 time to fit residues: 83.3133 Evaluate side-chains 124 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain R residue 271 ILE Chi-restraints excluded: chain R residue 301 ASP Chi-restraints excluded: chain R residue 359 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 325 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 103 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 46 optimal weight: 0.0870 chunk 80 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 0.4980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.104016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.075740 restraints weight = 16742.024| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.13 r_work: 0.2972 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8925 Z= 0.110 Angle : 0.488 6.960 12095 Z= 0.264 Chirality : 0.038 0.147 1347 Planarity : 0.003 0.030 1539 Dihedral : 4.288 78.131 1218 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.54 % Allowed : 17.03 % Favored : 81.43 % 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: 1.84 (0.26), residues: 1095 helix: 2.98 (0.24), residues: 429 sheet: 0.59 (0.34), residues: 226 loop : -0.22 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 379 TYR 0.024 0.001 TYR R 157 PHE 0.011 0.001 PHE A 376 TRP 0.013 0.001 TRP R 243 HIS 0.003 0.000 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 8919) covalent geometry : angle 0.48759 (12083) SS BOND : bond 0.00263 ( 6) SS BOND : angle 0.79024 ( 12) hydrogen bonds : bond 0.03545 ( 451) hydrogen bonds : angle 3.86221 ( 1278) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7461 (ttp-110) cc_final: 0.7233 (ttp-110) REVERT: B 172 GLU cc_start: 0.9218 (tp30) cc_final: 0.8920 (tp30) REVERT: B 292 PHE cc_start: 0.9091 (m-80) cc_final: 0.8809 (m-80) REVERT: G 36 ASP cc_start: 0.7800 (m-30) cc_final: 0.7493 (m-30) REVERT: G 58 GLU cc_start: 0.9077 (tp30) cc_final: 0.8601 (tm-30) REVERT: N 38 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.7857 (ttm170) REVERT: N 53 GLN cc_start: 0.8291 (mp10) cc_final: 0.7773 (mp10) REVERT: P 15 LYS cc_start: 0.8964 (ttmm) cc_final: 0.8344 (ttpp) REVERT: P 16 GLN cc_start: 0.8014 (mt0) cc_final: 0.7287 (mm110) REVERT: R 85 ASN cc_start: 0.8840 (m110) cc_final: 0.8411 (t0) REVERT: R 374 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8357 (mt-10) REVERT: R 380 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7088 (mp0) REVERT: R 406 GLU cc_start: 0.8422 (mp0) cc_final: 0.8162 (pm20) REVERT: R 412 LYS cc_start: 0.7427 (mptt) cc_final: 0.6759 (ptpt) REVERT: A 209 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8237 (tt0) REVERT: A 333 ARG cc_start: 0.8938 (mtp85) cc_final: 0.8561 (mmp80) outliers start: 14 outliers final: 10 residues processed: 123 average time/residue: 0.6356 time to fit residues: 82.7813 Evaluate side-chains 119 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain R residue 301 ASP Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 248 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 71 optimal weight: 0.0370 chunk 60 optimal weight: 0.7980 chunk 2 optimal weight: 0.0060 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.4874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN N 123 GLN ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.104722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.076560 restraints weight = 16822.973| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.14 r_work: 0.2989 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 8925 Z= 0.108 Angle : 0.499 7.169 12095 Z= 0.267 Chirality : 0.038 0.144 1347 Planarity : 0.003 0.031 1539 Dihedral : 4.263 79.543 1218 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.65 % Allowed : 16.92 % Favored : 81.43 % 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: 1.95 (0.26), residues: 1095 helix: 3.11 (0.24), residues: 422 sheet: 0.63 (0.33), residues: 231 loop : -0.13 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 379 TYR 0.023 0.001 TYR R 157 PHE 0.011 0.001 PHE A 376 TRP 0.013 0.001 TRP R 243 HIS 0.003 0.000 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 8919) covalent geometry : angle 0.49824 (12083) SS BOND : bond 0.00230 ( 6) SS BOND : angle 0.75399 ( 12) hydrogen bonds : bond 0.03447 ( 451) hydrogen bonds : angle 3.81968 ( 1278) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7494 (ttp-110) cc_final: 0.7267 (ttp-110) REVERT: B 172 GLU cc_start: 0.9213 (tp30) cc_final: 0.8956 (tp30) REVERT: B 246 ASP cc_start: 0.8204 (m-30) cc_final: 0.7872 (m-30) REVERT: B 292 PHE cc_start: 0.9025 (m-80) cc_final: 0.8765 (m-80) REVERT: G 36 ASP cc_start: 0.7805 (m-30) cc_final: 0.7498 (m-30) REVERT: G 58 GLU cc_start: 0.9083 (tp30) cc_final: 0.8611 (tm-30) REVERT: N 38 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.7828 (ttm170) REVERT: N 53 GLN cc_start: 0.8294 (mp10) cc_final: 0.7774 (mp10) REVERT: N 105 ARG cc_start: 0.8543 (mtm110) cc_final: 0.8322 (mtm110) REVERT: P 15 LYS cc_start: 0.8963 (ttmm) cc_final: 0.8347 (ttpp) REVERT: P 16 GLN cc_start: 0.7968 (mt0) cc_final: 0.7237 (mm110) REVERT: R 85 ASN cc_start: 0.8831 (m110) cc_final: 0.8403 (t0) REVERT: R 257 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7127 (mm-30) REVERT: R 292 ASP cc_start: 0.8461 (t0) cc_final: 0.7486 (t70) REVERT: R 380 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7126 (mp0) REVERT: R 406 GLU cc_start: 0.8413 (mp0) cc_final: 0.8176 (pm20) REVERT: R 412 LYS cc_start: 0.7425 (mptt) cc_final: 0.6766 (ptpt) REVERT: A 209 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8200 (tt0) REVERT: A 333 ARG cc_start: 0.8931 (mtp85) cc_final: 0.8551 (mmp80) outliers start: 15 outliers final: 10 residues processed: 126 average time/residue: 0.6700 time to fit residues: 89.2893 Evaluate side-chains 123 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain R residue 301 ASP Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 248 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 87 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN R 320 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.104168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.075836 restraints weight = 16771.410| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.14 r_work: 0.2977 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8925 Z= 0.116 Angle : 0.501 7.512 12095 Z= 0.270 Chirality : 0.039 0.224 1347 Planarity : 0.003 0.046 1539 Dihedral : 4.274 80.609 1218 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.76 % Allowed : 17.47 % Favored : 80.77 % 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: 1.94 (0.26), residues: 1095 helix: 3.11 (0.24), residues: 422 sheet: 0.65 (0.33), residues: 231 loop : -0.16 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 38 TYR 0.024 0.001 TYR R 157 PHE 0.011 0.001 PHE A 376 TRP 0.013 0.001 TRP R 243 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8919) covalent geometry : angle 0.50100 (12083) SS BOND : bond 0.00235 ( 6) SS BOND : angle 0.75168 ( 12) hydrogen bonds : bond 0.03479 ( 451) hydrogen bonds : angle 3.83390 ( 1278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2737.97 seconds wall clock time: 47 minutes 29.57 seconds (2849.57 seconds total)