Starting phenix.real_space_refine on Thu Jul 2 20:20:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vb4_64915/07_2026/9vb4_64915.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vb4_64915/07_2026/9vb4_64915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vb4_64915/07_2026/9vb4_64915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vb4_64915/07_2026/9vb4_64915.map" model { file = "/net/cci-nas-00/data/ceres_data/9vb4_64915/07_2026/9vb4_64915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vb4_64915/07_2026/9vb4_64915.cif" } resolution = 2.85 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= -0.006 sd= 0.094 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 65 5.16 5 C 6387 2.51 5 N 1722 2.21 5 O 1890 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10066 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2442 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "L" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 53 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 2793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2793 Classifications: {'peptide': 351} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 346} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2584 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 404 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1762 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.85, per 1000 atoms: 0.18 Number of scatterers: 10066 At special positions: 0 Unit cell: (105.133, 123.117, 130.033, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 P 2 15.00 O 1890 8.00 N 1722 7.00 C 6387 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 141 " - pdb=" SG CYS R 224 " distance=2.02 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.20 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.06 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: 0.73 Conformation dependent library (CDL) restraints added in 282.9 milliseconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2416 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 14 sheets defined 41.4% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'R' and resid 51 through 55 Processing helix chain 'R' and resid 59 through 90 Processing helix chain 'R' and resid 100 through 118 removed outlier: 3.742A pdb=" N HIS R 104 " --> pdb=" O THR R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 128 removed outlier: 3.528A pdb=" N ILE R 128 " --> pdb=" O LEU R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 172 Processing helix chain 'R' and resid 172 through 180 removed outlier: 3.779A pdb=" N LYS R 177 " --> pdb=" O PRO R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 201 Processing helix chain 'R' and resid 202 through 205 Processing helix chain 'R' and resid 218 through 220 No H-bonds generated for 'chain 'R' and resid 218 through 220' Processing helix chain 'R' and resid 229 through 245 Processing helix chain 'R' and resid 245 through 273 removed outlier: 3.913A pdb=" N ASN R 256 " --> pdb=" O ILE R 252 " (cutoff:3.500A) Processing helix chain 'R' and resid 296 through 329 removed outlier: 4.153A pdb=" N VAL R 302 " --> pdb=" O LEU R 298 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG R 303 " --> pdb=" O ARG R 299 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) Proline residue: R 318 - end of helix removed outlier: 3.505A pdb=" N CYS R 327 " --> pdb=" O ARG R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 365 removed outlier: 4.198A pdb=" N ASP R 340 " --> pdb=" O PRO R 336 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER R 357 " --> pdb=" O PHE R 353 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR R 358 " --> pdb=" O TYR R 354 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 370 through 374 Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.658A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 69 through 92 removed outlier: 3.765A pdb=" N GLY A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 111 removed outlier: 3.879A pdb=" N ASP A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 133 Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 143 through 146 removed outlier: 3.809A pdb=" N TYR A 146 " --> pdb=" O SER A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 143 through 146' Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.666A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.338A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.503A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 328 through 347 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.649A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 53 through 56 removed outlier: 4.244A pdb=" N GLY D 56 " --> pdb=" O SER D 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing sheet with id=AA1, first strand: chain 'R' and resid 209 through 211 Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 191 removed outlier: 8.454A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.714A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.769A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.526A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.550A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.698A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.159A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.275A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.796A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR D 59 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.107A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 128 through 130 removed outlier: 3.581A pdb=" N ALA D 199 " --> pdb=" O SER D 196 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.308A pdb=" N LEU D 162 " --> pdb=" O TYR D 178 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N TYR D 178 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) 523 hydrogen bonds defined for protein. 1476 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: 1.31 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.36: 3323 1.36 - 1.56: 6843 1.56 - 1.77: 14 1.77 - 1.97: 96 1.97 - 2.18: 1 Bond restraints: 10277 Sorted by residual: bond pdb=" CG LEU R 71 " pdb=" CD1 LEU R 71 " ideal model delta sigma weight residual 1.521 2.176 -0.655 3.30e-02 9.18e+02 3.94e+02 bond pdb=" CG LEU R 71 " pdb=" CD2 LEU R 71 " ideal model delta sigma weight residual 1.521 1.157 0.364 3.30e-02 9.18e+02 1.22e+02 bond pdb=" CG PHE R 174 " pdb=" CD1 PHE R 174 " ideal model delta sigma weight residual 1.384 1.192 0.192 2.10e-02 2.27e+03 8.36e+01 bond pdb=" CG LEU R 118 " pdb=" CD1 LEU R 118 " ideal model delta sigma weight residual 1.521 1.260 0.261 3.30e-02 9.18e+02 6.25e+01 bond pdb=" CA GLU R 332 " pdb=" CB GLU R 332 " ideal model delta sigma weight residual 1.529 1.405 0.124 1.63e-02 3.76e+03 5.82e+01 ... (remaining 10272 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.05: 13805 7.05 - 14.10: 121 14.10 - 21.15: 9 21.15 - 28.21: 2 28.21 - 35.26: 2 Bond angle restraints: 13939 Sorted by residual: angle pdb=" CD1 PHE R 174 " pdb=" CG PHE R 174 " pdb=" CD2 PHE R 174 " ideal model delta sigma weight residual 118.60 146.68 -28.08 1.50e+00 4.44e-01 3.51e+02 angle pdb=" CD1 LEU R 118 " pdb=" CG LEU R 118 " pdb=" CD2 LEU R 118 " ideal model delta sigma weight residual 110.80 142.29 -31.49 2.20e+00 2.07e-01 2.05e+02 angle pdb=" CB PHE R 174 " pdb=" CG PHE R 174 " pdb=" CD1 PHE R 174 " ideal model delta sigma weight residual 120.70 97.19 23.51 1.70e+00 3.46e-01 1.91e+02 angle pdb=" NE ARG R 148 " pdb=" CZ ARG R 148 " pdb=" NH2 ARG R 148 " ideal model delta sigma weight residual 119.20 106.84 12.36 9.00e-01 1.23e+00 1.89e+02 angle pdb=" CB LEU R 71 " pdb=" CG LEU R 71 " pdb=" CD2 LEU R 71 " ideal model delta sigma weight residual 110.70 145.96 -35.26 3.00e+00 1.11e-01 1.38e+02 ... (remaining 13934 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.97: 5836 29.97 - 59.95: 227 59.95 - 89.92: 28 89.92 - 119.90: 2 119.90 - 149.87: 1 Dihedral angle restraints: 6094 sinusoidal: 2345 harmonic: 3749 Sorted by residual: dihedral pdb=" CB CYS R 141 " pdb=" SG CYS R 141 " pdb=" SG CYS R 224 " pdb=" CB CYS R 224 " ideal model delta sinusoidal sigma weight residual 93.00 176.51 -83.51 1 1.00e+01 1.00e-02 8.52e+01 dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 169.58 -76.58 1 1.00e+01 1.00e-02 7.37e+01 dihedral pdb=" C ASP B 291 " pdb=" N ASP B 291 " pdb=" CA ASP B 291 " pdb=" CB ASP B 291 " ideal model delta harmonic sigma weight residual -122.60 -103.41 -19.19 0 2.50e+00 1.60e-01 5.89e+01 ... (remaining 6091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.409: 1574 0.409 - 0.818: 6 0.818 - 1.227: 2 1.227 - 1.636: 0 1.636 - 2.045: 1 Chirality restraints: 1583 Sorted by residual: chirality pdb=" CG LEU R 118 " pdb=" CB LEU R 118 " pdb=" CD1 LEU R 118 " pdb=" CD2 LEU R 118 " both_signs ideal model delta sigma weight residual False -2.59 -0.54 -2.05 2.00e-01 2.50e+01 1.05e+02 chirality pdb=" CB ILE R 60 " pdb=" CA ILE R 60 " pdb=" CG1 ILE R 60 " pdb=" CG2 ILE R 60 " both_signs ideal model delta sigma weight residual False 2.64 1.71 0.94 2.00e-01 2.50e+01 2.20e+01 chirality pdb=" CG LEU A 175 " pdb=" CB LEU A 175 " pdb=" CD1 LEU A 175 " pdb=" CD2 LEU A 175 " both_signs ideal model delta sigma weight residual False -2.59 -1.73 -0.86 2.00e-01 2.50e+01 1.86e+01 ... (remaining 1580 not shown) Planarity restraints: 1765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 148 " -0.825 9.50e-02 1.11e+02 3.80e-01 1.74e+02 pdb=" NE ARG R 148 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG R 148 " 0.174 2.00e-02 2.50e+03 pdb=" NH1 ARG R 148 " -0.059 2.00e-02 2.50e+03 pdb=" NH2 ARG R 148 " -0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 294 " 0.633 9.50e-02 1.11e+02 2.92e-01 1.09e+02 pdb=" NE ARG R 294 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG R 294 " -0.141 2.00e-02 2.50e+03 pdb=" NH1 ARG R 294 " 0.044 2.00e-02 2.50e+03 pdb=" NH2 ARG R 294 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 174 " 0.093 2.00e-02 2.50e+03 6.82e-02 8.15e+01 pdb=" CG PHE R 174 " -0.148 2.00e-02 2.50e+03 pdb=" CD1 PHE R 174 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE R 174 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE R 174 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE R 174 " 0.027 2.00e-02 2.50e+03 pdb=" CZ PHE R 174 " 0.033 2.00e-02 2.50e+03 ... (remaining 1762 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1064 2.80 - 3.32: 10193 3.32 - 3.85: 16311 3.85 - 4.37: 20432 4.37 - 4.90: 34407 Nonbonded interactions: 82407 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.272 3.040 nonbonded pdb=" NH1 ARG A 15 " pdb=" O VAL B 90 " model vdw 2.348 3.120 nonbonded pdb=" O SER D 105 " pdb=" NH2 ARG D 179 " model vdw 2.397 3.120 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.399 3.040 nonbonded pdb=" CG PHE R 174 " pdb=" CZ PHE R 174 " model vdw 2.408 2.848 ... (remaining 82402 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.110 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.840 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 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 : 0.015 0.655 10280 Z= 0.813 Angle : 2.332 35.257 13945 Z= 1.548 Chirality : 0.138 2.045 1583 Planarity : 0.022 0.380 1765 Dihedral : 16.233 149.870 3669 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 5.01 % Allowed : 10.85 % Favored : 84.14 % Cbeta Deviations : 2.32 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.58 (0.21), residues: 1272 helix: -1.93 (0.19), residues: 481 sheet: -1.03 (0.31), residues: 241 loop : -1.65 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.164 0.011 ARG R 148 TYR 0.050 0.009 TYR D 161 PHE 0.148 0.010 PHE R 174 TRP 0.063 0.011 TRP B 99 HIS 0.032 0.006 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.01516 / 0.81 (10277) covalent geometry : angle 2.32805 / 1.55 (13939) SS BOND : bond 0.10165 / 7.19 ( 3) SS BOND : angle 6.63094 / 4.07 ( 6) hydrogen bonds : bond 0.20988 / 14.23 ( 516) hydrogen bonds : angle 8.39302 / 5.92 ( 1476) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 232 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 123 GLU cc_start: 0.9252 (tm-30) cc_final: 0.8731 (tt0) REVERT: R 187 LYS cc_start: 0.8749 (mtpm) cc_final: 0.8323 (tttm) REVERT: R 211 ASN cc_start: 0.8339 (t0) cc_final: 0.8046 (t0) REVERT: R 292 PRO cc_start: 0.7541 (OUTLIER) cc_final: 0.6841 (Cg_endo) REVERT: R 296 GLN cc_start: 0.8710 (mm110) cc_final: 0.8474 (tp40) REVERT: R 333 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7488 (mp10) REVERT: R 350 ASN cc_start: 0.9217 (m110) cc_final: 0.8972 (m110) REVERT: R 360 ASN cc_start: 0.9104 (m-40) cc_final: 0.8662 (m110) REVERT: R 373 HIS cc_start: 0.8344 (t-170) cc_final: 0.8140 (t-170) REVERT: A 23 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.8963 (mp) REVERT: A 63 GLU cc_start: 0.8430 (tt0) cc_final: 0.8111 (tm-30) REVERT: A 66 CYS cc_start: 0.8978 (m) cc_final: 0.8625 (p) REVERT: A 67 LYS cc_start: 0.9526 (mtpt) cc_final: 0.9035 (tppp) REVERT: A 119 MET cc_start: 0.7672 (ptm) cc_final: 0.7435 (ttp) REVERT: A 181 THR cc_start: 0.9079 (OUTLIER) cc_final: 0.8398 (p) REVERT: A 192 LYS cc_start: 0.9078 (tppp) cc_final: 0.8771 (mttp) REVERT: A 248 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8757 (mttt) REVERT: A 353 LEU cc_start: 0.8674 (tt) cc_final: 0.8471 (tt) REVERT: B 8 ARG cc_start: 0.9294 (mmm-85) cc_final: 0.9081 (mtt-85) REVERT: B 42 ARG cc_start: 0.9208 (ttt-90) cc_final: 0.8996 (ttp-110) REVERT: B 46 ARG cc_start: 0.9268 (mtp-110) cc_final: 0.9040 (mtp85) REVERT: B 61 MET cc_start: 0.9058 (tmm) cc_final: 0.8716 (ttp) REVERT: B 142 HIS cc_start: 0.8947 (OUTLIER) cc_final: 0.8018 (m170) REVERT: B 268 ASN cc_start: 0.9305 (m110) cc_final: 0.9051 (t0) REVERT: C 18 GLN cc_start: 0.8598 (tp-100) cc_final: 0.8129 (tp-100) REVERT: C 19 LEU cc_start: 0.9318 (mt) cc_final: 0.9093 (mt) REVERT: C 22 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8541 (mt-10) REVERT: C 38 MET cc_start: 0.9246 (ttt) cc_final: 0.8997 (ttp) REVERT: D 3 GLN cc_start: 0.8768 (tp-100) cc_final: 0.8514 (tt0) REVERT: D 19 LYS cc_start: 0.9191 (ttpp) cc_final: 0.8896 (ttmt) REVERT: D 21 SER cc_start: 0.8986 (t) cc_final: 0.8784 (p) REVERT: D 83 MET cc_start: 0.8717 (mtm) cc_final: 0.8280 (mtp) REVERT: D 128 MET cc_start: 0.9254 (mmm) cc_final: 0.8897 (mmm) REVERT: D 206 ARG cc_start: 0.9270 (mtm-85) cc_final: 0.9064 (ttp-110) REVERT: D 234 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8546 (pp20) outliers start: 54 outliers final: 9 residues processed: 273 average time/residue: 0.6113 time to fit residues: 177.3675 Evaluate side-chains 172 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 251 VAL Chi-restraints excluded: chain R residue 258 ILE Chi-restraints excluded: chain R residue 292 PRO Chi-restraints excluded: chain R residue 333 GLN Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 51 LYS Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain D residue 51 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.0170 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.0170 chunk 51 optimal weight: 3.9990 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 104 HIS R 218 HIS R 238 GLN R 261 ASN R 269 GLN R 320 HIS R 333 GLN R 343 HIS R 350 ASN R 365 ASN A 57 HIS A 213 HIS A 241 ASN A 346 ASN B 88 ASN B 142 HIS B 311 HIS D 130 GLN D 171 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.096672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.066936 restraints weight = 19652.032| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.78 r_work: 0.2811 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10280 Z= 0.137 Angle : 0.667 9.355 13945 Z= 0.345 Chirality : 0.043 0.183 1583 Planarity : 0.004 0.041 1765 Dihedral : 7.347 97.050 1443 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.62 % Allowed : 17.63 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.23), residues: 1272 helix: 1.05 (0.23), residues: 481 sheet: -0.68 (0.31), residues: 265 loop : -1.18 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 96 TYR 0.016 0.001 TYR D 178 PHE 0.022 0.001 PHE A 336 TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (10277) covalent geometry : angle 0.66625 / 0.35 (13939) SS BOND : bond 0.00822 / 0.58 ( 3) SS BOND : angle 1.40796 / 1.06 ( 6) hydrogen bonds : bond 0.04506 / 3.07 ( 516) hydrogen bonds : angle 5.20189 / 3.68 ( 1476) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 123 GLU cc_start: 0.9028 (tm-30) cc_final: 0.8412 (tt0) REVERT: R 129 TRP cc_start: 0.8615 (m100) cc_final: 0.8323 (m100) REVERT: R 175 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7802 (mtmt) REVERT: R 187 LYS cc_start: 0.7876 (mtpm) cc_final: 0.7570 (tttm) REVERT: R 207 MET cc_start: 0.8770 (mmm) cc_final: 0.8405 (mmm) REVERT: R 296 GLN cc_start: 0.8404 (mm110) cc_final: 0.8079 (tp-100) REVERT: R 373 HIS cc_start: 0.7835 (t-170) cc_final: 0.7453 (t-170) REVERT: A 66 CYS cc_start: 0.8797 (m) cc_final: 0.8487 (p) REVERT: A 67 LYS cc_start: 0.9510 (mtpt) cc_final: 0.9085 (tppp) REVERT: A 208 ARG cc_start: 0.7885 (mtt90) cc_final: 0.7569 (mtm110) REVERT: A 248 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8068 (mttt) REVERT: A 269 ASN cc_start: 0.9200 (OUTLIER) cc_final: 0.8868 (t0) REVERT: A 347 ASN cc_start: 0.8844 (m-40) cc_final: 0.8642 (m-40) REVERT: B 23 LYS cc_start: 0.9261 (tptp) cc_final: 0.9042 (tppp) REVERT: B 36 ASN cc_start: 0.9386 (m-40) cc_final: 0.9046 (m-40) REVERT: B 46 ARG cc_start: 0.8259 (mtp-110) cc_final: 0.7716 (mtp85) REVERT: B 215 GLU cc_start: 0.8513 (mp0) cc_final: 0.8226 (mp0) REVERT: B 217 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8597 (pmm) REVERT: B 230 ASN cc_start: 0.8935 (m-40) cc_final: 0.8651 (m110) REVERT: B 323 ASP cc_start: 0.8592 (t0) cc_final: 0.8208 (t0) REVERT: C 17 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8682 (mm-30) REVERT: C 20 LYS cc_start: 0.8904 (mtpp) cc_final: 0.8443 (mtmm) REVERT: D 3 GLN cc_start: 0.8025 (tp-100) cc_final: 0.7802 (tt0) REVERT: D 19 LYS cc_start: 0.8923 (ttpp) cc_final: 0.8703 (ttmt) REVERT: D 83 MET cc_start: 0.8598 (mtm) cc_final: 0.8306 (mtm) REVERT: D 206 ARG cc_start: 0.8254 (mtm-85) cc_final: 0.7987 (ttp-110) outliers start: 39 outliers final: 7 residues processed: 195 average time/residue: 0.5922 time to fit residues: 122.9313 Evaluate side-chains 150 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 175 LYS Chi-restraints excluded: chain R residue 302 VAL Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 124 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 101 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 112 optimal weight: 2.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 269 GLN R 365 ASN B 268 ASN D 13 GLN D 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.091448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.061121 restraints weight = 20174.840| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.83 r_work: 0.2687 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 10280 Z= 0.249 Angle : 0.692 10.257 13945 Z= 0.357 Chirality : 0.045 0.167 1583 Planarity : 0.004 0.031 1765 Dihedral : 6.347 81.140 1419 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.08 % Allowed : 19.76 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.24), residues: 1272 helix: 1.61 (0.24), residues: 490 sheet: -0.52 (0.30), residues: 294 loop : -0.92 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 322 TYR 0.016 0.002 TYR D 94 PHE 0.014 0.002 PHE R 247 TRP 0.014 0.002 TRP B 82 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.25 (10277) covalent geometry : angle 0.68869 / 0.36 (13939) SS BOND : bond 0.01378 / 0.97 ( 3) SS BOND : angle 3.18755 / 2.78 ( 6) hydrogen bonds : bond 0.04682 / 3.19 ( 516) hydrogen bonds : angle 5.05358 / 3.59 ( 1476) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 141 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 93 SER cc_start: 0.8391 (m) cc_final: 0.8072 (t) REVERT: R 123 GLU cc_start: 0.9079 (tm-30) cc_final: 0.8340 (tt0) REVERT: R 129 TRP cc_start: 0.8723 (m100) cc_final: 0.8400 (m100) REVERT: R 175 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7832 (mtmt) REVERT: R 187 LYS cc_start: 0.8063 (mtpm) cc_final: 0.7732 (tttm) REVERT: R 207 MET cc_start: 0.8945 (mmm) cc_final: 0.8607 (mmm) REVERT: R 296 GLN cc_start: 0.8388 (mm110) cc_final: 0.7983 (tp-100) REVERT: R 373 HIS cc_start: 0.8068 (t-170) cc_final: 0.7675 (t-170) REVERT: A 23 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8146 (mt) REVERT: A 66 CYS cc_start: 0.8716 (m) cc_final: 0.8495 (p) REVERT: A 67 LYS cc_start: 0.9297 (mtpt) cc_final: 0.8942 (mmpt) REVERT: A 79 GLN cc_start: 0.8831 (tp-100) cc_final: 0.8620 (tp-100) REVERT: A 105 ARG cc_start: 0.9369 (ptt-90) cc_final: 0.9121 (ptt-90) REVERT: A 106 GLN cc_start: 0.9806 (mm110) cc_final: 0.9553 (mm110) REVERT: A 128 LYS cc_start: 0.9313 (pptt) cc_final: 0.9011 (pptt) REVERT: A 208 ARG cc_start: 0.8031 (mtt90) cc_final: 0.7682 (mtm110) REVERT: A 248 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8165 (mttt) REVERT: A 269 ASN cc_start: 0.9264 (OUTLIER) cc_final: 0.8899 (t0) REVERT: B 46 ARG cc_start: 0.8229 (mtp-110) cc_final: 0.7648 (mtp85) REVERT: B 142 HIS cc_start: 0.8599 (OUTLIER) cc_final: 0.8268 (t-90) REVERT: B 147 SER cc_start: 0.9061 (m) cc_final: 0.8853 (p) REVERT: B 198 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8439 (pp) REVERT: B 215 GLU cc_start: 0.8494 (mp0) cc_final: 0.8099 (mp0) REVERT: B 217 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8526 (pmm) REVERT: B 226 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8176 (mt-10) REVERT: B 262 MET cc_start: 0.8928 (tpp) cc_final: 0.8602 (ttm) REVERT: C 30 VAL cc_start: 0.8590 (t) cc_final: 0.8369 (p) REVERT: D 19 LYS cc_start: 0.8833 (ttpp) cc_final: 0.8394 (ttmt) REVERT: D 206 ARG cc_start: 0.8463 (mtm-85) cc_final: 0.8038 (ttp-110) outliers start: 44 outliers final: 19 residues processed: 170 average time/residue: 0.6133 time to fit residues: 110.7535 Evaluate side-chains 164 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 79 VAL Chi-restraints excluded: chain R residue 175 LYS Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 302 VAL Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain R residue 358 THR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 20 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 269 GLN R 365 ASN A 347 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.092342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.062455 restraints weight = 20053.414| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.88 r_work: 0.2689 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10280 Z= 0.188 Angle : 0.637 10.804 13945 Z= 0.326 Chirality : 0.043 0.151 1583 Planarity : 0.003 0.029 1765 Dihedral : 5.915 80.302 1419 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.99 % Allowed : 19.48 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.24), residues: 1272 helix: 1.88 (0.24), residues: 491 sheet: -0.29 (0.30), residues: 285 loop : -0.79 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 148 TYR 0.015 0.001 TYR D 178 PHE 0.011 0.001 PHE A 336 TRP 0.014 0.002 TRP B 82 HIS 0.004 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (10277) covalent geometry : angle 0.63384 / 0.32 (13939) SS BOND : bond 0.01207 / 0.85 ( 3) SS BOND : angle 2.95924 / 2.57 ( 6) hydrogen bonds : bond 0.04139 / 2.84 ( 516) hydrogen bonds : angle 4.81352 / 3.42 ( 1476) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 143 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 93 SER cc_start: 0.8294 (m) cc_final: 0.8011 (t) REVERT: R 123 GLU cc_start: 0.9145 (tm-30) cc_final: 0.8423 (tt0) REVERT: R 129 TRP cc_start: 0.8575 (m100) cc_final: 0.8195 (m100) REVERT: R 180 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8651 (ptm) REVERT: R 187 LYS cc_start: 0.8034 (mtpm) cc_final: 0.7692 (tttm) REVERT: R 203 MET cc_start: 0.8240 (tpp) cc_final: 0.7849 (tpp) REVERT: R 207 MET cc_start: 0.8917 (mmm) cc_final: 0.8521 (mmm) REVERT: R 225 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8603 (m) REVERT: R 296 GLN cc_start: 0.8367 (mm110) cc_final: 0.8020 (tp-100) REVERT: R 373 HIS cc_start: 0.8050 (t-170) cc_final: 0.7673 (t-170) REVERT: A 53 MET cc_start: 0.8115 (mmp) cc_final: 0.7896 (mmp) REVERT: A 66 CYS cc_start: 0.8926 (m) cc_final: 0.8701 (p) REVERT: A 67 LYS cc_start: 0.9325 (mtpt) cc_final: 0.8910 (mmpt) REVERT: A 79 GLN cc_start: 0.8843 (tp-100) cc_final: 0.8611 (tp-100) REVERT: A 106 GLN cc_start: 0.9794 (mm110) cc_final: 0.9525 (mm110) REVERT: A 208 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7679 (mtm110) REVERT: A 243 MET cc_start: 0.8494 (tpp) cc_final: 0.8219 (ttm) REVERT: A 269 ASN cc_start: 0.9215 (OUTLIER) cc_final: 0.8831 (t0) REVERT: A 310 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8513 (mm) REVERT: A 347 ASN cc_start: 0.8835 (m-40) cc_final: 0.8351 (m110) REVERT: B 5 ASP cc_start: 0.8883 (p0) cc_final: 0.8434 (p0) REVERT: B 20 ASP cc_start: 0.9163 (m-30) cc_final: 0.8853 (p0) REVERT: B 46 ARG cc_start: 0.8354 (mtp-110) cc_final: 0.7780 (mtp85) REVERT: B 198 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8356 (pp) REVERT: B 215 GLU cc_start: 0.8530 (mp0) cc_final: 0.8113 (OUTLIER) REVERT: B 217 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8559 (pmm) REVERT: B 254 ASP cc_start: 0.8078 (t0) cc_final: 0.7681 (t0) REVERT: B 262 MET cc_start: 0.8915 (tpp) cc_final: 0.8564 (ttm) REVERT: C 21 MET cc_start: 0.9241 (tpp) cc_final: 0.9026 (mmm) REVERT: C 25 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.7831 (tt) REVERT: C 30 VAL cc_start: 0.8557 (t) cc_final: 0.8331 (p) REVERT: C 58 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8917 (mt-10) REVERT: D 19 LYS cc_start: 0.8807 (ttpp) cc_final: 0.8401 (ttmt) REVERT: D 73 ASP cc_start: 0.7988 (t0) cc_final: 0.7593 (t0) REVERT: D 206 ARG cc_start: 0.8379 (mtm-85) cc_final: 0.8002 (ttp-110) outliers start: 43 outliers final: 20 residues processed: 165 average time/residue: 0.6259 time to fit residues: 109.6394 Evaluate side-chains 163 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 302 VAL Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain R residue 358 THR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 95 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 17 optimal weight: 30.0000 chunk 4 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 238 GLN R 350 ASN R 365 ASN B 88 ASN D 13 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.093639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.063939 restraints weight = 20112.016| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.88 r_work: 0.2721 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10280 Z= 0.132 Angle : 0.598 9.506 13945 Z= 0.305 Chirality : 0.041 0.155 1583 Planarity : 0.003 0.034 1765 Dihedral : 5.430 77.296 1415 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.06 % Allowed : 21.34 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.24), residues: 1272 helix: 2.11 (0.24), residues: 483 sheet: -0.30 (0.30), residues: 283 loop : -0.65 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 8 TYR 0.015 0.001 TYR D 178 PHE 0.009 0.001 PHE A 336 TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (10277) covalent geometry : angle 0.59698 / 0.30 (13939) SS BOND : bond 0.01034 / 0.73 ( 3) SS BOND : angle 2.07087 / 1.78 ( 6) hydrogen bonds : bond 0.03740 / 2.57 ( 516) hydrogen bonds : angle 4.59178 / 3.28 ( 1476) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 139 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 93 SER cc_start: 0.8277 (m) cc_final: 0.8007 (t) REVERT: R 123 GLU cc_start: 0.9098 (tm-30) cc_final: 0.8471 (tt0) REVERT: R 129 TRP cc_start: 0.8566 (m100) cc_final: 0.8071 (m100) REVERT: R 175 LYS cc_start: 0.8332 (mppt) cc_final: 0.7890 (mmmm) REVERT: R 180 MET cc_start: 0.9003 (ttm) cc_final: 0.8713 (ptm) REVERT: R 187 LYS cc_start: 0.8001 (mtpm) cc_final: 0.7628 (tttt) REVERT: R 203 MET cc_start: 0.8415 (tpp) cc_final: 0.8034 (tpp) REVERT: R 207 MET cc_start: 0.8873 (mmm) cc_final: 0.8508 (mmm) REVERT: R 225 THR cc_start: 0.8882 (OUTLIER) cc_final: 0.8635 (m) REVERT: R 296 GLN cc_start: 0.8326 (mm110) cc_final: 0.7986 (tp-100) REVERT: A 67 LYS cc_start: 0.9298 (mtpt) cc_final: 0.8909 (mmmm) REVERT: A 79 GLN cc_start: 0.8971 (tp-100) cc_final: 0.8733 (tp-100) REVERT: A 106 GLN cc_start: 0.9792 (mm110) cc_final: 0.9530 (mm110) REVERT: A 132 LYS cc_start: 0.9364 (mtmp) cc_final: 0.9162 (pttp) REVERT: A 208 ARG cc_start: 0.8020 (mtt90) cc_final: 0.7718 (mtm110) REVERT: A 218 VAL cc_start: 0.8711 (OUTLIER) cc_final: 0.8498 (p) REVERT: A 269 ASN cc_start: 0.9175 (OUTLIER) cc_final: 0.8777 (t0) REVERT: A 310 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8522 (mm) REVERT: A 347 ASN cc_start: 0.8852 (m-40) cc_final: 0.8341 (m110) REVERT: B 5 ASP cc_start: 0.8461 (p0) cc_final: 0.7864 (p0) REVERT: B 20 ASP cc_start: 0.9221 (m-30) cc_final: 0.8883 (p0) REVERT: B 46 ARG cc_start: 0.8379 (mtp-110) cc_final: 0.7805 (mtp85) REVERT: B 135 VAL cc_start: 0.9417 (OUTLIER) cc_final: 0.9161 (p) REVERT: B 198 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8316 (pp) REVERT: B 215 GLU cc_start: 0.8572 (mp0) cc_final: 0.8061 (OUTLIER) REVERT: B 217 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8669 (pmm) REVERT: B 226 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8296 (mt-10) REVERT: B 254 ASP cc_start: 0.8098 (t0) cc_final: 0.7622 (t0) REVERT: B 262 MET cc_start: 0.8925 (tpp) cc_final: 0.8554 (ttm) REVERT: C 17 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8763 (mm-30) REVERT: C 20 LYS cc_start: 0.9090 (mtmm) cc_final: 0.8646 (mtmm) REVERT: C 25 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.7978 (tt) REVERT: C 30 VAL cc_start: 0.8550 (t) cc_final: 0.8337 (p) REVERT: C 58 GLU cc_start: 0.9264 (mt-10) cc_final: 0.8970 (mt-10) REVERT: D 19 LYS cc_start: 0.8788 (ttpp) cc_final: 0.8416 (ttmt) REVERT: D 73 ASP cc_start: 0.7957 (t0) cc_final: 0.7585 (t0) REVERT: D 206 ARG cc_start: 0.8451 (mtm-85) cc_final: 0.8035 (ttp-110) outliers start: 33 outliers final: 16 residues processed: 159 average time/residue: 0.6204 time to fit residues: 104.8336 Evaluate side-chains 157 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 302 VAL Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 7 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 41 optimal weight: 30.0000 chunk 83 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 365 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.092022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.061922 restraints weight = 20184.946| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.89 r_work: 0.2672 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10280 Z= 0.195 Angle : 0.643 10.007 13945 Z= 0.326 Chirality : 0.043 0.193 1583 Planarity : 0.004 0.042 1765 Dihedral : 5.508 79.710 1415 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.36 % Allowed : 20.59 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.24), residues: 1272 helix: 2.06 (0.24), residues: 490 sheet: -0.33 (0.31), residues: 276 loop : -0.68 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 96 TYR 0.014 0.001 TYR D 178 PHE 0.012 0.001 PHE A 336 TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (10277) covalent geometry : angle 0.64059 / 0.33 (13939) SS BOND : bond 0.01447 / 1.02 ( 3) SS BOND : angle 2.56759 / 2.20 ( 6) hydrogen bonds : bond 0.04038 / 2.77 ( 516) hydrogen bonds : angle 4.64559 / 3.32 ( 1476) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 137 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 123 GLU cc_start: 0.9063 (tm-30) cc_final: 0.8433 (tt0) REVERT: R 129 TRP cc_start: 0.8606 (m100) cc_final: 0.8114 (m100) REVERT: R 175 LYS cc_start: 0.8369 (mppt) cc_final: 0.7948 (mmmm) REVERT: R 180 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8717 (ptm) REVERT: R 187 LYS cc_start: 0.8070 (mtpm) cc_final: 0.7685 (tttt) REVERT: R 207 MET cc_start: 0.8913 (mmm) cc_final: 0.8584 (mmm) REVERT: R 225 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8603 (m) REVERT: R 296 GLN cc_start: 0.8335 (mm110) cc_final: 0.7998 (tp-100) REVERT: A 23 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8157 (mt) REVERT: A 67 LYS cc_start: 0.9111 (mtpt) cc_final: 0.8841 (mmmm) REVERT: A 106 GLN cc_start: 0.9784 (mm110) cc_final: 0.9518 (mm110) REVERT: A 208 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7725 (mtm110) REVERT: A 243 MET cc_start: 0.8693 (tpp) cc_final: 0.8473 (ttm) REVERT: A 269 ASN cc_start: 0.9214 (OUTLIER) cc_final: 0.8833 (t0) REVERT: A 310 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8520 (mm) REVERT: A 346 ASN cc_start: 0.8570 (t0) cc_final: 0.8308 (p0) REVERT: B 20 ASP cc_start: 0.9220 (m-30) cc_final: 0.8908 (p0) REVERT: B 46 ARG cc_start: 0.8348 (mtp-110) cc_final: 0.7806 (mtp85) REVERT: B 135 VAL cc_start: 0.9394 (OUTLIER) cc_final: 0.9138 (p) REVERT: B 146 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8649 (tp) REVERT: B 198 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8335 (pp) REVERT: B 215 GLU cc_start: 0.8592 (mp0) cc_final: 0.8053 (OUTLIER) REVERT: B 217 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8519 (pmm) REVERT: B 226 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8214 (mt-10) REVERT: B 254 ASP cc_start: 0.8113 (t0) cc_final: 0.7691 (t0) REVERT: B 262 MET cc_start: 0.8977 (tpp) cc_final: 0.8496 (ttm) REVERT: B 286 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8743 (mt) REVERT: C 13 ARG cc_start: 0.9101 (mtm-85) cc_final: 0.8800 (mpp80) REVERT: C 25 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.7962 (tt) REVERT: C 58 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8981 (mt-10) REVERT: D 19 LYS cc_start: 0.8782 (ttpp) cc_final: 0.8397 (ttmt) REVERT: D 73 ASP cc_start: 0.7975 (t0) cc_final: 0.7631 (t0) REVERT: D 89 GLU cc_start: 0.8201 (pm20) cc_final: 0.7739 (pm20) REVERT: D 206 ARG cc_start: 0.8538 (mtm-85) cc_final: 0.8185 (ttp-110) REVERT: D 234 GLU cc_start: 0.7410 (tm-30) cc_final: 0.7168 (tm-30) outliers start: 47 outliers final: 21 residues processed: 163 average time/residue: 0.6143 time to fit residues: 106.6821 Evaluate side-chains 163 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 302 VAL Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain R residue 358 THR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 17 optimal weight: 30.0000 chunk 36 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 365 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.091027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.060712 restraints weight = 20081.730| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 2.88 r_work: 0.2639 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 10280 Z= 0.236 Angle : 0.687 10.561 13945 Z= 0.350 Chirality : 0.044 0.206 1583 Planarity : 0.004 0.045 1765 Dihedral : 5.616 81.347 1415 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.27 % Allowed : 21.24 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.24), residues: 1272 helix: 2.00 (0.24), residues: 490 sheet: -0.20 (0.31), residues: 281 loop : -0.71 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 96 TYR 0.014 0.002 TYR D 178 PHE 0.014 0.002 PHE A 336 TRP 0.013 0.002 TRP B 63 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.24 (10277) covalent geometry : angle 0.68461 / 0.35 (13939) SS BOND : bond 0.01626 / 1.15 ( 3) SS BOND : angle 2.80769 / 2.40 ( 6) hydrogen bonds : bond 0.04204 / 2.88 ( 516) hydrogen bonds : angle 4.71809 / 3.39 ( 1476) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 135 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 123 GLU cc_start: 0.9088 (tm-30) cc_final: 0.8460 (tt0) REVERT: R 129 TRP cc_start: 0.8651 (m100) cc_final: 0.8155 (m100) REVERT: R 175 LYS cc_start: 0.8385 (mppt) cc_final: 0.7972 (mmmm) REVERT: R 180 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8718 (ptm) REVERT: R 187 LYS cc_start: 0.8041 (mtpm) cc_final: 0.7653 (tttt) REVERT: R 207 MET cc_start: 0.8890 (mmm) cc_final: 0.8549 (mmm) REVERT: R 296 GLN cc_start: 0.8378 (mm110) cc_final: 0.8041 (tp-100) REVERT: A 23 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8170 (mt) REVERT: A 67 LYS cc_start: 0.9108 (mtpt) cc_final: 0.8768 (mmmm) REVERT: A 106 GLN cc_start: 0.9762 (mm110) cc_final: 0.9504 (mm110) REVERT: A 208 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7733 (mtm110) REVERT: A 243 MET cc_start: 0.8739 (tpp) cc_final: 0.8488 (ttm) REVERT: A 269 ASN cc_start: 0.9211 (OUTLIER) cc_final: 0.8846 (t0) REVERT: A 310 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8518 (mm) REVERT: A 346 ASN cc_start: 0.8578 (t0) cc_final: 0.8341 (p0) REVERT: B 20 ASP cc_start: 0.9230 (m-30) cc_final: 0.8911 (p0) REVERT: B 46 ARG cc_start: 0.8224 (mtp-110) cc_final: 0.7685 (mtp85) REVERT: B 135 VAL cc_start: 0.9403 (OUTLIER) cc_final: 0.9138 (p) REVERT: B 146 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8479 (tp) REVERT: B 198 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8383 (pp) REVERT: B 215 GLU cc_start: 0.8630 (mp0) cc_final: 0.8070 (OUTLIER) REVERT: B 217 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8476 (pmm) REVERT: B 226 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8279 (mt-10) REVERT: B 254 ASP cc_start: 0.8187 (t0) cc_final: 0.7725 (t0) REVERT: B 262 MET cc_start: 0.8979 (tpp) cc_final: 0.8522 (ttm) REVERT: B 286 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8754 (mt) REVERT: C 13 ARG cc_start: 0.9099 (mtm-85) cc_final: 0.8819 (mpp80) REVERT: C 17 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8916 (mm-30) REVERT: C 20 LYS cc_start: 0.9073 (mtmm) cc_final: 0.8647 (mtmm) REVERT: C 25 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.7990 (tt) REVERT: C 58 GLU cc_start: 0.9297 (mt-10) cc_final: 0.8933 (mt-10) REVERT: D 19 LYS cc_start: 0.8786 (ttpp) cc_final: 0.8369 (ttmt) REVERT: D 73 ASP cc_start: 0.7986 (t0) cc_final: 0.7649 (t0) REVERT: D 89 GLU cc_start: 0.8165 (pm20) cc_final: 0.7752 (pm20) REVERT: D 206 ARG cc_start: 0.8602 (mtm-85) cc_final: 0.8278 (ttp-110) outliers start: 46 outliers final: 26 residues processed: 163 average time/residue: 0.6292 time to fit residues: 109.0612 Evaluate side-chains 166 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 262 LYS Chi-restraints excluded: chain R residue 302 VAL Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain R residue 358 THR Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 56 optimal weight: 4.9990 chunk 65 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 102 optimal weight: 0.0370 chunk 23 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 365 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.092069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.062101 restraints weight = 20083.903| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.88 r_work: 0.2680 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10280 Z= 0.163 Angle : 0.656 9.260 13945 Z= 0.332 Chirality : 0.042 0.185 1583 Planarity : 0.003 0.042 1765 Dihedral : 5.424 79.012 1415 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.99 % Allowed : 22.17 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.24), residues: 1272 helix: 2.18 (0.24), residues: 484 sheet: -0.35 (0.30), residues: 286 loop : -0.56 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 96 TYR 0.014 0.001 TYR D 178 PHE 0.009 0.001 PHE A 336 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (10277) covalent geometry : angle 0.65506 / 0.33 (13939) SS BOND : bond 0.01215 / 0.86 ( 3) SS BOND : angle 2.18730 / 1.88 ( 6) hydrogen bonds : bond 0.03867 / 2.66 ( 516) hydrogen bonds : angle 4.62322 / 3.32 ( 1476) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 133 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 123 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8437 (tt0) REVERT: R 129 TRP cc_start: 0.8601 (m100) cc_final: 0.8022 (m100) REVERT: R 175 LYS cc_start: 0.8356 (mppt) cc_final: 0.7947 (mmmm) REVERT: R 180 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8820 (ttt) REVERT: R 187 LYS cc_start: 0.7986 (mtpm) cc_final: 0.7587 (tttt) REVERT: R 207 MET cc_start: 0.8850 (mmm) cc_final: 0.8557 (mmm) REVERT: R 225 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8522 (m) REVERT: R 296 GLN cc_start: 0.8342 (mm110) cc_final: 0.8009 (tp-100) REVERT: A 53 MET cc_start: 0.8411 (mmp) cc_final: 0.8002 (mmp) REVERT: A 67 LYS cc_start: 0.9112 (mtpt) cc_final: 0.8765 (mmmm) REVERT: A 88 MET cc_start: 0.7797 (ttp) cc_final: 0.7192 (ptm) REVERT: A 106 GLN cc_start: 0.9751 (mm110) cc_final: 0.9490 (mm110) REVERT: A 208 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7725 (mtm110) REVERT: A 243 MET cc_start: 0.8669 (tpp) cc_final: 0.8407 (ttm) REVERT: A 269 ASN cc_start: 0.9190 (OUTLIER) cc_final: 0.8795 (t0) REVERT: A 310 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8483 (mm) REVERT: A 346 ASN cc_start: 0.8544 (t0) cc_final: 0.8305 (p0) REVERT: B 20 ASP cc_start: 0.9255 (m-30) cc_final: 0.8892 (p0) REVERT: B 46 ARG cc_start: 0.8407 (mtp-110) cc_final: 0.7870 (mtp85) REVERT: B 135 VAL cc_start: 0.9411 (OUTLIER) cc_final: 0.9157 (p) REVERT: B 198 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8336 (pp) REVERT: B 215 GLU cc_start: 0.8650 (mp0) cc_final: 0.8073 (OUTLIER) REVERT: B 217 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8624 (pmm) REVERT: B 254 ASP cc_start: 0.8129 (t0) cc_final: 0.7723 (t0) REVERT: B 262 MET cc_start: 0.8958 (tpp) cc_final: 0.8524 (ttm) REVERT: B 286 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8724 (mt) REVERT: C 25 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.7969 (tt) REVERT: C 58 GLU cc_start: 0.9284 (mt-10) cc_final: 0.8948 (mt-10) REVERT: D 19 LYS cc_start: 0.8777 (ttpp) cc_final: 0.8388 (ttmt) REVERT: D 73 ASP cc_start: 0.7946 (t0) cc_final: 0.7615 (t0) REVERT: D 89 GLU cc_start: 0.8168 (pm20) cc_final: 0.7737 (pm20) REVERT: D 206 ARG cc_start: 0.8662 (mtm-85) cc_final: 0.8351 (ttp-110) outliers start: 43 outliers final: 20 residues processed: 158 average time/residue: 0.6030 time to fit residues: 101.2990 Evaluate side-chains 159 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 302 VAL Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain R residue 358 THR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 90 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 365 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS D 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.091213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.061265 restraints weight = 20073.382| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.87 r_work: 0.2647 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10280 Z= 0.215 Angle : 0.707 11.960 13945 Z= 0.355 Chirality : 0.043 0.191 1583 Planarity : 0.004 0.048 1765 Dihedral : 5.517 80.757 1415 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.34 % Allowed : 22.82 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.24), residues: 1272 helix: 2.15 (0.24), residues: 483 sheet: -0.29 (0.31), residues: 291 loop : -0.56 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 96 TYR 0.013 0.001 TYR D 178 PHE 0.012 0.001 PHE A 336 TRP 0.013 0.001 TRP B 63 HIS 0.024 0.002 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.21 (10277) covalent geometry : angle 0.70529 / 0.35 (13939) SS BOND : bond 0.01499 / 1.06 ( 3) SS BOND : angle 2.61181 / 2.24 ( 6) hydrogen bonds : bond 0.04058 / 2.79 ( 516) hydrogen bonds : angle 4.67233 / 3.36 ( 1476) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 136 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 123 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8451 (tt0) REVERT: R 129 TRP cc_start: 0.8620 (m100) cc_final: 0.8090 (m100) REVERT: R 175 LYS cc_start: 0.8372 (mppt) cc_final: 0.7965 (mmmm) REVERT: R 180 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8698 (ptm) REVERT: R 187 LYS cc_start: 0.7956 (mtpm) cc_final: 0.7555 (tttt) REVERT: R 207 MET cc_start: 0.8828 (mmm) cc_final: 0.8590 (mmm) REVERT: R 296 GLN cc_start: 0.8361 (mm110) cc_final: 0.8021 (tp-100) REVERT: A 53 MET cc_start: 0.8428 (mmp) cc_final: 0.8033 (mmp) REVERT: A 67 LYS cc_start: 0.9117 (mtpt) cc_final: 0.8768 (mmmm) REVERT: A 88 MET cc_start: 0.7922 (ttp) cc_final: 0.7285 (ptm) REVERT: A 106 GLN cc_start: 0.9738 (mm110) cc_final: 0.9292 (mm110) REVERT: A 208 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7735 (mtm110) REVERT: A 243 MET cc_start: 0.8705 (tpp) cc_final: 0.8463 (ttm) REVERT: A 269 ASN cc_start: 0.9192 (OUTLIER) cc_final: 0.8825 (t0) REVERT: A 310 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8490 (mm) REVERT: A 346 ASN cc_start: 0.8559 (t0) cc_final: 0.8310 (p0) REVERT: B 46 ARG cc_start: 0.8406 (mtp-110) cc_final: 0.7873 (mtp85) REVERT: B 135 VAL cc_start: 0.9393 (OUTLIER) cc_final: 0.9134 (p) REVERT: B 198 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8373 (pp) REVERT: B 215 GLU cc_start: 0.8659 (mp0) cc_final: 0.8097 (OUTLIER) REVERT: B 217 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8517 (pmm) REVERT: B 254 ASP cc_start: 0.8185 (t0) cc_final: 0.7732 (t0) REVERT: B 262 MET cc_start: 0.8981 (tpp) cc_final: 0.8511 (ttm) REVERT: B 286 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8696 (mt) REVERT: C 13 ARG cc_start: 0.9077 (mtm-85) cc_final: 0.8820 (mpp80) REVERT: C 17 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8948 (mm-30) REVERT: C 20 LYS cc_start: 0.9096 (mtmm) cc_final: 0.8686 (mtmm) REVERT: C 25 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.7998 (tt) REVERT: C 58 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8934 (mt-10) REVERT: D 19 LYS cc_start: 0.8780 (ttpp) cc_final: 0.8377 (ttmt) REVERT: D 89 GLU cc_start: 0.8184 (pm20) cc_final: 0.7757 (pm20) REVERT: D 206 ARG cc_start: 0.8682 (mtm-85) cc_final: 0.8374 (ttp-110) outliers start: 36 outliers final: 23 residues processed: 159 average time/residue: 0.5883 time to fit residues: 99.3462 Evaluate side-chains 161 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 302 VAL Chi-restraints excluded: chain R residue 308 VAL Chi-restraints excluded: chain R residue 328 TYR Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain R residue 358 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 102 optimal weight: 0.1980 chunk 119 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 365 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.094714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.064014 restraints weight = 19627.108| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.79 r_work: 0.2765 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10280 Z= 0.134 Angle : 0.687 13.346 13945 Z= 0.342 Chirality : 0.042 0.191 1583 Planarity : 0.003 0.043 1765 Dihedral : 5.216 76.460 1415 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.60 % Allowed : 24.03 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.24), residues: 1272 helix: 2.17 (0.24), residues: 484 sheet: -0.19 (0.31), residues: 272 loop : -0.58 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 96 TYR 0.014 0.001 TYR D 178 PHE 0.008 0.001 PHE B 151 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (10277) covalent geometry : angle 0.68668 / 0.34 (13939) SS BOND : bond 0.00921 / 0.64 ( 3) SS BOND : angle 1.71896 / 1.47 ( 6) hydrogen bonds : bond 0.03562 / 2.47 ( 516) hydrogen bonds : angle 4.54561 / 3.28 ( 1476) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 123 GLU cc_start: 0.9004 (tm-30) cc_final: 0.8382 (tt0) REVERT: R 129 TRP cc_start: 0.8635 (m100) cc_final: 0.7991 (m100) REVERT: R 175 LYS cc_start: 0.8413 (mppt) cc_final: 0.7982 (mmmm) REVERT: R 187 LYS cc_start: 0.7988 (mtpm) cc_final: 0.7598 (tttt) REVERT: R 207 MET cc_start: 0.8788 (mmm) cc_final: 0.8564 (mmm) REVERT: R 225 THR cc_start: 0.8898 (OUTLIER) cc_final: 0.8512 (m) REVERT: R 296 GLN cc_start: 0.8418 (mm110) cc_final: 0.8112 (tp-100) REVERT: A 53 MET cc_start: 0.8477 (mmp) cc_final: 0.8095 (mmp) REVERT: A 67 LYS cc_start: 0.9118 (mtpt) cc_final: 0.8771 (mmmm) REVERT: A 88 MET cc_start: 0.7847 (ttp) cc_final: 0.7303 (ptm) REVERT: A 208 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7720 (mtm110) REVERT: A 243 MET cc_start: 0.8736 (tpp) cc_final: 0.8484 (ttm) REVERT: A 269 ASN cc_start: 0.9138 (OUTLIER) cc_final: 0.8732 (t0) REVERT: A 310 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8565 (mm) REVERT: A 330 LYS cc_start: 0.9301 (mtpp) cc_final: 0.8855 (mppt) REVERT: A 346 ASN cc_start: 0.8557 (t0) cc_final: 0.8251 (p0) REVERT: B 46 ARG cc_start: 0.8427 (mtp-110) cc_final: 0.7889 (mtp85) REVERT: B 135 VAL cc_start: 0.9432 (OUTLIER) cc_final: 0.9178 (p) REVERT: B 198 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8372 (pp) REVERT: B 215 GLU cc_start: 0.8688 (mp0) cc_final: 0.8133 (OUTLIER) REVERT: B 217 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8608 (pmm) REVERT: B 254 ASP cc_start: 0.8134 (t0) cc_final: 0.7754 (t0) REVERT: B 262 MET cc_start: 0.8967 (tpp) cc_final: 0.8496 (ttm) REVERT: C 13 ARG cc_start: 0.9063 (mtm-85) cc_final: 0.8798 (mpp80) REVERT: C 25 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.8003 (tt) REVERT: C 58 GLU cc_start: 0.9296 (mt-10) cc_final: 0.8973 (mt-10) REVERT: D 73 ASP cc_start: 0.8101 (t0) cc_final: 0.7490 (t0) REVERT: D 76 LYS cc_start: 0.8909 (ptpp) cc_final: 0.8693 (ptpp) REVERT: D 89 GLU cc_start: 0.8189 (pm20) cc_final: 0.7755 (pm20) REVERT: D 129 THR cc_start: 0.9190 (m) cc_final: 0.8920 (p) REVERT: D 206 ARG cc_start: 0.8653 (mtm-85) cc_final: 0.8346 (ttp-110) outliers start: 28 outliers final: 14 residues processed: 151 average time/residue: 0.5782 time to fit residues: 93.0499 Evaluate side-chains 147 residues out of total 1098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 302 VAL Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain R residue 358 THR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 185 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 79 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 21 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 chunk 41 optimal weight: 0.0010 chunk 80 optimal weight: 5.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 365 ASN D 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.095812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.065250 restraints weight = 19788.238| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.80 r_work: 0.2787 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10280 Z= 0.128 Angle : 0.710 12.542 13945 Z= 0.350 Chirality : 0.042 0.303 1583 Planarity : 0.003 0.044 1765 Dihedral : 5.076 75.722 1415 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.86 % Allowed : 24.95 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.89 (0.24), residues: 1272 helix: 2.14 (0.24), residues: 486 sheet: -0.03 (0.31), residues: 281 loop : -0.54 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 8 TYR 0.014 0.001 TYR D 178 PHE 0.013 0.001 PHE A 108 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (10277) covalent geometry : angle 0.70913 / 0.35 (13939) SS BOND : bond 0.00793 / 0.55 ( 3) SS BOND : angle 1.56754 / 1.35 ( 6) hydrogen bonds : bond 0.03451 / 2.40 ( 516) hydrogen bonds : angle 4.47879 / 3.25 ( 1476) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3223.66 seconds wall clock time: 55 minutes 44.31 seconds (3344.31 seconds total)