Starting phenix.real_space_refine on Sat Jul 26 05:53:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z9o_39865/07_2025/8z9o_39865.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z9o_39865/07_2025/8z9o_39865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z9o_39865/07_2025/8z9o_39865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z9o_39865/07_2025/8z9o_39865.map" model { file = "/net/cci-nas-00/data/ceres_data/8z9o_39865/07_2025/8z9o_39865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z9o_39865/07_2025/8z9o_39865.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 5270 2.51 5 N 1443 2.21 5 O 1514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8279 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2558 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN%COO:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 1829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1829 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 213} Chain breaks: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 431 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG%COO:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 956 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2448 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 290} Chain: "R" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2, 'water': 1} Link IDs: {None: 2} Time building chain proxies: 5.24, per 1000 atoms: 0.63 Number of scatterers: 8279 At special positions: 0 Unit cell: (75.33, 101.37, 133.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1514 8.00 N 1443 7.00 C 5270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 9 " - pdb=" SG CYS R 258 " distance=2.03 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 168 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.1 seconds 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1964 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 11 sheets defined 42.6% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 12 through 39 removed outlier: 3.657A pdb=" N GLU C 16 " --> pdb=" O GLN C 12 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C 39 " --> pdb=" O GLN C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 239 removed outlier: 3.583A pdb=" N GLN C 236 " --> pdb=" O LYS C 233 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN C 239 " --> pdb=" O GLN C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 278 Processing helix chain 'C' and resid 293 through 303 Processing helix chain 'C' and resid 307 through 311 Processing helix chain 'C' and resid 312 through 318 removed outlier: 3.636A pdb=" N ALA C 316 " --> pdb=" O PRO C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 352 removed outlier: 3.768A pdb=" N THR C 335 " --> pdb=" O ASP C 331 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N SER C 352 " --> pdb=" O ILE C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 391 Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.955A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 18 through 47 Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 50 through 69 removed outlier: 3.766A pdb=" N VAL R 54 " --> pdb=" O ASN R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 79 removed outlier: 3.767A pdb=" N TYR R 76 " --> pdb=" O LEU R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 121 removed outlier: 3.612A pdb=" N TYR R 98 " --> pdb=" O GLY R 94 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE R 101 " --> pdb=" O PHE R 97 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE R 105 " --> pdb=" O ILE R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 129 Processing helix chain 'R' and resid 130 through 149 Processing helix chain 'R' and resid 150 through 155 Processing helix chain 'R' and resid 175 through 188 Processing helix chain 'R' and resid 190 through 210 Processing helix chain 'R' and resid 215 through 254 removed outlier: 3.519A pdb=" N CYS R 236 " --> pdb=" O ILE R 232 " (cutoff:3.500A) Proline residue: R 239 - end of helix Processing helix chain 'R' and resid 259 through 289 removed outlier: 5.469A pdb=" N SER R 266 " --> pdb=" O GLU R 262 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ALA R 267 " --> pdb=" O ARG R 263 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N HIS R 269 " --> pdb=" O PHE R 265 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER R 270 " --> pdb=" O SER R 266 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER R 276 " --> pdb=" O LEU R 272 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU R 277 " --> pdb=" O ALA R 273 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASN R 278 " --> pdb=" O PHE R 274 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N CYS R 279 " --> pdb=" O THR R 275 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 290 through 310 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.499A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.891A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.821A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.758A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.816A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.610A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.325A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 207 through 214 removed outlier: 3.663A pdb=" N PHE C 219 " --> pdb=" O PHE C 212 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL C 224 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 9.372A pdb=" N ALA C 243 " --> pdb=" O THR C 40 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ARG C 42 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE C 245 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU C 44 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL C 247 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LEU C 46 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ALA C 249 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE C 244 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N PHE C 290 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N PHE C 246 " --> pdb=" O PHE C 290 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ASN C 292 " --> pdb=" O PHE C 246 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL C 248 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL C 287 " --> pdb=" O TYR C 360 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N HIS C 362 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU C 289 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.283A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 158 through 160 432 hydrogen bonds defined for protein. 1221 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.22 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2217 1.33 - 1.45: 1656 1.45 - 1.57: 4521 1.57 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 8464 Sorted by residual: bond pdb=" C PRO R 20 " pdb=" N PRO R 21 " ideal model delta sigma weight residual 1.335 1.426 -0.091 1.30e-02 5.92e+03 4.86e+01 bond pdb=" CA TRP R 73 " pdb=" C TRP R 73 " ideal model delta sigma weight residual 1.519 1.468 0.051 1.19e-02 7.06e+03 1.83e+01 bond pdb=" N TRP R 73 " pdb=" CA TRP R 73 " ideal model delta sigma weight residual 1.458 1.403 0.054 1.35e-02 5.49e+03 1.60e+01 bond pdb=" CG HIS R 79 " pdb=" ND1 HIS R 79 " ideal model delta sigma weight residual 1.378 1.335 0.043 1.10e-02 8.26e+03 1.54e+01 bond pdb=" CG HIS R 85 " pdb=" ND1 HIS R 85 " ideal model delta sigma weight residual 1.378 1.335 0.043 1.10e-02 8.26e+03 1.50e+01 ... (remaining 8459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 11256 2.48 - 4.96: 196 4.96 - 7.45: 26 7.45 - 9.93: 7 9.93 - 12.41: 1 Bond angle restraints: 11486 Sorted by residual: angle pdb=" N TRP R 73 " pdb=" CA TRP R 73 " pdb=" C TRP R 73 " ideal model delta sigma weight residual 113.43 101.02 12.41 1.26e+00 6.30e-01 9.70e+01 angle pdb=" CA HIS R 10 " pdb=" CB HIS R 10 " pdb=" CG HIS R 10 " ideal model delta sigma weight residual 113.80 106.27 7.53 1.00e+00 1.00e+00 5.67e+01 angle pdb=" C PRO R 20 " pdb=" N PRO R 21 " pdb=" CA PRO R 21 " ideal model delta sigma weight residual 118.97 124.57 -5.60 1.04e+00 9.25e-01 2.90e+01 angle pdb=" CA HIS R 80 " pdb=" CB HIS R 80 " pdb=" CG HIS R 80 " ideal model delta sigma weight residual 113.80 109.12 4.68 1.00e+00 1.00e+00 2.19e+01 angle pdb=" CA HIS R 79 " pdb=" CB HIS R 79 " pdb=" CG HIS R 79 " ideal model delta sigma weight residual 113.80 109.19 4.61 1.00e+00 1.00e+00 2.13e+01 ... (remaining 11481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4680 17.93 - 35.85: 366 35.85 - 53.78: 49 53.78 - 71.71: 15 71.71 - 89.63: 7 Dihedral angle restraints: 5117 sinusoidal: 2080 harmonic: 3037 Sorted by residual: dihedral pdb=" CA PHE R 172 " pdb=" C PHE R 172 " pdb=" N PRO R 173 " pdb=" CA PRO R 173 " ideal model delta harmonic sigma weight residual 0.00 -28.46 28.46 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CB CYS R 9 " pdb=" SG CYS R 9 " pdb=" SG CYS R 258 " pdb=" CB CYS R 258 " ideal model delta sinusoidal sigma weight residual -86.00 -45.99 -40.01 1 1.00e+01 1.00e-02 2.25e+01 dihedral pdb=" CA PHE R 307 " pdb=" C PHE R 307 " pdb=" N LEU R 308 " pdb=" CA LEU R 308 " ideal model delta harmonic sigma weight residual 180.00 160.77 19.23 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 5114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1220 0.105 - 0.210: 55 0.210 - 0.314: 2 0.314 - 0.419: 2 0.419 - 0.524: 2 Chirality restraints: 1281 Sorted by residual: chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.84 0.52 2.00e-01 2.50e+01 6.85e+00 chirality pdb=" C14 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C15 CLR R 402 " pdb=" C8 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.84 0.52 2.00e-01 2.50e+01 6.72e+00 chirality pdb=" C10 CLR R 401 " pdb=" C1 CLR R 401 " pdb=" C5 CLR R 401 " pdb=" C9 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.85 -2.49 -0.36 2.00e-01 2.50e+01 3.23e+00 ... (remaining 1278 not shown) Planarity restraints: 1463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO R 20 " 0.043 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO R 21 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO R 21 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO R 21 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 188 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.84e+00 pdb=" C VAL R 188 " 0.045 2.00e-02 2.50e+03 pdb=" O VAL R 188 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY R 189 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 285 " 0.012 2.00e-02 2.50e+03 2.53e-02 6.39e+00 pdb=" C LEU R 285 " -0.044 2.00e-02 2.50e+03 pdb=" O LEU R 285 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR R 286 " 0.015 2.00e-02 2.50e+03 ... (remaining 1460 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 925 2.74 - 3.28: 8148 3.28 - 3.82: 14102 3.82 - 4.36: 17285 4.36 - 4.90: 29353 Nonbonded interactions: 69813 Sorted by model distance: nonbonded pdb=" O LEU R 146 " pdb=" OG SER R 150 " model vdw 2.203 3.040 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.251 3.040 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.275 3.120 nonbonded pdb=" OG SER B 147 " pdb=" OG SER B 160 " model vdw 2.290 3.040 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.298 3.040 ... (remaining 69808 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.350 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:11.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 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 : 0.006 0.091 8468 Z= 0.340 Angle : 0.818 12.408 11494 Z= 0.504 Chirality : 0.055 0.524 1281 Planarity : 0.005 0.066 1463 Dihedral : 13.392 89.632 3141 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.23), residues: 1026 helix: -0.82 (0.22), residues: 396 sheet: -0.35 (0.34), residues: 219 loop : -1.94 (0.27), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 73 HIS 0.015 0.002 HIS C 357 PHE 0.024 0.002 PHE R 159 TYR 0.018 0.002 TYR R 76 ARG 0.005 0.000 ARG N 38 Details of bonding type rmsd hydrogen bonds : bond 0.16402 ( 432) hydrogen bonds : angle 6.91238 ( 1221) SS BOND : bond 0.00129 ( 4) SS BOND : angle 1.32677 ( 8) covalent geometry : bond 0.00596 ( 8464) covalent geometry : angle 0.81774 (11486) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7284 (ttp-110) cc_final: 0.6883 (ttm-80) REVERT: B 45 MET cc_start: 0.8628 (mtt) cc_final: 0.8123 (mtm) REVERT: B 219 ARG cc_start: 0.7566 (mmt180) cc_final: 0.7358 (mmt180) REVERT: C 35 GLN cc_start: 0.8086 (mt0) cc_final: 0.7843 (mm-40) REVERT: C 339 TYR cc_start: 0.8429 (m-80) cc_final: 0.8026 (m-80) REVERT: C 392 GLU cc_start: 0.7423 (mp0) cc_final: 0.7122 (mp0) REVERT: G 38 MET cc_start: 0.8050 (ttp) cc_final: 0.7833 (ttp) REVERT: R 57 MET cc_start: 0.7559 (ttt) cc_final: 0.7313 (tpp) REVERT: R 263 ARG cc_start: 0.7420 (mtp-110) cc_final: 0.6960 (mtp85) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 1.3415 time to fit residues: 294.8382 Evaluate side-chains 134 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 52 optimal weight: 0.0970 chunk 41 optimal weight: 0.4980 chunk 79 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 59 optimal weight: 0.0040 chunk 92 optimal weight: 1.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN B 266 HIS C 14 ASN C 294 GLN ** C 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 45 GLN R 100 ASN R 164 ASN R 217 GLN ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.178844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.120678 restraints weight = 7974.196| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.84 r_work: 0.3222 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8468 Z= 0.122 Angle : 0.553 7.422 11494 Z= 0.298 Chirality : 0.043 0.175 1281 Planarity : 0.005 0.057 1463 Dihedral : 5.438 53.225 1276 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.29 % Allowed : 11.00 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.25), residues: 1026 helix: 1.01 (0.26), residues: 397 sheet: -0.00 (0.34), residues: 218 loop : -1.20 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.008 0.001 HIS C 357 PHE 0.030 0.002 PHE R 307 TYR 0.012 0.001 TYR R 102 ARG 0.007 0.001 ARG R 44 Details of bonding type rmsd hydrogen bonds : bond 0.04489 ( 432) hydrogen bonds : angle 4.98224 ( 1221) SS BOND : bond 0.00083 ( 4) SS BOND : angle 1.09526 ( 8) covalent geometry : bond 0.00243 ( 8464) covalent geometry : angle 0.55283 (11486) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: B 44 GLN cc_start: 0.8396 (mt0) cc_final: 0.8182 (mp10) REVERT: B 45 MET cc_start: 0.8962 (mtt) cc_final: 0.8419 (mtm) REVERT: B 46 ARG cc_start: 0.8427 (mmt-90) cc_final: 0.8213 (mmt180) REVERT: B 134 ARG cc_start: 0.7487 (mmp-170) cc_final: 0.6624 (mmm160) REVERT: B 217 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8247 (pmt) REVERT: B 303 ASP cc_start: 0.7958 (m-30) cc_final: 0.7716 (m-30) REVERT: C 20 ARG cc_start: 0.6395 (mtm110) cc_final: 0.6022 (mtt90) REVERT: C 35 GLN cc_start: 0.8220 (mt0) cc_final: 0.7745 (mm-40) REVERT: C 339 TYR cc_start: 0.8493 (m-80) cc_final: 0.8170 (m-80) REVERT: N 76 LYS cc_start: 0.8668 (mtmt) cc_final: 0.8359 (mtmm) REVERT: R 14 ARG cc_start: 0.7171 (mmt90) cc_final: 0.6664 (ptp90) REVERT: R 57 MET cc_start: 0.7849 (ttt) cc_final: 0.7580 (tpp) REVERT: R 263 ARG cc_start: 0.7069 (mtp-110) cc_final: 0.6503 (mtp85) outliers start: 20 outliers final: 9 residues processed: 150 average time/residue: 1.4119 time to fit residues: 223.7932 Evaluate side-chains 135 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain R residue 150 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 36 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 155 ASN B 176 GLN B 220 GLN C 41 HIS N 3 GLN N 35 ASN R 47 GLN R 165 HIS ** R 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.174010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.111991 restraints weight = 7968.932| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.99 r_work: 0.3088 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8468 Z= 0.163 Angle : 0.581 7.086 11494 Z= 0.314 Chirality : 0.044 0.179 1281 Planarity : 0.005 0.062 1463 Dihedral : 5.537 47.376 1276 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.78 % Allowed : 12.71 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.26), residues: 1026 helix: 1.48 (0.26), residues: 397 sheet: 0.33 (0.35), residues: 211 loop : -0.95 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.008 0.001 HIS C 357 PHE 0.028 0.002 PHE R 307 TYR 0.012 0.002 TYR R 102 ARG 0.006 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.05026 ( 432) hydrogen bonds : angle 4.89837 ( 1221) SS BOND : bond 0.00153 ( 4) SS BOND : angle 1.44394 ( 8) covalent geometry : bond 0.00358 ( 8464) covalent geometry : angle 0.57948 (11486) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: B 23 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7595 (ttpp) REVERT: B 44 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7985 (mp10) REVERT: B 45 MET cc_start: 0.8968 (mtt) cc_final: 0.8367 (mtm) REVERT: B 134 ARG cc_start: 0.7666 (mmp-170) cc_final: 0.6698 (mmm160) REVERT: B 172 GLU cc_start: 0.8090 (tp30) cc_final: 0.7849 (tp30) REVERT: B 217 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8293 (pmt) REVERT: B 303 ASP cc_start: 0.8238 (m-30) cc_final: 0.8018 (m-30) REVERT: C 20 ARG cc_start: 0.6694 (mtm110) cc_final: 0.6258 (mtt90) REVERT: C 24 LYS cc_start: 0.7695 (mttm) cc_final: 0.6832 (ttpt) REVERT: C 25 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8120 (ttmm) REVERT: C 35 GLN cc_start: 0.8232 (mt0) cc_final: 0.7675 (mm-40) REVERT: C 60 MET cc_start: 0.3074 (tpt) cc_final: 0.2811 (tpt) REVERT: C 339 TYR cc_start: 0.8428 (m-80) cc_final: 0.7987 (m-80) REVERT: G 42 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: R 57 MET cc_start: 0.7728 (ttt) cc_final: 0.7421 (tpp) REVERT: R 155 HIS cc_start: 0.8212 (m-70) cc_final: 0.7988 (m-70) REVERT: R 263 ARG cc_start: 0.7124 (mtp-110) cc_final: 0.6606 (mtp85) outliers start: 33 outliers final: 14 residues processed: 157 average time/residue: 1.5963 time to fit residues: 266.9123 Evaluate side-chains 144 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain C residue 25 LYS Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 212 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 74 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 38 optimal weight: 0.4980 chunk 54 optimal weight: 3.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 176 GLN N 35 ASN R 47 GLN R 269 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.172890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.111464 restraints weight = 7924.121| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.95 r_work: 0.3083 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8468 Z= 0.167 Angle : 0.579 6.938 11494 Z= 0.313 Chirality : 0.044 0.181 1281 Planarity : 0.005 0.056 1463 Dihedral : 5.506 43.205 1276 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.12 % Allowed : 13.97 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.26), residues: 1026 helix: 1.66 (0.26), residues: 397 sheet: 0.58 (0.36), residues: 200 loop : -0.82 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.006 0.001 HIS C 357 PHE 0.026 0.002 PHE R 307 TYR 0.012 0.002 TYR R 102 ARG 0.007 0.000 ARG R 44 Details of bonding type rmsd hydrogen bonds : bond 0.04939 ( 432) hydrogen bonds : angle 4.83104 ( 1221) SS BOND : bond 0.00251 ( 4) SS BOND : angle 1.25884 ( 8) covalent geometry : bond 0.00366 ( 8464) covalent geometry : angle 0.57801 (11486) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7600 (ttpp) REVERT: B 46 ARG cc_start: 0.8339 (mmt180) cc_final: 0.8111 (mmp80) REVERT: B 134 ARG cc_start: 0.7702 (mmp-170) cc_final: 0.6933 (mmm160) REVERT: B 186 ASP cc_start: 0.8517 (p0) cc_final: 0.8154 (p0) REVERT: B 217 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8324 (pmt) REVERT: B 303 ASP cc_start: 0.8264 (m-30) cc_final: 0.8055 (m-30) REVERT: C 20 ARG cc_start: 0.6693 (mtm110) cc_final: 0.6256 (mtt90) REVERT: C 24 LYS cc_start: 0.7711 (mttm) cc_final: 0.6852 (ttpt) REVERT: C 25 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8110 (ttmm) REVERT: C 35 GLN cc_start: 0.8187 (mt0) cc_final: 0.7663 (mm-40) REVERT: C 339 TYR cc_start: 0.8450 (m-80) cc_final: 0.7983 (m-80) REVERT: G 42 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.6904 (mp0) REVERT: N 120 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8236 (mp10) REVERT: R 57 MET cc_start: 0.7725 (ttt) cc_final: 0.7455 (tpp) REVERT: R 155 HIS cc_start: 0.8119 (m-70) cc_final: 0.7799 (m-70) REVERT: R 263 ARG cc_start: 0.7264 (mtp-110) cc_final: 0.6760 (mtp85) outliers start: 36 outliers final: 21 residues processed: 147 average time/residue: 1.4636 time to fit residues: 227.8020 Evaluate side-chains 148 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 25 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 212 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 98 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 31 optimal weight: 0.2980 chunk 68 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 93 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 69 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 176 GLN R 269 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.172976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.111582 restraints weight = 7884.269| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.94 r_work: 0.3083 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8468 Z= 0.158 Angle : 0.572 6.760 11494 Z= 0.308 Chirality : 0.044 0.192 1281 Planarity : 0.004 0.055 1463 Dihedral : 5.476 53.241 1276 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.01 % Allowed : 14.78 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.26), residues: 1026 helix: 1.76 (0.26), residues: 399 sheet: 0.58 (0.36), residues: 200 loop : -0.70 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS C 357 PHE 0.024 0.002 PHE N 108 TYR 0.012 0.002 TYR R 102 ARG 0.008 0.000 ARG R 14 Details of bonding type rmsd hydrogen bonds : bond 0.04789 ( 432) hydrogen bonds : angle 4.77060 ( 1221) SS BOND : bond 0.00250 ( 4) SS BOND : angle 1.07553 ( 8) covalent geometry : bond 0.00346 ( 8464) covalent geometry : angle 0.57113 (11486) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 0.754 Fit side-chains REVERT: B 23 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7571 (ttpp) REVERT: B 44 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.8032 (mp10) REVERT: B 46 ARG cc_start: 0.8386 (mmt180) cc_final: 0.8162 (mmp80) REVERT: B 134 ARG cc_start: 0.7702 (mmp-170) cc_final: 0.6966 (mmm160) REVERT: B 172 GLU cc_start: 0.7955 (tp30) cc_final: 0.7706 (mm-30) REVERT: B 217 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8384 (pmt) REVERT: C 20 ARG cc_start: 0.6741 (mtm110) cc_final: 0.6281 (mtt90) REVERT: C 24 LYS cc_start: 0.7744 (mttm) cc_final: 0.6910 (ttpt) REVERT: C 35 GLN cc_start: 0.8193 (mt0) cc_final: 0.7686 (mm-40) REVERT: C 339 TYR cc_start: 0.8426 (m-80) cc_final: 0.7998 (m-80) REVERT: G 42 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.6823 (mp0) REVERT: N 5 GLN cc_start: 0.8101 (mt0) cc_final: 0.7347 (mm-40) REVERT: N 38 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8411 (ttm170) REVERT: N 73 ASP cc_start: 0.8501 (t0) cc_final: 0.8077 (t0) REVERT: N 120 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8234 (mp10) REVERT: R 25 ILE cc_start: 0.7615 (mt) cc_final: 0.7339 (mm) REVERT: R 127 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.6421 (ptt90) REVERT: R 155 HIS cc_start: 0.8175 (m-70) cc_final: 0.7822 (m-70) REVERT: R 206 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7470 (ptp90) REVERT: R 263 ARG cc_start: 0.7290 (mtp-110) cc_final: 0.6773 (mtp85) outliers start: 35 outliers final: 19 residues processed: 146 average time/residue: 1.5453 time to fit residues: 237.7748 Evaluate side-chains 155 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 127 ARG Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 206 ARG Chi-restraints excluded: chain R residue 212 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 7 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 96 optimal weight: 0.3980 chunk 41 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 48 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 175 GLN B 176 GLN R 47 GLN R 269 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.173919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.112809 restraints weight = 7898.114| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.95 r_work: 0.3099 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8468 Z= 0.134 Angle : 0.545 6.618 11494 Z= 0.294 Chirality : 0.043 0.197 1281 Planarity : 0.004 0.053 1463 Dihedral : 5.321 54.468 1276 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.24 % Allowed : 15.01 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.26), residues: 1026 helix: 1.92 (0.26), residues: 399 sheet: 0.59 (0.35), residues: 200 loop : -0.67 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS C 41 PHE 0.021 0.002 PHE R 307 TYR 0.011 0.001 TYR R 102 ARG 0.007 0.000 ARG R 14 Details of bonding type rmsd hydrogen bonds : bond 0.04508 ( 432) hydrogen bonds : angle 4.65139 ( 1221) SS BOND : bond 0.00241 ( 4) SS BOND : angle 0.87488 ( 8) covalent geometry : bond 0.00288 ( 8464) covalent geometry : angle 0.54437 (11486) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 133 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7580 (ttpp) REVERT: B 44 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7912 (mp10) REVERT: B 134 ARG cc_start: 0.7719 (mmp-170) cc_final: 0.7009 (mmm160) REVERT: B 172 GLU cc_start: 0.7978 (tp30) cc_final: 0.7756 (mm-30) REVERT: B 217 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8415 (pmt) REVERT: C 20 ARG cc_start: 0.6716 (mtm110) cc_final: 0.6258 (mtt90) REVERT: C 24 LYS cc_start: 0.7695 (mttm) cc_final: 0.6798 (ttpt) REVERT: C 35 GLN cc_start: 0.8191 (mt0) cc_final: 0.7674 (mm-40) REVERT: C 339 TYR cc_start: 0.8392 (m-80) cc_final: 0.8004 (m-80) REVERT: N 5 GLN cc_start: 0.8137 (mt0) cc_final: 0.7371 (mm-40) REVERT: N 38 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8392 (ttm170) REVERT: N 73 ASP cc_start: 0.8530 (t0) cc_final: 0.8091 (t0) REVERT: R 127 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.6410 (ptt90) REVERT: R 155 HIS cc_start: 0.8195 (m-70) cc_final: 0.7856 (m-70) REVERT: R 206 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7476 (ptp90) REVERT: R 263 ARG cc_start: 0.7291 (mtp-110) cc_final: 0.6698 (mtp85) REVERT: R 269 HIS cc_start: 0.7295 (m-70) cc_final: 0.6970 (m90) outliers start: 37 outliers final: 21 residues processed: 154 average time/residue: 1.3482 time to fit residues: 219.2994 Evaluate side-chains 154 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 127 ARG Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 206 ARG Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 280 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 44 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 51 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 176 GLN C 357 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.173070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.111613 restraints weight = 7920.744| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.96 r_work: 0.3085 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8468 Z= 0.154 Angle : 0.569 6.548 11494 Z= 0.308 Chirality : 0.043 0.204 1281 Planarity : 0.004 0.052 1463 Dihedral : 5.428 57.664 1276 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.44 % Allowed : 16.27 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.26), residues: 1026 helix: 1.92 (0.26), residues: 399 sheet: 0.59 (0.35), residues: 200 loop : -0.62 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS C 357 PHE 0.021 0.002 PHE N 108 TYR 0.012 0.002 TYR R 102 ARG 0.007 0.000 ARG R 14 Details of bonding type rmsd hydrogen bonds : bond 0.04728 ( 432) hydrogen bonds : angle 4.68695 ( 1221) SS BOND : bond 0.00389 ( 4) SS BOND : angle 1.67985 ( 8) covalent geometry : bond 0.00335 ( 8464) covalent geometry : angle 0.56781 (11486) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 23 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7559 (ttpp) REVERT: B 44 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7999 (mp10) REVERT: B 134 ARG cc_start: 0.7678 (mmp-170) cc_final: 0.6994 (mmm160) REVERT: B 172 GLU cc_start: 0.7957 (tp30) cc_final: 0.7728 (mm-30) REVERT: B 217 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8414 (pmt) REVERT: B 237 ASN cc_start: 0.7682 (t0) cc_final: 0.7439 (t0) REVERT: C 20 ARG cc_start: 0.6747 (mtm110) cc_final: 0.6275 (mtt90) REVERT: C 24 LYS cc_start: 0.7698 (mttm) cc_final: 0.6809 (ttpt) REVERT: C 35 GLN cc_start: 0.8168 (mt0) cc_final: 0.7642 (mm-40) REVERT: C 339 TYR cc_start: 0.8395 (m-80) cc_final: 0.7967 (m-80) REVERT: N 5 GLN cc_start: 0.8113 (mt0) cc_final: 0.7337 (mm-40) REVERT: N 38 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8395 (ttm170) REVERT: N 73 ASP cc_start: 0.8527 (t0) cc_final: 0.8083 (t0) REVERT: R 127 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.6477 (ptt90) REVERT: R 155 HIS cc_start: 0.8171 (m-70) cc_final: 0.7821 (m-70) REVERT: R 206 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7482 (ptp90) REVERT: R 263 ARG cc_start: 0.7284 (mtp-110) cc_final: 0.6696 (mtp85) REVERT: R 269 HIS cc_start: 0.7272 (m-70) cc_final: 0.6961 (m90) outliers start: 30 outliers final: 21 residues processed: 141 average time/residue: 1.8835 time to fit residues: 280.6213 Evaluate side-chains 149 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 127 ARG Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 206 ARG Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 280 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 40 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 0.0010 chunk 47 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.173293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.111942 restraints weight = 7972.236| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.95 r_work: 0.3092 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8468 Z= 0.144 Angle : 0.557 6.290 11494 Z= 0.301 Chirality : 0.043 0.211 1281 Planarity : 0.004 0.051 1463 Dihedral : 5.366 58.906 1276 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.55 % Allowed : 16.49 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.26), residues: 1026 helix: 1.96 (0.26), residues: 399 sheet: 0.61 (0.35), residues: 200 loop : -0.62 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.007 0.001 HIS C 357 PHE 0.021 0.002 PHE N 108 TYR 0.012 0.001 TYR R 102 ARG 0.006 0.000 ARG R 44 Details of bonding type rmsd hydrogen bonds : bond 0.04623 ( 432) hydrogen bonds : angle 4.64892 ( 1221) SS BOND : bond 0.00229 ( 4) SS BOND : angle 1.43902 ( 8) covalent geometry : bond 0.00313 ( 8464) covalent geometry : angle 0.55630 (11486) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: B 23 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7532 (ttpp) REVERT: B 44 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.8046 (mp10) REVERT: B 46 ARG cc_start: 0.8435 (mmt180) cc_final: 0.8203 (mmp80) REVERT: B 134 ARG cc_start: 0.7717 (mmp-170) cc_final: 0.7067 (mmm160) REVERT: B 172 GLU cc_start: 0.7943 (tp30) cc_final: 0.7725 (mm-30) REVERT: B 197 ARG cc_start: 0.8277 (mtp-110) cc_final: 0.7813 (mmm160) REVERT: B 217 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8429 (pmt) REVERT: B 237 ASN cc_start: 0.7686 (t0) cc_final: 0.7430 (t0) REVERT: C 20 ARG cc_start: 0.6704 (mtm110) cc_final: 0.6250 (mtt90) REVERT: C 24 LYS cc_start: 0.7707 (mttm) cc_final: 0.6814 (ttpt) REVERT: C 35 GLN cc_start: 0.8165 (mt0) cc_final: 0.7645 (mm-40) REVERT: C 339 TYR cc_start: 0.8388 (m-80) cc_final: 0.7975 (m-80) REVERT: N 5 GLN cc_start: 0.8109 (mt0) cc_final: 0.7334 (mm-40) REVERT: N 38 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8372 (ttm170) REVERT: N 73 ASP cc_start: 0.8528 (t0) cc_final: 0.8095 (t0) REVERT: R 127 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.6429 (ptt90) REVERT: R 155 HIS cc_start: 0.8189 (m-70) cc_final: 0.7791 (m-70) REVERT: R 206 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7486 (ptp90) REVERT: R 263 ARG cc_start: 0.7244 (mtp-110) cc_final: 0.6639 (mtp85) REVERT: R 269 HIS cc_start: 0.7299 (m-70) cc_final: 0.7029 (m90) outliers start: 31 outliers final: 21 residues processed: 141 average time/residue: 1.8397 time to fit residues: 276.2313 Evaluate side-chains 150 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 127 ARG Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 206 ARG Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 280 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 84 optimal weight: 0.0670 chunk 29 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 175 GLN B 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.174948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.113974 restraints weight = 8027.246| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.96 r_work: 0.3122 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8468 Z= 0.117 Angle : 0.525 6.150 11494 Z= 0.283 Chirality : 0.042 0.213 1281 Planarity : 0.004 0.051 1463 Dihedral : 5.129 57.390 1276 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.75 % Allowed : 17.18 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.26), residues: 1026 helix: 2.09 (0.26), residues: 397 sheet: 0.58 (0.35), residues: 201 loop : -0.59 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS C 357 PHE 0.019 0.001 PHE R 307 TYR 0.011 0.001 TYR R 76 ARG 0.006 0.000 ARG R 44 Details of bonding type rmsd hydrogen bonds : bond 0.04217 ( 432) hydrogen bonds : angle 4.52556 ( 1221) SS BOND : bond 0.00211 ( 4) SS BOND : angle 1.10247 ( 8) covalent geometry : bond 0.00246 ( 8464) covalent geometry : angle 0.52391 (11486) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 2.257 Fit side-chains REVERT: B 23 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7491 (ttpp) REVERT: B 44 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.8016 (mp10) REVERT: B 46 ARG cc_start: 0.8426 (mmt180) cc_final: 0.8196 (mmp80) REVERT: B 134 ARG cc_start: 0.7685 (mmp-170) cc_final: 0.7215 (mmt180) REVERT: B 197 ARG cc_start: 0.8253 (mtp-110) cc_final: 0.7789 (mmm160) REVERT: B 217 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8451 (pmt) REVERT: C 20 ARG cc_start: 0.6709 (mtm110) cc_final: 0.6321 (ttm-80) REVERT: C 24 LYS cc_start: 0.7632 (mttm) cc_final: 0.6764 (ttpt) REVERT: C 35 GLN cc_start: 0.8112 (mt0) cc_final: 0.7603 (mm-40) REVERT: C 339 TYR cc_start: 0.8370 (m-80) cc_final: 0.8004 (m-80) REVERT: N 5 GLN cc_start: 0.8096 (mt0) cc_final: 0.7335 (mm-40) REVERT: N 73 ASP cc_start: 0.8508 (t0) cc_final: 0.8036 (t0) REVERT: R 57 MET cc_start: 0.7616 (ttp) cc_final: 0.7150 (mmm) REVERT: R 155 HIS cc_start: 0.8103 (m-70) cc_final: 0.7703 (m-70) REVERT: R 234 LEU cc_start: 0.7401 (tp) cc_final: 0.7187 (tp) REVERT: R 269 HIS cc_start: 0.7192 (m-70) cc_final: 0.6935 (m90) outliers start: 24 outliers final: 16 residues processed: 142 average time/residue: 2.3179 time to fit residues: 349.6386 Evaluate side-chains 147 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 280 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 36 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 72 optimal weight: 30.0000 chunk 61 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 175 GLN B 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.172770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.111559 restraints weight = 7922.420| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.94 r_work: 0.3085 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8468 Z= 0.158 Angle : 0.568 6.502 11494 Z= 0.308 Chirality : 0.044 0.214 1281 Planarity : 0.004 0.051 1463 Dihedral : 5.347 59.801 1276 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.41 % Allowed : 18.10 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.26), residues: 1026 helix: 2.01 (0.26), residues: 398 sheet: 0.61 (0.35), residues: 200 loop : -0.58 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.007 0.001 HIS C 357 PHE 0.021 0.002 PHE N 108 TYR 0.014 0.002 TYR R 76 ARG 0.006 0.000 ARG R 44 Details of bonding type rmsd hydrogen bonds : bond 0.04755 ( 432) hydrogen bonds : angle 4.70015 ( 1221) SS BOND : bond 0.00245 ( 4) SS BOND : angle 1.32705 ( 8) covalent geometry : bond 0.00348 ( 8464) covalent geometry : angle 0.56747 (11486) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.898 Fit side-chains REVERT: B 23 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7498 (ttpp) REVERT: B 44 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.8000 (mp10) REVERT: B 46 ARG cc_start: 0.8417 (mmt180) cc_final: 0.8186 (mmp80) REVERT: B 134 ARG cc_start: 0.7708 (mmp-170) cc_final: 0.7236 (mmt180) REVERT: B 197 ARG cc_start: 0.8276 (mtp-110) cc_final: 0.7798 (mmm160) REVERT: B 217 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8460 (pmt) REVERT: B 237 ASN cc_start: 0.7710 (t0) cc_final: 0.7443 (t0) REVERT: C 20 ARG cc_start: 0.6737 (mtm110) cc_final: 0.6350 (ttm-80) REVERT: C 24 LYS cc_start: 0.7711 (mttm) cc_final: 0.6834 (ttpt) REVERT: C 35 GLN cc_start: 0.8184 (mt0) cc_final: 0.7655 (mm-40) REVERT: C 339 TYR cc_start: 0.8392 (m-80) cc_final: 0.8022 (m-80) REVERT: N 5 GLN cc_start: 0.8069 (mt0) cc_final: 0.7321 (mm-40) REVERT: N 73 ASP cc_start: 0.8523 (t0) cc_final: 0.8141 (t0) REVERT: R 14 ARG cc_start: 0.6702 (mtm-85) cc_final: 0.5574 (pmm150) REVERT: R 25 ILE cc_start: 0.7387 (mt) cc_final: 0.7181 (mp) REVERT: R 127 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.6370 (ptt90) REVERT: R 155 HIS cc_start: 0.8126 (m-70) cc_final: 0.7789 (m-70) REVERT: R 234 LEU cc_start: 0.7482 (tp) cc_final: 0.7265 (tp) REVERT: R 269 HIS cc_start: 0.7231 (m-70) cc_final: 0.6958 (m90) outliers start: 21 outliers final: 17 residues processed: 137 average time/residue: 1.4076 time to fit residues: 203.6328 Evaluate side-chains 146 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain R residue 127 ARG Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 280 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 27 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.172199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.110822 restraints weight = 7977.194| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.95 r_work: 0.3076 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8468 Z= 0.169 Angle : 0.582 6.777 11494 Z= 0.315 Chirality : 0.044 0.217 1281 Planarity : 0.004 0.050 1463 Dihedral : 5.417 59.330 1276 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.52 % Allowed : 18.21 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.26), residues: 1026 helix: 1.96 (0.26), residues: 398 sheet: 0.59 (0.35), residues: 200 loop : -0.60 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.008 0.001 HIS C 357 PHE 0.022 0.002 PHE N 108 TYR 0.014 0.002 TYR R 76 ARG 0.006 0.000 ARG R 44 Details of bonding type rmsd hydrogen bonds : bond 0.04880 ( 432) hydrogen bonds : angle 4.74017 ( 1221) SS BOND : bond 0.00276 ( 4) SS BOND : angle 1.36620 ( 8) covalent geometry : bond 0.00375 ( 8464) covalent geometry : angle 0.58158 (11486) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10214.16 seconds wall clock time: 183 minutes 22.84 seconds (11002.84 seconds total)