Starting phenix.real_space_refine on Wed Feb 4 02:30:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vuz_32132/02_2026/7vuz_32132.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vuz_32132/02_2026/7vuz_32132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vuz_32132/02_2026/7vuz_32132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vuz_32132/02_2026/7vuz_32132.map" model { file = "/net/cci-nas-00/data/ceres_data/7vuz_32132/02_2026/7vuz_32132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vuz_32132/02_2026/7vuz_32132.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 64 5.16 5 C 5493 2.51 5 N 1439 2.21 5 O 1588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8584 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1995 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain: "A" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1750 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2598 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 427 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1786 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.07, per 1000 atoms: 0.24 Number of scatterers: 8584 At special positions: 0 Unit cell: (116.833, 114.347, 100.261, 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 64 16.00 O 1588 8.00 N 1439 7.00 C 5493 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.01 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.06 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 305.7 milliseconds 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2038 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 14 sheets defined 36.4% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'R' and resid 36 through 57 removed outlier: 3.521A pdb=" N LEU R 42 " --> pdb=" O LEU R 38 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL R 43 " --> pdb=" O PHE R 39 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL R 46 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N PHE R 50 " --> pdb=" O VAL R 46 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY R 56 " --> pdb=" O LEU R 52 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE R 57 " --> pdb=" O TRP R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 95 Processing helix chain 'R' and resid 103 through 133 removed outlier: 4.282A pdb=" N THR R 107 " --> pdb=" O SER R 103 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 139 Processing helix chain 'R' and resid 144 through 168 Processing helix chain 'R' and resid 179 through 212 removed outlier: 3.946A pdb=" N PHE R 183 " --> pdb=" O TRP R 179 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY R 212 " --> pdb=" O ARG R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 235 Processing helix chain 'R' and resid 236 through 245 removed outlier: 3.861A pdb=" N GLY R 240 " --> pdb=" O GLY R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 251 removed outlier: 3.658A pdb=" N LYS R 251 " --> pdb=" O LEU R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 260 removed outlier: 3.715A pdb=" N HIS R 259 " --> pdb=" O VAL R 255 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 279 Proline residue: R 276 - end of helix Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 208 through 214 Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.580A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.965A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.568A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 4.034A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.927A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN B 36 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.730A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.532A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.187A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.680A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.680A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.858A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.965A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.876A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.706A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.708A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.909A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.193A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.193A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 129 through 130 removed outlier: 3.899A pdb=" N PHE S 200 " --> pdb=" O CYS S 147 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER S 194 " --> pdb=" O THR S 201 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.895A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR S 231 " --> pdb=" O TYR S 215 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR S 216 " --> pdb=" O PHE S 165 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET S 218 " --> pdb=" O TYR S 163 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU S 166 " --> pdb=" O GLN S 174 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2523 1.34 - 1.46: 2378 1.46 - 1.59: 3780 1.59 - 1.72: 1 1.72 - 1.85: 89 Bond restraints: 8771 Sorted by residual: bond pdb=" C PRO R 238 " pdb=" N PHE R 239 " ideal model delta sigma weight residual 1.335 1.471 -0.137 1.31e-02 5.83e+03 1.09e+02 bond pdb=" C GLY R 236 " pdb=" N LEU R 237 " ideal model delta sigma weight residual 1.331 1.440 -0.109 2.07e-02 2.33e+03 2.77e+01 bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.626 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" C LEU R 237 " pdb=" N PRO R 238 " ideal model delta sigma weight residual 1.336 1.372 -0.036 1.20e-02 6.94e+03 9.25e+00 bond pdb=" CG LEU B 146 " pdb=" CD2 LEU B 146 " ideal model delta sigma weight residual 1.521 1.422 0.099 3.30e-02 9.18e+02 8.99e+00 ... (remaining 8766 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.08: 11385 3.08 - 6.15: 414 6.15 - 9.23: 64 9.23 - 12.31: 22 12.31 - 15.38: 3 Bond angle restraints: 11888 Sorted by residual: angle pdb=" N ASP R 254 " pdb=" CA ASP R 254 " pdb=" C ASP R 254 " ideal model delta sigma weight residual 111.28 120.50 -9.22 1.09e+00 8.42e-01 7.16e+01 angle pdb=" C ASN R 275 " pdb=" N PRO R 276 " pdb=" CA PRO R 276 " ideal model delta sigma weight residual 119.47 111.39 8.08 1.16e+00 7.43e-01 4.86e+01 angle pdb=" CA PRO R 276 " pdb=" N PRO R 276 " pdb=" CD PRO R 276 " ideal model delta sigma weight residual 112.00 102.58 9.42 1.40e+00 5.10e-01 4.53e+01 angle pdb=" N GLN B 17 " pdb=" CA GLN B 17 " pdb=" CB GLN B 17 " ideal model delta sigma weight residual 110.16 119.85 -9.69 1.48e+00 4.57e-01 4.29e+01 angle pdb=" N PRO R 276 " pdb=" CA PRO R 276 " pdb=" C PRO R 276 " ideal model delta sigma weight residual 113.81 123.17 -9.36 1.45e+00 4.76e-01 4.17e+01 ... (remaining 11883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.51: 4518 14.51 - 29.02: 538 29.02 - 43.54: 128 43.54 - 58.05: 18 58.05 - 72.56: 10 Dihedral angle restraints: 5212 sinusoidal: 2050 harmonic: 3162 Sorted by residual: dihedral pdb=" CA PHE R 172 " pdb=" C PHE R 172 " pdb=" N SER R 173 " pdb=" CA SER R 173 " ideal model delta harmonic sigma weight residual -180.00 -137.80 -42.20 0 5.00e+00 4.00e-02 7.12e+01 dihedral pdb=" CA GLY B 185 " pdb=" C GLY B 185 " pdb=" N ASP B 186 " pdb=" CA ASP B 186 " ideal model delta harmonic sigma weight residual 180.00 150.37 29.63 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 150.85 29.15 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 5209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 1212 0.122 - 0.244: 124 0.244 - 0.366: 13 0.366 - 0.488: 2 0.488 - 0.610: 3 Chirality restraints: 1354 Sorted by residual: chirality pdb=" CA PRO R 276 " pdb=" N PRO R 276 " pdb=" C PRO R 276 " pdb=" CB PRO R 276 " both_signs ideal model delta sigma weight residual False 2.72 2.11 0.61 2.00e-01 2.50e+01 9.30e+00 chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.02 -0.61 2.00e-01 2.50e+01 9.30e+00 chirality pdb=" CB VAL B 296 " pdb=" CA VAL B 296 " pdb=" CG1 VAL B 296 " pdb=" CG2 VAL B 296 " both_signs ideal model delta sigma weight residual False -2.63 -2.08 -0.55 2.00e-01 2.50e+01 7.54e+00 ... (remaining 1351 not shown) Planarity restraints: 1489 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 275 " 0.134 5.00e-02 4.00e+02 2.01e-01 6.47e+01 pdb=" N PRO R 276 " -0.348 5.00e-02 4.00e+02 pdb=" CA PRO R 276 " 0.104 5.00e-02 4.00e+02 pdb=" CD PRO R 276 " 0.110 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER R 273 " 0.020 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C SER R 273 " -0.071 2.00e-02 2.50e+03 pdb=" O SER R 273 " 0.027 2.00e-02 2.50e+03 pdb=" N ALA R 274 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 230 " -0.016 2.00e-02 2.50e+03 2.66e-02 1.41e+01 pdb=" CG TYR A 230 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR A 230 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A 230 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR A 230 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 230 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 230 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 230 " 0.002 2.00e-02 2.50e+03 ... (remaining 1486 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 88 2.61 - 3.18: 6696 3.18 - 3.75: 13745 3.75 - 4.33: 18610 4.33 - 4.90: 31109 Nonbonded interactions: 70248 Sorted by model distance: nonbonded pdb=" O CYS R 258 " pdb=" CD PRO R 262 " model vdw 2.035 3.440 nonbonded pdb=" OD1 ASN R 48 " pdb=" CG PRO R 276 " model vdw 2.170 3.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.286 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.294 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.295 3.040 ... (remaining 70243 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: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.740 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 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 : 0.010 0.137 8775 Z= 0.459 Angle : 1.398 15.384 11896 Z= 0.755 Chirality : 0.082 0.610 1354 Planarity : 0.010 0.201 1489 Dihedral : 13.540 72.560 3162 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.39 % Allowed : 1.28 % Favored : 97.33 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.23), residues: 1081 helix: -2.11 (0.22), residues: 355 sheet: -1.33 (0.30), residues: 276 loop : -1.94 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.002 ARG S 98 TYR 0.064 0.005 TYR A 230 PHE 0.035 0.004 PHE R 50 TRP 0.032 0.004 TRP R 133 HIS 0.026 0.004 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.01002 ( 8771) covalent geometry : angle 1.39514 (11888) SS BOND : bond 0.01987 ( 4) SS BOND : angle 3.64219 ( 8) hydrogen bonds : bond 0.20174 ( 405) hydrogen bonds : angle 8.25884 ( 1188) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 203 time to evaluate : 0.235 Fit side-chains REVERT: R 234 LEU cc_start: 0.8434 (mt) cc_final: 0.8093 (mp) REVERT: R 252 ASP cc_start: 0.7053 (OUTLIER) cc_final: 0.6711 (m-30) REVERT: A 294 ASN cc_start: 0.6673 (m110) cc_final: 0.6360 (t0) REVERT: A 318 GLU cc_start: 0.6400 (tp30) cc_final: 0.6000 (tp30) REVERT: S 206 ARG cc_start: 0.7390 (mmt-90) cc_final: 0.7145 (mmp80) outliers start: 13 outliers final: 4 residues processed: 214 average time/residue: 0.6430 time to fit residues: 145.4540 Evaluate side-chains 153 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 148 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 252 ASP Chi-restraints excluded: chain R residue 265 VAL Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 271 ASN Chi-restraints excluded: chain R residue 276 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 30.0000 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 82 GLN R 275 ASN A 52 GLN A 331 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS B 259 GLN B 268 ASN S 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.194158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.153444 restraints weight = 10692.155| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 2.95 r_work: 0.4030 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8775 Z= 0.161 Angle : 0.718 8.454 11896 Z= 0.371 Chirality : 0.047 0.346 1354 Planarity : 0.005 0.055 1489 Dihedral : 6.973 72.625 1254 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.53 % Allowed : 13.89 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.24), residues: 1081 helix: -0.21 (0.26), residues: 360 sheet: -1.16 (0.30), residues: 273 loop : -1.59 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 21 TYR 0.014 0.002 TYR S 223 PHE 0.012 0.001 PHE S 29 TRP 0.030 0.002 TRP B 82 HIS 0.007 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 8771) covalent geometry : angle 0.71710 (11888) SS BOND : bond 0.01152 ( 4) SS BOND : angle 1.75574 ( 8) hydrogen bonds : bond 0.04797 ( 405) hydrogen bonds : angle 5.46474 ( 1188) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 0.362 Fit side-chains REVERT: R 196 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8205 (ttp) REVERT: R 199 CYS cc_start: 0.7064 (p) cc_final: 0.6840 (m) REVERT: A 294 ASN cc_start: 0.6738 (m110) cc_final: 0.6531 (t0) REVERT: A 318 GLU cc_start: 0.6394 (tp30) cc_final: 0.5902 (tp30) REVERT: B 19 ARG cc_start: 0.7469 (mtm110) cc_final: 0.7123 (ttp-170) REVERT: B 59 TYR cc_start: 0.7505 (m-80) cc_final: 0.6675 (m-80) REVERT: B 75 GLN cc_start: 0.7457 (tt0) cc_final: 0.7165 (tt0) REVERT: B 304 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7659 (mmm-85) REVERT: G 37 LEU cc_start: 0.7746 (mm) cc_final: 0.7541 (mm) REVERT: S 163 TYR cc_start: 0.5992 (m-80) cc_final: 0.5756 (m-80) REVERT: S 206 ARG cc_start: 0.7561 (mmt-90) cc_final: 0.7260 (tpp-160) outliers start: 33 outliers final: 9 residues processed: 194 average time/residue: 0.5764 time to fit residues: 119.3976 Evaluate side-chains 163 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 196 MET Chi-restraints excluded: chain R residue 241 ILE Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 88 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 97 optimal weight: 50.0000 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 261 HIS A 304 GLN A 331 ASN B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 59 ASN S 159 ASN S 182 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.186992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.145623 restraints weight = 10868.992| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 2.90 r_work: 0.3920 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 8775 Z= 0.282 Angle : 0.797 8.549 11896 Z= 0.407 Chirality : 0.051 0.346 1354 Planarity : 0.005 0.058 1489 Dihedral : 6.752 75.271 1246 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 4.38 % Allowed : 18.27 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.25), residues: 1081 helix: 0.28 (0.26), residues: 366 sheet: -1.28 (0.29), residues: 276 loop : -1.60 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 21 TYR 0.025 0.002 TYR S 163 PHE 0.022 0.002 PHE B 151 TRP 0.030 0.002 TRP B 82 HIS 0.007 0.002 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00662 ( 8771) covalent geometry : angle 0.79456 (11888) SS BOND : bond 0.01149 ( 4) SS BOND : angle 2.28915 ( 8) hydrogen bonds : bond 0.05187 ( 405) hydrogen bonds : angle 5.44320 ( 1188) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 167 time to evaluate : 0.357 Fit side-chains REVERT: R 199 CYS cc_start: 0.7104 (p) cc_final: 0.6791 (m) REVERT: R 234 LEU cc_start: 0.8470 (mt) cc_final: 0.8206 (mp) REVERT: R 243 TRP cc_start: 0.6752 (t-100) cc_final: 0.6113 (t-100) REVERT: A 25 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6800 (tp30) REVERT: A 33 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.6476 (mp0) REVERT: A 241 ASN cc_start: 0.7964 (m-40) cc_final: 0.7501 (t0) REVERT: A 318 GLU cc_start: 0.6613 (tp30) cc_final: 0.6136 (tp30) REVERT: B 19 ARG cc_start: 0.7452 (mtm110) cc_final: 0.7050 (ttp80) REVERT: B 59 TYR cc_start: 0.7441 (m-80) cc_final: 0.6848 (m-80) REVERT: B 75 GLN cc_start: 0.7551 (tt0) cc_final: 0.7299 (tt0) REVERT: B 82 TRP cc_start: 0.7923 (OUTLIER) cc_final: 0.7339 (m-10) REVERT: G 27 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.4339 (mtt-85) REVERT: S 163 TYR cc_start: 0.6170 (m-80) cc_final: 0.5857 (m-80) REVERT: S 206 ARG cc_start: 0.7708 (mmt-90) cc_final: 0.7382 (tpp-160) outliers start: 41 outliers final: 17 residues processed: 188 average time/residue: 0.5504 time to fit residues: 110.9524 Evaluate side-chains 171 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 241 ILE Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 134 SER Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 84 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 56 optimal weight: 0.0770 chunk 37 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 97 optimal weight: 40.0000 chunk 53 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.195396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.155020 restraints weight = 10801.274| |-----------------------------------------------------------------------------| r_work (start): 0.4214 rms_B_bonded: 2.92 r_work: 0.4078 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8775 Z= 0.133 Angle : 0.659 8.605 11896 Z= 0.333 Chirality : 0.045 0.331 1354 Planarity : 0.004 0.042 1489 Dihedral : 6.299 75.470 1246 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.85 % Allowed : 21.15 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.26), residues: 1081 helix: 0.94 (0.27), residues: 364 sheet: -1.08 (0.30), residues: 270 loop : -1.38 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 21 TYR 0.013 0.001 TYR S 223 PHE 0.015 0.001 PHE R 104 TRP 0.029 0.002 TRP B 82 HIS 0.008 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8771) covalent geometry : angle 0.65831 (11888) SS BOND : bond 0.00552 ( 4) SS BOND : angle 1.24223 ( 8) hydrogen bonds : bond 0.03992 ( 405) hydrogen bonds : angle 4.90399 ( 1188) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: R 158 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7552 (tt) REVERT: R 199 CYS cc_start: 0.7105 (p) cc_final: 0.6726 (m) REVERT: R 234 LEU cc_start: 0.8300 (mt) cc_final: 0.8063 (mp) REVERT: R 243 TRP cc_start: 0.6689 (t-100) cc_final: 0.6340 (t-100) REVERT: A 25 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6678 (tp30) REVERT: A 33 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6056 (mp0) REVERT: A 53 MET cc_start: 0.7957 (mpt) cc_final: 0.7387 (mpt) REVERT: A 241 ASN cc_start: 0.7927 (m-40) cc_final: 0.7415 (t160) REVERT: A 318 GLU cc_start: 0.6470 (tp30) cc_final: 0.6077 (tp30) REVERT: B 15 LYS cc_start: 0.7231 (mmmt) cc_final: 0.6952 (tppp) REVERT: B 19 ARG cc_start: 0.7230 (mtm110) cc_final: 0.6902 (ttp80) REVERT: B 59 TYR cc_start: 0.7407 (m-80) cc_final: 0.6770 (m-80) REVERT: B 75 GLN cc_start: 0.7406 (tt0) cc_final: 0.7092 (tt0) REVERT: B 135 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8369 (p) REVERT: B 262 MET cc_start: 0.7038 (mmt) cc_final: 0.6737 (mmm) REVERT: S 206 ARG cc_start: 0.7642 (mmt-90) cc_final: 0.7284 (tpp-160) outliers start: 36 outliers final: 14 residues processed: 186 average time/residue: 0.5318 time to fit residues: 106.2201 Evaluate side-chains 177 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 33 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 261 HIS R 275 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN S 159 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.189692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.149512 restraints weight = 10903.269| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 2.73 r_work: 0.4098 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 8775 Z= 0.234 Angle : 0.729 8.754 11896 Z= 0.371 Chirality : 0.048 0.342 1354 Planarity : 0.004 0.049 1489 Dihedral : 6.432 75.813 1246 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.49 % Allowed : 22.65 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.26), residues: 1081 helix: 0.94 (0.27), residues: 365 sheet: -1.11 (0.30), residues: 277 loop : -1.42 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 313 TYR 0.018 0.002 TYR S 59 PHE 0.018 0.002 PHE B 151 TRP 0.025 0.002 TRP B 82 HIS 0.008 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00551 ( 8771) covalent geometry : angle 0.72769 (11888) SS BOND : bond 0.00938 ( 4) SS BOND : angle 1.87550 ( 8) hydrogen bonds : bond 0.04584 ( 405) hydrogen bonds : angle 5.10917 ( 1188) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 156 time to evaluate : 0.338 Fit side-chains REVERT: R 158 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7828 (tt) REVERT: R 199 CYS cc_start: 0.7279 (p) cc_final: 0.6822 (m) REVERT: R 243 TRP cc_start: 0.7117 (t-100) cc_final: 0.6838 (t-100) REVERT: A 25 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.7003 (tp30) REVERT: A 33 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.6469 (mp0) REVERT: A 53 MET cc_start: 0.7877 (mpt) cc_final: 0.7484 (mpt) REVERT: A 241 ASN cc_start: 0.7829 (m-40) cc_final: 0.7546 (t160) REVERT: A 318 GLU cc_start: 0.6684 (tp30) cc_final: 0.6391 (tp30) REVERT: B 15 LYS cc_start: 0.7513 (mmmt) cc_final: 0.7180 (tppp) REVERT: B 19 ARG cc_start: 0.7371 (mtm110) cc_final: 0.6966 (ttp80) REVERT: B 59 TYR cc_start: 0.7522 (m-80) cc_final: 0.6934 (m-80) REVERT: G 37 LEU cc_start: 0.8031 (mm) cc_final: 0.7822 (mm) REVERT: S 206 ARG cc_start: 0.7691 (mmt-90) cc_final: 0.7449 (tpp-160) outliers start: 42 outliers final: 23 residues processed: 180 average time/residue: 0.5324 time to fit residues: 102.6226 Evaluate side-chains 180 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 241 ILE Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 275 ASN Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 134 SER Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 98 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 261 HIS ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.186078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.144552 restraints weight = 10865.767| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 2.86 r_work: 0.3911 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 8775 Z= 0.284 Angle : 0.786 8.833 11896 Z= 0.400 Chirality : 0.051 0.345 1354 Planarity : 0.004 0.050 1489 Dihedral : 6.544 75.488 1246 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.70 % Allowed : 23.61 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.25), residues: 1081 helix: 0.83 (0.27), residues: 365 sheet: -1.23 (0.30), residues: 277 loop : -1.51 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 21 TYR 0.019 0.002 TYR S 59 PHE 0.021 0.002 PHE B 151 TRP 0.026 0.002 TRP B 82 HIS 0.007 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00669 ( 8771) covalent geometry : angle 0.78442 (11888) SS BOND : bond 0.01093 ( 4) SS BOND : angle 2.11120 ( 8) hydrogen bonds : bond 0.04859 ( 405) hydrogen bonds : angle 5.25809 ( 1188) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 155 time to evaluate : 0.402 Fit side-chains REVERT: R 158 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7667 (tt) REVERT: R 199 CYS cc_start: 0.7195 (p) cc_final: 0.6690 (m) REVERT: R 243 TRP cc_start: 0.6738 (t-100) cc_final: 0.6072 (t-100) REVERT: A 25 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6714 (tp30) REVERT: A 33 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6425 (mp0) REVERT: A 53 MET cc_start: 0.7889 (mpt) cc_final: 0.7423 (mpt) REVERT: A 296 TYR cc_start: 0.7105 (p90) cc_final: 0.6866 (p90) REVERT: A 318 GLU cc_start: 0.6624 (tp30) cc_final: 0.6206 (tp30) REVERT: B 4 LEU cc_start: 0.4883 (OUTLIER) cc_final: 0.4479 (tt) REVERT: B 15 LYS cc_start: 0.7276 (mmmt) cc_final: 0.6985 (tppp) REVERT: B 19 ARG cc_start: 0.7256 (mtm110) cc_final: 0.6871 (ttp80) REVERT: B 172 GLU cc_start: 0.7711 (pm20) cc_final: 0.7374 (pm20) REVERT: B 262 MET cc_start: 0.7396 (mmt) cc_final: 0.6843 (mmm) REVERT: G 37 LEU cc_start: 0.7985 (mm) cc_final: 0.7751 (mm) REVERT: S 70 ILE cc_start: 0.6870 (OUTLIER) cc_final: 0.6580 (tt) REVERT: S 206 ARG cc_start: 0.7712 (mmt-90) cc_final: 0.7316 (tpp-160) outliers start: 44 outliers final: 29 residues processed: 180 average time/residue: 0.5200 time to fit residues: 100.8692 Evaluate side-chains 177 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 241 ILE Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 134 SER Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 79 optimal weight: 0.1980 chunk 12 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 99 optimal weight: 0.3980 chunk 66 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 261 HIS R 275 ASN B 16 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.195033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.154081 restraints weight = 10759.541| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 2.92 r_work: 0.4077 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8775 Z= 0.137 Angle : 0.679 9.735 11896 Z= 0.342 Chirality : 0.045 0.352 1354 Planarity : 0.004 0.041 1489 Dihedral : 6.039 75.342 1246 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.95 % Allowed : 25.85 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.26), residues: 1081 helix: 1.23 (0.28), residues: 366 sheet: -1.09 (0.29), residues: 283 loop : -1.19 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 21 TYR 0.014 0.001 TYR S 223 PHE 0.020 0.001 PHE R 244 TRP 0.029 0.002 TRP B 82 HIS 0.009 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8771) covalent geometry : angle 0.67862 (11888) SS BOND : bond 0.00499 ( 4) SS BOND : angle 1.32969 ( 8) hydrogen bonds : bond 0.03901 ( 405) hydrogen bonds : angle 4.79063 ( 1188) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 163 time to evaluate : 0.340 Fit side-chains REVERT: R 199 CYS cc_start: 0.7149 (p) cc_final: 0.6643 (m) REVERT: A 25 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6653 (tp30) REVERT: A 53 MET cc_start: 0.7677 (mpt) cc_final: 0.7348 (mpt) REVERT: A 232 LEU cc_start: 0.7668 (tt) cc_final: 0.7427 (pp) REVERT: A 241 ASN cc_start: 0.7916 (m-40) cc_final: 0.7492 (t0) REVERT: A 305 CYS cc_start: 0.8096 (m) cc_final: 0.7551 (m) REVERT: A 318 GLU cc_start: 0.6473 (tp30) cc_final: 0.6155 (tp30) REVERT: B 15 LYS cc_start: 0.7237 (mmmt) cc_final: 0.6931 (tppp) REVERT: B 16 ASN cc_start: 0.8771 (m-40) cc_final: 0.8400 (m110) REVERT: B 19 ARG cc_start: 0.7189 (mtm110) cc_final: 0.6856 (ttp80) REVERT: B 135 VAL cc_start: 0.8590 (OUTLIER) cc_final: 0.8340 (p) REVERT: B 172 GLU cc_start: 0.7612 (pm20) cc_final: 0.7406 (pm20) REVERT: B 189 SER cc_start: 0.7989 (p) cc_final: 0.7510 (t) REVERT: G 37 LEU cc_start: 0.7874 (mm) cc_final: 0.7548 (mm) REVERT: S 206 ARG cc_start: 0.7662 (mmt-90) cc_final: 0.7158 (tpp-160) REVERT: S 234 GLU cc_start: 0.6114 (pm20) cc_final: 0.5615 (pm20) outliers start: 37 outliers final: 15 residues processed: 188 average time/residue: 0.4990 time to fit residues: 101.1704 Evaluate side-chains 171 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 241 ILE Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 275 ASN Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 134 SER Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 14 optimal weight: 50.0000 chunk 100 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 275 ASN A 195 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.191918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.150552 restraints weight = 10680.258| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 2.93 r_work: 0.3984 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8775 Z= 0.158 Angle : 0.697 9.989 11896 Z= 0.352 Chirality : 0.047 0.370 1354 Planarity : 0.004 0.045 1489 Dihedral : 6.047 75.862 1246 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.06 % Allowed : 27.24 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.26), residues: 1081 helix: 1.32 (0.27), residues: 365 sheet: -0.95 (0.30), residues: 273 loop : -1.19 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 21 TYR 0.026 0.002 TYR A 230 PHE 0.018 0.001 PHE R 244 TRP 0.025 0.002 TRP B 82 HIS 0.008 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 8771) covalent geometry : angle 0.69599 (11888) SS BOND : bond 0.00619 ( 4) SS BOND : angle 1.41036 ( 8) hydrogen bonds : bond 0.04035 ( 405) hydrogen bonds : angle 4.79523 ( 1188) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: R 199 CYS cc_start: 0.7022 (p) cc_final: 0.6531 (m) REVERT: A 25 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6523 (tp30) REVERT: A 33 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6192 (mp0) REVERT: A 53 MET cc_start: 0.7579 (mpt) cc_final: 0.7254 (mpt) REVERT: A 232 LEU cc_start: 0.7542 (tt) cc_final: 0.7287 (pp) REVERT: A 296 TYR cc_start: 0.7023 (p90) cc_final: 0.6572 (p90) REVERT: A 305 CYS cc_start: 0.8056 (m) cc_final: 0.7532 (m) REVERT: A 318 GLU cc_start: 0.6415 (tp30) cc_final: 0.5996 (tp30) REVERT: B 4 LEU cc_start: 0.4700 (OUTLIER) cc_final: 0.4367 (tt) REVERT: B 15 LYS cc_start: 0.7014 (mmmt) cc_final: 0.6695 (tppp) REVERT: B 16 ASN cc_start: 0.8786 (m-40) cc_final: 0.8525 (m110) REVERT: B 19 ARG cc_start: 0.7055 (mtm110) cc_final: 0.6751 (ttp80) REVERT: B 135 VAL cc_start: 0.8560 (OUTLIER) cc_final: 0.8354 (p) REVERT: B 189 SER cc_start: 0.7903 (p) cc_final: 0.7367 (t) REVERT: G 37 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7526 (mm) REVERT: S 206 ARG cc_start: 0.7594 (mmt-90) cc_final: 0.7212 (tpp-160) REVERT: S 234 GLU cc_start: 0.6187 (pm20) cc_final: 0.5862 (pm20) outliers start: 38 outliers final: 24 residues processed: 176 average time/residue: 0.5241 time to fit residues: 99.2304 Evaluate side-chains 170 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 241 ILE Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain R residue 272 SER Chi-restraints excluded: chain R residue 275 ASN Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 92 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 chunk 39 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 84 optimal weight: 0.0470 chunk 65 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.0480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.196844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.155798 restraints weight = 10635.528| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 2.92 r_work: 0.4104 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8775 Z= 0.139 Angle : 0.699 11.678 11896 Z= 0.349 Chirality : 0.046 0.356 1354 Planarity : 0.003 0.041 1489 Dihedral : 5.934 75.954 1246 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.95 % Allowed : 27.67 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.26), residues: 1081 helix: 1.45 (0.28), residues: 365 sheet: -0.89 (0.30), residues: 277 loop : -1.05 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 21 TYR 0.015 0.001 TYR S 223 PHE 0.018 0.001 PHE R 244 TRP 0.028 0.002 TRP A 211 HIS 0.009 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8771) covalent geometry : angle 0.69897 (11888) SS BOND : bond 0.00562 ( 4) SS BOND : angle 1.22034 ( 8) hydrogen bonds : bond 0.03795 ( 405) hydrogen bonds : angle 4.64048 ( 1188) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 153 time to evaluate : 0.351 Fit side-chains REVERT: R 199 CYS cc_start: 0.7128 (p) cc_final: 0.6611 (m) REVERT: R 243 TRP cc_start: 0.6893 (t-100) cc_final: 0.6312 (t-100) REVERT: R 259 HIS cc_start: 0.6458 (OUTLIER) cc_final: 0.6074 (t70) REVERT: A 25 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6613 (tp30) REVERT: A 33 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6295 (mp0) REVERT: A 305 CYS cc_start: 0.8091 (m) cc_final: 0.7565 (m) REVERT: A 318 GLU cc_start: 0.6557 (tp30) cc_final: 0.6164 (tp30) REVERT: B 4 LEU cc_start: 0.4721 (OUTLIER) cc_final: 0.4377 (tt) REVERT: B 16 ASN cc_start: 0.8810 (m-40) cc_final: 0.8496 (m110) REVERT: B 19 ARG cc_start: 0.7043 (mtm110) cc_final: 0.6826 (ttp80) REVERT: B 135 VAL cc_start: 0.8537 (OUTLIER) cc_final: 0.8303 (p) REVERT: B 189 SER cc_start: 0.7895 (p) cc_final: 0.7480 (t) REVERT: B 262 MET cc_start: 0.6979 (OUTLIER) cc_final: 0.6461 (mmm) REVERT: G 37 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7555 (mm) REVERT: S 34 MET cc_start: 0.5963 (tpp) cc_final: 0.5740 (mmm) REVERT: S 206 ARG cc_start: 0.7535 (mmt-90) cc_final: 0.7229 (tpp80) REVERT: S 234 GLU cc_start: 0.6070 (pm20) cc_final: 0.5795 (pm20) outliers start: 37 outliers final: 22 residues processed: 176 average time/residue: 0.4990 time to fit residues: 94.7907 Evaluate side-chains 177 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 241 ILE Chi-restraints excluded: chain R residue 259 HIS Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 103 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 75 optimal weight: 0.8980 chunk 98 optimal weight: 30.0000 chunk 29 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.194542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.152927 restraints weight = 10711.379| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 2.96 r_work: 0.4064 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8775 Z= 0.165 Angle : 0.731 11.208 11896 Z= 0.363 Chirality : 0.047 0.398 1354 Planarity : 0.004 0.044 1489 Dihedral : 6.031 76.356 1245 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.74 % Allowed : 28.10 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.26), residues: 1081 helix: 1.37 (0.28), residues: 365 sheet: -0.89 (0.30), residues: 280 loop : -1.06 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 21 TYR 0.024 0.002 TYR A 230 PHE 0.031 0.001 PHE S 227 TRP 0.042 0.002 TRP A 211 HIS 0.009 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 8771) covalent geometry : angle 0.73015 (11888) SS BOND : bond 0.00642 ( 4) SS BOND : angle 1.46641 ( 8) hydrogen bonds : bond 0.03973 ( 405) hydrogen bonds : angle 4.74063 ( 1188) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 0.333 Fit side-chains REVERT: R 199 CYS cc_start: 0.7133 (p) cc_final: 0.6626 (m) REVERT: R 243 TRP cc_start: 0.6930 (t-100) cc_final: 0.6347 (t-100) REVERT: R 259 HIS cc_start: 0.6523 (OUTLIER) cc_final: 0.6139 (t70) REVERT: A 25 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6615 (tp30) REVERT: A 33 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6304 (mp0) REVERT: A 305 CYS cc_start: 0.8089 (m) cc_final: 0.7554 (m) REVERT: A 318 GLU cc_start: 0.6576 (tp30) cc_final: 0.6150 (tp30) REVERT: B 4 LEU cc_start: 0.4701 (OUTLIER) cc_final: 0.4336 (tt) REVERT: B 16 ASN cc_start: 0.8783 (m-40) cc_final: 0.8490 (m110) REVERT: B 19 ARG cc_start: 0.7078 (mtm110) cc_final: 0.6840 (ttp80) REVERT: B 135 VAL cc_start: 0.8596 (OUTLIER) cc_final: 0.8390 (p) REVERT: B 189 SER cc_start: 0.7910 (p) cc_final: 0.7478 (t) REVERT: B 262 MET cc_start: 0.6944 (OUTLIER) cc_final: 0.6454 (mmm) REVERT: G 37 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7577 (mm) REVERT: S 34 MET cc_start: 0.6040 (tpp) cc_final: 0.5760 (mmm) REVERT: S 206 ARG cc_start: 0.7494 (mmt-90) cc_final: 0.7227 (tpp80) REVERT: S 234 GLU cc_start: 0.6082 (pm20) cc_final: 0.5821 (pm20) outliers start: 35 outliers final: 21 residues processed: 169 average time/residue: 0.5257 time to fit residues: 95.4586 Evaluate side-chains 170 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 222 TYR Chi-restraints excluded: chain R residue 241 ILE Chi-restraints excluded: chain R residue 259 HIS Chi-restraints excluded: chain R residue 263 VAL Chi-restraints excluded: chain R residue 267 LEU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 159 ASN Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 58 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.192855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.151826 restraints weight = 10769.521| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 2.82 r_work: 0.4031 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8775 Z= 0.204 Angle : 0.774 11.629 11896 Z= 0.385 Chirality : 0.049 0.425 1354 Planarity : 0.004 0.044 1489 Dihedral : 6.164 76.672 1245 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.31 % Allowed : 29.38 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.26), residues: 1081 helix: 1.34 (0.28), residues: 363 sheet: -1.00 (0.29), residues: 288 loop : -1.10 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 256 TYR 0.018 0.002 TYR S 223 PHE 0.045 0.002 PHE S 227 TRP 0.049 0.002 TRP A 211 HIS 0.009 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 8771) covalent geometry : angle 0.77262 (11888) SS BOND : bond 0.00771 ( 4) SS BOND : angle 1.63010 ( 8) hydrogen bonds : bond 0.04298 ( 405) hydrogen bonds : angle 4.86308 ( 1188) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3863.55 seconds wall clock time: 66 minutes 46.08 seconds (4006.08 seconds total)