Starting phenix.real_space_refine on Wed Mar 4 04:04:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vgz_31981/03_2026/7vgz_31981_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vgz_31981/03_2026/7vgz_31981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vgz_31981/03_2026/7vgz_31981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vgz_31981/03_2026/7vgz_31981.map" model { file = "/net/cci-nas-00/data/ceres_data/7vgz_31981/03_2026/7vgz_31981_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vgz_31981/03_2026/7vgz_31981_neut.cif" } resolution = 3.3 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2159 atoms to isotropic. 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 61 5.16 5 C 5631 2.51 5 N 1476 2.21 5 O 1622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8790 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2242 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1751 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2584 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 404 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1762 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Unusual residues: {'CLR': 1, 'JEV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.27, per 1000 atoms: 0.26 Number of scatterers: 8790 At special positions: 0 Unit cell: (90.47, 116.2, 125.33, 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 61 16.00 O 1622 8.00 N 1476 7.00 C 5631 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 177 " distance=2.03 Simple disulfide: pdb=" SG CYS D 121 " - pdb=" SG CYS D 149 " distance=2.04 Simple disulfide: pdb=" SG CYS F 159 " - pdb=" SG CYS F 229 " 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: 0.71 Conformation dependent library (CDL) restraints added in 352.2 milliseconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 14 sheets defined 39.1% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'B' and resid 23 through 55 Processing helix chain 'B' and resid 63 through 75 Processing helix chain 'B' and resid 79 through 91 Processing helix chain 'B' and resid 96 through 130 removed outlier: 3.754A pdb=" N SER B 103 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 105 " --> pdb=" O GLN B 101 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 139 Processing helix chain 'B' and resid 140 through 160 removed outlier: 3.614A pdb=" N LEU B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 166 Processing helix chain 'B' and resid 184 through 194 removed outlier: 3.550A pdb=" N THR B 188 " --> pdb=" O SER B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 220 removed outlier: 4.089A pdb=" N VAL B 203 " --> pdb=" O PRO B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 240 Processing helix chain 'B' and resid 240 through 245 Processing helix chain 'B' and resid 246 through 251 removed outlier: 3.790A pdb=" N CYS B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP B 251 " --> pdb=" O PHE B 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 246 through 251' Processing helix chain 'B' and resid 251 through 264 removed outlier: 3.833A pdb=" N LEU B 259 " --> pdb=" O ASN B 255 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 removed outlier: 3.960A pdb=" N VAL B 269 " --> pdb=" O PRO B 265 " (cutoff:3.500A) Proline residue: B 270 - end of helix Processing helix chain 'B' and resid 273 through 295 removed outlier: 3.524A pdb=" N PHE B 277 " --> pdb=" O PRO B 273 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N CYS B 289 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA B 292 " --> pdb=" O SER B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 313 removed outlier: 3.933A pdb=" N GLU B 305 " --> pdb=" O ASN B 301 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ARG B 307 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ARG B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 33 removed outlier: 3.510A pdb=" N ALA C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ARG C 24 " --> pdb=" O ASP C 20 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 55 removed outlier: 3.537A pdb=" N ILE C 55 " --> pdb=" O LYS C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 211 Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.770A pdb=" N GLU C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.899A pdb=" N ILE C 285 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 309 removed outlier: 3.551A pdb=" N ASP C 309 " --> pdb=" O CYS C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 352 Processing helix chain 'D' and resid 4 through 26 Processing helix chain 'D' and resid 29 through 35 Processing helix chain 'E' and resid 10 through 24 removed outlier: 3.736A pdb=" N ASN E 24 " --> pdb=" O LYS E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 Processing helix chain 'E' and resid 45 through 48 Processing helix chain 'F' and resid 53 through 56 removed outlier: 3.819A pdb=" N GLY F 56 " --> pdb=" O SER F 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 53 through 56' Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.509A pdb=" N THR F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 168 through 171 removed outlier: 3.506A pdb=" N GLN B 169 " --> pdb=" O THR B 178 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 185 through 187 removed outlier: 6.600A pdb=" N LEU C 36 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU C 39 " --> pdb=" O CYS C 224 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ALA C 226 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 47 through 51 removed outlier: 6.834A pdb=" N ILE D 338 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR D 50 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU D 336 " --> pdb=" O THR D 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 58 through 63 removed outlier: 4.121A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU D 79 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA D 92 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE D 81 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 100 through 105 removed outlier: 6.939A pdb=" N GLY D 115 " --> pdb=" O MET D 101 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N CYS D 103 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA D 113 " --> pdb=" O CYS D 103 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N TYR D 105 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N TYR D 111 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N CYS D 121 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N GLU D 138 " --> pdb=" O CYS D 121 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE D 123 " --> pdb=" O SER D 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 150 through 151 removed outlier: 3.756A pdb=" N ILE D 157 " --> pdb=" O TRP D 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 187 through 192 removed outlier: 6.576A pdb=" N GLY D 202 " --> pdb=" O MET D 188 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU D 190 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL D 200 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU D 192 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU D 198 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE D 199 " --> pdb=" O TRP D 211 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER D 207 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN D 220 " --> pdb=" O LEU D 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 229 through 234 removed outlier: 3.501A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 273 through 276 removed outlier: 6.558A pdb=" N GLY D 288 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL D 276 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU D 286 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASP D 298 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG D 304 " --> pdb=" O ASP D 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.203A pdb=" N GLY F 10 " --> pdb=" O THR F 118 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU F 117 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA F 92 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N MET F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N TYR F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.203A pdb=" N GLY F 10 " --> pdb=" O THR F 118 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU F 117 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA F 92 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE F 110 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 140 through 142 Processing sheet with id=AB5, first strand: chain 'F' and resid 146 through 148 removed outlier: 3.858A pdb=" N GLU F 246 " --> pdb=" O VAL F 147 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU F 174 " --> pdb=" O TYR F 190 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N TYR F 190 " --> pdb=" O LEU F 174 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TRP F 176 " --> pdb=" O LEU F 188 " (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: 1.46 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1419 1.31 - 1.44: 2495 1.44 - 1.56: 4981 1.56 - 1.69: 0 1.69 - 1.82: 87 Bond restraints: 8982 Sorted by residual: bond pdb=" CA TYR B 126 " pdb=" C TYR B 126 " ideal model delta sigma weight residual 1.523 1.437 0.087 1.30e-02 5.92e+03 4.45e+01 bond pdb=" C3 JEV B 401 " pdb=" N1 JEV B 401 " ideal model delta sigma weight residual 1.344 1.449 -0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" C15 JEV B 401 " pdb=" O1 JEV B 401 " ideal model delta sigma weight residual 1.439 1.351 0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" CA TYR B 281 " pdb=" C TYR B 281 " ideal model delta sigma weight residual 1.522 1.464 0.058 1.38e-02 5.25e+03 1.79e+01 bond pdb=" N TYR B 282 " pdb=" CA TYR B 282 " ideal model delta sigma weight residual 1.457 1.404 0.053 1.27e-02 6.20e+03 1.74e+01 ... (remaining 8977 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 11879 1.88 - 3.76: 247 3.76 - 5.64: 54 5.64 - 7.51: 11 7.51 - 9.39: 2 Bond angle restraints: 12193 Sorted by residual: angle pdb=" N TYR B 126 " pdb=" CA TYR B 126 " pdb=" C TYR B 126 " ideal model delta sigma weight residual 111.28 101.89 9.39 1.09e+00 8.42e-01 7.43e+01 angle pdb=" N PHE B 237 " pdb=" CA PHE B 237 " pdb=" C PHE B 237 " ideal model delta sigma weight residual 111.28 104.76 6.52 1.09e+00 8.42e-01 3.58e+01 angle pdb=" C TYR B 282 " pdb=" CA TYR B 282 " pdb=" CB TYR B 282 " ideal model delta sigma weight residual 109.24 118.49 -9.25 1.75e+00 3.27e-01 2.80e+01 angle pdb=" N ARG B 235 " pdb=" CA ARG B 235 " pdb=" C ARG B 235 " ideal model delta sigma weight residual 111.28 106.09 5.19 1.09e+00 8.42e-01 2.27e+01 angle pdb=" N TYR B 282 " pdb=" CA TYR B 282 " pdb=" C TYR B 282 " ideal model delta sigma weight residual 113.41 107.63 5.78 1.22e+00 6.72e-01 2.24e+01 ... (remaining 12188 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.85: 5081 24.85 - 49.69: 249 49.69 - 74.54: 26 74.54 - 99.39: 3 99.39 - 124.23: 3 Dihedral angle restraints: 5362 sinusoidal: 2093 harmonic: 3269 Sorted by residual: dihedral pdb=" CB CYS D 121 " pdb=" SG CYS D 121 " pdb=" SG CYS D 149 " pdb=" CB CYS D 149 " ideal model delta sinusoidal sigma weight residual 93.00 167.31 -74.31 1 1.00e+01 1.00e-02 7.00e+01 dihedral pdb=" CB CYS B 100 " pdb=" SG CYS B 100 " pdb=" SG CYS B 177 " pdb=" CB CYS B 177 " ideal model delta sinusoidal sigma weight residual -86.00 -124.54 38.54 1 1.00e+01 1.00e-02 2.09e+01 dihedral pdb=" C1 CLR B 402 " pdb=" C2 CLR B 402 " pdb=" C3 CLR B 402 " pdb=" O1 CLR B 402 " ideal model delta sinusoidal sigma weight residual 180.04 55.81 124.23 1 3.00e+01 1.11e-03 1.67e+01 ... (remaining 5359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1255 0.076 - 0.152: 127 0.152 - 0.229: 3 0.229 - 0.305: 4 0.305 - 0.381: 2 Chirality restraints: 1391 Sorted by residual: chirality pdb=" CA CYS B 127 " pdb=" N CYS B 127 " pdb=" C CYS B 127 " pdb=" CB CYS B 127 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CA TYR B 282 " pdb=" N TYR B 282 " pdb=" C TYR B 282 " pdb=" CB TYR B 282 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CA TYR B 281 " pdb=" N TYR B 281 " pdb=" C TYR B 281 " pdb=" CB TYR B 281 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 1388 not shown) Planarity restraints: 1532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 279 " 0.027 2.00e-02 2.50e+03 5.49e-02 3.02e+01 pdb=" C ALA B 279 " -0.095 2.00e-02 2.50e+03 pdb=" O ALA B 279 " 0.036 2.00e-02 2.50e+03 pdb=" N SER B 280 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 193 " -0.019 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C VAL B 193 " 0.062 2.00e-02 2.50e+03 pdb=" O VAL B 193 " -0.023 2.00e-02 2.50e+03 pdb=" N PHE B 194 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 150 " -0.043 5.00e-02 4.00e+02 6.59e-02 6.94e+00 pdb=" N PRO F 151 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO F 151 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO F 151 " -0.036 5.00e-02 4.00e+02 ... (remaining 1529 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 217 2.69 - 3.24: 8642 3.24 - 3.79: 13989 3.79 - 4.35: 18367 4.35 - 4.90: 31157 Nonbonded interactions: 72372 Sorted by model distance: nonbonded pdb=" OG SER D 331 " pdb=" OD1 ASP D 333 " model vdw 2.137 3.040 nonbonded pdb=" OG1 THR D 274 " pdb=" O VAL D 315 " model vdw 2.184 3.040 nonbonded pdb=" OG SER D 74 " pdb=" OD1 ASP D 76 " model vdw 2.193 3.040 nonbonded pdb=" OH TYR C 290 " pdb=" OE1 GLU C 298 " model vdw 2.251 3.040 nonbonded pdb=" O SER D 67 " pdb=" OG SER D 67 " model vdw 2.272 3.040 ... (remaining 72367 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: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.890 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 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 : 0.005 0.105 8985 Z= 0.299 Angle : 0.689 9.393 12199 Z= 0.395 Chirality : 0.048 0.381 1391 Planarity : 0.005 0.066 1532 Dihedral : 14.104 124.233 3247 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.21 % Allowed : 0.96 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.10 (0.26), residues: 1107 helix: 1.03 (0.28), residues: 386 sheet: -0.23 (0.32), residues: 276 loop : -0.85 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 19 TYR 0.019 0.002 TYR B 126 PHE 0.014 0.001 PHE B 196 TRP 0.012 0.001 TRP B 275 HIS 0.007 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00507 ( 8982) covalent geometry : angle 0.68926 (12193) SS BOND : bond 0.00388 ( 3) SS BOND : angle 0.97602 ( 6) hydrogen bonds : bond 0.17918 ( 420) hydrogen bonds : angle 6.94945 ( 1188) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 129 time to evaluate : 0.229 Fit side-chains REVERT: B 169 GLN cc_start: 0.6863 (pp30) cc_final: 0.6415 (pp30) REVERT: B 287 ASN cc_start: 0.8591 (t0) cc_final: 0.8280 (t0) REVERT: C 26 ASP cc_start: 0.8306 (m-30) cc_final: 0.8041 (m-30) REVERT: D 226 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7732 (mt-10) REVERT: E 18 GLN cc_start: 0.8012 (tp40) cc_final: 0.7650 (tp40) outliers start: 2 outliers final: 1 residues processed: 131 average time/residue: 0.1020 time to fit residues: 18.1742 Evaluate side-chains 105 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 238 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 ASN ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.102850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.076257 restraints weight = 19151.227| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.14 r_work: 0.3019 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8985 Z= 0.207 Angle : 0.625 9.868 12199 Z= 0.326 Chirality : 0.044 0.191 1391 Planarity : 0.004 0.055 1532 Dihedral : 7.358 87.095 1305 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.74 % Allowed : 9.45 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.04 (0.26), residues: 1107 helix: 1.26 (0.27), residues: 391 sheet: -0.38 (0.32), residues: 274 loop : -0.88 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 19 TYR 0.017 0.002 TYR B 282 PHE 0.016 0.002 PHE C 354 TRP 0.018 0.001 TRP D 82 HIS 0.005 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 8982) covalent geometry : angle 0.62409 (12193) SS BOND : bond 0.00564 ( 3) SS BOND : angle 1.65304 ( 6) hydrogen bonds : bond 0.04383 ( 420) hydrogen bonds : angle 5.13625 ( 1188) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.275 Fit side-chains REVERT: B 287 ASN cc_start: 0.8670 (t0) cc_final: 0.8331 (t0) REVERT: C 26 ASP cc_start: 0.8591 (m-30) cc_final: 0.8288 (m-30) REVERT: D 226 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8334 (mt-10) outliers start: 7 outliers final: 6 residues processed: 117 average time/residue: 0.1111 time to fit residues: 17.3812 Evaluate side-chains 108 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain F residue 17 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 46 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.103600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.076870 restraints weight = 19044.891| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 3.16 r_work: 0.3031 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8985 Z= 0.156 Angle : 0.577 9.346 12199 Z= 0.298 Chirality : 0.043 0.160 1391 Planarity : 0.004 0.050 1532 Dihedral : 5.528 50.221 1305 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.27 % Allowed : 11.68 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.04 (0.26), residues: 1107 helix: 1.39 (0.27), residues: 390 sheet: -0.39 (0.32), residues: 276 loop : -0.86 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 19 TYR 0.016 0.001 TYR B 282 PHE 0.016 0.001 PHE C 354 TRP 0.015 0.001 TRP D 82 HIS 0.003 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 8982) covalent geometry : angle 0.57584 (12193) SS BOND : bond 0.00698 ( 3) SS BOND : angle 1.56270 ( 6) hydrogen bonds : bond 0.03696 ( 420) hydrogen bonds : angle 4.83438 ( 1188) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.328 Fit side-chains REVERT: B 169 GLN cc_start: 0.6933 (pp30) cc_final: 0.6504 (pp30) REVERT: B 171 ASP cc_start: 0.7523 (t70) cc_final: 0.7093 (t70) REVERT: C 26 ASP cc_start: 0.8613 (m-30) cc_final: 0.8317 (m-30) REVERT: D 226 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8352 (mt-10) outliers start: 12 outliers final: 8 residues processed: 126 average time/residue: 0.0993 time to fit residues: 16.8359 Evaluate side-chains 112 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 89 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 83 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 94 optimal weight: 0.0000 chunk 15 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 16 optimal weight: 7.9990 chunk 79 optimal weight: 7.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.104970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.077775 restraints weight = 19447.817| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 3.25 r_work: 0.3020 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8985 Z= 0.158 Angle : 0.569 8.818 12199 Z= 0.297 Chirality : 0.043 0.157 1391 Planarity : 0.004 0.046 1532 Dihedral : 5.162 49.372 1305 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.91 % Allowed : 12.95 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.05 (0.26), residues: 1107 helix: 1.43 (0.27), residues: 389 sheet: -0.38 (0.32), residues: 279 loop : -0.89 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 19 TYR 0.021 0.001 TYR B 281 PHE 0.017 0.001 PHE C 354 TRP 0.015 0.001 TRP D 82 HIS 0.003 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 8982) covalent geometry : angle 0.56788 (12193) SS BOND : bond 0.01077 ( 3) SS BOND : angle 1.35865 ( 6) hydrogen bonds : bond 0.03496 ( 420) hydrogen bonds : angle 4.70796 ( 1188) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.335 Fit side-chains REVERT: B 169 GLN cc_start: 0.6866 (pp30) cc_final: 0.6470 (pp30) REVERT: B 171 ASP cc_start: 0.7569 (t70) cc_final: 0.7086 (t70) REVERT: C 26 ASP cc_start: 0.8613 (m-30) cc_final: 0.8304 (m-30) REVERT: D 226 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8372 (mt-10) REVERT: E 27 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7784 (mtt-85) outliers start: 18 outliers final: 9 residues processed: 129 average time/residue: 0.1025 time to fit residues: 17.9658 Evaluate side-chains 117 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 89 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 64 optimal weight: 2.9990 chunk 105 optimal weight: 0.0770 chunk 12 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 169 GLN ** D 17 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 = 0.3613 r_free = 0.3613 target = 0.102797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.075775 restraints weight = 19228.661| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 3.17 r_work: 0.3007 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8985 Z= 0.197 Angle : 0.614 10.151 12199 Z= 0.317 Chirality : 0.044 0.194 1391 Planarity : 0.004 0.044 1532 Dihedral : 5.157 48.510 1304 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.23 % Allowed : 13.91 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.05 (0.26), residues: 1107 helix: 1.46 (0.27), residues: 390 sheet: -0.42 (0.31), residues: 285 loop : -0.90 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 19 TYR 0.019 0.002 TYR B 281 PHE 0.029 0.002 PHE F 212 TRP 0.016 0.001 TRP D 82 HIS 0.004 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 8982) covalent geometry : angle 0.61388 (12193) SS BOND : bond 0.01138 ( 3) SS BOND : angle 0.50616 ( 6) hydrogen bonds : bond 0.03599 ( 420) hydrogen bonds : angle 4.75240 ( 1188) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.274 Fit side-chains REVERT: B 169 GLN cc_start: 0.6961 (OUTLIER) cc_final: 0.6564 (pp30) REVERT: B 171 ASP cc_start: 0.7637 (t70) cc_final: 0.7241 (t70) REVERT: C 26 ASP cc_start: 0.8624 (m-30) cc_final: 0.8316 (m-30) REVERT: C 306 GLN cc_start: 0.7786 (tm-30) cc_final: 0.7518 (pp30) REVERT: D 226 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8362 (mt-10) REVERT: E 18 GLN cc_start: 0.8183 (tp40) cc_final: 0.7636 (tp40) REVERT: E 21 MET cc_start: 0.8822 (tpp) cc_final: 0.8529 (ppp) REVERT: E 27 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7784 (mtt-85) REVERT: F 11 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.9000 (tt) outliers start: 21 outliers final: 13 residues processed: 121 average time/residue: 0.1046 time to fit residues: 17.0158 Evaluate side-chains 117 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 169 GLN Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 89 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 44 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 90 optimal weight: 0.4980 chunk 95 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 304 GLN ** D 17 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 = 0.3622 r_free = 0.3622 target = 0.103346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.076435 restraints weight = 19151.818| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 3.17 r_work: 0.3021 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8985 Z= 0.160 Angle : 0.595 10.482 12199 Z= 0.305 Chirality : 0.043 0.166 1391 Planarity : 0.003 0.043 1532 Dihedral : 5.049 46.783 1304 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.44 % Allowed : 14.97 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.09 (0.26), residues: 1107 helix: 1.50 (0.27), residues: 390 sheet: -0.45 (0.32), residues: 270 loop : -0.84 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 19 TYR 0.015 0.001 TYR B 281 PHE 0.016 0.001 PHE C 354 TRP 0.016 0.001 TRP D 82 HIS 0.003 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8982) covalent geometry : angle 0.59459 (12193) SS BOND : bond 0.01288 ( 3) SS BOND : angle 0.89181 ( 6) hydrogen bonds : bond 0.03406 ( 420) hydrogen bonds : angle 4.69510 ( 1188) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.329 Fit side-chains REVERT: B 169 GLN cc_start: 0.6790 (pp30) cc_final: 0.6395 (pp30) REVERT: B 171 ASP cc_start: 0.7649 (t70) cc_final: 0.7226 (t70) REVERT: C 26 ASP cc_start: 0.8633 (m-30) cc_final: 0.8329 (m-30) REVERT: D 226 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8332 (mt-10) REVERT: E 18 GLN cc_start: 0.8291 (tp40) cc_final: 0.7679 (tp40) REVERT: E 21 MET cc_start: 0.8796 (tpp) cc_final: 0.8381 (ppp) REVERT: E 27 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7713 (mtt-85) REVERT: F 11 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.9040 (tt) outliers start: 23 outliers final: 15 residues processed: 126 average time/residue: 0.1042 time to fit residues: 17.8687 Evaluate side-chains 121 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 139 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 56 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 31 optimal weight: 0.0050 chunk 93 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 46 optimal weight: 0.2980 chunk 7 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 GLN C 294 ASN C 304 GLN D 17 GLN D 142 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.105049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.078358 restraints weight = 19011.457| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 3.17 r_work: 0.3056 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8985 Z= 0.117 Angle : 0.575 11.224 12199 Z= 0.293 Chirality : 0.042 0.181 1391 Planarity : 0.003 0.041 1532 Dihedral : 4.841 44.190 1304 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.65 % Allowed : 15.61 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.15 (0.26), residues: 1107 helix: 1.52 (0.27), residues: 389 sheet: -0.24 (0.32), residues: 274 loop : -0.91 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 19 TYR 0.016 0.001 TYR F 190 PHE 0.018 0.001 PHE C 354 TRP 0.015 0.001 TRP D 82 HIS 0.003 0.001 HIS C 322 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8982) covalent geometry : angle 0.57511 (12193) SS BOND : bond 0.00951 ( 3) SS BOND : angle 0.53499 ( 6) hydrogen bonds : bond 0.03131 ( 420) hydrogen bonds : angle 4.57374 ( 1188) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.235 Fit side-chains REVERT: B 169 GLN cc_start: 0.6723 (pp30) cc_final: 0.6334 (pp30) REVERT: C 26 ASP cc_start: 0.8611 (m-30) cc_final: 0.8305 (m-30) REVERT: C 247 MET cc_start: 0.7989 (ptm) cc_final: 0.7680 (mtm) REVERT: C 287 TYR cc_start: 0.7965 (m-10) cc_final: 0.7599 (m-10) REVERT: D 142 HIS cc_start: 0.8517 (OUTLIER) cc_final: 0.7374 (t-90) REVERT: D 226 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8364 (mt-10) REVERT: E 18 GLN cc_start: 0.8375 (tp40) cc_final: 0.7668 (tp40) REVERT: E 21 MET cc_start: 0.8765 (tpp) cc_final: 0.8398 (ppp) REVERT: E 27 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7803 (mtt-85) outliers start: 25 outliers final: 13 residues processed: 131 average time/residue: 0.1010 time to fit residues: 17.8279 Evaluate side-chains 119 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 142 HIS Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 139 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 70 optimal weight: 0.1980 chunk 21 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 100 optimal weight: 0.2980 chunk 94 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 GLN ** C 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.106864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.079925 restraints weight = 19101.867| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 3.22 r_work: 0.3068 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8985 Z= 0.116 Angle : 0.586 10.749 12199 Z= 0.300 Chirality : 0.042 0.184 1391 Planarity : 0.003 0.041 1532 Dihedral : 4.771 42.331 1304 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.12 % Allowed : 16.88 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.16 (0.26), residues: 1107 helix: 1.50 (0.27), residues: 388 sheet: -0.21 (0.32), residues: 275 loop : -0.89 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 180 TYR 0.012 0.001 TYR F 190 PHE 0.026 0.001 PHE F 212 TRP 0.014 0.001 TRP D 82 HIS 0.012 0.001 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8982) covalent geometry : angle 0.58568 (12193) SS BOND : bond 0.00968 ( 3) SS BOND : angle 1.07009 ( 6) hydrogen bonds : bond 0.03049 ( 420) hydrogen bonds : angle 4.54014 ( 1188) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.278 Fit side-chains REVERT: B 169 GLN cc_start: 0.6760 (pp30) cc_final: 0.6342 (pp30) REVERT: C 26 ASP cc_start: 0.8637 (m-30) cc_final: 0.8332 (m-30) REVERT: D 226 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8296 (mt-10) REVERT: E 18 GLN cc_start: 0.8413 (tp40) cc_final: 0.7663 (tp40) REVERT: E 21 MET cc_start: 0.8704 (tpp) cc_final: 0.8377 (ppp) REVERT: E 27 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7774 (mtt-85) outliers start: 20 outliers final: 14 residues processed: 124 average time/residue: 0.0996 time to fit residues: 16.5119 Evaluate side-chains 120 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 204 GLN Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 139 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 29 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 35 optimal weight: 0.1980 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 27 optimal weight: 0.7980 chunk 56 optimal weight: 0.0970 chunk 54 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.106779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.080015 restraints weight = 19131.881| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.22 r_work: 0.3075 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8985 Z= 0.116 Angle : 0.588 10.488 12199 Z= 0.299 Chirality : 0.042 0.185 1391 Planarity : 0.003 0.040 1532 Dihedral : 4.712 41.074 1304 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.02 % Allowed : 16.24 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.19 (0.26), residues: 1107 helix: 1.51 (0.27), residues: 388 sheet: -0.16 (0.32), residues: 275 loop : -0.86 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 205 TYR 0.012 0.001 TYR F 190 PHE 0.037 0.001 PHE F 212 TRP 0.013 0.001 TRP D 82 HIS 0.003 0.001 HIS C 322 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8982) covalent geometry : angle 0.58777 (12193) SS BOND : bond 0.01058 ( 3) SS BOND : angle 1.03833 ( 6) hydrogen bonds : bond 0.03029 ( 420) hydrogen bonds : angle 4.55437 ( 1188) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.261 Fit side-chains REVERT: B 169 GLN cc_start: 0.6716 (pp30) cc_final: 0.6303 (pp30) REVERT: C 26 ASP cc_start: 0.8632 (m-30) cc_final: 0.8333 (m-30) REVERT: C 306 GLN cc_start: 0.8059 (pp30) cc_final: 0.7725 (pp30) REVERT: C 307 PHE cc_start: 0.9197 (OUTLIER) cc_final: 0.8106 (t80) REVERT: D 13 GLN cc_start: 0.8422 (pp30) cc_final: 0.8156 (pp30) REVERT: D 226 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8298 (mt-10) REVERT: E 18 GLN cc_start: 0.8432 (tp40) cc_final: 0.7561 (tp40) REVERT: E 21 MET cc_start: 0.8720 (tpp) cc_final: 0.8366 (ppp) REVERT: E 27 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7735 (mtt-85) outliers start: 19 outliers final: 14 residues processed: 123 average time/residue: 0.0986 time to fit residues: 16.4638 Evaluate side-chains 120 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 139 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 59 optimal weight: 0.0370 chunk 51 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 ASN C 204 GLN ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.104549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.077340 restraints weight = 19337.116| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.23 r_work: 0.3029 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8985 Z= 0.170 Angle : 0.630 10.371 12199 Z= 0.323 Chirality : 0.043 0.189 1391 Planarity : 0.003 0.041 1532 Dihedral : 4.841 42.447 1304 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.12 % Allowed : 16.99 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.10 (0.26), residues: 1107 helix: 1.48 (0.27), residues: 388 sheet: -0.38 (0.32), residues: 270 loop : -0.83 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 19 TYR 0.015 0.001 TYR F 190 PHE 0.029 0.002 PHE F 212 TRP 0.011 0.001 TRP D 82 HIS 0.003 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 8982) covalent geometry : angle 0.62985 (12193) SS BOND : bond 0.01288 ( 3) SS BOND : angle 1.11173 ( 6) hydrogen bonds : bond 0.03363 ( 420) hydrogen bonds : angle 4.69861 ( 1188) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.335 Fit side-chains REVERT: B 169 GLN cc_start: 0.6716 (pp30) cc_final: 0.6315 (pp30) REVERT: C 26 ASP cc_start: 0.8642 (m-30) cc_final: 0.8349 (m-30) REVERT: C 307 PHE cc_start: 0.9272 (OUTLIER) cc_final: 0.8344 (t80) REVERT: D 226 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8249 (mt-10) REVERT: E 18 GLN cc_start: 0.8436 (tp40) cc_final: 0.7525 (tp40) REVERT: E 21 MET cc_start: 0.8747 (tpp) cc_final: 0.8384 (ppp) REVERT: E 27 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7717 (mtt-85) outliers start: 20 outliers final: 15 residues processed: 122 average time/residue: 0.1028 time to fit residues: 16.9627 Evaluate side-chains 120 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 224 CYS Chi-restraints excluded: chain C residue 307 PHE Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain E residue 27 ARG Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 52 SER Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 229 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.0040 chunk 30 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 overall best weight: 1.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 204 GLN C 255 ASN ** D 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 ASN D 142 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.103695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.076543 restraints weight = 19065.982| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.20 r_work: 0.3013 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8985 Z= 0.197 Angle : 0.648 10.410 12199 Z= 0.333 Chirality : 0.044 0.193 1391 Planarity : 0.004 0.040 1532 Dihedral : 4.945 42.659 1304 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.12 % Allowed : 16.99 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.09 (0.26), residues: 1107 helix: 1.51 (0.27), residues: 390 sheet: -0.42 (0.31), residues: 289 loop : -0.88 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 19 TYR 0.016 0.002 TYR F 190 PHE 0.026 0.002 PHE F 212 TRP 0.013 0.001 TRP D 82 HIS 0.003 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 8982) covalent geometry : angle 0.64742 (12193) SS BOND : bond 0.01400 ( 3) SS BOND : angle 1.26721 ( 6) hydrogen bonds : bond 0.03483 ( 420) hydrogen bonds : angle 4.75452 ( 1188) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2094.95 seconds wall clock time: 36 minutes 41.98 seconds (2201.98 seconds total)