Starting phenix.real_space_refine on Wed Feb 4 08:09:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9doo_47086/02_2026/9doo_47086.cif Found real_map, /net/cci-nas-00/data/ceres_data/9doo_47086/02_2026/9doo_47086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9doo_47086/02_2026/9doo_47086.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9doo_47086/02_2026/9doo_47086.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9doo_47086/02_2026/9doo_47086.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9doo_47086/02_2026/9doo_47086.map" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 37 5.16 5 C 6043 2.51 5 N 1611 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 9363 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1849 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain: "A" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1841 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain: "G" Number of atoms: 2763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2763 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 15, 'TRANS': 338} Chain: "F" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2738 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 335} Chain breaks: 2 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 30 Chain: "G" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 128 Unusual residues: {'3PE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 27 Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 2.11, per 1000 atoms: 0.23 Number of scatterers: 9363 At special positions: 0 Unit cell: (69.12, 98.28, 142.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 37 16.00 P 4 15.00 O 1668 8.00 N 1611 7.00 C 6043 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 346.3 milliseconds 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2168 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 9 sheets defined 58.3% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'B' and resid 41 through 51 Processing helix chain 'B' and resid 94 through 104 removed outlier: 4.143A pdb=" N ILE B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 125 removed outlier: 3.673A pdb=" N PHE B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 131 removed outlier: 3.665A pdb=" N ARG B 131 " --> pdb=" O HIS B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 removed outlier: 3.910A pdb=" N LEU B 138 " --> pdb=" O GLY B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 153 removed outlier: 4.103A pdb=" N ARG B 144 " --> pdb=" O GLY B 140 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 187 removed outlier: 3.666A pdb=" N GLN B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 204 Processing helix chain 'B' and resid 220 through 226 Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'A' and resid 42 through 51 Processing helix chain 'A' and resid 71 through 79 Processing helix chain 'A' and resid 94 through 104 removed outlier: 3.794A pdb=" N ILE A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N MET A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 125 removed outlier: 3.619A pdb=" N PHE A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.727A pdb=" N ARG A 131 " --> pdb=" O HIS A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 139 through 154 removed outlier: 3.670A pdb=" N ARG A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 185 removed outlier: 3.628A pdb=" N GLN A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 204 Processing helix chain 'A' and resid 220 through 226 Processing helix chain 'A' and resid 228 through 234 Processing helix chain 'G' and resid 2 through 37 removed outlier: 3.929A pdb=" N ASN G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 55 Processing helix chain 'G' and resid 55 through 81 Proline residue: G 65 - end of helix removed outlier: 3.622A pdb=" N LEU G 69 " --> pdb=" O PRO G 65 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU G 79 " --> pdb=" O GLY G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 91 removed outlier: 3.887A pdb=" N MET G 88 " --> pdb=" O GLU G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 120 removed outlier: 3.503A pdb=" N ILE G 98 " --> pdb=" O SER G 94 " (cutoff:3.500A) Proline residue: G 105 - end of helix removed outlier: 3.603A pdb=" N VAL G 108 " --> pdb=" O LYS G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 136 removed outlier: 3.533A pdb=" N ALA G 133 " --> pdb=" O GLN G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 239 removed outlier: 3.546A pdb=" N VAL G 238 " --> pdb=" O LEU G 234 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET G 239 " --> pdb=" O ASN G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 244 removed outlier: 3.526A pdb=" N LEU G 244 " --> pdb=" O PRO G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 260 removed outlier: 3.697A pdb=" N GLN G 251 " --> pdb=" O SER G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 263 through 275 removed outlier: 3.697A pdb=" N LEU G 268 " --> pdb=" O ASN G 264 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA G 269 " --> pdb=" O ARG G 265 " (cutoff:3.500A) Processing helix chain 'G' and resid 275 through 293 Processing helix chain 'G' and resid 299 through 322 Processing helix chain 'G' and resid 323 through 328 removed outlier: 3.675A pdb=" N VAL G 327 " --> pdb=" O PRO G 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 331 through 354 removed outlier: 4.223A pdb=" N ALA G 335 " --> pdb=" O PRO G 331 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL G 336 " --> pdb=" O PRO G 332 " (cutoff:3.500A) Proline residue: G 339 - end of helix Processing helix chain 'F' and resid 3 through 41 removed outlier: 5.074A pdb=" N ARG F 9 " --> pdb=" O ARG F 5 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL F 11 " --> pdb=" O LEU F 7 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU F 12 " --> pdb=" O SER F 8 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 46 No H-bonds generated for 'chain 'F' and resid 44 through 46' Processing helix chain 'F' and resid 47 through 55 removed outlier: 4.158A pdb=" N ILE F 51 " --> pdb=" O SER F 47 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N MET F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 82 removed outlier: 3.645A pdb=" N PHE F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) Proline residue: F 65 - end of helix Processing helix chain 'F' and resid 85 through 90 Processing helix chain 'F' and resid 95 through 103 removed outlier: 3.652A pdb=" N LEU F 99 " --> pdb=" O GLN F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 119 removed outlier: 3.628A pdb=" N LEU F 108 " --> pdb=" O ALA F 104 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU F 118 " --> pdb=" O ALA F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 135 Processing helix chain 'F' and resid 221 through 225 Processing helix chain 'F' and resid 241 through 248 removed outlier: 3.589A pdb=" N SER F 245 " --> pdb=" O LYS F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 253 Processing helix chain 'F' and resid 255 through 261 removed outlier: 4.436A pdb=" N GLY F 261 " --> pdb=" O ALA F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 275 removed outlier: 3.505A pdb=" N GLN F 272 " --> pdb=" O GLN F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 292 removed outlier: 3.509A pdb=" N VAL F 281 " --> pdb=" O THR F 277 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE F 282 " --> pdb=" O PRO F 278 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU F 286 " --> pdb=" O PHE F 282 " (cutoff:3.500A) Proline residue: F 290 - end of helix Processing helix chain 'F' and resid 303 through 327 Processing helix chain 'F' and resid 336 through 352 removed outlier: 3.616A pdb=" N HIS F 340 " --> pdb=" O LEU F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 365 Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'B' and resid 16 through 22 removed outlier: 6.066A pdb=" N VAL B 18 " --> pdb=" O TYR B 13 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N TYR B 13 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ARG B 20 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LYS B 11 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU B 9 " --> pdb=" O GLN B 57 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLN B 57 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 80 through 83 removed outlier: 3.668A pdb=" N LEU B 160 " --> pdb=" O GLY B 81 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU B 83 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR B 193 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE B 31 " --> pdb=" O THR B 206 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N TYR B 208 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLY B 33 " --> pdb=" O TYR B 208 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL B 210 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU B 35 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA B 217 " --> pdb=" O ILE B 209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 17 through 27 removed outlier: 6.400A pdb=" N VAL A 18 " --> pdb=" O SER A 12 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N SER A 12 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG A 20 " --> pdb=" O ALA A 10 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA A 10 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VAL A 22 " --> pdb=" O HIS A 8 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LEU A 9 " --> pdb=" O GLN A 57 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLN A 57 " --> pdb=" O LEU A 9 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 160 through 162 removed outlier: 7.124A pdb=" N LEU A 161 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N GLY A 33 " --> pdb=" O TYR A 208 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL A 210 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU A 35 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA A 207 " --> pdb=" O GLU A 218 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU A 218 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE A 209 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 148 through 151 removed outlier: 6.789A pdb=" N GLY G 170 " --> pdb=" O ASN G 160 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL G 162 " --> pdb=" O LEU G 168 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU G 168 " --> pdb=" O VAL G 162 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 193 through 194 removed outlier: 3.613A pdb=" N GLU G 223 " --> pdb=" O LEU G 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 205 through 207 removed outlier: 3.972A pdb=" N THR G 205 " --> pdb=" O VAL G 218 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 157 through 158 476 hydrogen bonds defined for protein. 1377 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: 1.05 Time building geometry restraints manager: 0.91 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: 1517 1.31 - 1.43: 2413 1.43 - 1.56: 5526 1.56 - 1.68: 8 1.68 - 1.81: 68 Bond restraints: 9532 Sorted by residual: bond pdb=" C21 3PE G 401 " pdb=" O21 3PE G 401 " ideal model delta sigma weight residual 1.316 1.457 -0.141 2.00e-02 2.50e+03 5.00e+01 bond pdb=" C21 3PE G 403 " pdb=" O21 3PE G 403 " ideal model delta sigma weight residual 1.316 1.453 -0.137 2.00e-02 2.50e+03 4.71e+01 bond pdb=" C21 3PE F 401 " pdb=" O21 3PE F 401 " ideal model delta sigma weight residual 1.316 1.452 -0.136 2.00e-02 2.50e+03 4.63e+01 bond pdb=" C21 3PE G 402 " pdb=" O21 3PE G 402 " ideal model delta sigma weight residual 1.316 1.451 -0.135 2.00e-02 2.50e+03 4.58e+01 bond pdb=" C31 3PE G 402 " pdb=" O31 3PE G 402 " ideal model delta sigma weight residual 1.331 1.455 -0.124 2.00e-02 2.50e+03 3.84e+01 ... (remaining 9527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 12478 3.48 - 6.96: 307 6.96 - 10.44: 71 10.44 - 13.91: 13 13.91 - 17.39: 5 Bond angle restraints: 12874 Sorted by residual: angle pdb=" N GLY G 139 " pdb=" CA GLY G 139 " pdb=" C GLY G 139 " ideal model delta sigma weight residual 112.77 129.66 -16.89 1.28e+00 6.10e-01 1.74e+02 angle pdb=" N PHE F 301 " pdb=" CA PHE F 301 " pdb=" C PHE F 301 " ideal model delta sigma weight residual 113.18 125.90 -12.72 1.21e+00 6.83e-01 1.10e+02 angle pdb=" N SER F 249 " pdb=" CA SER F 249 " pdb=" C SER F 249 " ideal model delta sigma weight residual 109.85 95.15 14.70 1.58e+00 4.01e-01 8.66e+01 angle pdb=" N ALA G 227 " pdb=" CA ALA G 227 " pdb=" C ALA G 227 " ideal model delta sigma weight residual 107.99 123.70 -15.71 1.76e+00 3.23e-01 7.97e+01 angle pdb=" N TYR F 232 " pdb=" CA TYR F 232 " pdb=" C TYR F 232 " ideal model delta sigma weight residual 110.23 122.98 -12.75 1.45e+00 4.76e-01 7.73e+01 ... (remaining 12869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.36: 5239 20.36 - 40.71: 424 40.71 - 61.07: 89 61.07 - 81.43: 7 81.43 - 101.79: 2 Dihedral angle restraints: 5761 sinusoidal: 2377 harmonic: 3384 Sorted by residual: dihedral pdb=" C LYS F 329 " pdb=" N LYS F 329 " pdb=" CA LYS F 329 " pdb=" CB LYS F 329 " ideal model delta harmonic sigma weight residual -122.60 -137.03 14.43 0 2.50e+00 1.60e-01 3.33e+01 dihedral pdb=" C THR F 277 " pdb=" N THR F 277 " pdb=" CA THR F 277 " pdb=" CB THR F 277 " ideal model delta harmonic sigma weight residual -122.00 -135.82 13.82 0 2.50e+00 1.60e-01 3.06e+01 dihedral pdb=" N LYS F 329 " pdb=" C LYS F 329 " pdb=" CA LYS F 329 " pdb=" CB LYS F 329 " ideal model delta harmonic sigma weight residual 122.80 135.74 -12.94 0 2.50e+00 1.60e-01 2.68e+01 ... (remaining 5758 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 1285 0.126 - 0.252: 136 0.252 - 0.378: 36 0.378 - 0.504: 13 0.504 - 0.630: 6 Chirality restraints: 1476 Sorted by residual: chirality pdb=" CA LYS F 329 " pdb=" N LYS F 329 " pdb=" C LYS F 329 " pdb=" CB LYS F 329 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.92e+00 chirality pdb=" CA SER G 186 " pdb=" N SER G 186 " pdb=" C SER G 186 " pdb=" CB SER G 186 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.10e+00 chirality pdb=" CA THR F 277 " pdb=" N THR F 277 " pdb=" C THR F 277 " pdb=" CB THR F 277 " both_signs ideal model delta sigma weight residual False 2.53 1.98 0.55 2.00e-01 2.50e+01 7.47e+00 ... (remaining 1473 not shown) Planarity restraints: 1621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER F 276 " 0.024 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C SER F 276 " -0.079 2.00e-02 2.50e+03 pdb=" O SER F 276 " 0.028 2.00e-02 2.50e+03 pdb=" N THR F 277 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 277 " -0.074 5.00e-02 4.00e+02 1.12e-01 1.99e+01 pdb=" N PRO F 278 " 0.193 5.00e-02 4.00e+02 pdb=" CA PRO F 278 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO F 278 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 64 " -0.052 5.00e-02 4.00e+02 7.73e-02 9.56e+00 pdb=" N PRO G 65 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO G 65 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO G 65 " -0.045 5.00e-02 4.00e+02 ... (remaining 1618 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 13 2.40 - 3.03: 5571 3.03 - 3.65: 13293 3.65 - 4.28: 20598 4.28 - 4.90: 35098 Nonbonded interactions: 74573 Sorted by model distance: nonbonded pdb=" OG1 THR F 137 " pdb=" CE1 PHE F 141 " model vdw 1.780 3.340 nonbonded pdb=" CE1 PHE F 141 " pdb=" NH2 ARG F 208 " model vdw 2.015 3.420 nonbonded pdb=" OG1 THR F 137 " pdb=" CD1 PHE F 141 " model vdw 2.121 3.340 nonbonded pdb=" NZ LYS B 177 " pdb=" OD2 ASP B 202 " model vdw 2.218 3.120 nonbonded pdb=" OE1 GLN F 61 " pdb=" OG SER F 117 " model vdw 2.236 3.040 ... (remaining 74568 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 2 through 240) } 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: 2.930 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.980 Find NCS groups from input model: 0.090 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 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 0.141 9532 Z= 0.713 Angle : 1.383 17.392 12874 Z= 0.873 Chirality : 0.101 0.630 1476 Planarity : 0.007 0.112 1621 Dihedral : 14.958 101.786 3593 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.83 % Favored : 96.00 % Rotamer: Outliers : 4.14 % Allowed : 4.66 % Favored : 91.20 % Cbeta Deviations : 0.55 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.24), residues: 1174 helix: 0.76 (0.21), residues: 616 sheet: -0.30 (0.64), residues: 81 loop : -1.31 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 173 TYR 0.024 0.002 TYR F 209 PHE 0.032 0.002 PHE F 69 TRP 0.015 0.002 TRP G 149 HIS 0.004 0.001 HIS G 197 Details of bonding type rmsd covalent geometry : bond 0.01031 ( 9532) covalent geometry : angle 1.38307 (12874) hydrogen bonds : bond 0.19870 ( 476) hydrogen bonds : angle 6.68690 ( 1377) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 124 time to evaluate : 0.241 Fit side-chains REVERT: A 196 ASN cc_start: 0.8554 (t0) cc_final: 0.8217 (t0) REVERT: G 212 GLU cc_start: 0.5038 (OUTLIER) cc_final: 0.4730 (pm20) REVERT: G 214 ARG cc_start: 0.5888 (OUTLIER) cc_final: 0.5646 (ptp90) REVERT: G 286 MET cc_start: 0.7410 (ttp) cc_final: 0.6977 (ttt) REVERT: G 312 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.6692 (m-10) REVERT: F 130 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7434 (tp) REVERT: F 227 TYR cc_start: 0.3261 (OUTLIER) cc_final: -0.0865 (m-80) outliers start: 40 outliers final: 7 residues processed: 161 average time/residue: 0.0973 time to fit residues: 21.6207 Evaluate side-chains 114 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 43 TYR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain G residue 214 ARG Chi-restraints excluded: chain G residue 312 PHE Chi-restraints excluded: chain F residue 128 PHE Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 317 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 GLN G 37 ASN G 150 HIS G 179 GLN G 199 GLN F 127 GLN F 221 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.168945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.130268 restraints weight = 11205.273| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.58 r_work: 0.3295 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9532 Z= 0.156 Angle : 0.622 8.140 12874 Z= 0.331 Chirality : 0.043 0.179 1476 Planarity : 0.005 0.071 1621 Dihedral : 9.421 94.353 1482 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.26 % Favored : 95.66 % Rotamer: Outliers : 2.59 % Allowed : 9.01 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.25), residues: 1174 helix: 1.00 (0.21), residues: 625 sheet: -0.80 (0.58), residues: 93 loop : -1.37 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 180 TYR 0.013 0.001 TYR F 218 PHE 0.022 0.001 PHE F 69 TRP 0.016 0.002 TRP G 225 HIS 0.008 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 9532) covalent geometry : angle 0.62164 (12874) hydrogen bonds : bond 0.05152 ( 476) hydrogen bonds : angle 4.57085 ( 1377) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.355 Fit side-chains REVERT: A 73 HIS cc_start: 0.7247 (OUTLIER) cc_final: 0.5801 (m90) REVERT: A 112 ASN cc_start: 0.7985 (t0) cc_final: 0.7775 (t0) REVERT: G 184 SER cc_start: 0.6226 (m) cc_final: 0.5995 (t) REVERT: G 212 GLU cc_start: 0.4300 (OUTLIER) cc_final: 0.3992 (pm20) REVERT: G 214 ARG cc_start: 0.6178 (OUTLIER) cc_final: 0.5612 (ptp90) REVERT: G 286 MET cc_start: 0.8123 (ttp) cc_final: 0.7663 (ttt) REVERT: F 130 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7053 (tp) REVERT: F 227 TYR cc_start: 0.2961 (OUTLIER) cc_final: -0.0197 (m-80) REVERT: F 260 PHE cc_start: 0.7789 (OUTLIER) cc_final: 0.6905 (t80) REVERT: F 279 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8288 (mp) outliers start: 25 outliers final: 9 residues processed: 128 average time/residue: 0.0953 time to fit residues: 17.1637 Evaluate side-chains 122 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 43 TYR Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain G residue 214 ARG Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 260 PHE Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 317 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 80 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 115 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.166975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.127528 restraints weight = 11382.576| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.69 r_work: 0.3233 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9532 Z= 0.190 Angle : 0.607 7.622 12874 Z= 0.319 Chirality : 0.044 0.143 1476 Planarity : 0.005 0.062 1621 Dihedral : 8.965 89.025 1474 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.00 % Allowed : 11.08 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.25), residues: 1174 helix: 0.98 (0.22), residues: 626 sheet: -0.69 (0.58), residues: 90 loop : -1.43 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 78 TYR 0.007 0.001 TYR A 234 PHE 0.020 0.002 PHE F 69 TRP 0.024 0.002 TRP G 198 HIS 0.006 0.001 HIS G 197 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 9532) covalent geometry : angle 0.60707 (12874) hydrogen bonds : bond 0.04922 ( 476) hydrogen bonds : angle 4.38645 ( 1377) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.293 Fit side-chains REVERT: A 73 HIS cc_start: 0.7486 (OUTLIER) cc_final: 0.6176 (m170) REVERT: G 184 SER cc_start: 0.6047 (m) cc_final: 0.5809 (t) REVERT: G 212 GLU cc_start: 0.4188 (OUTLIER) cc_final: 0.3957 (pm20) REVERT: G 214 ARG cc_start: 0.6387 (OUTLIER) cc_final: 0.5443 (ptp90) REVERT: G 286 MET cc_start: 0.8140 (ttp) cc_final: 0.7713 (ttt) REVERT: G 312 PHE cc_start: 0.7537 (OUTLIER) cc_final: 0.7227 (m-80) REVERT: F 130 LEU cc_start: 0.7588 (mp) cc_final: 0.7114 (tp) REVERT: F 227 TYR cc_start: 0.2891 (OUTLIER) cc_final: -0.0311 (m-80) REVERT: F 260 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.6854 (t80) REVERT: F 279 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8414 (mp) REVERT: F 326 ASP cc_start: 0.7913 (p0) cc_final: 0.7491 (p0) REVERT: F 356 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7844 (mp) outliers start: 29 outliers final: 11 residues processed: 135 average time/residue: 0.0915 time to fit residues: 17.7639 Evaluate side-chains 123 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain G residue 214 ARG Chi-restraints excluded: chain G residue 312 PHE Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 260 PHE Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 356 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 93 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.165597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.128562 restraints weight = 11529.431| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.59 r_work: 0.3228 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9532 Z= 0.210 Angle : 0.615 7.383 12874 Z= 0.320 Chirality : 0.044 0.137 1476 Planarity : 0.005 0.063 1621 Dihedral : 8.999 83.922 1470 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.52 % Allowed : 12.11 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.25), residues: 1174 helix: 0.89 (0.21), residues: 627 sheet: -0.75 (0.57), residues: 90 loop : -1.46 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 78 TYR 0.008 0.001 TYR G 119 PHE 0.020 0.002 PHE F 69 TRP 0.032 0.002 TRP G 198 HIS 0.005 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00518 ( 9532) covalent geometry : angle 0.61506 (12874) hydrogen bonds : bond 0.04929 ( 476) hydrogen bonds : angle 4.40096 ( 1377) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.256 Fit side-chains REVERT: A 73 HIS cc_start: 0.7545 (OUTLIER) cc_final: 0.6193 (m90) REVERT: G 61 TYR cc_start: 0.8683 (t80) cc_final: 0.8432 (t80) REVERT: G 184 SER cc_start: 0.6099 (m) cc_final: 0.5891 (t) REVERT: G 212 GLU cc_start: 0.4152 (OUTLIER) cc_final: 0.3932 (pm20) REVERT: G 214 ARG cc_start: 0.6346 (OUTLIER) cc_final: 0.5394 (ptp90) REVERT: G 286 MET cc_start: 0.8283 (ttp) cc_final: 0.7845 (ttt) REVERT: G 312 PHE cc_start: 0.7757 (OUTLIER) cc_final: 0.7412 (m-80) REVERT: F 130 LEU cc_start: 0.7689 (mp) cc_final: 0.7188 (tp) REVERT: F 227 TYR cc_start: 0.3055 (OUTLIER) cc_final: -0.0143 (m-80) REVERT: F 260 PHE cc_start: 0.7739 (OUTLIER) cc_final: 0.6917 (t80) REVERT: F 279 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8441 (mp) REVERT: F 326 ASP cc_start: 0.7822 (p0) cc_final: 0.7333 (p0) REVERT: F 356 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7885 (mp) outliers start: 34 outliers final: 19 residues processed: 139 average time/residue: 0.0840 time to fit residues: 16.7637 Evaluate side-chains 133 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain G residue 214 ARG Chi-restraints excluded: chain G residue 312 PHE Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 260 PHE Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 360 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN G 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.167253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.127316 restraints weight = 11451.774| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.67 r_work: 0.3229 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9532 Z= 0.159 Angle : 0.567 8.127 12874 Z= 0.296 Chirality : 0.042 0.187 1476 Planarity : 0.004 0.062 1621 Dihedral : 8.852 82.123 1470 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.31 % Allowed : 13.77 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.25), residues: 1174 helix: 1.06 (0.22), residues: 627 sheet: -0.77 (0.58), residues: 90 loop : -1.47 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 78 TYR 0.008 0.001 TYR F 235 PHE 0.015 0.001 PHE F 69 TRP 0.022 0.001 TRP G 198 HIS 0.006 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 9532) covalent geometry : angle 0.56746 (12874) hydrogen bonds : bond 0.04397 ( 476) hydrogen bonds : angle 4.23072 ( 1377) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.317 Fit side-chains REVERT: A 73 HIS cc_start: 0.7326 (OUTLIER) cc_final: 0.5953 (m90) REVERT: A 198 ARG cc_start: 0.8291 (ttm110) cc_final: 0.7975 (mtt90) REVERT: G 61 TYR cc_start: 0.8686 (t80) cc_final: 0.8309 (t80) REVERT: G 214 ARG cc_start: 0.6273 (OUTLIER) cc_final: 0.5303 (ptp90) REVERT: G 286 MET cc_start: 0.8185 (ttp) cc_final: 0.7729 (ttt) REVERT: G 312 PHE cc_start: 0.7726 (OUTLIER) cc_final: 0.7382 (m-80) REVERT: F 130 LEU cc_start: 0.7621 (mp) cc_final: 0.7106 (tp) REVERT: F 227 TYR cc_start: 0.3146 (OUTLIER) cc_final: -0.0113 (m-80) REVERT: F 279 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8414 (mp) REVERT: F 326 ASP cc_start: 0.7637 (p0) cc_final: 0.7072 (p0) REVERT: F 356 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7872 (mp) outliers start: 32 outliers final: 20 residues processed: 136 average time/residue: 0.0915 time to fit residues: 17.8121 Evaluate side-chains 132 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 TYR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 214 ARG Chi-restraints excluded: chain G residue 312 PHE Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 260 PHE Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 356 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 17 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 0.0870 chunk 98 optimal weight: 20.0000 chunk 40 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.167650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.127599 restraints weight = 11362.415| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.62 r_work: 0.3268 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9532 Z= 0.140 Angle : 0.551 7.287 12874 Z= 0.286 Chirality : 0.041 0.168 1476 Planarity : 0.004 0.061 1621 Dihedral : 8.665 80.213 1467 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.31 % Allowed : 14.80 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.25), residues: 1174 helix: 1.19 (0.22), residues: 629 sheet: -1.14 (0.56), residues: 96 loop : -1.49 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 303 TYR 0.007 0.001 TYR F 218 PHE 0.013 0.001 PHE F 69 TRP 0.018 0.001 TRP G 198 HIS 0.005 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9532) covalent geometry : angle 0.55062 (12874) hydrogen bonds : bond 0.04171 ( 476) hydrogen bonds : angle 4.12859 ( 1377) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.361 Fit side-chains REVERT: A 73 HIS cc_start: 0.7311 (OUTLIER) cc_final: 0.5853 (m90) REVERT: G 61 TYR cc_start: 0.8684 (t80) cc_final: 0.8422 (t80) REVERT: G 214 ARG cc_start: 0.6220 (OUTLIER) cc_final: 0.5259 (ptp90) REVERT: G 286 MET cc_start: 0.8151 (ttp) cc_final: 0.7728 (ttt) REVERT: G 312 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.7344 (m-80) REVERT: F 130 LEU cc_start: 0.7654 (mp) cc_final: 0.7113 (tp) REVERT: F 227 TYR cc_start: 0.3001 (OUTLIER) cc_final: -0.0283 (m-80) REVERT: F 279 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8414 (mp) REVERT: F 326 ASP cc_start: 0.7690 (p0) cc_final: 0.7371 (p0) REVERT: F 356 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7874 (mp) outliers start: 32 outliers final: 17 residues processed: 135 average time/residue: 0.1011 time to fit residues: 19.2604 Evaluate side-chains 127 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 TYR Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 204 CYS Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 214 ARG Chi-restraints excluded: chain G residue 312 PHE Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain F residue 260 PHE Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 356 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 106 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 16 optimal weight: 0.0870 chunk 21 optimal weight: 0.0980 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN A 128 HIS G 158 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.169371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.129645 restraints weight = 11378.381| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.61 r_work: 0.3275 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9532 Z= 0.115 Angle : 0.528 9.266 12874 Z= 0.275 Chirality : 0.040 0.158 1476 Planarity : 0.005 0.075 1621 Dihedral : 8.475 78.639 1467 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.59 % Allowed : 15.22 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.25), residues: 1174 helix: 1.44 (0.22), residues: 628 sheet: -1.19 (0.54), residues: 103 loop : -1.53 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 198 TYR 0.008 0.001 TYR F 218 PHE 0.011 0.001 PHE F 69 TRP 0.017 0.001 TRP G 198 HIS 0.004 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9532) covalent geometry : angle 0.52820 (12874) hydrogen bonds : bond 0.03816 ( 476) hydrogen bonds : angle 4.02291 ( 1377) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: B 196 ASN cc_start: 0.9082 (t0) cc_final: 0.8864 (t0) REVERT: A 73 HIS cc_start: 0.7165 (OUTLIER) cc_final: 0.5386 (m170) REVERT: A 198 ARG cc_start: 0.8215 (ttm110) cc_final: 0.7897 (mtt90) REVERT: G 61 TYR cc_start: 0.8667 (t80) cc_final: 0.8404 (t80) REVERT: G 214 ARG cc_start: 0.6117 (OUTLIER) cc_final: 0.5659 (pmt170) REVERT: G 286 MET cc_start: 0.8120 (ttp) cc_final: 0.7722 (ttt) REVERT: G 312 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.7330 (m-80) REVERT: F 130 LEU cc_start: 0.7642 (mp) cc_final: 0.7145 (tp) REVERT: F 238 MET cc_start: 0.5409 (mmm) cc_final: 0.5166 (mmm) REVERT: F 326 ASP cc_start: 0.7513 (p0) cc_final: 0.7183 (p0) REVERT: F 356 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7898 (mp) outliers start: 25 outliers final: 15 residues processed: 130 average time/residue: 0.0886 time to fit residues: 16.5883 Evaluate side-chains 126 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain A residue 13 TYR Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 214 ARG Chi-restraints excluded: chain G residue 312 PHE Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain F residue 260 PHE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 360 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 7 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.169221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.133151 restraints weight = 11320.693| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.62 r_work: 0.3275 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9532 Z= 0.131 Angle : 0.550 12.094 12874 Z= 0.281 Chirality : 0.041 0.176 1476 Planarity : 0.004 0.060 1621 Dihedral : 8.473 77.305 1467 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.38 % Allowed : 15.94 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.25), residues: 1174 helix: 1.43 (0.22), residues: 630 sheet: -0.95 (0.55), residues: 106 loop : -1.41 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 175 TYR 0.012 0.001 TYR F 235 PHE 0.011 0.001 PHE F 128 TRP 0.016 0.001 TRP G 198 HIS 0.005 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9532) covalent geometry : angle 0.54988 (12874) hydrogen bonds : bond 0.03935 ( 476) hydrogen bonds : angle 4.02501 ( 1377) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 73 HIS cc_start: 0.7271 (OUTLIER) cc_final: 0.5875 (m90) REVERT: A 123 GLN cc_start: 0.8676 (mm-40) cc_final: 0.8381 (mm110) REVERT: A 198 ARG cc_start: 0.8205 (ttm110) cc_final: 0.7916 (mtt90) REVERT: G 61 TYR cc_start: 0.8659 (t80) cc_final: 0.8401 (t80) REVERT: G 214 ARG cc_start: 0.6227 (OUTLIER) cc_final: 0.5754 (pmt170) REVERT: G 286 MET cc_start: 0.8167 (ttp) cc_final: 0.7778 (ttt) REVERT: G 312 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.7382 (m-80) REVERT: F 130 LEU cc_start: 0.7586 (mp) cc_final: 0.7055 (tp) REVERT: F 227 TYR cc_start: 0.2706 (OUTLIER) cc_final: -0.0572 (m-80) REVERT: F 279 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8392 (mp) REVERT: F 326 ASP cc_start: 0.7590 (p0) cc_final: 0.7257 (p0) REVERT: F 356 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7923 (mp) outliers start: 23 outliers final: 15 residues processed: 129 average time/residue: 0.0835 time to fit residues: 15.2751 Evaluate side-chains 127 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 214 ARG Chi-restraints excluded: chain G residue 312 PHE Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain F residue 260 PHE Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 356 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 54 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 96 optimal weight: 0.0570 chunk 50 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 ASN ** B 214 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 = 0.3939 r_free = 0.3939 target = 0.168753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.129037 restraints weight = 11335.403| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.72 r_work: 0.3263 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9532 Z= 0.138 Angle : 0.541 8.942 12874 Z= 0.281 Chirality : 0.041 0.146 1476 Planarity : 0.004 0.060 1621 Dihedral : 8.488 76.116 1467 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.80 % Allowed : 16.36 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.25), residues: 1174 helix: 1.45 (0.22), residues: 631 sheet: -1.17 (0.52), residues: 116 loop : -1.44 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 175 TYR 0.012 0.001 TYR F 235 PHE 0.010 0.001 PHE F 69 TRP 0.015 0.001 TRP G 198 HIS 0.006 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9532) covalent geometry : angle 0.54072 (12874) hydrogen bonds : bond 0.03996 ( 476) hydrogen bonds : angle 4.03718 ( 1377) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 73 HIS cc_start: 0.7330 (OUTLIER) cc_final: 0.5892 (m90) REVERT: G 61 TYR cc_start: 0.8688 (t80) cc_final: 0.8436 (t80) REVERT: G 214 ARG cc_start: 0.6346 (OUTLIER) cc_final: 0.5924 (pmt170) REVERT: G 286 MET cc_start: 0.8220 (ttp) cc_final: 0.7831 (ttt) REVERT: G 312 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.7433 (m-80) REVERT: F 130 LEU cc_start: 0.7446 (mp) cc_final: 0.6925 (tp) REVERT: F 227 TYR cc_start: 0.2659 (OUTLIER) cc_final: -0.0525 (m-80) REVERT: F 238 MET cc_start: 0.5416 (mmm) cc_final: 0.5094 (mtm) REVERT: F 279 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8398 (mp) REVERT: F 326 ASP cc_start: 0.7600 (p0) cc_final: 0.7269 (p0) REVERT: F 356 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7927 (mp) outliers start: 27 outliers final: 18 residues processed: 130 average time/residue: 0.0851 time to fit residues: 15.8113 Evaluate side-chains 132 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 204 CYS Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain A residue 13 TYR Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 214 ARG Chi-restraints excluded: chain G residue 312 PHE Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain F residue 260 PHE Chi-restraints excluded: chain F residue 279 LEU Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain F residue 360 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 0.3980 chunk 105 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 70 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 67 optimal weight: 0.0870 chunk 35 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.170063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.130466 restraints weight = 11253.604| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.66 r_work: 0.3277 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9532 Z= 0.112 Angle : 0.521 8.639 12874 Z= 0.272 Chirality : 0.040 0.151 1476 Planarity : 0.004 0.059 1621 Dihedral : 8.350 75.523 1467 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.17 % Allowed : 16.87 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.25), residues: 1174 helix: 1.58 (0.22), residues: 631 sheet: -1.12 (0.52), residues: 116 loop : -1.39 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 175 TYR 0.017 0.001 TYR G 119 PHE 0.010 0.001 PHE F 128 TRP 0.017 0.001 TRP G 198 HIS 0.005 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9532) covalent geometry : angle 0.52119 (12874) hydrogen bonds : bond 0.03723 ( 476) hydrogen bonds : angle 3.94842 ( 1377) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2348 Ramachandran restraints generated. 1174 Oldfield, 0 Emsley, 1174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 73 HIS cc_start: 0.7121 (OUTLIER) cc_final: 0.5341 (m170) REVERT: G 61 TYR cc_start: 0.8696 (t80) cc_final: 0.8422 (t80) REVERT: G 119 TYR cc_start: 0.8675 (m-10) cc_final: 0.8462 (m-10) REVERT: G 214 ARG cc_start: 0.6282 (OUTLIER) cc_final: 0.5887 (pmt170) REVERT: G 286 MET cc_start: 0.8051 (ttp) cc_final: 0.7702 (ttp) REVERT: G 312 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.7335 (m-80) REVERT: F 130 LEU cc_start: 0.7551 (mp) cc_final: 0.7134 (tp) REVERT: F 227 TYR cc_start: 0.2532 (OUTLIER) cc_final: -0.0570 (m-80) REVERT: F 238 MET cc_start: 0.5497 (mmm) cc_final: 0.5087 (mtm) REVERT: F 326 ASP cc_start: 0.7458 (p0) cc_final: 0.7099 (p0) REVERT: F 356 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7899 (mp) outliers start: 21 outliers final: 15 residues processed: 125 average time/residue: 0.0907 time to fit residues: 16.4509 Evaluate side-chains 128 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 TYR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 62 ASP Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 214 ARG Chi-restraints excluded: chain G residue 312 PHE Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 227 TYR Chi-restraints excluded: chain F residue 260 PHE Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 356 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 chunk 33 optimal weight: 0.0970 chunk 19 optimal weight: 1.9990 chunk 113 optimal weight: 0.0470 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 211 ASN ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 = 0.3914 r_free = 0.3914 target = 0.166440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.126236 restraints weight = 11217.701| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.62 r_work: 0.3264 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9532 Z= 0.160 Angle : 0.554 8.592 12874 Z= 0.286 Chirality : 0.041 0.142 1476 Planarity : 0.004 0.060 1621 Dihedral : 8.493 74.569 1467 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.48 % Allowed : 16.67 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.25), residues: 1174 helix: 1.46 (0.22), residues: 624 sheet: -1.19 (0.52), residues: 116 loop : -1.46 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 198 TYR 0.017 0.001 TYR G 119 PHE 0.012 0.001 PHE F 128 TRP 0.015 0.001 TRP G 198 HIS 0.006 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 9532) covalent geometry : angle 0.55364 (12874) hydrogen bonds : bond 0.04183 ( 476) hydrogen bonds : angle 4.05904 ( 1377) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2313.11 seconds wall clock time: 40 minutes 15.46 seconds (2415.46 seconds total)