Starting phenix.real_space_refine on Thu Jul 2 14:46:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vv5_32138/07_2026/7vv5_32138.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vv5_32138/07_2026/7vv5_32138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vv5_32138/07_2026/7vv5_32138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vv5_32138/07_2026/7vv5_32138.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7vv5_32138/07_2026/7vv5_32138.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vv5_32138/07_2026/7vv5_32138.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vv5_32138/07_2026/7vv5_32138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vv5_32138/07_2026/7vv5_32138.map" } resolution = 2.76 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 5660 2.51 5 N 1474 2.21 5 O 1629 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8829 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1813 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2598 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 427 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1786 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "R" Number of atoms: 2139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2139 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 8, 'TRANS': 259} Chain: "R" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'6IB': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.53, per 1000 atoms: 0.17 Number of scatterers: 8829 At special positions: 0 Unit cell: (116.772, 108.356, 104.148, 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 66 16.00 O 1629 8.00 N 1474 7.00 C 5660 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.06 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.05 Simple disulfide: pdb=" SG CYS R 26 " - pdb=" SG CYS R 258 " distance=2.04 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " 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: 0.41 Conformation dependent library (CDL) restraints added in 358.6 milliseconds 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 13 sheets defined 37.5% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.671A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.505A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.492A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.819A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 4.123A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 43 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.338A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.640A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.730A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 57 removed outlier: 3.529A pdb=" N VAL R 34 " --> pdb=" O THR R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 94 removed outlier: 3.831A pdb=" N VAL R 66 " --> pdb=" O ASN R 62 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYR R 67 " --> pdb=" O ALA R 63 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 133 removed outlier: 3.602A pdb=" N VAL R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 139 Processing helix chain 'R' and resid 144 through 168 Processing helix chain 'R' and resid 176 through 212 removed outlier: 3.926A pdb=" N THR R 182 " --> pdb=" O GLY R 178 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE R 186 " --> pdb=" O THR R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 236 Processing helix chain 'R' and resid 236 through 245 removed outlier: 4.339A pdb=" N GLY R 240 " --> pdb=" O GLY R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 250 Processing helix chain 'R' and resid 256 through 280 Proline residue: R 262 - end of helix Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 280 through 285 Processing helix chain 'R' and resid 286 through 288 No H-bonds generated for 'chain 'R' and resid 286 through 288' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.303A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.442A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.853A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.892A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.788A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.444A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.520A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.594A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.698A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.137A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.464A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1257 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.35: 2811 1.35 - 1.48: 2505 1.48 - 1.61: 3616 1.61 - 1.75: 2 1.75 - 1.88: 90 Bond restraints: 9024 Sorted by residual: bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.669 -0.134 2.00e-02 2.50e+03 4.52e+01 bond pdb=" C ALA S 40 " pdb=" N PRO S 41 " ideal model delta sigma weight residual 1.333 1.415 -0.082 1.44e-02 4.82e+03 3.26e+01 bond pdb=" CG LEU B 79 " pdb=" CD2 LEU B 79 " ideal model delta sigma weight residual 1.521 1.419 0.102 3.30e-02 9.18e+02 9.62e+00 bond pdb=" CG1 ILE B 123 " pdb=" CD1 ILE B 123 " ideal model delta sigma weight residual 1.513 1.406 0.107 3.90e-02 6.57e+02 7.51e+00 bond pdb=" C LEU R 237 " pdb=" N PRO R 238 " ideal model delta sigma weight residual 1.335 1.368 -0.034 1.28e-02 6.10e+03 6.99e+00 ... (remaining 9019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 11938 3.21 - 6.43: 258 6.43 - 9.64: 26 9.64 - 12.86: 3 12.86 - 16.07: 5 Bond angle restraints: 12230 Sorted by residual: angle pdb=" N PRO S 41 " pdb=" CA PRO S 41 " pdb=" C PRO S 41 " ideal model delta sigma weight residual 113.81 121.95 -8.14 1.45e+00 4.76e-01 3.15e+01 angle pdb=" C ASP B 333 " pdb=" N SER B 334 " pdb=" CA SER B 334 " ideal model delta sigma weight residual 122.74 130.63 -7.89 1.44e+00 4.82e-01 3.01e+01 angle pdb=" N LEU R 237 " pdb=" CA LEU R 237 " pdb=" C LEU R 237 " ideal model delta sigma weight residual 113.45 120.88 -7.43 1.39e+00 5.18e-01 2.85e+01 angle pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta sigma weight residual 121.54 131.52 -9.98 1.91e+00 2.74e-01 2.73e+01 angle pdb=" C TRP R 250 " pdb=" N LYS R 251 " pdb=" CA LYS R 251 " ideal model delta sigma weight residual 122.08 129.29 -7.21 1.47e+00 4.63e-01 2.41e+01 ... (remaining 12225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 4478 17.14 - 34.27: 572 34.27 - 51.41: 197 51.41 - 68.55: 52 68.55 - 85.69: 12 Dihedral angle restraints: 5311 sinusoidal: 2075 harmonic: 3236 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 159.43 -66.43 1 1.00e+01 1.00e-02 5.76e+01 dihedral pdb=" CA THR R 30 " pdb=" C THR R 30 " pdb=" N LEU R 31 " pdb=" CA LEU R 31 " ideal model delta harmonic sigma weight residual -180.00 -154.56 -25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ASP R 254 " pdb=" C ASP R 254 " pdb=" N VAL R 255 " pdb=" CA VAL R 255 " ideal model delta harmonic sigma weight residual -180.00 -154.78 -25.22 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 5308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1130 0.082 - 0.164: 227 0.164 - 0.246: 20 0.246 - 0.329: 7 0.329 - 0.411: 1 Chirality restraints: 1385 Sorted by residual: chirality pdb=" CB VAL A 218 " pdb=" CA VAL A 218 " pdb=" CG1 VAL A 218 " pdb=" CG2 VAL A 218 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.62 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CG LEU S 162 " pdb=" CB LEU S 162 " pdb=" CD1 LEU S 162 " pdb=" CD2 LEU S 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 1382 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER S 172 " -0.046 5.00e-02 4.00e+02 6.95e-02 7.72e+00 pdb=" N PRO S 173 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO S 173 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO S 173 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.046 5.00e-02 4.00e+02 6.78e-02 7.35e+00 pdb=" N PRO S 75 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 149 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.78e+00 pdb=" C VAL R 149 " -0.042 2.00e-02 2.50e+03 pdb=" O VAL R 149 " 0.016 2.00e-02 2.50e+03 pdb=" N CYS R 150 " 0.014 2.00e-02 2.50e+03 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1853 2.77 - 3.30: 7280 3.30 - 3.83: 15787 3.83 - 4.37: 18448 4.37 - 4.90: 32102 Nonbonded interactions: 75470 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.236 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.286 3.040 nonbonded pdb=" O GLY R 27 " pdb=" OH TYR R 89 " model vdw 2.291 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.297 3.040 nonbonded pdb=" O SER R 264 " pdb=" OG SER R 268 " model vdw 2.306 3.040 ... (remaining 75465 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.230 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.620 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 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 : 0.012 0.134 9028 Z= 0.506 Angle : 1.177 16.073 12238 Z= 0.634 Chirality : 0.067 0.411 1385 Planarity : 0.008 0.069 1530 Dihedral : 18.032 85.686 3213 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 10.86 % Allowed : 18.27 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.82 (0.21), residues: 1108 helix: -2.79 (0.16), residues: 387 sheet: -0.57 (0.29), residues: 279 loop : -1.65 (0.25), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 314 TYR 0.023 0.004 TYR S 50 PHE 0.028 0.004 PHE B 151 TRP 0.015 0.004 TRP S 47 HIS 0.011 0.003 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.01165 / 0.51 ( 9024) covalent geometry : angle 1.17381 / 0.63 (12230) SS BOND : bond 0.01765 / 0.91 ( 4) SS BOND : angle 3.32485 / 1.88 ( 8) hydrogen bonds : bond 0.16487 / 11.02 ( 437) hydrogen bonds : angle 7.57451 / 5.32 ( 1257) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 216 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.8256 (m-30) cc_final: 0.8052 (m-30) REVERT: A 29 LYS cc_start: 0.7879 (tppt) cc_final: 0.7514 (tppt) REVERT: A 32 ARG cc_start: 0.8335 (ptp90) cc_final: 0.7887 (ptp-170) REVERT: A 205 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.6654 (mtm180) REVERT: A 248 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8127 (mttp) REVERT: A 273 LEU cc_start: 0.8539 (tp) cc_final: 0.8185 (tp) REVERT: A 305 CYS cc_start: 0.8128 (t) cc_final: 0.7844 (p) REVERT: B 10 GLU cc_start: 0.8181 (tp30) cc_final: 0.7699 (tp30) REVERT: B 15 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8502 (mtmt) REVERT: B 127 LYS cc_start: 0.9073 (mptm) cc_final: 0.8839 (mmtp) REVERT: B 146 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8855 (tp) REVERT: B 172 GLU cc_start: 0.7580 (pp20) cc_final: 0.7308 (tm-30) REVERT: B 188 MET cc_start: 0.8860 (mmm) cc_final: 0.8496 (mmm) REVERT: S 23 SER cc_start: 0.8905 (OUTLIER) cc_final: 0.8646 (p) REVERT: R 22 LEU cc_start: 0.6317 (OUTLIER) cc_final: 0.5832 (tm) REVERT: R 24 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6586 (mm) REVERT: R 28 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7115 (mmpt) REVERT: R 32 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7658 (tp) REVERT: R 52 LEU cc_start: 0.9279 (mt) cc_final: 0.9052 (mt) REVERT: R 58 ARG cc_start: 0.7892 (mmt-90) cc_final: 0.7662 (mmp80) REVERT: R 152 LEU cc_start: 0.8596 (mt) cc_final: 0.8371 (mt) REVERT: R 278 ILE cc_start: 0.9025 (mt) cc_final: 0.8749 (mt) REVERT: R 289 TRP cc_start: 0.5361 (p-90) cc_final: 0.4343 (m-10) outliers start: 104 outliers final: 34 residues processed: 303 average time/residue: 0.4363 time to fit residues: 141.3745 Evaluate side-chains 223 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 125 ASP Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 28 LYS Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 91 SER Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 248 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS A 195 HIS A 204 GLN A 213 HIS A 255 ASN B 175 GLN B 259 GLN B 311 HIS S 3 GLN ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.133953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.092347 restraints weight = 11575.574| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.34 r_work: 0.2920 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9028 Z= 0.140 Angle : 0.605 9.779 12238 Z= 0.311 Chirality : 0.043 0.223 1385 Planarity : 0.005 0.039 1530 Dihedral : 9.788 82.102 1312 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.91 % Allowed : 24.53 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.49 (0.24), residues: 1108 helix: 0.32 (0.25), residues: 381 sheet: 0.05 (0.31), residues: 262 loop : -1.00 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 129 TYR 0.017 0.001 TYR R 222 PHE 0.020 0.001 PHE R 257 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 9024) covalent geometry : angle 0.60320 / 0.31 (12230) SS BOND : bond 0.01262 / 0.65 ( 4) SS BOND : angle 2.09116 / 1.11 ( 8) hydrogen bonds : bond 0.04081 / 2.78 ( 437) hydrogen bonds : angle 4.93170 / 3.43 ( 1257) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 207 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8684 (tt0) REVERT: A 20 ASP cc_start: 0.8730 (m-30) cc_final: 0.8429 (m-30) REVERT: A 21 ARG cc_start: 0.8333 (mtm110) cc_final: 0.8039 (ttm-80) REVERT: A 29 LYS cc_start: 0.7994 (tppt) cc_final: 0.7694 (tppt) REVERT: A 305 CYS cc_start: 0.8749 (t) cc_final: 0.8150 (t) REVERT: A 306 GLN cc_start: 0.8596 (mm110) cc_final: 0.8363 (mm110) REVERT: B 8 ARG cc_start: 0.7639 (mpt-90) cc_final: 0.7378 (mpt-90) REVERT: B 9 GLN cc_start: 0.8400 (mm110) cc_final: 0.8017 (tm-30) REVERT: B 10 GLU cc_start: 0.8433 (tp30) cc_final: 0.7954 (tp30) REVERT: B 23 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8738 (tmmm) REVERT: B 101 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8952 (mtm) REVERT: B 127 LYS cc_start: 0.9232 (mptm) cc_final: 0.8842 (mmtp) REVERT: B 146 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8961 (tp) REVERT: B 188 MET cc_start: 0.9160 (mmm) cc_final: 0.8940 (mmm) REVERT: B 197 ARG cc_start: 0.8541 (mtp-110) cc_final: 0.8035 (mmp-170) REVERT: B 266 HIS cc_start: 0.8844 (t-90) cc_final: 0.8432 (t70) REVERT: G 20 LYS cc_start: 0.8916 (ttmt) cc_final: 0.8697 (ttmm) REVERT: G 32 LYS cc_start: 0.8837 (tttt) cc_final: 0.8577 (tmtp) REVERT: G 37 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8649 (mp) REVERT: S 43 LYS cc_start: 0.8759 (mppt) cc_final: 0.8504 (mppt) REVERT: S 62 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8450 (p0) REVERT: S 87 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7240 (mtp85) REVERT: S 168 ARG cc_start: 0.9075 (mtt90) cc_final: 0.8656 (mtt90) REVERT: S 206 ARG cc_start: 0.8332 (tmm-80) cc_final: 0.8036 (tmm-80) REVERT: S 222 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8306 (mt-10) REVERT: R 22 LEU cc_start: 0.5735 (OUTLIER) cc_final: 0.5261 (tm) REVERT: R 52 LEU cc_start: 0.9217 (mt) cc_final: 0.8992 (mt) REVERT: R 58 ARG cc_start: 0.8076 (mmt-90) cc_final: 0.7680 (mmp80) REVERT: R 221 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8053 (mp) REVERT: R 249 ILE cc_start: 0.8311 (mt) cc_final: 0.8034 (mm) REVERT: R 278 ILE cc_start: 0.8930 (mt) cc_final: 0.8650 (mt) outliers start: 47 outliers final: 15 residues processed: 231 average time/residue: 0.5285 time to fit residues: 129.1318 Evaluate side-chains 207 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 128 CYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 248 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 101 optimal weight: 9.9990 chunk 25 optimal weight: 0.0040 overall best weight: 2.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS A 195 HIS A 255 ASN B 36 ASN G 24 ASN S 3 GLN S 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.131831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.090220 restraints weight = 11483.710| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.34 r_work: 0.2890 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9028 Z= 0.190 Angle : 0.615 10.791 12238 Z= 0.313 Chirality : 0.044 0.226 1385 Planarity : 0.004 0.033 1530 Dihedral : 8.540 81.720 1262 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.85 % Allowed : 24.95 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.13 (0.25), residues: 1108 helix: 1.20 (0.26), residues: 391 sheet: 0.01 (0.31), residues: 271 loop : -0.80 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 129 TYR 0.018 0.002 TYR R 222 PHE 0.019 0.002 PHE R 257 TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 ( 9024) covalent geometry : angle 0.61177 / 0.31 (12230) SS BOND : bond 0.01506 / 0.78 ( 4) SS BOND : angle 2.43573 / 1.29 ( 8) hydrogen bonds : bond 0.04216 / 2.88 ( 437) hydrogen bonds : angle 4.66159 / 3.24 ( 1257) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 186 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8300 (ptp90) REVERT: A 308 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8084 (mt-10) REVERT: B 9 GLN cc_start: 0.8456 (mm110) cc_final: 0.8113 (tm-30) REVERT: B 10 GLU cc_start: 0.8433 (tp30) cc_final: 0.7960 (tp30) REVERT: B 15 LYS cc_start: 0.8881 (ttmt) cc_final: 0.8572 (mtmt) REVERT: B 23 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8736 (tmmm) REVERT: B 101 MET cc_start: 0.9309 (OUTLIER) cc_final: 0.8952 (mtm) REVERT: B 127 LYS cc_start: 0.9289 (mptm) cc_final: 0.8938 (mmtp) REVERT: B 146 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9052 (tp) REVERT: B 172 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8471 (mm-30) REVERT: B 188 MET cc_start: 0.9243 (mmm) cc_final: 0.8945 (mmm) REVERT: B 197 ARG cc_start: 0.8638 (mtp-110) cc_final: 0.8134 (mmp-170) REVERT: B 226 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7970 (mp0) REVERT: B 266 HIS cc_start: 0.8893 (t-90) cc_final: 0.8684 (t-90) REVERT: G 17 GLU cc_start: 0.8178 (tp30) cc_final: 0.7954 (tp30) REVERT: G 20 LYS cc_start: 0.8945 (ttmt) cc_final: 0.8699 (ttmm) REVERT: G 37 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8671 (mp) REVERT: S 43 LYS cc_start: 0.8819 (mppt) cc_final: 0.8582 (mppt) REVERT: S 87 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7254 (mtp85) REVERT: S 168 ARG cc_start: 0.9059 (mtt90) cc_final: 0.8851 (mtt90) REVERT: S 206 ARG cc_start: 0.8350 (tmm-80) cc_final: 0.7981 (tmm-80) REVERT: R 22 LEU cc_start: 0.5788 (OUTLIER) cc_final: 0.5341 (tm) REVERT: R 52 LEU cc_start: 0.9213 (mt) cc_final: 0.8990 (mt) REVERT: R 58 ARG cc_start: 0.8088 (mmt-90) cc_final: 0.7737 (mmp80) REVERT: R 152 LEU cc_start: 0.8629 (mt) cc_final: 0.8386 (tt) REVERT: R 249 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.8042 (mm) REVERT: R 278 ILE cc_start: 0.8944 (mt) cc_final: 0.8640 (mt) outliers start: 56 outliers final: 27 residues processed: 218 average time/residue: 0.5079 time to fit residues: 117.1415 Evaluate side-chains 216 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 179 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 128 CYS Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 248 TRP Chi-restraints excluded: chain R residue 249 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 88 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 16 optimal weight: 0.2980 chunk 5 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS A 195 HIS B 36 ASN G 24 ASN S 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.134026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.094917 restraints weight = 11813.162| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.23 r_work: 0.2982 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9028 Z= 0.132 Angle : 0.575 10.266 12238 Z= 0.289 Chirality : 0.042 0.211 1385 Planarity : 0.004 0.035 1530 Dihedral : 8.227 81.088 1260 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.91 % Allowed : 25.68 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.57 (0.25), residues: 1108 helix: 1.72 (0.27), residues: 383 sheet: 0.10 (0.30), residues: 275 loop : -0.55 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 129 TYR 0.018 0.001 TYR R 222 PHE 0.016 0.001 PHE R 257 TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 9024) covalent geometry : angle 0.57261 / 0.29 (12230) SS BOND : bond 0.01136 / 0.59 ( 4) SS BOND : angle 2.01103 / 1.06 ( 8) hydrogen bonds : bond 0.03770 / 2.57 ( 437) hydrogen bonds : angle 4.48381 / 3.11 ( 1257) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 197 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8200 (tppt) cc_final: 0.7934 (tppt) REVERT: A 308 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8131 (mt-10) REVERT: B 8 ARG cc_start: 0.7724 (mpt180) cc_final: 0.7517 (mpt180) REVERT: B 9 GLN cc_start: 0.8430 (mm110) cc_final: 0.8153 (tm-30) REVERT: B 10 GLU cc_start: 0.8407 (tp30) cc_final: 0.8026 (tp30) REVERT: B 15 LYS cc_start: 0.8947 (ttmt) cc_final: 0.8550 (mtmt) REVERT: B 101 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8810 (mtm) REVERT: B 127 LYS cc_start: 0.9235 (mptm) cc_final: 0.8837 (mmtm) REVERT: B 135 VAL cc_start: 0.9174 (t) cc_final: 0.8935 (p) REVERT: B 146 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8966 (tp) REVERT: B 188 MET cc_start: 0.9189 (mmm) cc_final: 0.8864 (mmm) REVERT: B 197 ARG cc_start: 0.8615 (mtp-110) cc_final: 0.8134 (mmp-170) REVERT: B 217 MET cc_start: 0.9055 (pmm) cc_final: 0.8818 (ppp) REVERT: B 226 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7945 (mp0) REVERT: G 20 LYS cc_start: 0.8998 (ttmt) cc_final: 0.8764 (ttmm) REVERT: G 37 LEU cc_start: 0.8951 (tp) cc_final: 0.8651 (mp) REVERT: S 43 LYS cc_start: 0.8811 (mppt) cc_final: 0.8593 (mppt) REVERT: S 65 LYS cc_start: 0.8812 (ttmt) cc_final: 0.8608 (ttmt) REVERT: S 87 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.8138 (ptp-170) REVERT: S 206 ARG cc_start: 0.8325 (tmm-80) cc_final: 0.7737 (ttp80) REVERT: R 22 LEU cc_start: 0.5807 (OUTLIER) cc_final: 0.5427 (tm) REVERT: R 58 ARG cc_start: 0.8144 (mmt-90) cc_final: 0.7617 (mmp80) REVERT: R 208 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7625 (mmm160) REVERT: R 249 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.8039 (mm) REVERT: R 270 LEU cc_start: 0.8826 (tp) cc_final: 0.8518 (tm) REVERT: R 278 ILE cc_start: 0.8933 (mt) cc_final: 0.8611 (mt) outliers start: 47 outliers final: 25 residues processed: 224 average time/residue: 0.5306 time to fit residues: 125.9603 Evaluate side-chains 214 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 128 CYS Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 248 TRP Chi-restraints excluded: chain R residue 249 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 105 optimal weight: 0.3980 chunk 106 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS A 195 HIS B 36 ASN G 24 ASN S 3 GLN S 77 ASN S 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.130670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.090469 restraints weight = 11895.532| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.31 r_work: 0.2900 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9028 Z= 0.129 Angle : 0.567 10.101 12238 Z= 0.285 Chirality : 0.042 0.199 1385 Planarity : 0.004 0.041 1530 Dihedral : 7.957 80.728 1258 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 5.22 % Allowed : 26.30 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.77 (0.25), residues: 1108 helix: 2.04 (0.27), residues: 377 sheet: 0.12 (0.31), residues: 258 loop : -0.47 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 21 TYR 0.018 0.001 TYR R 222 PHE 0.014 0.001 PHE R 257 TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 9024) covalent geometry : angle 0.56510 / 0.28 (12230) SS BOND : bond 0.01173 / 0.61 ( 4) SS BOND : angle 2.07662 / 1.10 ( 8) hydrogen bonds : bond 0.03657 / 2.50 ( 437) hydrogen bonds : angle 4.36525 / 3.03 ( 1257) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 197 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8182 (tppt) cc_final: 0.7519 (tppt) REVERT: A 244 HIS cc_start: 0.8407 (m90) cc_final: 0.7884 (m90) REVERT: A 304 GLN cc_start: 0.8452 (tm-30) cc_final: 0.7968 (tm-30) REVERT: A 308 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8015 (mt-10) REVERT: B 8 ARG cc_start: 0.7772 (mpt180) cc_final: 0.7451 (mpt-90) REVERT: B 9 GLN cc_start: 0.8434 (mm110) cc_final: 0.8128 (tm-30) REVERT: B 10 GLU cc_start: 0.8429 (tp30) cc_final: 0.7987 (tp30) REVERT: B 15 LYS cc_start: 0.8813 (ttmt) cc_final: 0.8444 (mtmt) REVERT: B 101 MET cc_start: 0.9296 (OUTLIER) cc_final: 0.8843 (mtm) REVERT: B 127 LYS cc_start: 0.9201 (mptm) cc_final: 0.8765 (mmtm) REVERT: B 135 VAL cc_start: 0.9202 (t) cc_final: 0.8997 (p) REVERT: B 170 ASP cc_start: 0.8771 (t70) cc_final: 0.8536 (t0) REVERT: B 188 MET cc_start: 0.9243 (mmm) cc_final: 0.8990 (mmm) REVERT: B 197 ARG cc_start: 0.8612 (mtp-110) cc_final: 0.8105 (mmp-170) REVERT: B 226 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: B 262 MET cc_start: 0.8905 (tpt) cc_final: 0.8535 (ttm) REVERT: B 266 HIS cc_start: 0.8826 (t-90) cc_final: 0.8544 (t70) REVERT: G 17 GLU cc_start: 0.7987 (tp30) cc_final: 0.7659 (tp30) REVERT: G 20 LYS cc_start: 0.8927 (ttmt) cc_final: 0.8667 (ttmm) REVERT: G 29 LYS cc_start: 0.8644 (mmmt) cc_final: 0.8405 (mptp) REVERT: G 37 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8588 (mp) REVERT: S 43 LYS cc_start: 0.8806 (mppt) cc_final: 0.8526 (mppt) REVERT: S 62 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.8438 (p0) REVERT: S 87 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.8116 (ptp-170) REVERT: S 206 ARG cc_start: 0.8315 (tmm-80) cc_final: 0.8054 (tmm-80) REVERT: R 22 LEU cc_start: 0.5785 (OUTLIER) cc_final: 0.5357 (tm) REVERT: R 58 ARG cc_start: 0.8085 (mmt-90) cc_final: 0.7566 (mmp80) REVERT: R 181 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.6831 (tt0) REVERT: R 249 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8121 (mm) REVERT: R 270 LEU cc_start: 0.8745 (tp) cc_final: 0.8453 (tm) REVERT: R 278 ILE cc_start: 0.8845 (mt) cc_final: 0.8514 (mt) outliers start: 50 outliers final: 25 residues processed: 227 average time/residue: 0.4824 time to fit residues: 116.1852 Evaluate side-chains 221 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 128 CYS Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 248 TRP Chi-restraints excluded: chain R residue 249 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 106 optimal weight: 20.0000 chunk 91 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS A 195 HIS B 36 ASN G 24 ASN S 3 GLN S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.129992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.088106 restraints weight = 11654.854| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.32 r_work: 0.2854 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 9028 Z= 0.284 Angle : 0.668 11.935 12238 Z= 0.340 Chirality : 0.047 0.212 1385 Planarity : 0.004 0.043 1530 Dihedral : 8.240 80.012 1257 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.85 % Allowed : 26.20 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.70 (0.25), residues: 1108 helix: 1.97 (0.27), residues: 382 sheet: 0.06 (0.31), residues: 274 loop : -0.53 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 21 TYR 0.020 0.002 TYR R 222 PHE 0.022 0.002 PHE R 183 TRP 0.015 0.002 TRP S 47 HIS 0.006 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00652 / 0.28 ( 9024) covalent geometry : angle 0.66302 / 0.34 (12230) SS BOND : bond 0.02068 / 1.08 ( 4) SS BOND : angle 3.20685 / 1.71 ( 8) hydrogen bonds : bond 0.04321 / 2.94 ( 437) hydrogen bonds : angle 4.59168 / 3.19 ( 1257) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 188 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 HIS cc_start: 0.8417 (m90) cc_final: 0.7961 (m90) REVERT: A 273 LEU cc_start: 0.8533 (tp) cc_final: 0.8222 (tp) REVERT: A 306 GLN cc_start: 0.8614 (tp40) cc_final: 0.8367 (mm110) REVERT: A 308 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8158 (mt-10) REVERT: B 8 ARG cc_start: 0.7818 (mpt180) cc_final: 0.7581 (mpt-90) REVERT: B 9 GLN cc_start: 0.8471 (mm110) cc_final: 0.8142 (tm-30) REVERT: B 10 GLU cc_start: 0.8450 (tp30) cc_final: 0.8034 (tp30) REVERT: B 15 LYS cc_start: 0.8859 (ttmt) cc_final: 0.8569 (mtmt) REVERT: B 101 MET cc_start: 0.9361 (OUTLIER) cc_final: 0.8990 (mtm) REVERT: B 127 LYS cc_start: 0.9254 (mptm) cc_final: 0.8898 (mmtp) REVERT: B 188 MET cc_start: 0.9290 (mmm) cc_final: 0.8995 (mmm) REVERT: B 226 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: G 17 GLU cc_start: 0.8127 (tp30) cc_final: 0.7894 (tp30) REVERT: G 20 LYS cc_start: 0.8954 (ttmt) cc_final: 0.8689 (ttmm) REVERT: S 43 LYS cc_start: 0.8861 (mppt) cc_final: 0.8578 (mppt) REVERT: S 87 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7533 (mtp85) REVERT: R 22 LEU cc_start: 0.5780 (OUTLIER) cc_final: 0.5362 (tm) REVERT: R 52 LEU cc_start: 0.9194 (mt) cc_final: 0.8948 (mt) REVERT: R 58 ARG cc_start: 0.8120 (mmt-90) cc_final: 0.7675 (mmp80) REVERT: R 141 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8198 (ttp80) REVERT: R 181 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.6941 (tt0) REVERT: R 208 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7502 (mmm160) REVERT: R 249 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8125 (mm) REVERT: R 270 LEU cc_start: 0.8821 (tp) cc_final: 0.8543 (tm) REVERT: R 278 ILE cc_start: 0.9005 (mt) cc_final: 0.8678 (mt) outliers start: 56 outliers final: 27 residues processed: 226 average time/residue: 0.4657 time to fit residues: 111.7764 Evaluate side-chains 215 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 141 ARG Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 248 TRP Chi-restraints excluded: chain R residue 249 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 88 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 35 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS A 195 HIS B 36 ASN G 24 ASN S 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.133459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.092025 restraints weight = 11586.978| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.34 r_work: 0.2923 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9028 Z= 0.131 Angle : 0.576 9.998 12238 Z= 0.292 Chirality : 0.042 0.190 1385 Planarity : 0.004 0.042 1530 Dihedral : 7.833 79.028 1257 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.49 % Allowed : 27.56 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.97 (0.26), residues: 1108 helix: 2.26 (0.27), residues: 380 sheet: 0.21 (0.31), residues: 274 loop : -0.43 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 129 TYR 0.019 0.001 TYR R 222 PHE 0.011 0.001 PHE A 189 TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 9024) covalent geometry : angle 0.57381 / 0.29 (12230) SS BOND : bond 0.01143 / 0.59 ( 4) SS BOND : angle 1.96418 / 1.04 ( 8) hydrogen bonds : bond 0.03601 / 2.45 ( 437) hydrogen bonds : angle 4.29414 / 2.98 ( 1257) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 195 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 HIS cc_start: 0.8426 (m90) cc_final: 0.8029 (m90) REVERT: A 273 LEU cc_start: 0.8534 (tp) cc_final: 0.8182 (tp) REVERT: A 306 GLN cc_start: 0.8508 (tp40) cc_final: 0.8233 (mm110) REVERT: A 308 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8146 (mt-10) REVERT: B 8 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7526 (mpt-90) REVERT: B 9 GLN cc_start: 0.8465 (mm110) cc_final: 0.8115 (tm-30) REVERT: B 10 GLU cc_start: 0.8419 (tp30) cc_final: 0.7960 (tp30) REVERT: B 15 LYS cc_start: 0.8834 (ttmt) cc_final: 0.8446 (mtmt) REVERT: B 46 ARG cc_start: 0.8507 (mtm-85) cc_final: 0.8265 (ttp80) REVERT: B 101 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.8774 (mtm) REVERT: B 127 LYS cc_start: 0.9242 (mptm) cc_final: 0.8840 (mmtm) REVERT: B 170 ASP cc_start: 0.8826 (t70) cc_final: 0.8591 (t0) REVERT: B 188 MET cc_start: 0.9236 (mmm) cc_final: 0.8940 (mmm) REVERT: B 197 ARG cc_start: 0.8678 (mmm160) cc_final: 0.8020 (mmp-170) REVERT: B 217 MET cc_start: 0.9142 (pmm) cc_final: 0.8902 (ppp) REVERT: B 226 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7853 (mp0) REVERT: G 17 GLU cc_start: 0.8083 (tp30) cc_final: 0.7794 (tp30) REVERT: G 20 LYS cc_start: 0.8972 (ttmt) cc_final: 0.8722 (ttmm) REVERT: G 29 LYS cc_start: 0.8598 (mmmt) cc_final: 0.8354 (mptp) REVERT: G 37 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8577 (mp) REVERT: S 43 LYS cc_start: 0.8832 (mppt) cc_final: 0.8532 (mppt) REVERT: S 62 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8433 (p0) REVERT: S 87 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7924 (mtp85) REVERT: R 22 LEU cc_start: 0.5768 (OUTLIER) cc_final: 0.5387 (tm) REVERT: R 58 ARG cc_start: 0.8118 (mmt-90) cc_final: 0.7506 (mmp80) REVERT: R 181 GLN cc_start: 0.7433 (OUTLIER) cc_final: 0.6846 (tt0) REVERT: R 208 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7474 (mmm160) REVERT: R 249 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8125 (mm) REVERT: R 270 LEU cc_start: 0.8752 (tp) cc_final: 0.8471 (tm) REVERT: R 278 ILE cc_start: 0.8876 (mt) cc_final: 0.8524 (mt) outliers start: 43 outliers final: 22 residues processed: 220 average time/residue: 0.4998 time to fit residues: 116.5308 Evaluate side-chains 218 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 248 TRP Chi-restraints excluded: chain R residue 249 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 6.9990 chunk 108 optimal weight: 0.0020 chunk 59 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 48 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS A 195 HIS B 36 ASN G 24 ASN S 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.132750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.093877 restraints weight = 11871.845| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.20 r_work: 0.2968 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9028 Z= 0.133 Angle : 0.591 10.028 12238 Z= 0.298 Chirality : 0.042 0.176 1385 Planarity : 0.004 0.047 1530 Dihedral : 7.585 79.128 1255 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.18 % Allowed : 28.71 % Favored : 67.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.08 (0.26), residues: 1108 helix: 2.36 (0.27), residues: 381 sheet: 0.20 (0.31), residues: 274 loop : -0.34 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 129 TYR 0.019 0.001 TYR R 222 PHE 0.014 0.001 PHE R 183 TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 9024) covalent geometry : angle 0.58882 / 0.30 (12230) SS BOND : bond 0.01170 / 0.61 ( 4) SS BOND : angle 2.18927 / 1.16 ( 8) hydrogen bonds : bond 0.03594 / 2.44 ( 437) hydrogen bonds : angle 4.25037 / 2.95 ( 1257) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 197 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 HIS cc_start: 0.8433 (m90) cc_final: 0.8040 (m90) REVERT: A 306 GLN cc_start: 0.8519 (tp40) cc_final: 0.8241 (mm110) REVERT: A 308 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8146 (mt-10) REVERT: B 8 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7582 (mpt-90) REVERT: B 9 GLN cc_start: 0.8469 (mm110) cc_final: 0.8152 (tm-30) REVERT: B 10 GLU cc_start: 0.8480 (tp30) cc_final: 0.8022 (tp30) REVERT: B 15 LYS cc_start: 0.8893 (ttmt) cc_final: 0.8508 (mtmt) REVERT: B 46 ARG cc_start: 0.8513 (mtm-85) cc_final: 0.8281 (ttp80) REVERT: B 101 MET cc_start: 0.9200 (OUTLIER) cc_final: 0.8703 (mtm) REVERT: B 127 LYS cc_start: 0.9225 (mptm) cc_final: 0.8837 (mmtm) REVERT: B 146 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8910 (tm) REVERT: B 188 MET cc_start: 0.9195 (mmm) cc_final: 0.8868 (mmm) REVERT: B 226 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7819 (mp0) REVERT: B 266 HIS cc_start: 0.8857 (t-90) cc_final: 0.8642 (t70) REVERT: G 17 GLU cc_start: 0.8150 (tp30) cc_final: 0.7891 (tp30) REVERT: G 20 LYS cc_start: 0.9038 (ttmt) cc_final: 0.8789 (ttmm) REVERT: G 29 LYS cc_start: 0.8673 (mmmt) cc_final: 0.8434 (mptp) REVERT: S 62 ASP cc_start: 0.8724 (OUTLIER) cc_final: 0.8494 (p0) REVERT: S 87 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.8033 (ptp-170) REVERT: S 148 ARG cc_start: 0.7893 (mmm-85) cc_final: 0.7313 (mmm-85) REVERT: S 168 ARG cc_start: 0.8934 (mtt180) cc_final: 0.8678 (mtt180) REVERT: R 22 LEU cc_start: 0.5798 (OUTLIER) cc_final: 0.5439 (tm) REVERT: R 58 ARG cc_start: 0.8113 (mmt-90) cc_final: 0.7522 (mmp80) REVERT: R 60 ARG cc_start: 0.7775 (ttm170) cc_final: 0.7556 (ttp-170) REVERT: R 181 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6826 (tt0) REVERT: R 208 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7538 (mmm160) REVERT: R 249 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8237 (mm) REVERT: R 270 LEU cc_start: 0.8766 (tp) cc_final: 0.8508 (tm) REVERT: R 278 ILE cc_start: 0.8863 (mt) cc_final: 0.8530 (mt) outliers start: 40 outliers final: 21 residues processed: 219 average time/residue: 0.4786 time to fit residues: 111.5185 Evaluate side-chains 217 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 248 TRP Chi-restraints excluded: chain R residue 249 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS A 195 HIS B 36 ASN G 24 ASN S 3 GLN S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.130882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.091555 restraints weight = 11816.416| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.22 r_work: 0.2924 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 9028 Z= 0.198 Angle : 0.643 10.603 12238 Z= 0.325 Chirality : 0.044 0.177 1385 Planarity : 0.004 0.051 1530 Dihedral : 7.735 78.679 1255 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.59 % Allowed : 28.39 % Favored : 67.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.05 (0.26), residues: 1108 helix: 2.34 (0.27), residues: 379 sheet: 0.12 (0.30), residues: 279 loop : -0.29 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 129 TYR 0.020 0.002 TYR R 222 PHE 0.024 0.002 PHE R 257 TRP 0.013 0.001 TRP S 47 HIS 0.005 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 ( 9024) covalent geometry : angle 0.63904 / 0.32 (12230) SS BOND : bond 0.01649 / 0.86 ( 4) SS BOND : angle 2.74034 / 1.45 ( 8) hydrogen bonds : bond 0.03920 / 2.66 ( 437) hydrogen bonds : angle 4.40881 / 3.07 ( 1257) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 184 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 HIS cc_start: 0.8511 (m90) cc_final: 0.8066 (m90) REVERT: A 273 LEU cc_start: 0.8583 (tp) cc_final: 0.8300 (tp) REVERT: A 306 GLN cc_start: 0.8555 (tp40) cc_final: 0.8327 (mm110) REVERT: B 8 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7588 (mpt-90) REVERT: B 9 GLN cc_start: 0.8475 (mm110) cc_final: 0.8166 (tm-30) REVERT: B 10 GLU cc_start: 0.8498 (tp30) cc_final: 0.8061 (tp30) REVERT: B 15 LYS cc_start: 0.8923 (ttmt) cc_final: 0.8578 (mtmt) REVERT: B 101 MET cc_start: 0.9300 (OUTLIER) cc_final: 0.8816 (mtm) REVERT: B 127 LYS cc_start: 0.9273 (mptm) cc_final: 0.8940 (mmtp) REVERT: B 130 GLU cc_start: 0.8783 (mp0) cc_final: 0.8487 (mp0) REVERT: B 188 MET cc_start: 0.9241 (mmm) cc_final: 0.8921 (mmm) REVERT: B 197 ARG cc_start: 0.8590 (mtp-110) cc_final: 0.8292 (mmp-170) REVERT: B 226 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: B 266 HIS cc_start: 0.8870 (t-90) cc_final: 0.8624 (t70) REVERT: G 17 GLU cc_start: 0.8195 (tp30) cc_final: 0.7943 (tp30) REVERT: G 20 LYS cc_start: 0.9026 (ttmt) cc_final: 0.8802 (ttmm) REVERT: S 62 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8473 (p0) REVERT: S 87 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8121 (ptp-170) REVERT: S 148 ARG cc_start: 0.7996 (mmm-85) cc_final: 0.7437 (mmm-85) REVERT: S 168 ARG cc_start: 0.8924 (mtt180) cc_final: 0.8701 (mtt180) REVERT: R 22 LEU cc_start: 0.5833 (OUTLIER) cc_final: 0.5485 (tm) REVERT: R 58 ARG cc_start: 0.8121 (mmt-90) cc_final: 0.7513 (mmp80) REVERT: R 181 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.6870 (tt0) REVERT: R 208 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7576 (mmm160) REVERT: R 249 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8444 (mm) REVERT: R 270 LEU cc_start: 0.8826 (tp) cc_final: 0.8572 (tm) REVERT: R 278 ILE cc_start: 0.8928 (mt) cc_final: 0.8602 (mt) outliers start: 44 outliers final: 26 residues processed: 210 average time/residue: 0.4665 time to fit residues: 104.2717 Evaluate side-chains 218 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 248 TRP Chi-restraints excluded: chain R residue 249 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 8 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 16 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS A 195 HIS B 36 ASN G 24 ASN S 3 GLN S 77 ASN S 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.133540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.095082 restraints weight = 11728.982| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.19 r_work: 0.2987 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9028 Z= 0.126 Angle : 0.607 10.025 12238 Z= 0.305 Chirality : 0.042 0.160 1385 Planarity : 0.004 0.057 1530 Dihedral : 7.444 78.452 1255 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.65 % Allowed : 29.75 % Favored : 66.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.14 (0.26), residues: 1108 helix: 2.38 (0.27), residues: 382 sheet: 0.13 (0.31), residues: 271 loop : -0.19 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 21 TYR 0.013 0.001 TYR R 222 PHE 0.026 0.001 PHE R 257 TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 9024) covalent geometry : angle 0.60466 / 0.30 (12230) SS BOND : bond 0.01094 / 0.57 ( 4) SS BOND : angle 1.98648 / 1.05 ( 8) hydrogen bonds : bond 0.03508 / 2.39 ( 437) hydrogen bonds : angle 4.27004 / 2.97 ( 1257) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 192 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8701 (tmtt) cc_final: 0.8499 (pttp) REVERT: A 273 LEU cc_start: 0.8538 (tp) cc_final: 0.8249 (tp) REVERT: A 306 GLN cc_start: 0.8431 (tp40) cc_final: 0.8189 (mt0) REVERT: B 8 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7558 (mpt-90) REVERT: B 9 GLN cc_start: 0.8462 (mm110) cc_final: 0.8153 (tm-30) REVERT: B 10 GLU cc_start: 0.8478 (tp30) cc_final: 0.8021 (tp30) REVERT: B 15 LYS cc_start: 0.8900 (ttmt) cc_final: 0.8555 (mtmt) REVERT: B 46 ARG cc_start: 0.8500 (mtm-85) cc_final: 0.8248 (ttp80) REVERT: B 101 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8658 (mtm) REVERT: B 127 LYS cc_start: 0.9200 (mptm) cc_final: 0.8812 (mmtm) REVERT: B 130 GLU cc_start: 0.8745 (mp0) cc_final: 0.8482 (mp0) REVERT: B 146 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8897 (tm) REVERT: B 188 MET cc_start: 0.9195 (mmm) cc_final: 0.8876 (mmm) REVERT: B 197 ARG cc_start: 0.8515 (mtp-110) cc_final: 0.8246 (mmp-170) REVERT: B 226 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7791 (mp0) REVERT: B 266 HIS cc_start: 0.8840 (t-90) cc_final: 0.8600 (t70) REVERT: G 17 GLU cc_start: 0.8186 (tp30) cc_final: 0.7746 (tp30) REVERT: G 20 LYS cc_start: 0.9018 (ttmt) cc_final: 0.8815 (ttmm) REVERT: G 29 LYS cc_start: 0.8640 (mmmt) cc_final: 0.8372 (mptp) REVERT: S 19 LYS cc_start: 0.8976 (tttm) cc_final: 0.8750 (tptm) REVERT: S 43 LYS cc_start: 0.8620 (mppt) cc_final: 0.8276 (mtmm) REVERT: S 87 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8080 (ptp-170) REVERT: S 148 ARG cc_start: 0.7978 (mmm-85) cc_final: 0.7475 (mmm-85) REVERT: S 234 GLU cc_start: 0.6661 (mp0) cc_final: 0.6452 (mp0) REVERT: R 22 LEU cc_start: 0.5848 (OUTLIER) cc_final: 0.5576 (tm) REVERT: R 58 ARG cc_start: 0.8098 (mmt-90) cc_final: 0.7503 (mmp80) REVERT: R 60 ARG cc_start: 0.7789 (ttm170) cc_final: 0.7559 (ttp-170) REVERT: R 181 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.6825 (tt0) REVERT: R 208 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7533 (mmm160) REVERT: R 249 ILE cc_start: 0.8672 (mt) cc_final: 0.8455 (mm) REVERT: R 270 LEU cc_start: 0.8774 (tp) cc_final: 0.8514 (tm) REVERT: R 278 ILE cc_start: 0.8774 (mt) cc_final: 0.8448 (mt) outliers start: 35 outliers final: 22 residues processed: 214 average time/residue: 0.4678 time to fit residues: 106.4752 Evaluate side-chains 211 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 174 GLN Chi-restraints excluded: chain S residue 203 THR Chi-restraints excluded: chain S residue 205 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 42 LEU Chi-restraints excluded: chain R residue 86 CYS Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 208 ARG Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 248 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 58 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 70 optimal weight: 0.4980 chunk 24 optimal weight: 0.0980 chunk 4 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 HIS A 195 HIS B 36 ASN G 24 ASN S 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.134692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.096631 restraints weight = 11732.597| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.18 r_work: 0.3013 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9028 Z= 0.116 Angle : 0.600 9.948 12238 Z= 0.302 Chirality : 0.042 0.154 1385 Planarity : 0.004 0.059 1530 Dihedral : 7.247 78.596 1254 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.24 % Allowed : 30.48 % Favored : 66.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.20 (0.26), residues: 1108 helix: 2.46 (0.27), residues: 379 sheet: 0.14 (0.30), residues: 269 loop : -0.15 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 21 TYR 0.019 0.001 TYR R 222 PHE 0.028 0.001 PHE R 257 TRP 0.018 0.001 TRP B 169 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 9024) covalent geometry : angle 0.59835 / 0.30 (12230) SS BOND : bond 0.00921 / 0.48 ( 4) SS BOND : angle 1.80194 / 0.94 ( 8) hydrogen bonds : bond 0.03406 / 2.32 ( 437) hydrogen bonds : angle 4.19856 / 2.92 ( 1257) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3460.09 seconds wall clock time: 59 minutes 30.15 seconds (3570.15 seconds total)