Starting phenix.real_space_refine on Sat Aug 23 02:35:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jjp_36364/08_2025/8jjp_36364.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jjp_36364/08_2025/8jjp_36364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jjp_36364/08_2025/8jjp_36364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jjp_36364/08_2025/8jjp_36364.map" model { file = "/net/cci-nas-00/data/ceres_data/8jjp_36364/08_2025/8jjp_36364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jjp_36364/08_2025/8jjp_36364.cif" } resolution = 2.9 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= 0.048 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 60 5.16 5 C 5893 2.51 5 N 1544 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9165 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2415 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 10, 'TRANS': 281} Chain: "C" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1853 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2589 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 431 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1772 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "L" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 77 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.10, per 1000 atoms: 0.23 Number of scatterers: 9165 At special positions: 0 Unit cell: (88.4, 124.95, 133.45, 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 60 16.00 O 1668 8.00 N 1544 7.00 C 5893 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 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: 0.81 Conformation dependent library (CDL) restraints added in 345.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 35.6% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 35 through 65 removed outlier: 4.395A pdb=" N TRP A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) Proline residue: A 54 - end of helix removed outlier: 3.547A pdb=" N VAL A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE A 65 " --> pdb=" O TRP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 89 removed outlier: 4.103A pdb=" N TRP A 75 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE A 76 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 99 removed outlier: 4.401A pdb=" N TYR A 93 " --> pdb=" O PHE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 141 removed outlier: 3.738A pdb=" N LYS A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N PHE A 122 " --> pdb=" O GLN A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 175 removed outlier: 3.882A pdb=" N LEU A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 157 " --> pdb=" O ASN A 153 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 166 " --> pdb=" O TRP A 162 " (cutoff:3.500A) Proline residue: A 171 - end of helix Processing helix chain 'A' and resid 198 through 215 removed outlier: 3.560A pdb=" N ARG A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 235 removed outlier: 3.606A pdb=" N LYS A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS A 235 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 268 removed outlier: 3.654A pdb=" N TRP A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR A 247 " --> pdb=" O ARG A 243 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Proline residue: A 261 - end of helix Processing helix chain 'A' and resid 279 through 304 removed outlier: 3.723A pdb=" N GLN A 283 " --> pdb=" O HIS A 279 " (cutoff:3.500A) Proline residue: A 287 - end of helix removed outlier: 3.564A pdb=" N CYS A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) Proline residue: A 301 - end of helix Processing helix chain 'A' and resid 308 through 325 removed outlier: 3.821A pdb=" N SER A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 30 removed outlier: 3.841A pdb=" N ALA C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA C 12 " --> pdb=" O GLU C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 53 removed outlier: 4.343A pdb=" N MET C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 removed outlier: 4.129A pdb=" N TRP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 216 Processing helix chain 'C' and resid 241 through 255 Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.974A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.589A pdb=" N ILE C 285 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 309 Processing helix chain 'C' and resid 329 through 351 removed outlier: 3.716A pdb=" N GLN C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N CYS C 351 " --> pdb=" O ASN C 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 22 Processing helix chain 'G' and resid 23 through 25 No H-bonds generated for 'chain 'G' and resid 23 through 25' Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 4.008A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'S' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 181 Processing sheet with id=AA2, first strand: chain 'C' and resid 185 through 190 removed outlier: 3.632A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ILE C 264 " --> pdb=" O TYR C 320 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N HIS C 322 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU C 266 " --> pdb=" O HIS C 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.498A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.618A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.099A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.518A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.693A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.575A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.678A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.015A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.317A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.757A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.60 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2904 1.34 - 1.46: 2366 1.46 - 1.58: 4029 1.58 - 1.70: 1 1.70 - 1.82: 86 Bond restraints: 9386 Sorted by residual: bond pdb=" CG PRO A 301 " pdb=" CD PRO A 301 " ideal model delta sigma weight residual 1.503 1.368 0.135 3.40e-02 8.65e+02 1.58e+01 bond pdb=" CB PRO A 301 " pdb=" CG PRO A 301 " ideal model delta sigma weight residual 1.492 1.664 -0.172 5.00e-02 4.00e+02 1.19e+01 bond pdb=" N PRO A 301 " pdb=" CD PRO A 301 " ideal model delta sigma weight residual 1.473 1.518 -0.045 1.40e-02 5.10e+03 1.05e+01 bond pdb=" N PRO A 301 " pdb=" CA PRO A 301 " ideal model delta sigma weight residual 1.469 1.443 0.025 1.28e-02 6.10e+03 3.97e+00 bond pdb=" C LEU A 90 " pdb=" N PRO A 91 " ideal model delta sigma weight residual 1.334 1.368 -0.034 2.34e-02 1.83e+03 2.08e+00 ... (remaining 9381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.57: 12688 3.57 - 7.13: 40 7.13 - 10.70: 4 10.70 - 14.27: 1 14.27 - 17.83: 1 Bond angle restraints: 12734 Sorted by residual: angle pdb=" CA PRO A 301 " pdb=" N PRO A 301 " pdb=" CD PRO A 301 " ideal model delta sigma weight residual 112.00 94.17 17.83 1.40e+00 5.10e-01 1.62e+02 angle pdb=" N PRO A 301 " pdb=" CD PRO A 301 " pdb=" CG PRO A 301 " ideal model delta sigma weight residual 103.20 92.27 10.93 1.50e+00 4.44e-01 5.31e+01 angle pdb=" CA PRO A 301 " pdb=" CB PRO A 301 " pdb=" CG PRO A 301 " ideal model delta sigma weight residual 104.50 96.53 7.97 1.90e+00 2.77e-01 1.76e+01 angle pdb=" CA GLU S 222 " pdb=" CB GLU S 222 " pdb=" CG GLU S 222 " ideal model delta sigma weight residual 114.10 120.03 -5.93 2.00e+00 2.50e-01 8.79e+00 angle pdb=" CA TYR A 96 " pdb=" CB TYR A 96 " pdb=" CG TYR A 96 " ideal model delta sigma weight residual 113.90 119.13 -5.23 1.80e+00 3.09e-01 8.43e+00 ... (remaining 12729 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.45: 5017 22.45 - 44.90: 435 44.90 - 67.35: 80 67.35 - 89.80: 12 89.80 - 112.25: 3 Dihedral angle restraints: 5547 sinusoidal: 2178 harmonic: 3369 Sorted by residual: dihedral pdb=" CB CYS A 110 " pdb=" SG CYS A 110 " pdb=" SG CYS A 187 " pdb=" CB CYS A 187 " ideal model delta sinusoidal sigma weight residual 93.00 -178.92 -88.08 1 1.00e+01 1.00e-02 9.28e+01 dihedral pdb=" CA TRP B 332 " pdb=" C TRP B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta harmonic sigma weight residual 180.00 157.69 22.31 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 160.53 19.47 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 5544 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 839 0.029 - 0.057: 386 0.057 - 0.086: 118 0.086 - 0.115: 72 0.115 - 0.144: 23 Chirality restraints: 1438 Sorted by residual: chirality pdb=" CA THR A 260 " pdb=" N THR A 260 " pdb=" C THR A 260 " pdb=" CB THR A 260 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA HIS A 279 " pdb=" N HIS A 279 " pdb=" C HIS A 279 " pdb=" CB HIS A 279 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CB ILE A 240 " pdb=" CA ILE A 240 " pdb=" CG1 ILE A 240 " pdb=" CG2 ILE A 240 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 1435 not shown) Planarity restraints: 1591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 300 " 0.119 5.00e-02 4.00e+02 1.62e-01 4.20e+01 pdb=" N PRO A 301 " -0.279 5.00e-02 4.00e+02 pdb=" CA PRO A 301 " 0.080 5.00e-02 4.00e+02 pdb=" CD PRO A 301 " 0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 286 " 0.068 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO A 287 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO A 287 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 287 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 170 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.01e+00 pdb=" N PRO A 171 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 171 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 171 " 0.028 5.00e-02 4.00e+02 ... (remaining 1588 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 738 2.74 - 3.28: 8612 3.28 - 3.82: 14619 3.82 - 4.36: 17758 4.36 - 4.90: 31588 Nonbonded interactions: 73315 Sorted by model distance: nonbonded pdb=" O ILE A 286 " pdb=" OG1 THR A 290 " model vdw 2.202 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.241 3.040 nonbonded pdb=" NH1 ARG A 176 " pdb=" OG SER L 137 " model vdw 2.248 3.120 nonbonded pdb=" OE2 GLU C 8 " pdb=" OH TYR S 175 " model vdw 2.250 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.254 3.040 ... (remaining 73310 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.400 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.550 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 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 : 0.003 0.172 9389 Z= 0.132 Angle : 0.600 17.832 12740 Z= 0.327 Chirality : 0.042 0.144 1438 Planarity : 0.006 0.162 1591 Dihedral : 16.865 112.246 3364 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.84 % Allowed : 24.47 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.25), residues: 1144 helix: 1.35 (0.29), residues: 366 sheet: 0.64 (0.30), residues: 278 loop : -1.05 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 197 TYR 0.030 0.002 TYR A 45 PHE 0.018 0.001 PHE A 62 TRP 0.026 0.001 TRP A 268 HIS 0.008 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 9386) covalent geometry : angle 0.59837 (12734) SS BOND : bond 0.00479 ( 3) SS BOND : angle 2.27117 ( 6) hydrogen bonds : bond 0.14782 ( 415) hydrogen bonds : angle 6.00050 ( 1188) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 101 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 158 SER cc_start: 0.8703 (m) cc_final: 0.8327 (p) REVERT: S 192 MET cc_start: 0.8591 (ttt) cc_final: 0.8284 (tmm) outliers start: 38 outliers final: 34 residues processed: 133 average time/residue: 0.4376 time to fit residues: 63.3456 Evaluate side-chains 135 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 106 SER Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.0070 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 HIS A 296 ASN B 340 ASN G 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.177367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.104613 restraints weight = 9942.349| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.12 r_work: 0.3049 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9389 Z= 0.144 Angle : 0.570 8.672 12740 Z= 0.298 Chirality : 0.043 0.141 1438 Planarity : 0.004 0.069 1591 Dihedral : 7.032 70.513 1366 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.15 % Allowed : 22.85 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.25), residues: 1144 helix: 1.45 (0.28), residues: 375 sheet: 0.67 (0.30), residues: 290 loop : -1.02 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 197 TYR 0.017 0.001 TYR A 188 PHE 0.013 0.001 PHE C 189 TRP 0.020 0.001 TRP A 268 HIS 0.006 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9386) covalent geometry : angle 0.56964 (12734) SS BOND : bond 0.00733 ( 3) SS BOND : angle 1.21744 ( 6) hydrogen bonds : bond 0.04575 ( 415) hydrogen bonds : angle 4.61834 ( 1188) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 95 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 303 LEU cc_start: 0.7995 (mp) cc_final: 0.7747 (mt) REVERT: B 198 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8054 (pt) REVERT: B 256 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.6312 (mtp85) outliers start: 41 outliers final: 19 residues processed: 123 average time/residue: 0.4903 time to fit residues: 65.3010 Evaluate side-chains 116 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 155 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 23 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.178337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.106988 restraints weight = 9968.812| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.08 r_work: 0.3015 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9389 Z= 0.137 Angle : 0.550 8.033 12740 Z= 0.287 Chirality : 0.043 0.141 1438 Planarity : 0.004 0.051 1591 Dihedral : 5.594 61.108 1330 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 5.26 % Allowed : 21.64 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.25), residues: 1144 helix: 1.53 (0.28), residues: 374 sheet: 0.67 (0.30), residues: 290 loop : -1.00 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 197 TYR 0.014 0.001 TYR A 188 PHE 0.013 0.001 PHE A 62 TRP 0.016 0.001 TRP A 268 HIS 0.006 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9386) covalent geometry : angle 0.54961 (12734) SS BOND : bond 0.00713 ( 3) SS BOND : angle 0.98860 ( 6) hydrogen bonds : bond 0.04229 ( 415) hydrogen bonds : angle 4.44890 ( 1188) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 102 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 VAL cc_start: 0.8934 (m) cc_final: 0.8705 (t) REVERT: A 139 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6620 (mp) REVERT: B 198 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8003 (pt) REVERT: B 256 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.6305 (mtp85) outliers start: 52 outliers final: 27 residues processed: 140 average time/residue: 0.4556 time to fit residues: 69.4665 Evaluate side-chains 129 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 214 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 19 optimal weight: 8.9990 chunk 5 optimal weight: 0.6980 chunk 110 optimal weight: 0.0470 chunk 46 optimal weight: 10.0000 chunk 93 optimal weight: 0.5980 chunk 86 optimal weight: 0.1980 chunk 3 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 HIS A 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.180230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.109206 restraints weight = 10112.337| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.11 r_work: 0.3058 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9389 Z= 0.106 Angle : 0.510 6.885 12740 Z= 0.269 Chirality : 0.041 0.197 1438 Planarity : 0.004 0.050 1591 Dihedral : 5.185 56.181 1327 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.84 % Allowed : 22.65 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.25), residues: 1144 helix: 1.64 (0.28), residues: 376 sheet: 0.66 (0.30), residues: 290 loop : -0.92 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 197 TYR 0.014 0.001 TYR S 190 PHE 0.026 0.001 PHE A 84 TRP 0.010 0.001 TRP B 82 HIS 0.006 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 9386) covalent geometry : angle 0.50966 (12734) SS BOND : bond 0.00522 ( 3) SS BOND : angle 0.78996 ( 6) hydrogen bonds : bond 0.03620 ( 415) hydrogen bonds : angle 4.29213 ( 1188) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 106 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6638 (mp) REVERT: A 303 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7685 (mt) REVERT: C 324 THR cc_start: 0.7790 (OUTLIER) cc_final: 0.7417 (m) REVERT: B 198 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8001 (pt) REVERT: B 256 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.6295 (mtp85) outliers start: 38 outliers final: 20 residues processed: 131 average time/residue: 0.5081 time to fit residues: 72.0286 Evaluate side-chains 124 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 155 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 10 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 18 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN B 340 ASN G 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.178872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.108407 restraints weight = 9997.440| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.28 r_work: 0.3009 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9389 Z= 0.130 Angle : 0.531 7.069 12740 Z= 0.279 Chirality : 0.042 0.149 1438 Planarity : 0.004 0.050 1591 Dihedral : 5.032 51.086 1324 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 5.06 % Allowed : 22.35 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.25), residues: 1144 helix: 1.75 (0.28), residues: 374 sheet: 0.72 (0.30), residues: 288 loop : -0.94 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 197 TYR 0.012 0.001 TYR S 190 PHE 0.027 0.001 PHE A 84 TRP 0.012 0.001 TRP B 82 HIS 0.006 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9386) covalent geometry : angle 0.53037 (12734) SS BOND : bond 0.00680 ( 3) SS BOND : angle 0.91749 ( 6) hydrogen bonds : bond 0.03897 ( 415) hydrogen bonds : angle 4.32505 ( 1188) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 100 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6627 (mp) REVERT: A 303 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7771 (mt) REVERT: C 324 THR cc_start: 0.7853 (OUTLIER) cc_final: 0.7482 (m) REVERT: B 198 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8018 (pt) REVERT: B 256 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.6310 (mtp85) outliers start: 50 outliers final: 30 residues processed: 136 average time/residue: 0.4573 time to fit residues: 67.6117 Evaluate side-chains 133 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 98 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 214 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 83 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 109 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 96 optimal weight: 0.7980 chunk 78 optimal weight: 0.0050 chunk 90 optimal weight: 0.0570 chunk 16 optimal weight: 5.9990 overall best weight: 0.4512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.180267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.109317 restraints weight = 10022.315| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.09 r_work: 0.3057 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9389 Z= 0.103 Angle : 0.500 6.620 12740 Z= 0.263 Chirality : 0.041 0.139 1438 Planarity : 0.003 0.050 1591 Dihedral : 4.892 50.401 1324 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.65 % Allowed : 23.05 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.25), residues: 1144 helix: 1.84 (0.28), residues: 374 sheet: 0.69 (0.30), residues: 283 loop : -0.84 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 197 TYR 0.013 0.001 TYR S 190 PHE 0.029 0.001 PHE A 84 TRP 0.011 0.001 TRP B 82 HIS 0.006 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 9386) covalent geometry : angle 0.50014 (12734) SS BOND : bond 0.00521 ( 3) SS BOND : angle 0.70273 ( 6) hydrogen bonds : bond 0.03467 ( 415) hydrogen bonds : angle 4.21599 ( 1188) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 105 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 67 TRP cc_start: 0.8117 (OUTLIER) cc_final: 0.7544 (t-100) REVERT: A 139 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6537 (mp) REVERT: A 303 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7727 (mt) REVERT: C 298 GLU cc_start: 0.7860 (tp30) cc_final: 0.6881 (tp30) REVERT: C 324 THR cc_start: 0.7752 (OUTLIER) cc_final: 0.7395 (m) REVERT: B 198 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7953 (pt) REVERT: B 256 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.6214 (mtp85) outliers start: 46 outliers final: 27 residues processed: 142 average time/residue: 0.4522 time to fit residues: 69.4911 Evaluate side-chains 132 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 99 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 67 TRP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 184 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 23 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 92 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN G 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.178592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.107285 restraints weight = 10099.633| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.10 r_work: 0.3015 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9389 Z= 0.135 Angle : 0.536 6.962 12740 Z= 0.281 Chirality : 0.042 0.143 1438 Planarity : 0.004 0.050 1591 Dihedral : 5.002 48.510 1324 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.95 % Allowed : 23.86 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.25), residues: 1144 helix: 1.82 (0.28), residues: 374 sheet: 0.72 (0.30), residues: 294 loop : -0.87 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 197 TYR 0.012 0.001 TYR S 190 PHE 0.031 0.001 PHE A 84 TRP 0.012 0.001 TRP B 82 HIS 0.005 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9386) covalent geometry : angle 0.53556 (12734) SS BOND : bond 0.00724 ( 3) SS BOND : angle 0.89954 ( 6) hydrogen bonds : bond 0.03885 ( 415) hydrogen bonds : angle 4.30216 ( 1188) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 100 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 67 TRP cc_start: 0.8185 (OUTLIER) cc_final: 0.7578 (t-100) REVERT: A 139 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6617 (mp) REVERT: A 303 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7756 (mt) REVERT: C 298 GLU cc_start: 0.7795 (tp30) cc_final: 0.6842 (tp30) REVERT: C 324 THR cc_start: 0.7798 (OUTLIER) cc_final: 0.7465 (m) REVERT: B 198 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7992 (pt) REVERT: B 219 ARG cc_start: 0.8052 (mtp85) cc_final: 0.7841 (mtp85) REVERT: B 256 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6243 (mtp85) outliers start: 49 outliers final: 32 residues processed: 136 average time/residue: 0.4543 time to fit residues: 66.9705 Evaluate side-chains 135 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 97 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 67 TRP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 214 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 89 optimal weight: 0.4980 chunk 40 optimal weight: 7.9990 chunk 106 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.179405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.110253 restraints weight = 9948.654| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.41 r_work: 0.3021 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9389 Z= 0.118 Angle : 0.522 7.779 12740 Z= 0.272 Chirality : 0.042 0.141 1438 Planarity : 0.004 0.049 1591 Dihedral : 4.949 48.909 1324 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.65 % Allowed : 24.17 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.25), residues: 1144 helix: 1.84 (0.28), residues: 375 sheet: 0.69 (0.30), residues: 295 loop : -0.84 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 197 TYR 0.013 0.001 TYR S 190 PHE 0.035 0.001 PHE A 84 TRP 0.011 0.001 TRP B 82 HIS 0.006 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9386) covalent geometry : angle 0.52153 (12734) SS BOND : bond 0.00584 ( 3) SS BOND : angle 0.75186 ( 6) hydrogen bonds : bond 0.03636 ( 415) hydrogen bonds : angle 4.27102 ( 1188) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 102 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 67 TRP cc_start: 0.8145 (OUTLIER) cc_final: 0.7569 (t-100) REVERT: A 139 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6643 (mp) REVERT: C 298 GLU cc_start: 0.7774 (tp30) cc_final: 0.6831 (tp30) REVERT: C 324 THR cc_start: 0.7774 (OUTLIER) cc_final: 0.7439 (m) REVERT: B 198 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7979 (pt) REVERT: B 256 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6239 (mtp85) outliers start: 46 outliers final: 32 residues processed: 137 average time/residue: 0.4291 time to fit residues: 63.7673 Evaluate side-chains 134 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 97 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 67 TRP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 184 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 10 optimal weight: 0.0770 chunk 75 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN G 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.176238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.105065 restraints weight = 9955.709| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.15 r_work: 0.3021 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9389 Z= 0.159 Angle : 0.576 10.835 12740 Z= 0.298 Chirality : 0.043 0.145 1438 Planarity : 0.004 0.050 1591 Dihedral : 5.089 48.885 1324 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.55 % Allowed : 24.67 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.25), residues: 1144 helix: 1.81 (0.28), residues: 374 sheet: 0.73 (0.30), residues: 294 loop : -0.88 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 197 TYR 0.011 0.001 TYR S 190 PHE 0.035 0.002 PHE A 84 TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 9386) covalent geometry : angle 0.57574 (12734) SS BOND : bond 0.00770 ( 3) SS BOND : angle 1.01556 ( 6) hydrogen bonds : bond 0.04161 ( 415) hydrogen bonds : angle 4.37574 ( 1188) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 100 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 67 TRP cc_start: 0.8171 (OUTLIER) cc_final: 0.7542 (t-100) REVERT: A 139 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.6738 (mp) REVERT: C 298 GLU cc_start: 0.7748 (tp30) cc_final: 0.6818 (tp30) REVERT: B 198 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8008 (pt) REVERT: B 256 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.6362 (mtp85) outliers start: 45 outliers final: 34 residues processed: 135 average time/residue: 0.4402 time to fit residues: 64.1754 Evaluate side-chains 135 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 97 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 67 TRP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 97 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 34 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.177217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.106825 restraints weight = 9948.636| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.28 r_work: 0.3016 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9389 Z= 0.133 Angle : 0.549 10.045 12740 Z= 0.286 Chirality : 0.042 0.151 1438 Planarity : 0.004 0.049 1591 Dihedral : 5.041 49.117 1324 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.35 % Allowed : 24.77 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.25), residues: 1144 helix: 1.85 (0.28), residues: 374 sheet: 0.68 (0.30), residues: 295 loop : -0.87 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 197 TYR 0.012 0.001 TYR S 190 PHE 0.037 0.001 PHE A 84 TRP 0.012 0.001 TRP B 82 HIS 0.006 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9386) covalent geometry : angle 0.54890 (12734) SS BOND : bond 0.00662 ( 3) SS BOND : angle 0.88718 ( 6) hydrogen bonds : bond 0.03881 ( 415) hydrogen bonds : angle 4.33469 ( 1188) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 101 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 67 TRP cc_start: 0.8162 (OUTLIER) cc_final: 0.7534 (t-100) REVERT: A 139 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.6739 (mp) REVERT: A 149 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7807 (mtp85) REVERT: C 298 GLU cc_start: 0.7743 (tp30) cc_final: 0.6822 (tp30) REVERT: C 306 GLN cc_start: 0.8003 (mm110) cc_final: 0.7219 (mp10) REVERT: B 198 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8017 (pt) REVERT: B 256 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6343 (mtp85) outliers start: 43 outliers final: 34 residues processed: 134 average time/residue: 0.4997 time to fit residues: 72.4541 Evaluate side-chains 137 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 98 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 67 TRP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 149 ARG Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 2 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 33 optimal weight: 0.0980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 HIS B 175 GLN G 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.177768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.108170 restraints weight = 9881.525| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.24 r_work: 0.3001 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9389 Z= 0.123 Angle : 0.537 9.606 12740 Z= 0.279 Chirality : 0.042 0.142 1438 Planarity : 0.004 0.050 1591 Dihedral : 4.982 49.347 1324 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.35 % Allowed : 24.67 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.25), residues: 1144 helix: 1.88 (0.28), residues: 374 sheet: 0.69 (0.30), residues: 294 loop : -0.86 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 197 TYR 0.012 0.001 TYR S 190 PHE 0.037 0.001 PHE A 84 TRP 0.011 0.001 TRP B 82 HIS 0.006 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9386) covalent geometry : angle 0.53643 (12734) SS BOND : bond 0.00601 ( 3) SS BOND : angle 0.81092 ( 6) hydrogen bonds : bond 0.03763 ( 415) hydrogen bonds : angle 4.31086 ( 1188) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3742.26 seconds wall clock time: 64 minutes 25.05 seconds (3865.05 seconds total)