Starting phenix.real_space_refine on Mon May 12 17:29:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jjp_36364/05_2025/8jjp_36364.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jjp_36364/05_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_36364/05_2025/8jjp_36364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jjp_36364/05_2025/8jjp_36364.map" model { file = "/net/cci-nas-00/data/ceres_data/8jjp_36364/05_2025/8jjp_36364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jjp_36364/05_2025/8jjp_36364.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLU:plan': 1, 'ASP:plan': 3} 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: 5.93, per 1000 atoms: 0.65 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: 2.27 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.04 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: 2.56 Time building geometry restraints manager: 2.69 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: 1.790 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.420 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:11.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.350 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.026 0.001 TRP A 268 HIS 0.008 0.001 HIS A 244 PHE 0.018 0.001 PHE A 62 TYR 0.030 0.002 TYR A 45 ARG 0.010 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.14782 ( 415) hydrogen bonds : angle 6.00050 ( 1188) SS BOND : bond 0.00479 ( 3) SS BOND : angle 2.27117 ( 6) covalent geometry : bond 0.00334 ( 9386) covalent geometry : angle 0.59837 (12734) *********************** 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 : 0.951 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: 0.9104 time to fit residues: 132.4516 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 : 0.938 ------------------------------------------------------------------------------- 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 95 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 0.3980 chunk 57 optimal weight: 0.1980 chunk 45 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 0.2980 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 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 = 0.3991 r_free = 0.3991 target = 0.179226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.111478 restraints weight = 9900.055| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.19 r_work: 0.3050 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.0738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9389 Z= 0.114 Angle : 0.537 7.617 12740 Z= 0.282 Chirality : 0.042 0.137 1438 Planarity : 0.004 0.071 1591 Dihedral : 6.751 72.590 1366 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.25 % Allowed : 21.84 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.25), residues: 1144 helix: 1.54 (0.28), residues: 373 sheet: 0.73 (0.31), residues: 285 loop : -0.99 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 268 HIS 0.007 0.001 HIS A 244 PHE 0.013 0.001 PHE A 62 TYR 0.028 0.001 TYR A 45 ARG 0.007 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04042 ( 415) hydrogen bonds : angle 4.51843 ( 1188) SS BOND : bond 0.00585 ( 3) SS BOND : angle 1.14478 ( 6) covalent geometry : bond 0.00242 ( 9386) covalent geometry : angle 0.53688 (12734) *********************** 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 151 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 109 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 303 LEU cc_start: 0.7946 (mp) cc_final: 0.7697 (mt) REVERT: B 198 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8086 (pt) REVERT: B 256 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.6307 (mtp85) outliers start: 42 outliers final: 17 residues processed: 136 average time/residue: 0.9677 time to fit residues: 143.0702 Evaluate side-chains 120 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 PHE 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 55 ILE Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain B residue 70 LEU 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 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 91 THR 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 19 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 75 optimal weight: 0.0040 chunk 46 optimal weight: 10.0000 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 A 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.179764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.112578 restraints weight = 10024.177| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.34 r_work: 0.3049 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.0949 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= 0.114 Angle : 0.522 8.083 12740 Z= 0.273 Chirality : 0.042 0.138 1438 Planarity : 0.004 0.052 1591 Dihedral : 5.323 63.413 1328 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.65 % Allowed : 21.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.25), residues: 1144 helix: 1.66 (0.28), residues: 372 sheet: 0.71 (0.30), residues: 289 loop : -0.94 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 268 HIS 0.006 0.001 HIS A 244 PHE 0.013 0.001 PHE A 62 TYR 0.019 0.001 TYR A 96 ARG 0.007 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03870 ( 415) hydrogen bonds : angle 4.37145 ( 1188) SS BOND : bond 0.00600 ( 3) SS BOND : angle 0.88788 ( 6) covalent geometry : bond 0.00252 ( 9386) covalent geometry : angle 0.52194 (12734) *********************** 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 152 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 106 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6439 (mp) REVERT: A 279 HIS cc_start: 0.7337 (m90) cc_final: 0.7073 (m90) REVERT: A 303 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7602 (mt) REVERT: B 198 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7983 (pt) REVERT: B 246 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8288 (t0) REVERT: B 256 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.6221 (mtp85) outliers start: 46 outliers final: 17 residues processed: 136 average time/residue: 0.9254 time to fit residues: 137.1677 Evaluate side-chains 123 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 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 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 246 ASP Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 274 THR 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 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 155 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 41 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 85 optimal weight: 9.9990 chunk 20 optimal weight: 0.0020 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 overall best weight: 1.1192 ------------------------------------------------------------------------------- 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 273 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 = 0.4000 r_free = 0.4000 target = 0.177631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.106179 restraints weight = 9947.880| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.07 r_work: 0.3006 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1174 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= 0.162 Angle : 0.570 7.893 12740 Z= 0.299 Chirality : 0.043 0.188 1438 Planarity : 0.004 0.051 1591 Dihedral : 5.226 52.193 1324 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.55 % Allowed : 22.14 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.25), residues: 1144 helix: 1.61 (0.28), residues: 375 sheet: 0.68 (0.30), residues: 290 loop : -0.96 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 268 HIS 0.005 0.001 HIS A 244 PHE 0.015 0.002 PHE L 134 TYR 0.013 0.002 TYR A 96 ARG 0.010 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04351 ( 415) hydrogen bonds : angle 4.44933 ( 1188) SS BOND : bond 0.00831 ( 3) SS BOND : angle 1.14625 ( 6) covalent geometry : bond 0.00384 ( 9386) covalent geometry : angle 0.56926 (12734) *********************** 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 147 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 102 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6687 (mp) REVERT: B 198 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7964 (pt) REVERT: B 256 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.6322 (mtp85) outliers start: 45 outliers final: 26 residues processed: 133 average time/residue: 0.9611 time to fit residues: 139.0113 Evaluate side-chains 131 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 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 324 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 112 VAL 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 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 155 VAL Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 214 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 39 optimal weight: 0.4980 chunk 94 optimal weight: 0.0040 chunk 48 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 97 optimal weight: 0.0000 chunk 78 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.180179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.115570 restraints weight = 9966.833| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.14 r_work: 0.3085 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1298 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= 0.104 Angle : 0.502 6.606 12740 Z= 0.266 Chirality : 0.041 0.150 1438 Planarity : 0.003 0.051 1591 Dihedral : 4.957 51.966 1324 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.04 % Allowed : 22.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.25), residues: 1144 helix: 1.78 (0.28), residues: 375 sheet: 0.69 (0.30), residues: 290 loop : -0.89 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.006 0.001 HIS A 244 PHE 0.026 0.001 PHE A 84 TYR 0.014 0.001 TYR S 190 ARG 0.007 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03530 ( 415) hydrogen bonds : angle 4.26272 ( 1188) SS BOND : bond 0.00543 ( 3) SS BOND : angle 0.72209 ( 6) covalent geometry : bond 0.00222 ( 9386) covalent geometry : angle 0.50174 (12734) *********************** 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 148 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 108 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6386 (mp) REVERT: A 303 LEU cc_start: 0.7958 (mp) cc_final: 0.7691 (mt) REVERT: B 198 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7852 (pt) REVERT: B 256 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6162 (mtp85) outliers start: 40 outliers final: 25 residues processed: 136 average time/residue: 0.9611 time to fit residues: 141.9943 Evaluate side-chains 130 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 251 VAL 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 63 optimal weight: 2.9990 chunk 110 optimal weight: 0.0170 chunk 7 optimal weight: 0.0370 chunk 28 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 0.1980 chunk 10 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN A 189 ASN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.181297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.110451 restraints weight = 9952.309| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.10 r_work: 0.3071 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9389 Z= 0.098 Angle : 0.496 6.620 12740 Z= 0.260 Chirality : 0.041 0.140 1438 Planarity : 0.003 0.050 1591 Dihedral : 4.842 49.556 1324 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.85 % Allowed : 22.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.25), residues: 1144 helix: 1.91 (0.28), residues: 373 sheet: 0.72 (0.30), residues: 283 loop : -0.80 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.006 0.001 HIS A 244 PHE 0.031 0.001 PHE A 84 TYR 0.013 0.001 TYR S 190 ARG 0.007 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03347 ( 415) hydrogen bonds : angle 4.18583 ( 1188) SS BOND : bond 0.00493 ( 3) SS BOND : angle 0.69591 ( 6) covalent geometry : bond 0.00207 ( 9386) covalent geometry : angle 0.49611 (12734) *********************** 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 150 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 102 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 37 VAL cc_start: 0.8837 (OUTLIER) cc_final: 0.8628 (t) REVERT: A 67 TRP cc_start: 0.8113 (OUTLIER) cc_final: 0.7544 (t-100) REVERT: A 303 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7711 (mt) REVERT: C 298 GLU cc_start: 0.7788 (tp30) cc_final: 0.6838 (tp30) REVERT: C 324 THR cc_start: 0.7738 (OUTLIER) cc_final: 0.7376 (m) REVERT: B 198 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7921 (pt) REVERT: B 256 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6229 (mtp85) REVERT: S 192 MET cc_start: 0.8683 (ttt) cc_final: 0.8460 (tmm) outliers start: 48 outliers final: 28 residues processed: 138 average time/residue: 0.9583 time to fit residues: 144.4897 Evaluate side-chains 130 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 96 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 67 TRP 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 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 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 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 184 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 83 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 60 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.178085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.106440 restraints weight = 9969.843| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.32 r_work: 0.2996 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9389 Z= 0.158 Angle : 0.562 7.344 12740 Z= 0.295 Chirality : 0.043 0.147 1438 Planarity : 0.004 0.049 1591 Dihedral : 5.089 48.689 1324 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 5.16 % Allowed : 22.45 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.25), residues: 1144 helix: 1.82 (0.28), residues: 375 sheet: 0.71 (0.30), residues: 290 loop : -0.88 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS A 244 PHE 0.031 0.002 PHE A 84 TYR 0.011 0.001 TYR S 190 ARG 0.009 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04111 ( 415) hydrogen bonds : angle 4.34706 ( 1188) SS BOND : bond 0.00792 ( 3) SS BOND : angle 1.09703 ( 6) covalent geometry : bond 0.00374 ( 9386) covalent geometry : angle 0.56149 (12734) *********************** 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 153 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 102 time to evaluate : 1.128 Fit side-chains revert: symmetry clash REVERT: A 67 TRP cc_start: 0.8213 (OUTLIER) cc_final: 0.7593 (t-100) REVERT: A 139 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6589 (mp) REVERT: C 298 GLU cc_start: 0.7819 (tp30) cc_final: 0.6858 (tp30) REVERT: B 198 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7977 (pt) REVERT: B 256 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.6321 (mtp85) outliers start: 51 outliers final: 33 residues processed: 139 average time/residue: 0.9340 time to fit residues: 141.5164 Evaluate side-chains 135 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL 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 50 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 227 LEU 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 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 277 SER Chi-restraints excluded: chain B residue 336 LEU 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 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 43 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 74 optimal weight: 0.0770 chunk 68 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.178065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.111955 restraints weight = 10092.074| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.22 r_work: 0.3078 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1479 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= 0.117 Angle : 0.523 7.764 12740 Z= 0.274 Chirality : 0.042 0.142 1438 Planarity : 0.004 0.050 1591 Dihedral : 4.963 49.052 1324 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.55 % Allowed : 23.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.25), residues: 1144 helix: 1.88 (0.28), residues: 375 sheet: 0.73 (0.30), residues: 289 loop : -0.87 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.006 0.001 HIS A 244 PHE 0.034 0.001 PHE A 84 TYR 0.013 0.001 TYR S 190 ARG 0.009 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03640 ( 415) hydrogen bonds : angle 4.25307 ( 1188) SS BOND : bond 0.00586 ( 3) SS BOND : angle 0.84712 ( 6) covalent geometry : bond 0.00261 ( 9386) covalent geometry : angle 0.52311 (12734) *********************** 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: 45 poor density : 103 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 67 TRP cc_start: 0.8174 (OUTLIER) cc_final: 0.7568 (t-100) REVERT: A 139 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6591 (mp) REVERT: C 298 GLU cc_start: 0.7775 (tp30) cc_final: 0.6859 (tp30) REVERT: C 306 GLN cc_start: 0.7899 (mm110) cc_final: 0.7127 (mp10) REVERT: B 46 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.8069 (mtt-85) REVERT: B 198 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7939 (pt) REVERT: B 256 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.6306 (mtp85) outliers start: 45 outliers final: 28 residues processed: 136 average time/residue: 0.9792 time to fit residues: 144.4075 Evaluate side-chains 131 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 98 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 251 VAL 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 227 LEU 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 46 ARG 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 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 Chi-restraints excluded: chain S residue 214 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 27 optimal weight: 0.6980 chunk 24 optimal weight: 30.0000 chunk 60 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 87 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.177796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.106303 restraints weight = 9880.458| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.01 r_work: 0.3082 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1531 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= 0.126 Angle : 0.539 10.207 12740 Z= 0.281 Chirality : 0.042 0.142 1438 Planarity : 0.004 0.049 1591 Dihedral : 4.989 49.256 1324 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.25 % Allowed : 23.96 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.25), residues: 1144 helix: 1.90 (0.28), residues: 374 sheet: 0.69 (0.30), residues: 295 loop : -0.84 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.006 0.001 HIS A 244 PHE 0.034 0.001 PHE A 84 TYR 0.012 0.001 TYR S 190 ARG 0.009 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03774 ( 415) hydrogen bonds : angle 4.27982 ( 1188) SS BOND : bond 0.00636 ( 3) SS BOND : angle 0.94715 ( 6) covalent geometry : bond 0.00290 ( 9386) covalent geometry : angle 0.53841 (12734) *********************** 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 146 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 104 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 67 TRP cc_start: 0.8163 (OUTLIER) cc_final: 0.7540 (t-100) REVERT: A 139 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6658 (mp) REVERT: C 243 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7659 (mmt) REVERT: C 298 GLU cc_start: 0.7724 (tp30) cc_final: 0.6797 (tp30) REVERT: C 306 GLN cc_start: 0.7895 (mm110) cc_final: 0.7125 (mp10) REVERT: B 46 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.8027 (mtt-85) REVERT: B 198 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7925 (pt) REVERT: B 256 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6280 (mtp85) outliers start: 42 outliers final: 30 residues processed: 135 average time/residue: 0.9621 time to fit residues: 141.4574 Evaluate side-chains 136 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL 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 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 243 MET Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 46 ARG 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 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 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: 1.9990 chunk 80 optimal weight: 2.9990 chunk 89 optimal weight: 0.0070 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 57 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.3004 ------------------------------------------------------------------------------- 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 340 ASN G 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.175924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.107300 restraints weight = 9954.260| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.21 r_work: 0.3001 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9389 Z= 0.182 Angle : 0.601 9.340 12740 Z= 0.312 Chirality : 0.044 0.153 1438 Planarity : 0.004 0.050 1591 Dihedral : 5.213 49.047 1324 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.74 % Allowed : 25.18 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.25), residues: 1144 helix: 1.77 (0.28), residues: 374 sheet: 0.70 (0.29), residues: 298 loop : -0.94 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.037 0.002 PHE A 84 TYR 0.011 0.002 TYR B 59 ARG 0.009 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04435 ( 415) hydrogen bonds : angle 4.43367 ( 1188) SS BOND : bond 0.00852 ( 3) SS BOND : angle 1.24843 ( 6) covalent geometry : bond 0.00437 ( 9386) covalent geometry : angle 0.60059 (12734) ********************** 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 139 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 102 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: A 67 TRP cc_start: 0.8206 (OUTLIER) cc_final: 0.7577 (t-100) REVERT: A 139 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.6885 (mp) REVERT: C 243 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7755 (mmt) REVERT: C 298 GLU cc_start: 0.7780 (tp30) cc_final: 0.6861 (tp30) REVERT: C 306 GLN cc_start: 0.8014 (mm110) cc_final: 0.7211 (mp10) REVERT: B 198 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8017 (pt) REVERT: B 256 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.6356 (mtp85) outliers start: 37 outliers final: 28 residues processed: 131 average time/residue: 0.9407 time to fit residues: 134.1508 Evaluate side-chains 131 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 98 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL 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 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 243 MET Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 332 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 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 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 112 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 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 B 340 ASN G 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.178283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.106768 restraints weight = 9923.259| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.19 r_work: 0.3036 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1629 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= 0.121 Angle : 0.534 9.159 12740 Z= 0.279 Chirality : 0.042 0.163 1438 Planarity : 0.004 0.049 1591 Dihedral : 5.015 49.403 1324 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.44 % Allowed : 25.08 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.25), residues: 1144 helix: 1.91 (0.28), residues: 374 sheet: 0.70 (0.30), residues: 290 loop : -0.91 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.006 0.001 HIS A 244 PHE 0.037 0.001 PHE A 84 TYR 0.012 0.001 TYR S 190 ARG 0.009 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03744 ( 415) hydrogen bonds : angle 4.29308 ( 1188) SS BOND : bond 0.00576 ( 3) SS BOND : angle 0.84699 ( 6) covalent geometry : bond 0.00272 ( 9386) covalent geometry : angle 0.53400 (12734) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7786.52 seconds wall clock time: 134 minutes 32.58 seconds (8072.58 seconds total)