Starting phenix.real_space_refine on Tue May 13 06:12:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yk0_39356/05_2025/8yk0_39356.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yk0_39356/05_2025/8yk0_39356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yk0_39356/05_2025/8yk0_39356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yk0_39356/05_2025/8yk0_39356.map" model { file = "/net/cci-nas-00/data/ceres_data/8yk0_39356/05_2025/8yk0_39356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yk0_39356/05_2025/8yk0_39356.cif" } resolution = 2.4 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= -0.004 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 66 5.16 5 C 6444 2.51 5 N 1559 2.21 5 O 1758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 9831 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2226 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 10, 'TRANS': 287} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 2506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2506 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'GLU:plan': 2, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 72 Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 424 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1754 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 2401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2401 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 11, 'TRANS': 305} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 274 Unusual residues: {'CLR': 6, 'MW9': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "A" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 246 Unusual residues: {'CLR': 5, 'MW9': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 6.13, per 1000 atoms: 0.62 Number of scatterers: 9831 At special positions: 0 Unit cell: (95.79, 91.14, 154.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 4 15.00 O 1758 8.00 N 1559 7.00 C 6444 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 191 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 216 " distance=2.02 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 1.1 seconds 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2312 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 52.6% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'B' and resid 22 through 34 removed outlier: 3.756A pdb=" N ASP B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU B 27 " --> pdb=" O PRO B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 74 Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 84 through 105 Processing helix chain 'B' and resid 114 through 149 removed outlier: 3.790A pdb=" N THR B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Proline residue: B 137 - end of helix Processing helix chain 'B' and resid 161 through 187 removed outlier: 3.574A pdb=" N LEU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 246 Processing helix chain 'B' and resid 251 through 256 Processing helix chain 'B' and resid 256 through 281 Processing helix chain 'B' and resid 284 through 319 Proline residue: B 310 - end of helix removed outlier: 3.564A pdb=" N GLN B 314 " --> pdb=" O PRO B 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 26 Processing helix chain 'D' and resid 29 through 34 removed outlier: 4.030A pdb=" N ILE D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 25 removed outlier: 4.181A pdb=" N ARG G 13 " --> pdb=" O ILE G 9 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'C' and resid 7 through 31 Processing helix chain 'C' and resid 45 through 56 Processing helix chain 'C' and resid 207 through 212 removed outlier: 4.090A pdb=" N TRP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 232 removed outlier: 4.197A pdb=" N ASP C 231 " --> pdb=" O SER C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 255 Processing helix chain 'C' and resid 256 through 260 removed outlier: 4.034A pdb=" N THR C 260 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 278 Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 295 through 310 removed outlier: 3.821A pdb=" N ALA C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU C 310 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 351 Processing helix chain 'A' and resid 23 through 34 removed outlier: 3.660A pdb=" N THR A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER A 34 " --> pdb=" O THR A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 74 Processing helix chain 'A' and resid 77 through 83 Processing helix chain 'A' and resid 84 through 105 Processing helix chain 'A' and resid 112 through 151 Proline residue: A 137 - end of helix Processing helix chain 'A' and resid 161 through 187 Processing helix chain 'A' and resid 220 through 246 removed outlier: 3.688A pdb=" N TRP A 224 " --> pdb=" O TYR A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.673A pdb=" N GLN A 256 " --> pdb=" O PRO A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 281 Processing helix chain 'A' and resid 284 through 316 Proline residue: A 310 - end of helix removed outlier: 4.343A pdb=" N LYS A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing sheet with id=AA1, first strand: chain 'B' and resid 206 through 217 removed outlier: 4.246A pdb=" N THR B 209 " --> pdb=" O SER B 198 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER B 198 " --> pdb=" O THR B 209 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR B 211 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 194 " --> pdb=" O THR B 213 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE B 215 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU B 192 " --> pdb=" O PHE B 215 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 217 " --> pdb=" O GLN B 190 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 192 " --> pdb=" O PHE A 215 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N PHE A 215 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE A 194 " --> pdb=" O THR A 213 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR A 213 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 47 through 51 removed outlier: 6.763A pdb=" N ILE D 338 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR D 50 " --> pdb=" O LEU D 336 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU D 336 " --> pdb=" O THR D 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 58 through 63 removed outlier: 3.754A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LEU D 79 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA D 92 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE D 81 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 100 through 105 removed outlier: 6.764A pdb=" N GLY D 115 " --> pdb=" O MET D 101 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N CYS D 103 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA D 113 " --> pdb=" O CYS D 103 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N TYR D 105 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N TYR D 111 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 146 through 151 removed outlier: 3.552A pdb=" N CYS D 148 " --> pdb=" O SER D 160 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASP D 170 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N GLN D 176 " --> pdb=" O ASP D 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 189 through 192 removed outlier: 6.637A pdb=" N ALA D 208 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR D 221 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU D 210 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 229 through 234 removed outlier: 6.393A pdb=" N GLY D 244 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE D 232 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ALA D 242 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE D 234 " --> pdb=" O ALA D 240 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ALA D 240 " --> pdb=" O PHE D 234 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 273 through 278 removed outlier: 3.884A pdb=" N SER D 275 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N CYS D 294 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL D 307 " --> pdb=" O CYS D 294 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL D 296 " --> pdb=" O ALA D 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 185 through 191 removed outlier: 3.543A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE C 264 " --> pdb=" O TYR C 320 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N HIS C 322 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU C 266 " --> pdb=" O HIS C 322 " (cutoff:3.500A) 582 hydrogen bonds defined for protein. 1707 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: 2.97 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1513 1.31 - 1.44: 2555 1.44 - 1.56: 5868 1.56 - 1.69: 9 1.69 - 1.82: 92 Bond restraints: 10037 Sorted by residual: bond pdb=" C8 MW9 B 401 " pdb=" C9 MW9 B 401 " ideal model delta sigma weight residual 1.548 1.310 0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C MET A 82 " pdb=" N SER A 83 " ideal model delta sigma weight residual 1.333 1.487 -0.154 1.34e-02 5.57e+03 1.32e+02 bond pdb=" C8 MW9 B 402 " pdb=" C9 MW9 B 402 " ideal model delta sigma weight residual 1.548 1.332 0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C8 MW9 A 403 " pdb=" C9 MW9 A 403 " ideal model delta sigma weight residual 1.548 1.333 0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C8 MW9 A 404 " pdb=" C9 MW9 A 404 " ideal model delta sigma weight residual 1.548 1.333 0.215 2.00e-02 2.50e+03 1.15e+02 ... (remaining 10032 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.61: 13529 5.61 - 11.23: 115 11.23 - 16.84: 14 16.84 - 22.45: 0 22.45 - 28.07: 4 Bond angle restraints: 13662 Sorted by residual: angle pdb=" C32 MW9 A 403 " pdb=" C33 MW9 A 403 " pdb=" C34 MW9 A 403 " ideal model delta sigma weight residual 125.32 153.39 -28.07 3.00e+00 1.11e-01 8.75e+01 angle pdb=" C32 MW9 A 404 " pdb=" C33 MW9 A 404 " pdb=" C34 MW9 A 404 " ideal model delta sigma weight residual 125.32 152.57 -27.25 3.00e+00 1.11e-01 8.25e+01 angle pdb=" C32 MW9 B 401 " pdb=" C33 MW9 B 401 " pdb=" C34 MW9 B 401 " ideal model delta sigma weight residual 125.32 151.94 -26.62 3.00e+00 1.11e-01 7.87e+01 angle pdb=" C32 MW9 B 402 " pdb=" C33 MW9 B 402 " pdb=" C34 MW9 B 402 " ideal model delta sigma weight residual 125.32 151.90 -26.58 3.00e+00 1.11e-01 7.85e+01 angle pdb=" N ARG C 242 " pdb=" CA ARG C 242 " pdb=" C ARG C 242 " ideal model delta sigma weight residual 112.87 103.31 9.56 1.20e+00 6.94e-01 6.34e+01 ... (remaining 13657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 6282 35.97 - 71.95: 217 71.95 - 107.92: 35 107.92 - 143.89: 12 143.89 - 179.86: 6 Dihedral angle restraints: 6552 sinusoidal: 2984 harmonic: 3568 Sorted by residual: dihedral pdb=" C21 MW9 B 401 " pdb=" O5 MW9 B 401 " pdb=" P MW9 B 401 " pdb=" O4 MW9 B 401 " ideal model delta sinusoidal sigma weight residual 282.01 102.15 179.86 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C20 MW9 A 403 " pdb=" O2 MW9 A 403 " pdb=" P MW9 A 403 " pdb=" O5 MW9 A 403 " ideal model delta sinusoidal sigma weight residual 301.77 123.70 178.07 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O MW9 A 404 " pdb=" C16 MW9 A 404 " pdb=" C17 MW9 A 404 " pdb=" C15 MW9 A 404 " ideal model delta sinusoidal sigma weight residual 102.59 -61.44 164.03 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 6549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1503 0.106 - 0.212: 115 0.212 - 0.317: 14 0.317 - 0.423: 14 0.423 - 0.529: 8 Chirality restraints: 1654 Sorted by residual: chirality pdb=" C14 CLR A 402 " pdb=" C13 CLR A 402 " pdb=" C15 CLR A 402 " pdb=" C8 CLR A 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.85 0.53 2.00e-01 2.50e+01 6.99e+00 chirality pdb=" C14 CLR B 404 " pdb=" C13 CLR B 404 " pdb=" C15 CLR B 404 " pdb=" C8 CLR B 404 " both_signs ideal model delta sigma weight residual False -2.32 -2.84 0.52 2.00e-01 2.50e+01 6.87e+00 chirality pdb=" C14 CLR A 405 " pdb=" C13 CLR A 405 " pdb=" C15 CLR A 405 " pdb=" C8 CLR A 405 " both_signs ideal model delta sigma weight residual False -2.32 -2.84 0.52 2.00e-01 2.50e+01 6.86e+00 ... (remaining 1651 not shown) Planarity restraints: 1612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 231 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.92e+00 pdb=" C ASP C 231 " -0.049 2.00e-02 2.50e+03 pdb=" O ASP C 231 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU C 232 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 244 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.51e+00 pdb=" C HIS C 244 " -0.044 2.00e-02 2.50e+03 pdb=" O HIS C 244 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA C 245 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 315 " 0.014 2.00e-02 2.50e+03 1.55e-02 6.02e+00 pdb=" CG TRP A 315 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP A 315 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 315 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 315 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 315 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 315 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 315 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 315 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 315 " -0.000 2.00e-02 2.50e+03 ... (remaining 1609 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 135 2.60 - 3.18: 9009 3.18 - 3.75: 15296 3.75 - 4.33: 21534 4.33 - 4.90: 35378 Nonbonded interactions: 81352 Sorted by model distance: nonbonded pdb=" OG1 THR B 202 " pdb=" OD1 ASP B 205 " model vdw 2.029 3.040 nonbonded pdb=" OG SER G 57 " pdb=" OE1 GLU G 58 " model vdw 2.181 3.040 nonbonded pdb=" OH TYR C 230 " pdb=" OG SER C 281 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR D 264 " pdb=" O ALA D 299 " model vdw 2.221 3.040 nonbonded pdb=" O ILE D 58 " pdb=" OG SER D 316 " model vdw 2.223 3.040 ... (remaining 81347 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 72 or (resid 73 and (name N or name CA or name \ C or name O or name CB )) or resid 74 through 107 or (resid 108 and (name N or n \ ame CA or name C or name O or name CB )) or resid 109 through 115 or (resid 116 \ and (name N or name CA or name C or name O or name CB )) or resid 117 through 17 \ 5 or (resid 176 and (name N or name CA or name C or name O or name CB )) or resi \ d 177 through 319 or resid 402 or resid 405 through 407)) selection = (chain 'B' and (resid 22 through 319 or resid 403 or resid 406 through 408)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 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: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 24.640 Find NCS groups from input model: 0.270 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: 0.010 Load rotamer database and sin/cos tables:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.862 10040 Z= 0.967 Angle : 1.302 28.066 13666 Z= 0.592 Chirality : 0.077 0.529 1654 Planarity : 0.006 0.069 1612 Dihedral : 19.603 179.865 4234 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.10 % Allowed : 19.94 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.09 (0.24), residues: 1218 helix: 1.43 (0.21), residues: 594 sheet: -0.37 (0.34), residues: 220 loop : -1.76 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 315 HIS 0.005 0.001 HIS B 282 PHE 0.038 0.002 PHE B 275 TYR 0.017 0.002 TYR B 220 ARG 0.016 0.001 ARG C 24 Details of bonding type rmsd hydrogen bonds : bond 0.16523 ( 582) hydrogen bonds : angle 6.50435 ( 1707) SS BOND : bond 0.00515 ( 2) SS BOND : angle 1.50435 ( 4) covalent geometry : bond 0.00848 (10037) covalent geometry : angle 1.30195 (13662) Misc. bond : bond 0.86212 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 103 TYR cc_start: 0.8159 (m-80) cc_final: 0.7908 (m-80) REVERT: B 190 GLN cc_start: 0.8408 (mt0) cc_final: 0.8184 (mt0) REVERT: B 313 LYS cc_start: 0.8648 (mtpp) cc_final: 0.8419 (mtmm) REVERT: C 282 PRO cc_start: 0.8819 (Cg_endo) cc_final: 0.8607 (Cg_exo) REVERT: C 306 GLN cc_start: 0.8401 (tp40) cc_final: 0.8180 (mm110) REVERT: A 75 ARG cc_start: 0.8683 (ptt90) cc_final: 0.8325 (ptt90) REVERT: A 76 LYS cc_start: 0.9332 (mmtm) cc_final: 0.8994 (mppt) REVERT: A 164 GLN cc_start: 0.8659 (mt0) cc_final: 0.8352 (mt0) REVERT: A 176 ASP cc_start: 0.7928 (m-30) cc_final: 0.7540 (m-30) REVERT: A 181 MET cc_start: 0.8234 (tpt) cc_final: 0.7962 (tpp) REVERT: A 193 GLN cc_start: 0.7268 (mm-40) cc_final: 0.6544 (mm-40) REVERT: A 219 ARG cc_start: 0.8321 (mtp-110) cc_final: 0.7946 (mtp-110) REVERT: A 238 TYR cc_start: 0.8936 (t80) cc_final: 0.8574 (t80) REVERT: A 328 MET cc_start: 0.8559 (mpt) cc_final: 0.8024 (mpt) outliers start: 1 outliers final: 2 residues processed: 225 average time/residue: 1.3086 time to fit residues: 313.7275 Evaluate side-chains 187 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 185 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain C residue 272 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 2.9990 chunk 90 optimal weight: 30.0000 chunk 50 optimal weight: 0.4980 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 70 optimal weight: 0.3980 chunk 108 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 GLN B 256 GLN G 44 HIS C 244 HIS A 151 GLN A 256 GLN A 265 ASN A 304 ASN A 322 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.115229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.081726 restraints weight = 17903.816| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 3.16 r_work: 0.3072 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10040 Z= 0.143 Angle : 0.685 8.489 13666 Z= 0.341 Chirality : 0.046 0.237 1654 Planarity : 0.005 0.063 1612 Dihedral : 17.625 166.254 2243 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.34 % Allowed : 18.93 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.93 (0.24), residues: 1218 helix: 2.02 (0.21), residues: 605 sheet: 0.43 (0.36), residues: 203 loop : -1.49 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 315 HIS 0.004 0.001 HIS G 44 PHE 0.026 0.001 PHE B 215 TYR 0.019 0.001 TYR G 40 ARG 0.007 0.001 ARG A 152 Details of bonding type rmsd hydrogen bonds : bond 0.04685 ( 582) hydrogen bonds : angle 4.69731 ( 1707) SS BOND : bond 0.02678 ( 2) SS BOND : angle 2.79268 ( 4) covalent geometry : bond 0.00301 (10037) covalent geometry : angle 0.68355 (13662) Misc. bond : bond 0.00218 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 79 ILE cc_start: 0.8711 (mm) cc_final: 0.8331 (tp) REVERT: B 103 TYR cc_start: 0.8356 (m-80) cc_final: 0.8081 (m-80) REVERT: B 117 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8395 (mt-10) REVERT: B 190 GLN cc_start: 0.8715 (mt0) cc_final: 0.8308 (mm110) REVERT: B 313 LYS cc_start: 0.8682 (mtpp) cc_final: 0.8429 (mtmm) REVERT: D 22 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8356 (mmt-90) REVERT: D 258 ASP cc_start: 0.7864 (t0) cc_final: 0.7317 (t0) REVERT: G 47 GLU cc_start: 0.8569 (mt-10) cc_final: 0.7671 (mp0) REVERT: C 18 MET cc_start: 0.8139 (tpp) cc_final: 0.7921 (tpp) REVERT: C 20 ASP cc_start: 0.8524 (m-30) cc_final: 0.8278 (m-30) REVERT: C 21 ARG cc_start: 0.8487 (ttm-80) cc_final: 0.8243 (ttm-80) REVERT: C 205 ARG cc_start: 0.8761 (mmp80) cc_final: 0.8518 (mmp80) REVERT: C 232 LEU cc_start: 0.9035 (mm) cc_final: 0.8739 (mp) REVERT: C 242 ARG cc_start: 0.8740 (mtt90) cc_final: 0.8061 (mtt90) REVERT: C 333 GLN cc_start: 0.8765 (tp40) cc_final: 0.8358 (tp40) REVERT: A 75 ARG cc_start: 0.8764 (ptt90) cc_final: 0.8507 (ptt90) REVERT: A 164 GLN cc_start: 0.8701 (mt0) cc_final: 0.8314 (tt0) REVERT: A 176 ASP cc_start: 0.8445 (m-30) cc_final: 0.8078 (m-30) REVERT: A 181 MET cc_start: 0.9008 (tpt) cc_final: 0.8724 (tpp) REVERT: A 193 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7567 (mm-40) REVERT: A 214 HIS cc_start: 0.8425 (t70) cc_final: 0.8106 (t70) REVERT: A 325 ILE cc_start: 0.7317 (mm) cc_final: 0.6941 (mm) REVERT: A 326 ARG cc_start: 0.8051 (tpm170) cc_final: 0.7709 (mpt90) outliers start: 33 outliers final: 11 residues processed: 222 average time/residue: 1.1931 time to fit residues: 283.8391 Evaluate side-chains 192 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 180 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 192 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 282 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 21 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 33 optimal weight: 0.2980 chunk 4 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 256 GLN C 306 GLN A 151 GLN A 304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.115266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.082105 restraints weight = 18232.033| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 3.16 r_work: 0.3074 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10040 Z= 0.134 Angle : 0.632 11.034 13666 Z= 0.316 Chirality : 0.044 0.316 1654 Planarity : 0.004 0.059 1612 Dihedral : 16.410 163.911 2240 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.85 % Allowed : 18.83 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.36 (0.24), residues: 1218 helix: 2.39 (0.20), residues: 604 sheet: 0.81 (0.36), residues: 202 loop : -1.43 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 315 HIS 0.003 0.001 HIS G 44 PHE 0.010 0.001 PHE G 61 TYR 0.009 0.001 TYR A 220 ARG 0.009 0.001 ARG A 219 Details of bonding type rmsd hydrogen bonds : bond 0.04164 ( 582) hydrogen bonds : angle 4.41686 ( 1707) SS BOND : bond 0.00666 ( 2) SS BOND : angle 2.69046 ( 4) covalent geometry : bond 0.00286 (10037) covalent geometry : angle 0.63003 (13662) Misc. bond : bond 0.00064 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 193 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 LYS cc_start: 0.8989 (mmmt) cc_final: 0.8630 (mtmm) REVERT: B 82 MET cc_start: 0.8997 (mtp) cc_final: 0.8649 (ptp) REVERT: B 103 TYR cc_start: 0.8315 (m-80) cc_final: 0.7998 (m-80) REVERT: B 117 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8352 (mt-10) REVERT: B 190 GLN cc_start: 0.8652 (mt0) cc_final: 0.8209 (mm110) REVERT: B 193 GLN cc_start: 0.8961 (tp40) cc_final: 0.8433 (mm110) REVERT: B 195 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8821 (mm) REVERT: B 313 LYS cc_start: 0.8685 (mtpp) cc_final: 0.8267 (mtmm) REVERT: B 314 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.7559 (mp10) REVERT: D 22 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8343 (mmt-90) REVERT: D 258 ASP cc_start: 0.7776 (t0) cc_final: 0.7368 (t0) REVERT: G 47 GLU cc_start: 0.8405 (mt-10) cc_final: 0.7931 (mp0) REVERT: C 18 MET cc_start: 0.8144 (tpp) cc_final: 0.7930 (tpp) REVERT: C 20 ASP cc_start: 0.8424 (m-30) cc_final: 0.8042 (m-30) REVERT: C 333 GLN cc_start: 0.8761 (tp40) cc_final: 0.8285 (tp40) REVERT: A 75 ARG cc_start: 0.8731 (ptt90) cc_final: 0.8366 (ptt90) REVERT: A 76 LYS cc_start: 0.9498 (mmtm) cc_final: 0.9277 (mmmt) REVERT: A 164 GLN cc_start: 0.8702 (mt0) cc_final: 0.8280 (tt0) REVERT: A 176 ASP cc_start: 0.8466 (m-30) cc_final: 0.8092 (m-30) REVERT: A 181 MET cc_start: 0.8977 (tpt) cc_final: 0.8717 (tpp) REVERT: A 211 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8967 (p) REVERT: A 325 ILE cc_start: 0.7538 (mm) cc_final: 0.7157 (mm) REVERT: A 326 ARG cc_start: 0.8109 (tpm170) cc_final: 0.7750 (mpt90) outliers start: 38 outliers final: 15 residues processed: 218 average time/residue: 1.2324 time to fit residues: 287.0052 Evaluate side-chains 194 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 192 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 249 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 44 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 91 optimal weight: 0.0170 chunk 17 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 95 optimal weight: 0.7980 chunk 0 optimal weight: 60.0000 chunk 36 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 256 GLN ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.115660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.082775 restraints weight = 17952.343| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.15 r_work: 0.3088 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10040 Z= 0.124 Angle : 0.607 8.282 13666 Z= 0.304 Chirality : 0.043 0.269 1654 Planarity : 0.004 0.062 1612 Dihedral : 15.719 161.011 2240 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.54 % Allowed : 21.26 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.43 (0.24), residues: 1218 helix: 2.43 (0.20), residues: 608 sheet: 0.70 (0.35), residues: 207 loop : -1.32 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 315 HIS 0.004 0.001 HIS G 44 PHE 0.024 0.001 PHE B 215 TYR 0.020 0.001 TYR G 40 ARG 0.010 0.001 ARG A 219 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 582) hydrogen bonds : angle 4.29261 ( 1707) SS BOND : bond 0.00276 ( 2) SS BOND : angle 1.79401 ( 4) covalent geometry : bond 0.00269 (10037) covalent geometry : angle 0.60597 (13662) Misc. bond : bond 0.00028 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 LYS cc_start: 0.8981 (mmmt) cc_final: 0.8598 (mtmm) REVERT: B 82 MET cc_start: 0.9002 (mtp) cc_final: 0.8790 (ptp) REVERT: B 103 TYR cc_start: 0.8293 (m-80) cc_final: 0.7926 (m-80) REVERT: B 193 GLN cc_start: 0.8947 (tp40) cc_final: 0.8450 (mm110) REVERT: B 313 LYS cc_start: 0.8679 (mtpp) cc_final: 0.8329 (mtmm) REVERT: B 314 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.7548 (mp10) REVERT: D 22 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8248 (mmt-90) REVERT: D 258 ASP cc_start: 0.7773 (t0) cc_final: 0.7353 (t0) REVERT: G 47 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8038 (mp0) REVERT: C 20 ASP cc_start: 0.8442 (m-30) cc_final: 0.7992 (m-30) REVERT: C 242 ARG cc_start: 0.8791 (mtt90) cc_final: 0.8032 (mtt90) REVERT: C 333 GLN cc_start: 0.8766 (tp40) cc_final: 0.8393 (tp40) REVERT: A 75 ARG cc_start: 0.8750 (ptt90) cc_final: 0.8403 (ptt90) REVERT: A 76 LYS cc_start: 0.9500 (mmtm) cc_final: 0.9257 (mmmt) REVERT: A 164 GLN cc_start: 0.8740 (mt0) cc_final: 0.8406 (mt0) REVERT: A 176 ASP cc_start: 0.8406 (m-30) cc_final: 0.8062 (m-30) REVERT: A 181 MET cc_start: 0.8984 (tpt) cc_final: 0.8644 (tpp) REVERT: A 211 THR cc_start: 0.9072 (OUTLIER) cc_final: 0.8841 (p) REVERT: A 325 ILE cc_start: 0.7599 (mm) cc_final: 0.6950 (mm) REVERT: A 326 ARG cc_start: 0.8107 (tpm170) cc_final: 0.7755 (mpt90) outliers start: 35 outliers final: 14 residues processed: 213 average time/residue: 1.2030 time to fit residues: 275.3221 Evaluate side-chains 192 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 249 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 16 optimal weight: 5.9990 chunk 75 optimal weight: 0.1980 chunk 105 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 38 optimal weight: 0.1980 chunk 35 optimal weight: 0.0670 chunk 70 optimal weight: 0.3980 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN B 256 GLN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS A 304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.116767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.083409 restraints weight = 18016.318| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.21 r_work: 0.3108 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10040 Z= 0.118 Angle : 0.616 10.524 13666 Z= 0.307 Chirality : 0.043 0.280 1654 Planarity : 0.004 0.062 1612 Dihedral : 15.246 156.955 2240 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.54 % Allowed : 21.76 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.48 (0.24), residues: 1218 helix: 2.51 (0.20), residues: 608 sheet: 0.56 (0.35), residues: 209 loop : -1.27 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 315 HIS 0.003 0.000 HIS G 44 PHE 0.024 0.001 PHE B 215 TYR 0.010 0.001 TYR A 220 ARG 0.010 0.001 ARG A 219 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 582) hydrogen bonds : angle 4.23182 ( 1707) SS BOND : bond 0.00646 ( 2) SS BOND : angle 1.65663 ( 4) covalent geometry : bond 0.00252 (10037) covalent geometry : angle 0.61514 (13662) Misc. bond : bond 0.00021 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 190 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: B 81 LYS cc_start: 0.8913 (mmmt) cc_final: 0.8554 (mtmm) REVERT: B 103 TYR cc_start: 0.8232 (m-80) cc_final: 0.7858 (m-80) REVERT: B 193 GLN cc_start: 0.8897 (tp40) cc_final: 0.8514 (mm-40) REVERT: B 195 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8887 (mm) REVERT: B 214 HIS cc_start: 0.8400 (t-90) cc_final: 0.8061 (t-90) REVERT: B 313 LYS cc_start: 0.8668 (mtpp) cc_final: 0.8312 (mtmm) REVERT: B 314 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.7515 (mp10) REVERT: D 22 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8279 (mmt-90) REVERT: D 258 ASP cc_start: 0.7763 (t0) cc_final: 0.7401 (t0) REVERT: C 20 ASP cc_start: 0.8434 (m-30) cc_final: 0.7956 (m-30) REVERT: C 242 ARG cc_start: 0.8776 (mtt90) cc_final: 0.8008 (mtt90) REVERT: C 333 GLN cc_start: 0.8763 (tp40) cc_final: 0.8293 (tp40) REVERT: A 75 ARG cc_start: 0.8726 (ptt90) cc_final: 0.8386 (ptt90) REVERT: A 76 LYS cc_start: 0.9491 (mmtm) cc_final: 0.9247 (mmmt) REVERT: A 164 GLN cc_start: 0.8778 (mt0) cc_final: 0.8445 (mt0) REVERT: A 176 ASP cc_start: 0.8454 (m-30) cc_final: 0.8040 (m-30) REVERT: A 181 MET cc_start: 0.8943 (tpt) cc_final: 0.8643 (tpp) REVERT: A 211 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8794 (p) outliers start: 35 outliers final: 15 residues processed: 215 average time/residue: 1.1923 time to fit residues: 274.6095 Evaluate side-chains 196 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 281 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 67 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 18 optimal weight: 30.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 256 GLN B 304 ASN ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 ASN A 304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.110998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.077706 restraints weight = 18181.499| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.12 r_work: 0.2977 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10040 Z= 0.224 Angle : 0.703 9.049 13666 Z= 0.352 Chirality : 0.046 0.255 1654 Planarity : 0.005 0.064 1612 Dihedral : 15.298 160.053 2240 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.54 % Allowed : 22.87 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.38 (0.24), residues: 1218 helix: 2.37 (0.20), residues: 608 sheet: 0.51 (0.34), residues: 214 loop : -1.23 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 315 HIS 0.004 0.001 HIS A 282 PHE 0.021 0.002 PHE B 215 TYR 0.018 0.001 TYR G 40 ARG 0.010 0.001 ARG C 24 Details of bonding type rmsd hydrogen bonds : bond 0.04517 ( 582) hydrogen bonds : angle 4.44286 ( 1707) SS BOND : bond 0.00319 ( 2) SS BOND : angle 2.18042 ( 4) covalent geometry : bond 0.00511 (10037) covalent geometry : angle 0.70232 (13662) Misc. bond : bond 0.00027 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 189 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8609 (ptp) REVERT: B 103 TYR cc_start: 0.8414 (m-80) cc_final: 0.8062 (m-80) REVERT: B 193 GLN cc_start: 0.8864 (tp40) cc_final: 0.8442 (mm110) REVERT: B 195 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8902 (mm) REVERT: B 313 LYS cc_start: 0.8657 (mtpp) cc_final: 0.8293 (mtmm) REVERT: B 314 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.7569 (mp10) REVERT: D 22 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8427 (mmt-90) REVERT: D 258 ASP cc_start: 0.7837 (t0) cc_final: 0.7622 (t0) REVERT: D 262 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7556 (tmt) REVERT: G 48 ASP cc_start: 0.8281 (t0) cc_final: 0.7816 (m-30) REVERT: C 20 ASP cc_start: 0.8513 (m-30) cc_final: 0.8114 (m-30) REVERT: C 25 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: C 229 ASP cc_start: 0.8697 (m-30) cc_final: 0.8195 (m-30) REVERT: C 241 ASN cc_start: 0.8541 (m-40) cc_final: 0.8197 (t0) REVERT: C 333 GLN cc_start: 0.8771 (tp40) cc_final: 0.8414 (tp40) REVERT: A 75 ARG cc_start: 0.8692 (ptt90) cc_final: 0.8355 (ptt90) REVERT: A 76 LYS cc_start: 0.9512 (mmtm) cc_final: 0.9294 (mmmt) REVERT: A 164 GLN cc_start: 0.8725 (mt0) cc_final: 0.8375 (mt0) REVERT: A 176 ASP cc_start: 0.8448 (m-30) cc_final: 0.8056 (m-30) REVERT: A 181 MET cc_start: 0.8963 (tpt) cc_final: 0.8682 (tpp) REVERT: A 190 GLN cc_start: 0.8301 (mt0) cc_final: 0.7848 (pt0) REVERT: A 211 THR cc_start: 0.9017 (OUTLIER) cc_final: 0.8798 (p) REVERT: A 328 MET cc_start: 0.8647 (mpt) cc_final: 0.8351 (mpt) outliers start: 35 outliers final: 13 residues processed: 214 average time/residue: 1.2202 time to fit residues: 279.2116 Evaluate side-chains 202 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 192 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 191 CYS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 249 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 114 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 1 optimal weight: 0.0470 chunk 89 optimal weight: 50.0000 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 256 GLN ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 ASN A 151 GLN A 304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.113690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.080613 restraints weight = 18204.119| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 3.18 r_work: 0.3042 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10040 Z= 0.138 Angle : 0.665 10.337 13666 Z= 0.334 Chirality : 0.044 0.366 1654 Planarity : 0.005 0.064 1612 Dihedral : 14.961 153.396 2240 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.34 % Allowed : 24.60 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.46 (0.24), residues: 1218 helix: 2.43 (0.20), residues: 608 sheet: 0.65 (0.34), residues: 210 loop : -1.24 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 315 HIS 0.003 0.001 HIS B 214 PHE 0.025 0.001 PHE B 215 TYR 0.013 0.001 TYR D 124 ARG 0.012 0.001 ARG A 219 Details of bonding type rmsd hydrogen bonds : bond 0.04036 ( 582) hydrogen bonds : angle 4.33363 ( 1707) SS BOND : bond 0.00684 ( 2) SS BOND : angle 2.82257 ( 4) covalent geometry : bond 0.00305 (10037) covalent geometry : angle 0.66379 (13662) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: B 103 TYR cc_start: 0.8341 (m-80) cc_final: 0.7982 (m-80) REVERT: B 141 LYS cc_start: 0.9025 (mtpm) cc_final: 0.8658 (mtmt) REVERT: B 193 GLN cc_start: 0.8962 (tp40) cc_final: 0.8543 (mm110) REVERT: B 195 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8921 (mm) REVERT: B 313 LYS cc_start: 0.8677 (mtpp) cc_final: 0.8305 (mtmm) REVERT: B 314 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.7538 (mp10) REVERT: D 22 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8354 (mmt-90) REVERT: D 258 ASP cc_start: 0.7872 (t0) cc_final: 0.7539 (t0) REVERT: D 262 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7733 (tmt) REVERT: G 47 GLU cc_start: 0.8074 (mp0) cc_final: 0.7761 (mp0) REVERT: G 48 ASP cc_start: 0.8300 (t0) cc_final: 0.7912 (m-30) REVERT: C 20 ASP cc_start: 0.8502 (m-30) cc_final: 0.8002 (m-30) REVERT: C 25 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7648 (mp0) REVERT: C 229 ASP cc_start: 0.8668 (m-30) cc_final: 0.8103 (m-30) REVERT: C 241 ASN cc_start: 0.8468 (m-40) cc_final: 0.8216 (t0) REVERT: C 242 ARG cc_start: 0.8807 (mtt90) cc_final: 0.8294 (mtt90) REVERT: C 333 GLN cc_start: 0.8765 (tp40) cc_final: 0.8413 (tp40) REVERT: A 75 ARG cc_start: 0.8713 (ptt90) cc_final: 0.8398 (ptt90) REVERT: A 76 LYS cc_start: 0.9496 (OUTLIER) cc_final: 0.9282 (mmmt) REVERT: A 164 GLN cc_start: 0.8823 (mt0) cc_final: 0.8446 (mt0) REVERT: A 176 ASP cc_start: 0.8421 (m-30) cc_final: 0.8037 (m-30) REVERT: A 181 MET cc_start: 0.8998 (tpt) cc_final: 0.8720 (tpp) REVERT: A 190 GLN cc_start: 0.8173 (mt0) cc_final: 0.7733 (pt0) REVERT: A 192 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.6839 (mt) REVERT: A 193 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7796 (mm-40) REVERT: A 323 GLN cc_start: 0.7761 (pm20) cc_final: 0.7535 (pm20) REVERT: A 326 ARG cc_start: 0.7359 (mpt90) cc_final: 0.7079 (mmp80) REVERT: A 328 MET cc_start: 0.8843 (mpt) cc_final: 0.8412 (mpt) REVERT: A 337 LYS cc_start: 0.6979 (tptt) cc_final: 0.6668 (tmtt) outliers start: 33 outliers final: 12 residues processed: 210 average time/residue: 1.2032 time to fit residues: 269.9444 Evaluate side-chains 195 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 321 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 45 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 311 GLN ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.112930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.079520 restraints weight = 18249.201| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.18 r_work: 0.3025 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10040 Z= 0.168 Angle : 0.691 11.746 13666 Z= 0.345 Chirality : 0.045 0.351 1654 Planarity : 0.005 0.064 1612 Dihedral : 14.889 151.524 2240 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.63 % Allowed : 25.71 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.42 (0.24), residues: 1218 helix: 2.40 (0.20), residues: 608 sheet: 0.56 (0.35), residues: 206 loop : -1.21 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 315 HIS 0.003 0.001 HIS B 214 PHE 0.024 0.001 PHE B 215 TYR 0.021 0.001 TYR G 40 ARG 0.011 0.001 ARG A 152 Details of bonding type rmsd hydrogen bonds : bond 0.04107 ( 582) hydrogen bonds : angle 4.38813 ( 1707) SS BOND : bond 0.00636 ( 2) SS BOND : angle 2.96807 ( 4) covalent geometry : bond 0.00381 (10037) covalent geometry : angle 0.68953 (13662) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 LYS cc_start: 0.8969 (mmmt) cc_final: 0.8410 (mppt) REVERT: B 103 TYR cc_start: 0.8360 (m-80) cc_final: 0.8006 (m-80) REVERT: B 193 GLN cc_start: 0.8937 (tp40) cc_final: 0.8508 (mm110) REVERT: B 313 LYS cc_start: 0.8671 (mtpp) cc_final: 0.8292 (mtmm) REVERT: B 314 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.7544 (mp10) REVERT: D 22 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8299 (mmt-90) REVERT: D 258 ASP cc_start: 0.7893 (t0) cc_final: 0.7524 (t0) REVERT: D 262 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7704 (tmt) REVERT: G 47 GLU cc_start: 0.8151 (mp0) cc_final: 0.7840 (mp0) REVERT: G 48 ASP cc_start: 0.8327 (t0) cc_final: 0.7903 (m-30) REVERT: C 20 ASP cc_start: 0.8530 (m-30) cc_final: 0.8028 (m-30) REVERT: C 229 ASP cc_start: 0.8672 (m-30) cc_final: 0.8091 (m-30) REVERT: C 241 ASN cc_start: 0.8488 (m-40) cc_final: 0.8234 (t0) REVERT: C 242 ARG cc_start: 0.8815 (mtt90) cc_final: 0.8277 (mtt90) REVERT: C 333 GLN cc_start: 0.8786 (tp40) cc_final: 0.8419 (tp40) REVERT: A 75 ARG cc_start: 0.8715 (ptt90) cc_final: 0.8407 (ptt90) REVERT: A 76 LYS cc_start: 0.9496 (OUTLIER) cc_final: 0.9295 (mmmt) REVERT: A 109 ASP cc_start: 0.8211 (t0) cc_final: 0.7661 (m-30) REVERT: A 164 GLN cc_start: 0.8837 (mt0) cc_final: 0.8466 (mt0) REVERT: A 176 ASP cc_start: 0.8390 (m-30) cc_final: 0.8011 (m-30) REVERT: A 181 MET cc_start: 0.8987 (tpt) cc_final: 0.8726 (tpp) REVERT: A 190 GLN cc_start: 0.8150 (mt0) cc_final: 0.7683 (pt0) REVERT: A 192 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.6728 (mt) REVERT: A 193 GLN cc_start: 0.8241 (mm-40) cc_final: 0.7945 (mm-40) REVERT: A 326 ARG cc_start: 0.7348 (mpt90) cc_final: 0.7050 (mmp80) REVERT: A 337 LYS cc_start: 0.7006 (tptt) cc_final: 0.6530 (tmtt) outliers start: 26 outliers final: 11 residues processed: 207 average time/residue: 1.1965 time to fit residues: 265.3592 Evaluate side-chains 196 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 321 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 76 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 18 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 114 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.114055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.081022 restraints weight = 18125.455| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.17 r_work: 0.3035 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10040 Z= 0.140 Angle : 0.697 13.622 13666 Z= 0.349 Chirality : 0.044 0.349 1654 Planarity : 0.005 0.064 1612 Dihedral : 14.705 151.829 2240 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.13 % Allowed : 26.42 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.46 (0.24), residues: 1218 helix: 2.40 (0.20), residues: 608 sheet: 0.72 (0.35), residues: 200 loop : -1.17 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 315 HIS 0.003 0.001 HIS G 44 PHE 0.024 0.001 PHE B 215 TYR 0.014 0.001 TYR D 124 ARG 0.012 0.001 ARG C 24 Details of bonding type rmsd hydrogen bonds : bond 0.03995 ( 582) hydrogen bonds : angle 4.37337 ( 1707) SS BOND : bond 0.00436 ( 2) SS BOND : angle 2.74195 ( 4) covalent geometry : bond 0.00316 (10037) covalent geometry : angle 0.69520 (13662) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 TYR cc_start: 0.8307 (m-80) cc_final: 0.7932 (m-80) REVERT: B 193 GLN cc_start: 0.8886 (tp40) cc_final: 0.8552 (mm110) REVERT: B 313 LYS cc_start: 0.8587 (mtpp) cc_final: 0.8203 (mtmm) REVERT: B 314 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.7429 (mp10) REVERT: D 22 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8318 (mmt-90) REVERT: D 258 ASP cc_start: 0.7790 (t0) cc_final: 0.7513 (t0) REVERT: D 262 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7701 (tmt) REVERT: G 48 ASP cc_start: 0.8248 (t0) cc_final: 0.7828 (m-30) REVERT: C 229 ASP cc_start: 0.8617 (m-30) cc_final: 0.8006 (m-30) REVERT: C 232 LEU cc_start: 0.9155 (mm) cc_final: 0.8520 (mp) REVERT: C 241 ASN cc_start: 0.8437 (m-40) cc_final: 0.8218 (t0) REVERT: C 242 ARG cc_start: 0.8764 (mtt90) cc_final: 0.8276 (mtt90) REVERT: C 333 GLN cc_start: 0.8753 (tp40) cc_final: 0.8393 (tp40) REVERT: A 75 ARG cc_start: 0.8684 (ptt90) cc_final: 0.8385 (ptt90) REVERT: A 109 ASP cc_start: 0.8234 (t0) cc_final: 0.7558 (m-30) REVERT: A 164 GLN cc_start: 0.8792 (mt0) cc_final: 0.8364 (mt0) REVERT: A 176 ASP cc_start: 0.8441 (m-30) cc_final: 0.7968 (m-30) REVERT: A 181 MET cc_start: 0.8962 (tpt) cc_final: 0.8687 (tpp) REVERT: A 190 GLN cc_start: 0.8056 (mt0) cc_final: 0.7606 (pt0) REVERT: A 192 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6728 (mt) REVERT: A 193 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7937 (mm-40) REVERT: A 326 ARG cc_start: 0.7393 (mpt90) cc_final: 0.7085 (mmp80) REVERT: A 337 LYS cc_start: 0.6955 (tptt) cc_final: 0.6515 (tmtt) outliers start: 21 outliers final: 8 residues processed: 208 average time/residue: 1.2247 time to fit residues: 271.8854 Evaluate side-chains 198 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 249 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 7 optimal weight: 2.9990 chunk 97 optimal weight: 0.1980 chunk 109 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 89 optimal weight: 30.0000 chunk 37 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS A 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.110989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.076760 restraints weight = 18346.168| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.23 r_work: 0.2980 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10040 Z= 0.219 Angle : 0.784 13.426 13666 Z= 0.387 Chirality : 0.047 0.377 1654 Planarity : 0.005 0.064 1612 Dihedral : 14.900 150.599 2240 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.13 % Allowed : 26.32 % Favored : 71.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.30 (0.24), residues: 1218 helix: 2.24 (0.20), residues: 610 sheet: 0.52 (0.35), residues: 206 loop : -1.17 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 315 HIS 0.002 0.001 HIS A 282 PHE 0.025 0.002 PHE B 215 TYR 0.021 0.002 TYR G 40 ARG 0.013 0.001 ARG C 24 Details of bonding type rmsd hydrogen bonds : bond 0.04401 ( 582) hydrogen bonds : angle 4.49878 ( 1707) SS BOND : bond 0.00430 ( 2) SS BOND : angle 3.03461 ( 4) covalent geometry : bond 0.00504 (10037) covalent geometry : angle 0.78280 (13662) Misc. bond : bond 0.00022 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 81 LYS cc_start: 0.8959 (mmmt) cc_final: 0.8369 (mppt) REVERT: B 103 TYR cc_start: 0.8377 (m-80) cc_final: 0.8005 (m-80) REVERT: B 313 LYS cc_start: 0.8610 (mtpp) cc_final: 0.8231 (mtmm) REVERT: B 314 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.7584 (mp10) REVERT: D 22 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8339 (mmt-90) REVERT: D 258 ASP cc_start: 0.7832 (t0) cc_final: 0.7587 (t0) REVERT: D 262 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.7676 (tmt) REVERT: G 48 ASP cc_start: 0.8313 (t0) cc_final: 0.7932 (m-30) REVERT: C 20 ASP cc_start: 0.8507 (m-30) cc_final: 0.8112 (m-30) REVERT: C 53 MET cc_start: 0.9096 (mpm) cc_final: 0.8845 (mmt) REVERT: C 229 ASP cc_start: 0.8659 (m-30) cc_final: 0.8032 (m-30) REVERT: C 232 LEU cc_start: 0.9117 (mm) cc_final: 0.8426 (mp) REVERT: C 241 ASN cc_start: 0.8479 (m-40) cc_final: 0.8225 (t0) REVERT: C 242 ARG cc_start: 0.8794 (mtt90) cc_final: 0.8185 (mtt90) REVERT: A 75 ARG cc_start: 0.8644 (ptt90) cc_final: 0.8189 (ptt90) REVERT: A 76 LYS cc_start: 0.9550 (mmmt) cc_final: 0.9087 (mppt) REVERT: A 109 ASP cc_start: 0.8341 (t0) cc_final: 0.7536 (m-30) REVERT: A 164 GLN cc_start: 0.8716 (mt0) cc_final: 0.8308 (mt0) REVERT: A 176 ASP cc_start: 0.8466 (m-30) cc_final: 0.8009 (m-30) REVERT: A 181 MET cc_start: 0.8976 (tpt) cc_final: 0.8745 (tpp) REVERT: A 190 GLN cc_start: 0.8196 (mt0) cc_final: 0.7755 (pt0) REVERT: A 192 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6747 (mt) REVERT: A 193 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7988 (mm-40) REVERT: A 195 LEU cc_start: 0.9244 (mt) cc_final: 0.8961 (mm) REVERT: A 199 MET cc_start: 0.8946 (ppp) cc_final: 0.8263 (ttt) REVERT: A 337 LYS cc_start: 0.6949 (tptt) cc_final: 0.6523 (tmtt) outliers start: 21 outliers final: 11 residues processed: 201 average time/residue: 1.2196 time to fit residues: 262.7680 Evaluate side-chains 195 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 321 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 73 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 GLN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS C 306 GLN C 333 GLN A 304 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.113368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.080329 restraints weight = 17999.417| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 3.13 r_work: 0.3043 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10040 Z= 0.150 Angle : 0.773 13.330 13666 Z= 0.379 Chirality : 0.046 0.360 1654 Planarity : 0.005 0.064 1612 Dihedral : 14.718 151.595 2240 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.82 % Allowed : 26.42 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.35 (0.24), residues: 1218 helix: 2.25 (0.20), residues: 610 sheet: 0.71 (0.35), residues: 200 loop : -1.17 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A 315 HIS 0.007 0.001 HIS B 214 PHE 0.018 0.001 PHE A 275 TYR 0.013 0.001 TYR B 220 ARG 0.013 0.001 ARG C 24 Details of bonding type rmsd hydrogen bonds : bond 0.04085 ( 582) hydrogen bonds : angle 4.42774 ( 1707) SS BOND : bond 0.00715 ( 2) SS BOND : angle 3.23037 ( 4) covalent geometry : bond 0.00343 (10037) covalent geometry : angle 0.77091 (13662) Misc. bond : bond 0.00002 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9351.34 seconds wall clock time: 161 minutes 22.24 seconds (9682.24 seconds total)