Starting phenix.real_space_refine on Fri Feb 14 04:54:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yk0_39356/02_2025/8yk0_39356.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yk0_39356/02_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_39356/02_2025/8yk0_39356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yk0_39356/02_2025/8yk0_39356.map" model { file = "/net/cci-nas-00/data/ceres_data/8yk0_39356/02_2025/8yk0_39356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yk0_39356/02_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-5592/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: 6.05, 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 1.2 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: 0.93 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: 3.14 Time building geometry restraints manager: 3.02 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: 0.690 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.610 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.190 ------------------------------------------------------------------------------- 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 : 0.008 0.238 10037 Z= 0.571 Angle : 1.302 28.066 13662 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 *********************** 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 : 1.063 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: 1.3407 time to fit residues: 321.3635 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 : 1.071 ------------------------------------------------------------------------------- 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: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.115828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.082606 restraints weight = 17879.910| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.15 r_work: 0.3086 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10037 Z= 0.189 Angle : 0.678 7.866 13662 Z= 0.338 Chirality : 0.046 0.232 1654 Planarity : 0.005 0.064 1612 Dihedral : 17.551 165.708 2243 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.34 % Allowed : 18.72 % Favored : 77.94 % 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: 0.96 (0.24), residues: 1218 helix: 2.03 (0.21), residues: 605 sheet: 0.48 (0.36), residues: 205 loop : -1.47 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 315 HIS 0.005 0.001 HIS G 44 PHE 0.026 0.001 PHE B 215 TYR 0.020 0.001 TYR G 40 ARG 0.007 0.001 ARG A 219 *********************** 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 236 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 1.091 Fit side-chains revert: symmetry clash REVERT: B 79 ILE cc_start: 0.8702 (mm) cc_final: 0.8303 (tp) REVERT: B 103 TYR cc_start: 0.8349 (m-80) cc_final: 0.8066 (m-80) REVERT: B 117 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8382 (mt-10) REVERT: B 190 GLN cc_start: 0.8703 (mt0) cc_final: 0.8299 (mm110) REVERT: B 313 LYS cc_start: 0.8676 (mtpp) cc_final: 0.8421 (mtmm) REVERT: D 22 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8356 (mmt-90) REVERT: D 258 ASP cc_start: 0.7824 (t0) cc_final: 0.7283 (t0) REVERT: C 18 MET cc_start: 0.8120 (tpp) cc_final: 0.7875 (tpp) REVERT: C 20 ASP cc_start: 0.8532 (m-30) cc_final: 0.8283 (m-30) REVERT: C 205 ARG cc_start: 0.8768 (mmp80) cc_final: 0.8547 (mmp80) REVERT: C 232 LEU cc_start: 0.9055 (mm) cc_final: 0.8765 (mp) REVERT: C 242 ARG cc_start: 0.8726 (mtt90) cc_final: 0.8052 (mtt90) REVERT: C 333 GLN cc_start: 0.8766 (tp40) cc_final: 0.8291 (tp40) REVERT: A 75 ARG cc_start: 0.8762 (ptt90) cc_final: 0.8507 (ptt90) REVERT: A 78 ARG cc_start: 0.7704 (ptp-110) cc_final: 0.7492 (ptp-110) REVERT: A 81 LYS cc_start: 0.9117 (ttmm) cc_final: 0.8892 (ptmm) REVERT: A 164 GLN cc_start: 0.8692 (mt0) cc_final: 0.8310 (tt0) REVERT: A 176 ASP cc_start: 0.8444 (m-30) cc_final: 0.8080 (m-30) REVERT: A 181 MET cc_start: 0.8998 (tpt) cc_final: 0.8718 (tpp) REVERT: A 193 GLN cc_start: 0.7966 (mm-40) cc_final: 0.7362 (mm-40) REVERT: A 214 HIS cc_start: 0.8430 (t70) cc_final: 0.7980 (t-170) REVERT: A 238 TYR cc_start: 0.9098 (t80) cc_final: 0.8829 (t80) REVERT: A 325 ILE cc_start: 0.7361 (mm) cc_final: 0.6970 (mm) REVERT: A 326 ARG cc_start: 0.8030 (tpm170) cc_final: 0.7708 (mpt90) outliers start: 33 outliers final: 10 residues processed: 224 average time/residue: 1.2705 time to fit residues: 304.4881 Evaluate side-chains 189 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 178 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 68 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 33 optimal weight: 0.0770 chunk 4 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 GLN G 44 HIS C 306 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 = 0.3778 r_free = 0.3778 target = 0.115157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.081737 restraints weight = 18295.298| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.18 r_work: 0.3073 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10037 Z= 0.192 Angle : 0.626 10.607 13662 Z= 0.313 Chirality : 0.044 0.212 1654 Planarity : 0.004 0.059 1612 Dihedral : 16.408 163.722 2240 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.54 % Allowed : 19.23 % Favored : 77.23 % 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: 2.42 (0.20), residues: 603 sheet: 0.83 (0.36), residues: 202 loop : -1.42 (0.30), residues: 413 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 0.009 0.001 PHE G 61 TYR 0.010 0.001 TYR D 59 ARG 0.009 0.001 ARG A 219 *********************** 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 228 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 81 LYS cc_start: 0.8996 (mmmt) cc_final: 0.8642 (mtmm) REVERT: B 82 MET cc_start: 0.8997 (mtp) cc_final: 0.8648 (ptp) REVERT: B 103 TYR cc_start: 0.8332 (m-80) cc_final: 0.8006 (m-80) REVERT: B 117 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8360 (mt-10) REVERT: B 190 GLN cc_start: 0.8686 (mt0) cc_final: 0.8232 (mm110) REVERT: B 193 GLN cc_start: 0.8954 (tp40) cc_final: 0.8431 (mm110) REVERT: B 195 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8824 (mm) REVERT: B 313 LYS cc_start: 0.8686 (mtpp) cc_final: 0.8254 (mtmm) REVERT: B 314 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.7562 (mp10) REVERT: D 22 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8354 (mmt-90) REVERT: D 258 ASP cc_start: 0.7771 (t0) cc_final: 0.7353 (t0) REVERT: G 47 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7932 (mp0) REVERT: C 20 ASP cc_start: 0.8399 (m-30) cc_final: 0.7945 (m-30) REVERT: C 228 SER cc_start: 0.8975 (t) cc_final: 0.8759 (m) REVERT: C 333 GLN cc_start: 0.8769 (tp40) cc_final: 0.8294 (tp40) REVERT: A 75 ARG cc_start: 0.8750 (ptt90) cc_final: 0.8360 (ptt90) REVERT: A 76 LYS cc_start: 0.9481 (mmtm) cc_final: 0.9248 (mmmt) REVERT: A 164 GLN cc_start: 0.8703 (mt0) cc_final: 0.8353 (mt0) REVERT: A 176 ASP cc_start: 0.8472 (m-30) cc_final: 0.8073 (m-30) REVERT: A 181 MET cc_start: 0.8966 (tpt) cc_final: 0.8679 (tpp) REVERT: A 211 THR cc_start: 0.9191 (OUTLIER) cc_final: 0.8973 (p) REVERT: A 315 TRP cc_start: 0.8752 (t60) cc_final: 0.8546 (t60) REVERT: A 328 MET cc_start: 0.8741 (mpt) cc_final: 0.8084 (mpt) outliers start: 35 outliers final: 14 residues processed: 216 average time/residue: 1.3300 time to fit residues: 306.7680 Evaluate side-chains 190 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 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 192 LEU 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: 0.7980 chunk 27 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 91 optimal weight: 0.1980 chunk 17 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 0 optimal weight: 60.0000 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 256 GLN A 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.114566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.081095 restraints weight = 18054.201| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.18 r_work: 0.3063 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10037 Z= 0.200 Angle : 0.617 8.339 13662 Z= 0.309 Chirality : 0.043 0.185 1654 Planarity : 0.005 0.063 1612 Dihedral : 15.733 162.326 2240 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % 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: 1.40 (0.24), residues: 1218 helix: 2.42 (0.20), residues: 609 sheet: 0.67 (0.35), residues: 202 loop : -1.34 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 169 HIS 0.004 0.001 HIS G 44 PHE 0.025 0.001 PHE B 215 TYR 0.008 0.001 TYR A 220 ARG 0.010 0.001 ARG A 219 *********************** 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 221 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 186 time to evaluate : 1.203 Fit side-chains REVERT: B 81 LYS cc_start: 0.9005 (mmmt) cc_final: 0.8632 (mtmm) REVERT: B 82 MET cc_start: 0.8990 (mtp) cc_final: 0.8786 (ptp) REVERT: B 103 TYR cc_start: 0.8321 (m-80) cc_final: 0.7968 (m-80) REVERT: B 193 GLN cc_start: 0.8948 (tp40) cc_final: 0.8473 (mm-40) REVERT: B 214 HIS cc_start: 0.8450 (t-90) cc_final: 0.8079 (t-90) REVERT: B 313 LYS cc_start: 0.8689 (mtpp) cc_final: 0.8328 (mtmm) REVERT: B 314 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.7558 (mp10) REVERT: D 22 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8250 (mmt-90) REVERT: D 172 GLU cc_start: 0.8582 (mp0) cc_final: 0.8351 (mp0) REVERT: D 258 ASP cc_start: 0.7761 (t0) cc_final: 0.7311 (t0) REVERT: D 262 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7691 (ttt) REVERT: G 47 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8038 (mp0) REVERT: C 20 ASP cc_start: 0.8475 (m-30) cc_final: 0.7935 (m-30) REVERT: C 242 ARG cc_start: 0.8801 (mtt90) cc_final: 0.8053 (mtt90) REVERT: C 333 GLN cc_start: 0.8785 (tp40) cc_final: 0.8415 (tp40) REVERT: A 75 ARG cc_start: 0.8715 (ptt90) cc_final: 0.8350 (ptt90) REVERT: A 76 LYS cc_start: 0.9510 (mmtm) cc_final: 0.9260 (mmmt) REVERT: A 89 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.9186 (mp) REVERT: A 164 GLN cc_start: 0.8755 (mt0) cc_final: 0.8455 (mt0) REVERT: A 176 ASP cc_start: 0.8403 (m-30) cc_final: 0.8035 (m-30) REVERT: A 181 MET cc_start: 0.8982 (tpt) cc_final: 0.8665 (tpp) REVERT: A 211 THR cc_start: 0.9091 (OUTLIER) cc_final: 0.8855 (p) REVERT: A 315 TRP cc_start: 0.8796 (t60) cc_final: 0.8516 (t60) outliers start: 35 outliers final: 16 residues processed: 211 average time/residue: 1.2500 time to fit residues: 283.9998 Evaluate side-chains 196 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 D residue 262 MET 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 49 ILE Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 172 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 16 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 0.0980 chunk 35 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 GLN B 304 ASN D 13 GLN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.112795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.079235 restraints weight = 18085.625| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.16 r_work: 0.3029 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10037 Z= 0.256 Angle : 0.645 10.312 13662 Z= 0.322 Chirality : 0.044 0.303 1654 Planarity : 0.005 0.065 1612 Dihedral : 15.415 163.798 2240 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.05 % Allowed : 21.86 % Favored : 74.09 % 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: 2.33 (0.21), residues: 615 sheet: 0.54 (0.35), residues: 204 loop : -1.25 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 169 HIS 0.002 0.001 HIS G 44 PHE 0.023 0.001 PHE B 215 TYR 0.019 0.001 TYR G 40 ARG 0.010 0.001 ARG A 219 *********************** 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 224 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.8965 (mtp) cc_final: 0.8695 (ptp) REVERT: B 103 TYR cc_start: 0.8350 (m-80) cc_final: 0.8017 (m-80) REVERT: B 193 GLN cc_start: 0.8901 (tp40) cc_final: 0.8254 (mm110) REVERT: B 195 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8879 (mm) REVERT: B 313 LYS cc_start: 0.8662 (mtpp) cc_final: 0.8294 (mtmm) REVERT: B 314 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.7559 (mp10) REVERT: D 22 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8342 (mmt-90) REVERT: D 172 GLU cc_start: 0.8582 (mp0) cc_final: 0.8333 (mp0) REVERT: D 258 ASP cc_start: 0.7833 (t0) cc_final: 0.7430 (t0) REVERT: D 262 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7848 (ttt) REVERT: G 47 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8061 (mp0) REVERT: G 48 ASP cc_start: 0.8386 (t0) cc_final: 0.7953 (m-30) REVERT: C 20 ASP cc_start: 0.8495 (m-30) cc_final: 0.7945 (m-30) REVERT: C 229 ASP cc_start: 0.8775 (m-30) cc_final: 0.8362 (m-30) REVERT: C 241 ASN cc_start: 0.8570 (m-40) cc_final: 0.8242 (t0) REVERT: C 333 GLN cc_start: 0.8775 (tp40) cc_final: 0.8393 (tp40) REVERT: A 75 ARG cc_start: 0.8720 (ptt90) cc_final: 0.8351 (ptt90) REVERT: A 76 LYS cc_start: 0.9515 (OUTLIER) cc_final: 0.9296 (mmmt) REVERT: A 89 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.9089 (mp) REVERT: A 164 GLN cc_start: 0.8839 (mt0) cc_final: 0.8525 (mt0) REVERT: A 176 ASP cc_start: 0.8445 (m-30) cc_final: 0.8051 (m-30) REVERT: A 181 MET cc_start: 0.8976 (tpt) cc_final: 0.8706 (tpp) REVERT: A 190 GLN cc_start: 0.8233 (mt0) cc_final: 0.7658 (mm-40) REVERT: A 211 THR cc_start: 0.9037 (OUTLIER) cc_final: 0.8822 (p) REVERT: A 315 TRP cc_start: 0.8774 (t60) cc_final: 0.8485 (t60) REVERT: A 328 MET cc_start: 0.8778 (mpt) cc_final: 0.8274 (mpt) outliers start: 40 outliers final: 18 residues processed: 211 average time/residue: 1.2739 time to fit residues: 287.5223 Evaluate side-chains 202 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 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 13 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 47 ASN Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 192 LYS Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 172 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 67 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 18 optimal weight: 40.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 256 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.110819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.077071 restraints weight = 18197.096| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.19 r_work: 0.2966 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10037 Z= 0.347 Angle : 0.686 9.092 13662 Z= 0.342 Chirality : 0.046 0.302 1654 Planarity : 0.005 0.064 1612 Dihedral : 15.459 166.904 2240 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.85 % Allowed : 22.98 % Favored : 73.18 % 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: 615 sheet: 0.48 (0.34), residues: 214 loop : -1.23 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 169 HIS 0.003 0.001 HIS A 282 PHE 0.023 0.002 PHE B 215 TYR 0.012 0.001 TYR D 59 ARG 0.013 0.001 ARG A 219 *********************** 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 227 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.8947 (mtp) cc_final: 0.8585 (ptp) REVERT: B 103 TYR cc_start: 0.8363 (m-80) cc_final: 0.8037 (m-80) REVERT: B 193 GLN cc_start: 0.8872 (tp40) cc_final: 0.8620 (mm-40) REVERT: B 195 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8891 (mm) REVERT: B 313 LYS cc_start: 0.8656 (mtpp) cc_final: 0.8288 (mtmm) REVERT: B 314 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.7568 (mp10) REVERT: D 22 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8379 (mmt-90) REVERT: D 172 GLU cc_start: 0.8600 (mp0) cc_final: 0.8357 (mp0) REVERT: D 258 ASP cc_start: 0.7826 (t0) cc_final: 0.7595 (t0) REVERT: G 48 ASP cc_start: 0.8399 (t0) cc_final: 0.7959 (m-30) REVERT: C 20 ASP cc_start: 0.8515 (m-30) cc_final: 0.8123 (m-30) REVERT: C 25 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: C 241 ASN cc_start: 0.8537 (m-40) cc_final: 0.8202 (t0) REVERT: C 242 ARG cc_start: 0.8779 (mtt90) cc_final: 0.8118 (mtt90) REVERT: C 271 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8720 (ttmm) REVERT: C 333 GLN cc_start: 0.8778 (tp40) cc_final: 0.8434 (tp40) REVERT: A 75 ARG cc_start: 0.8707 (ptt90) cc_final: 0.8351 (ptt90) REVERT: A 76 LYS cc_start: 0.9523 (OUTLIER) cc_final: 0.9309 (mmmt) REVERT: A 164 GLN cc_start: 0.8726 (mt0) cc_final: 0.8378 (mt0) REVERT: A 176 ASP cc_start: 0.8416 (m-30) cc_final: 0.8031 (m-30) REVERT: A 181 MET cc_start: 0.8973 (tpt) cc_final: 0.8709 (tpp) REVERT: A 190 GLN cc_start: 0.8334 (mt0) cc_final: 0.7855 (pt0) REVERT: A 211 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8852 (p) REVERT: A 315 TRP cc_start: 0.8766 (t60) cc_final: 0.8481 (t60) REVERT: A 328 MET cc_start: 0.8758 (mpt) cc_final: 0.8341 (mpt) outliers start: 38 outliers final: 15 residues processed: 217 average time/residue: 1.2446 time to fit residues: 288.7893 Evaluate side-chains 202 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 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 G residue 52 THR Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 192 LYS Chi-restraints excluded: chain C residue 271 LYS Chi-restraints excluded: chain A residue 76 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: 1.9990 chunk 119 optimal weight: 0.2980 chunk 92 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 89 optimal weight: 40.0000 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 HIS 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 193 GLN A 304 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.112770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.079743 restraints weight = 18299.579| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.17 r_work: 0.3032 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10037 Z= 0.211 Angle : 0.668 10.226 13662 Z= 0.332 Chirality : 0.044 0.354 1654 Planarity : 0.005 0.064 1612 Dihedral : 15.160 162.546 2240 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.24 % Allowed : 24.70 % 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: 1.42 (0.24), residues: 1218 helix: 2.35 (0.20), residues: 613 sheet: 0.64 (0.34), residues: 210 loop : -1.23 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 169 HIS 0.004 0.001 HIS B 214 PHE 0.026 0.001 PHE B 215 TYR 0.013 0.001 TYR D 124 ARG 0.013 0.001 ARG A 219 *********************** 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 224 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.8922 (mtp) cc_final: 0.8535 (ptp) REVERT: B 103 TYR cc_start: 0.8332 (m-80) cc_final: 0.7958 (m-80) REVERT: B 193 GLN cc_start: 0.8902 (tp40) cc_final: 0.8630 (mm-40) REVERT: B 313 LYS cc_start: 0.8653 (mtpp) cc_final: 0.8276 (mtmm) REVERT: B 314 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.7542 (mp10) REVERT: D 22 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8422 (mmt-90) REVERT: D 172 GLU cc_start: 0.8610 (mp0) cc_final: 0.8394 (mp0) REVERT: G 48 ASP cc_start: 0.8384 (t0) cc_final: 0.7921 (m-30) REVERT: C 20 ASP cc_start: 0.8489 (m-30) cc_final: 0.7917 (m-30) REVERT: C 229 ASP cc_start: 0.8710 (m-30) cc_final: 0.8207 (m-30) REVERT: C 241 ASN cc_start: 0.8482 (m-40) cc_final: 0.8227 (t0) REVERT: C 333 GLN cc_start: 0.8762 (tp40) cc_final: 0.8411 (tp40) REVERT: A 75 ARG cc_start: 0.8707 (ptt90) cc_final: 0.8386 (ptt90) REVERT: A 76 LYS cc_start: 0.9502 (OUTLIER) cc_final: 0.9298 (mmmt) REVERT: A 164 GLN cc_start: 0.8827 (mt0) cc_final: 0.8447 (mt0) REVERT: A 176 ASP cc_start: 0.8404 (m-30) cc_final: 0.8023 (m-30) REVERT: A 181 MET cc_start: 0.8991 (tpt) cc_final: 0.8706 (tpp) REVERT: A 190 GLN cc_start: 0.8117 (mt0) cc_final: 0.7570 (mm-40) REVERT: A 192 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.6742 (mt) REVERT: A 193 GLN cc_start: 0.8229 (mm110) cc_final: 0.7817 (mm-40) REVERT: A 315 TRP cc_start: 0.8786 (t60) cc_final: 0.8498 (t60) REVERT: A 328 MET cc_start: 0.8852 (mpt) cc_final: 0.8351 (mpt) outliers start: 32 outliers final: 13 residues processed: 217 average time/residue: 1.3286 time to fit residues: 309.2505 Evaluate side-chains 195 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 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 110 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 198 SER 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: 1.9990 chunk 105 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 HIS B 256 GLN B 311 GLN D 13 GLN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS A 151 GLN A 304 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.112396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.079402 restraints weight = 18227.111| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.16 r_work: 0.3006 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10037 Z= 0.239 Angle : 0.695 11.676 13662 Z= 0.346 Chirality : 0.045 0.352 1654 Planarity : 0.005 0.063 1612 Dihedral : 15.086 159.497 2240 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.94 % Allowed : 25.71 % Favored : 71.36 % 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: 1.37 (0.24), residues: 1218 helix: 2.31 (0.20), residues: 614 sheet: 0.56 (0.34), residues: 206 loop : -1.20 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 169 HIS 0.006 0.001 HIS B 214 PHE 0.025 0.001 PHE B 215 TYR 0.013 0.001 TYR D 124 ARG 0.014 0.001 ARG A 219 *********************** 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 216 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: B 82 MET cc_start: 0.8930 (mtp) cc_final: 0.8587 (ptp) REVERT: B 103 TYR cc_start: 0.8313 (m-80) cc_final: 0.7928 (m-80) REVERT: B 313 LYS cc_start: 0.8607 (mtpp) cc_final: 0.8219 (mtmm) REVERT: B 314 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.7523 (mp10) REVERT: D 172 GLU cc_start: 0.8638 (mp0) cc_final: 0.8371 (mp0) REVERT: D 262 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7970 (ttt) REVERT: C 20 ASP cc_start: 0.8441 (m-30) cc_final: 0.7842 (m-30) REVERT: C 242 ARG cc_start: 0.8748 (mtt90) cc_final: 0.8140 (mtt90) REVERT: C 333 GLN cc_start: 0.8764 (tp40) cc_final: 0.8408 (tp40) REVERT: A 75 ARG cc_start: 0.8685 (ptt90) cc_final: 0.8362 (ptt90) REVERT: A 164 GLN cc_start: 0.8821 (mt0) cc_final: 0.8446 (mt0) REVERT: A 176 ASP cc_start: 0.8415 (m-30) cc_final: 0.8028 (m-30) REVERT: A 181 MET cc_start: 0.8960 (tpt) cc_final: 0.8698 (tpp) REVERT: A 190 GLN cc_start: 0.8097 (mt0) cc_final: 0.7527 (mm-40) REVERT: A 192 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.6724 (mt) REVERT: A 193 GLN cc_start: 0.8303 (mm110) cc_final: 0.7974 (mm-40) REVERT: A 315 TRP cc_start: 0.8761 (t60) cc_final: 0.8537 (t60) REVERT: A 328 MET cc_start: 0.8753 (mpt) cc_final: 0.8542 (mpt) outliers start: 29 outliers final: 15 residues processed: 207 average time/residue: 1.2906 time to fit residues: 285.2846 Evaluate side-chains 198 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 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 49 ILE Chi-restraints excluded: chain C residue 192 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 198 SER 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: 0.7980 chunk 84 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 18 optimal weight: 30.0000 chunk 46 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS 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 = 0.3733 r_free = 0.3733 target = 0.112068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.078406 restraints weight = 18202.523| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 3.23 r_work: 0.2999 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10037 Z= 0.271 Angle : 0.732 13.630 13662 Z= 0.364 Chirality : 0.045 0.351 1654 Planarity : 0.005 0.064 1612 Dihedral : 15.065 157.978 2240 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.43 % Allowed : 26.01 % 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: 1.33 (0.24), residues: 1218 helix: 2.31 (0.20), residues: 609 sheet: 0.55 (0.35), residues: 200 loop : -1.22 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 169 HIS 0.010 0.001 HIS B 214 PHE 0.026 0.001 PHE B 215 TYR 0.021 0.001 TYR G 40 ARG 0.016 0.001 ARG A 219 *********************** 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 210 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.8931 (mtp) cc_final: 0.8559 (ptp) REVERT: B 103 TYR cc_start: 0.8342 (m-80) cc_final: 0.7999 (m-80) REVERT: B 193 GLN cc_start: 0.8976 (mm-40) cc_final: 0.8592 (mm110) REVERT: B 313 LYS cc_start: 0.8582 (mtpp) cc_final: 0.8193 (mtmm) REVERT: B 314 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.7523 (mp10) REVERT: D 172 GLU cc_start: 0.8644 (mp0) cc_final: 0.8281 (mp0) REVERT: G 48 ASP cc_start: 0.8302 (t0) cc_final: 0.7878 (m-30) REVERT: C 229 ASP cc_start: 0.8572 (m-30) cc_final: 0.7955 (m-30) REVERT: C 232 LEU cc_start: 0.9000 (mm) cc_final: 0.8462 (mp) REVERT: C 241 ASN cc_start: 0.8079 (m-40) cc_final: 0.7620 (t0) REVERT: C 242 ARG cc_start: 0.8742 (mtt90) cc_final: 0.8306 (mtt90) REVERT: C 333 GLN cc_start: 0.8768 (tp40) cc_final: 0.8412 (tp40) REVERT: A 75 ARG cc_start: 0.8625 (ptt90) cc_final: 0.7985 (ptt90) REVERT: A 76 LYS cc_start: 0.9569 (mmmt) cc_final: 0.9082 (mppt) REVERT: A 89 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.8993 (mp) REVERT: A 164 GLN cc_start: 0.8746 (mt0) cc_final: 0.8371 (mt0) REVERT: A 176 ASP cc_start: 0.8417 (m-30) cc_final: 0.8033 (m-30) REVERT: A 181 MET cc_start: 0.8970 (tpt) cc_final: 0.8705 (tpp) REVERT: A 190 GLN cc_start: 0.8166 (mt0) cc_final: 0.7692 (pt0) REVERT: A 192 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.6681 (mt) REVERT: A 193 GLN cc_start: 0.8327 (mm110) cc_final: 0.8000 (mm-40) REVERT: A 315 TRP cc_start: 0.8780 (t60) cc_final: 0.8569 (t60) REVERT: A 328 MET cc_start: 0.8764 (mpt) cc_final: 0.8222 (mpt) outliers start: 24 outliers final: 15 residues processed: 204 average time/residue: 1.2916 time to fit residues: 281.4424 Evaluate side-chains 197 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 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 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 89 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 198 SER 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: 3.9990 chunk 109 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS C 306 GLN A 151 GLN ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.110276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.076377 restraints weight = 18324.530| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.23 r_work: 0.2957 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10037 Z= 0.357 Angle : 0.791 13.461 13662 Z= 0.391 Chirality : 0.047 0.342 1654 Planarity : 0.005 0.065 1612 Dihedral : 15.270 159.038 2240 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.53 % Allowed : 26.52 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.19 (0.24), residues: 1218 helix: 2.14 (0.20), residues: 611 sheet: 0.46 (0.34), residues: 212 loop : -1.24 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 169 HIS 0.010 0.001 HIS B 214 PHE 0.016 0.002 PHE A 275 TYR 0.014 0.001 TYR B 220 ARG 0.016 0.001 ARG A 219 ********************** 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 210 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 185 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 103 TYR cc_start: 0.8453 (m-80) cc_final: 0.8108 (m-80) REVERT: B 193 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8768 (mm110) REVERT: B 313 LYS cc_start: 0.8598 (mtpp) cc_final: 0.8217 (mtmm) REVERT: B 314 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.7553 (mp10) REVERT: D 172 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8360 (mp0) REVERT: G 48 ASP cc_start: 0.8353 (t0) cc_final: 0.7909 (m-30) REVERT: C 20 ASP cc_start: 0.8497 (m-30) cc_final: 0.8114 (m-30) REVERT: C 229 ASP cc_start: 0.8561 (m-30) cc_final: 0.7998 (m-30) REVERT: C 232 LEU cc_start: 0.9024 (mm) cc_final: 0.8486 (mp) REVERT: C 241 ASN cc_start: 0.8047 (m-40) cc_final: 0.7603 (t0) REVERT: A 75 ARG cc_start: 0.8651 (ptt90) cc_final: 0.8201 (ptt90) REVERT: A 76 LYS cc_start: 0.9573 (mmmt) cc_final: 0.9110 (mppt) REVERT: A 89 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.9013 (mp) REVERT: A 164 GLN cc_start: 0.8728 (mt0) cc_final: 0.8320 (mt0) REVERT: A 176 ASP cc_start: 0.8451 (m-30) cc_final: 0.8012 (m-30) REVERT: A 190 GLN cc_start: 0.8290 (mt0) cc_final: 0.7864 (pt0) REVERT: A 193 GLN cc_start: 0.8391 (mm110) cc_final: 0.8090 (mm-40) REVERT: A 195 LEU cc_start: 0.9221 (mt) cc_final: 0.8950 (mm) REVERT: A 199 MET cc_start: 0.8946 (ppp) cc_final: 0.8226 (ttt) REVERT: A 315 TRP cc_start: 0.8783 (t60) cc_final: 0.8575 (t60) outliers start: 25 outliers final: 12 residues processed: 204 average time/residue: 1.2708 time to fit residues: 277.1831 Evaluate side-chains 193 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 178 time to evaluate : 1.087 ------------------------------------------------------------------------------- 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 172 GLU 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 192 LYS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 198 SER 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 73 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 ASN G 44 HIS C 306 GLN C 333 GLN A 151 GLN A 304 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.111227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.077551 restraints weight = 18109.695| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.21 r_work: 0.2980 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10037 Z= 0.300 Angle : 0.785 13.383 13662 Z= 0.386 Chirality : 0.047 0.374 1654 Planarity : 0.005 0.065 1612 Dihedral : 15.132 157.188 2240 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.43 % Allowed : 26.32 % Favored : 71.26 % 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: 1.14 (0.24), residues: 1218 helix: 2.02 (0.20), residues: 617 sheet: 0.56 (0.34), residues: 211 loop : -1.25 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 169 HIS 0.011 0.001 HIS B 214 PHE 0.027 0.001 PHE B 215 TYR 0.020 0.002 TYR G 40 ARG 0.016 0.001 ARG D 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9179.64 seconds wall clock time: 162 minutes 25.31 seconds (9745.31 seconds total)