Starting phenix.real_space_refine on Wed Sep 17 16:36:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yk0_39356/09_2025/8yk0_39356.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yk0_39356/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8yk0_39356/09_2025/8yk0_39356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yk0_39356/09_2025/8yk0_39356.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yk0_39356/09_2025/8yk0_39356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yk0_39356/09_2025/8yk0_39356.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 1, 'HIS:plan': 4, 'ASP:plan': 2, 'GLN:plan1': 1} 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: {'ASP:plan': 5, 'ARG:plan': 7, 'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 1} 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: {'ASP:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1} 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, 'HIS:plan': 3, 'ASP:plan': 1} 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: 2.07, per 1000 atoms: 0.21 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: 1.02 Conformation dependent library (CDL) restraints added in 374.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.39 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: 1.52 Time building geometry restraints manager: 1.31 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: 1.100 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.990 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.862 10040 Z= 0.967 Angle : 1.302 28.066 13666 Z= 0.592 Chirality : 0.077 0.529 1654 Planarity : 0.006 0.069 1612 Dihedral : 19.603 179.865 4234 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 17.37 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (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 ARG 0.016 0.001 ARG C 24 TYR 0.017 0.002 TYR B 220 PHE 0.038 0.002 PHE B 275 TRP 0.042 0.002 TRP A 315 HIS 0.005 0.001 HIS B 282 Details of bonding type rmsd covalent geometry : bond 0.00848 (10037) covalent geometry : angle 1.30195 (13662) SS BOND : bond 0.00515 ( 2) SS BOND : angle 1.50435 ( 4) hydrogen bonds : bond 0.16523 ( 582) hydrogen bonds : angle 6.50435 ( 1707) Misc. bond : bond 0.86212 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 0.346 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: 0.8351 (mt0) REVERT: A 176 ASP cc_start: 0.7928 (m-30) cc_final: 0.7539 (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: 0.6554 (mm-40) REVERT: A 214 HIS cc_start: 0.8066 (t-170) cc_final: 0.7866 (t70) 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: 0.6553 time to fit residues: 156.6466 Evaluate side-chains 186 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 184 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 GLN B 256 GLN G 44 HIS C 244 HIS C 255 ASN A 151 GLN A 256 GLN A 265 ASN A 304 ASN A 322 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.115286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.081689 restraints weight = 17967.957| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 3.17 r_work: 0.3071 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10040 Z= 0.146 Angle : 0.689 8.789 13666 Z= 0.343 Chirality : 0.046 0.237 1654 Planarity : 0.005 0.063 1612 Dihedral : 17.702 166.300 2243 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.24 % Allowed : 18.83 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.24), residues: 1218 helix: 2.10 (0.21), residues: 599 sheet: 0.43 (0.36), residues: 203 loop : -1.55 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 152 TYR 0.019 0.001 TYR G 40 PHE 0.026 0.001 PHE B 215 TRP 0.021 0.001 TRP A 315 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00304 (10037) covalent geometry : angle 0.68629 (13662) SS BOND : bond 0.01175 ( 2) SS BOND : angle 3.60024 ( 4) hydrogen bonds : bond 0.04681 ( 582) hydrogen bonds : angle 4.72901 ( 1707) Misc. bond : bond 0.00065 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 202 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 ILE cc_start: 0.8713 (mm) cc_final: 0.8331 (tp) REVERT: B 103 TYR cc_start: 0.8357 (m-80) cc_final: 0.8083 (m-80) REVERT: B 117 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8398 (mt-10) REVERT: B 190 GLN cc_start: 0.8710 (mt0) cc_final: 0.8306 (mm110) REVERT: B 313 LYS cc_start: 0.8674 (mtpp) cc_final: 0.8419 (mtmm) REVERT: D 22 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8371 (mmt-90) REVERT: D 258 ASP cc_start: 0.7871 (t0) cc_final: 0.7336 (t0) REVERT: G 47 GLU cc_start: 0.8563 (mt-10) cc_final: 0.7688 (mp0) REVERT: C 20 ASP cc_start: 0.8531 (m-30) cc_final: 0.8303 (m-30) REVERT: C 205 ARG cc_start: 0.8760 (mmp80) cc_final: 0.8519 (mmp80) REVERT: C 232 LEU cc_start: 0.9005 (mm) cc_final: 0.8703 (mp) REVERT: C 242 ARG cc_start: 0.8743 (mtt90) cc_final: 0.8090 (mtt90) REVERT: C 306 GLN cc_start: 0.8352 (tp40) cc_final: 0.8150 (mm110) REVERT: C 333 GLN cc_start: 0.8765 (tp40) cc_final: 0.8355 (tp40) REVERT: A 81 LYS cc_start: 0.9125 (ttmm) cc_final: 0.8633 (ttpp) REVERT: A 164 GLN cc_start: 0.8707 (mt0) cc_final: 0.8322 (tt0) REVERT: A 176 ASP cc_start: 0.8429 (m-30) cc_final: 0.8069 (m-30) REVERT: A 181 MET cc_start: 0.9007 (tpt) cc_final: 0.8719 (tpp) REVERT: A 193 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7266 (mm-40) REVERT: A 214 HIS cc_start: 0.8428 (t-170) cc_final: 0.8142 (t70) outliers start: 32 outliers final: 9 residues processed: 221 average time/residue: 0.5951 time to fit residues: 140.3555 Evaluate side-chains 191 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 181 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 14 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 40 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 100 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.113945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.080219 restraints weight = 18174.088| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.17 r_work: 0.3044 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10040 Z= 0.160 Angle : 0.650 10.309 13666 Z= 0.325 Chirality : 0.045 0.319 1654 Planarity : 0.005 0.059 1612 Dihedral : 16.673 165.640 2240 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.34 % Allowed : 19.74 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.24), residues: 1218 helix: 2.34 (0.20), residues: 604 sheet: 0.75 (0.36), residues: 203 loop : -1.48 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 219 TYR 0.010 0.001 TYR A 220 PHE 0.011 0.001 PHE G 61 TRP 0.024 0.001 TRP A 315 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00355 (10037) covalent geometry : angle 0.64885 (13662) SS BOND : bond 0.00410 ( 2) SS BOND : angle 2.58122 ( 4) hydrogen bonds : bond 0.04377 ( 582) hydrogen bonds : angle 4.47503 ( 1707) Misc. bond : bond 0.00072 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 LYS cc_start: 0.9007 (mmmt) cc_final: 0.8655 (mtmm) REVERT: B 82 MET cc_start: 0.8993 (mtp) cc_final: 0.8605 (ptp) REVERT: B 103 TYR cc_start: 0.8341 (m-80) cc_final: 0.8053 (m-80) REVERT: B 117 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8411 (mt-10) REVERT: B 190 GLN cc_start: 0.8695 (mt0) cc_final: 0.8269 (mm110) REVERT: B 193 GLN cc_start: 0.8949 (tp40) cc_final: 0.8558 (mm110) REVERT: B 195 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8780 (mm) REVERT: B 313 LYS cc_start: 0.8693 (mtpp) cc_final: 0.8318 (mtmm) REVERT: B 314 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.7611 (mp10) REVERT: D 22 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8453 (mmt-90) REVERT: D 172 GLU cc_start: 0.8577 (mp0) cc_final: 0.8296 (mp0) REVERT: D 258 ASP cc_start: 0.7841 (t0) cc_final: 0.7521 (t0) REVERT: G 47 GLU cc_start: 0.8496 (mt-10) cc_final: 0.7983 (mp0) REVERT: C 20 ASP cc_start: 0.8423 (m-30) cc_final: 0.8043 (m-30) REVERT: C 242 ARG cc_start: 0.8789 (mtt90) cc_final: 0.8578 (mmm-85) REVERT: C 306 GLN cc_start: 0.8501 (tp40) cc_final: 0.8248 (mm110) REVERT: C 318 GLU cc_start: 0.8224 (tt0) cc_final: 0.8022 (tt0) REVERT: C 333 GLN cc_start: 0.8778 (tp40) cc_final: 0.8299 (tp40) REVERT: A 164 GLN cc_start: 0.8707 (mt0) cc_final: 0.8292 (tt0) REVERT: A 176 ASP cc_start: 0.8467 (m-30) cc_final: 0.8094 (m-30) REVERT: A 181 MET cc_start: 0.8994 (tpt) cc_final: 0.8692 (tpp) REVERT: A 193 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7584 (mm110) REVERT: A 211 THR cc_start: 0.9243 (OUTLIER) cc_final: 0.9030 (p) REVERT: A 328 MET cc_start: 0.8816 (mpt) cc_final: 0.8501 (mpt) outliers start: 33 outliers final: 15 residues processed: 214 average time/residue: 0.6185 time to fit residues: 140.7884 Evaluate side-chains 199 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 180 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 146 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 192 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 249 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 0.8980 chunk 63 optimal weight: 20.0000 chunk 1 optimal weight: 0.0040 chunk 92 optimal weight: 0.8980 chunk 37 optimal weight: 0.2980 chunk 20 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- 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 ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 ASN G 44 HIS A 304 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.115730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.082712 restraints weight = 18242.034| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.16 r_work: 0.3084 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10040 Z= 0.123 Angle : 0.610 8.333 13666 Z= 0.306 Chirality : 0.043 0.265 1654 Planarity : 0.005 0.063 1612 Dihedral : 15.837 161.982 2240 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.54 % Allowed : 20.65 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.25), residues: 1218 helix: 2.42 (0.20), residues: 610 sheet: 0.71 (0.35), residues: 207 loop : -1.33 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 219 TYR 0.010 0.001 TYR D 59 PHE 0.024 0.001 PHE B 215 TRP 0.026 0.001 TRP A 315 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00262 (10037) covalent geometry : angle 0.60946 (13662) SS BOND : bond 0.00337 ( 2) SS BOND : angle 2.00216 ( 4) hydrogen bonds : bond 0.03943 ( 582) hydrogen bonds : angle 4.29475 ( 1707) Misc. bond : bond 0.00027 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 194 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 LYS cc_start: 0.8999 (mmmt) cc_final: 0.8619 (mtmm) REVERT: B 82 MET cc_start: 0.8982 (mtp) cc_final: 0.8751 (OUTLIER) REVERT: B 103 TYR cc_start: 0.8276 (m-80) cc_final: 0.7955 (m-80) REVERT: B 146 TYR cc_start: 0.9104 (t80) cc_final: 0.8882 (t80) REVERT: B 193 GLN cc_start: 0.8948 (tp40) cc_final: 0.8537 (mm110) REVERT: B 313 LYS cc_start: 0.8669 (mtpp) cc_final: 0.8318 (mtmm) REVERT: B 314 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.7562 (mp10) REVERT: D 22 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8264 (mmt-90) REVERT: D 172 GLU cc_start: 0.8592 (mp0) cc_final: 0.8363 (mp0) REVERT: D 258 ASP cc_start: 0.7775 (t0) cc_final: 0.7346 (t0) REVERT: G 47 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8057 (mp0) REVERT: C 20 ASP cc_start: 0.8429 (m-30) cc_final: 0.7946 (m-30) REVERT: C 25 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: C 306 GLN cc_start: 0.8399 (tp40) cc_final: 0.8146 (mm110) REVERT: C 333 GLN cc_start: 0.8782 (tp40) cc_final: 0.8326 (tp40) REVERT: A 76 LYS cc_start: 0.9510 (mmtm) cc_final: 0.9267 (mmmt) REVERT: A 164 GLN cc_start: 0.8746 (mt0) cc_final: 0.8425 (mt0) REVERT: A 176 ASP cc_start: 0.8405 (m-30) cc_final: 0.8059 (m-30) REVERT: A 181 MET cc_start: 0.8974 (tpt) cc_final: 0.8663 (tpp) REVERT: A 192 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.6852 (tt) REVERT: A 193 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7592 (mm110) REVERT: A 211 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8839 (p) REVERT: A 326 ARG cc_start: 0.8283 (tpp-160) cc_final: 0.8075 (mpt90) outliers start: 35 outliers final: 13 residues processed: 220 average time/residue: 0.5798 time to fit residues: 136.4809 Evaluate side-chains 196 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 249 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 33 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 B 311 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 = 0.3766 r_free = 0.3766 target = 0.114390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.080820 restraints weight = 18251.883| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.20 r_work: 0.3058 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10040 Z= 0.145 Angle : 0.626 10.228 13666 Z= 0.313 Chirality : 0.044 0.293 1654 Planarity : 0.005 0.063 1612 Dihedral : 15.450 161.840 2240 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.24 % Allowed : 21.86 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.24), residues: 1218 helix: 2.41 (0.20), residues: 610 sheet: 0.68 (0.35), residues: 202 loop : -1.32 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 219 TYR 0.009 0.001 TYR A 220 PHE 0.023 0.001 PHE B 215 TRP 0.027 0.001 TRP A 315 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00322 (10037) covalent geometry : angle 0.62519 (13662) SS BOND : bond 0.00591 ( 2) SS BOND : angle 1.94950 ( 4) hydrogen bonds : bond 0.04022 ( 582) hydrogen bonds : angle 4.29686 ( 1707) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 LYS cc_start: 0.8976 (mmmt) cc_final: 0.8624 (mtmm) REVERT: B 82 MET cc_start: 0.8983 (mtp) cc_final: 0.8716 (ptp) REVERT: B 103 TYR cc_start: 0.8335 (m-80) cc_final: 0.7975 (m-80) REVERT: B 193 GLN cc_start: 0.8897 (tp40) cc_final: 0.8429 (mm-40) REVERT: B 195 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8880 (mm) REVERT: B 214 HIS cc_start: 0.8458 (t-90) cc_final: 0.8063 (t-90) REVERT: B 313 LYS cc_start: 0.8663 (mtpp) cc_final: 0.8302 (mtmm) REVERT: B 314 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.7574 (mp10) REVERT: D 22 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8208 (mmt-90) REVERT: D 172 GLU cc_start: 0.8625 (mp0) cc_final: 0.8398 (mp0) REVERT: D 258 ASP cc_start: 0.7806 (t0) cc_final: 0.7363 (t0) REVERT: G 47 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8058 (mp0) REVERT: C 20 ASP cc_start: 0.8469 (m-30) cc_final: 0.7878 (m-30) REVERT: C 25 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: C 232 LEU cc_start: 0.9179 (mm) cc_final: 0.8899 (mp) REVERT: C 306 GLN cc_start: 0.8508 (tp40) cc_final: 0.8243 (mm110) REVERT: C 333 GLN cc_start: 0.8769 (tp40) cc_final: 0.8375 (tp40) REVERT: A 76 LYS cc_start: 0.9506 (mmtm) cc_final: 0.9268 (mmmt) REVERT: A 164 GLN cc_start: 0.8792 (mt0) cc_final: 0.8513 (mt0) REVERT: A 176 ASP cc_start: 0.8449 (m-30) cc_final: 0.8017 (m-30) REVERT: A 181 MET cc_start: 0.8980 (tpt) cc_final: 0.8621 (tpp) REVERT: A 190 GLN cc_start: 0.8187 (mt0) cc_final: 0.7613 (mm-40) REVERT: A 193 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7802 (mm110) REVERT: A 211 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8858 (p) outliers start: 32 outliers final: 13 residues processed: 210 average time/residue: 0.5942 time to fit residues: 133.3301 Evaluate side-chains 195 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 197 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 254 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 17 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 91 optimal weight: 0.0060 chunk 87 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.5802 ------------------------------------------------------------------------------- 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 ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.110545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.076901 restraints weight = 18473.175| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.20 r_work: 0.2978 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 10040 Z= 0.250 Angle : 0.701 9.106 13666 Z= 0.348 Chirality : 0.046 0.295 1654 Planarity : 0.005 0.065 1612 Dihedral : 15.528 166.922 2240 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.05 % Allowed : 22.06 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.24), residues: 1218 helix: 2.29 (0.20), residues: 609 sheet: 0.48 (0.34), residues: 214 loop : -1.32 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 219 TYR 0.019 0.001 TYR G 40 PHE 0.022 0.002 PHE B 215 TRP 0.033 0.002 TRP A 315 HIS 0.004 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00569 (10037) covalent geometry : angle 0.70002 (13662) SS BOND : bond 0.00274 ( 2) SS BOND : angle 2.26242 ( 4) hydrogen bonds : bond 0.04537 ( 582) hydrogen bonds : angle 4.46089 ( 1707) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.8941 (mtp) cc_final: 0.8583 (ptp) REVERT: B 103 TYR cc_start: 0.8408 (m-80) cc_final: 0.8084 (m-80) REVERT: B 193 GLN cc_start: 0.8891 (tp40) cc_final: 0.8565 (mm-40) REVERT: B 195 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8899 (mm) REVERT: B 214 HIS cc_start: 0.8552 (t-90) cc_final: 0.8224 (t-90) REVERT: B 313 LYS cc_start: 0.8718 (mtpp) cc_final: 0.8360 (mtmm) REVERT: B 314 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.7612 (mp10) REVERT: D 22 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8404 (mmt-90) REVERT: D 172 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8347 (mp0) REVERT: D 258 ASP cc_start: 0.7883 (t0) cc_final: 0.7640 (t0) REVERT: D 262 MET cc_start: 0.7891 (ttt) cc_final: 0.7508 (tmt) REVERT: D 303 ASP cc_start: 0.8200 (p0) cc_final: 0.7738 (p0) REVERT: G 48 ASP cc_start: 0.8471 (t0) cc_final: 0.8070 (m-30) REVERT: C 20 ASP cc_start: 0.8508 (m-30) cc_final: 0.8126 (m-30) REVERT: C 25 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: C 229 ASP cc_start: 0.8783 (m-30) cc_final: 0.8251 (m-30) REVERT: C 232 LEU cc_start: 0.9180 (mm) cc_final: 0.8543 (mp) REVERT: C 241 ASN cc_start: 0.8568 (m-40) cc_final: 0.8243 (t0) REVERT: C 242 ARG cc_start: 0.8859 (mtt90) cc_final: 0.8321 (mtt90) REVERT: C 271 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8728 (ttmm) REVERT: C 306 GLN cc_start: 0.8808 (tp40) cc_final: 0.8239 (mp10) REVERT: A 76 LYS cc_start: 0.9547 (mmtm) cc_final: 0.9319 (mmmt) REVERT: A 164 GLN cc_start: 0.8787 (mt0) cc_final: 0.8460 (mt0) REVERT: A 176 ASP cc_start: 0.8447 (m-30) cc_final: 0.8070 (m-30) REVERT: A 181 MET cc_start: 0.8998 (tpt) cc_final: 0.8736 (tpp) REVERT: A 190 GLN cc_start: 0.8306 (mt0) cc_final: 0.7875 (pt0) REVERT: A 193 GLN cc_start: 0.8334 (mm-40) cc_final: 0.7882 (mm-40) REVERT: A 211 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8865 (p) outliers start: 40 outliers final: 15 residues processed: 220 average time/residue: 0.6147 time to fit residues: 144.2052 Evaluate side-chains 203 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 181 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 186 THR 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 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 25 GLU 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 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 33 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 49 optimal weight: 8.9990 chunk 74 optimal weight: 0.5980 chunk 91 optimal weight: 0.0010 chunk 47 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 256 GLN ** D 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 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 = 0.3760 r_free = 0.3760 target = 0.114083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.081082 restraints weight = 18215.097| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 3.19 r_work: 0.3055 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10040 Z= 0.129 Angle : 0.662 11.151 13666 Z= 0.329 Chirality : 0.044 0.371 1654 Planarity : 0.005 0.064 1612 Dihedral : 15.076 159.921 2240 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.04 % Allowed : 24.80 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.24), residues: 1218 helix: 2.40 (0.20), residues: 609 sheet: 0.71 (0.34), residues: 210 loop : -1.26 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 219 TYR 0.013 0.001 TYR D 124 PHE 0.024 0.001 PHE B 215 TRP 0.033 0.001 TRP A 315 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00281 (10037) covalent geometry : angle 0.65990 (13662) SS BOND : bond 0.00074 ( 2) SS BOND : angle 2.79114 ( 4) hydrogen bonds : bond 0.03939 ( 582) hydrogen bonds : angle 4.31539 ( 1707) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: B 82 MET cc_start: 0.8908 (mtp) cc_final: 0.8531 (ptp) REVERT: B 103 TYR cc_start: 0.8320 (m-80) cc_final: 0.7935 (m-80) REVERT: B 141 LYS cc_start: 0.8959 (mtpm) cc_final: 0.8635 (mtmt) REVERT: B 193 GLN cc_start: 0.8928 (tp40) cc_final: 0.8502 (mm110) REVERT: B 195 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8886 (mm) REVERT: B 313 LYS cc_start: 0.8627 (mtpp) cc_final: 0.8386 (mtmm) REVERT: D 22 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8372 (mmt-90) REVERT: D 172 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8390 (mp0) REVERT: D 258 ASP cc_start: 0.7896 (t0) cc_final: 0.7577 (t0) REVERT: G 47 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8086 (mp0) REVERT: G 48 ASP cc_start: 0.8335 (t0) cc_final: 0.7955 (m-30) REVERT: C 20 ASP cc_start: 0.8469 (m-30) cc_final: 0.7903 (m-30) REVERT: C 25 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: C 229 ASP cc_start: 0.8717 (m-30) cc_final: 0.8135 (m-30) REVERT: C 232 LEU cc_start: 0.9228 (mm) cc_final: 0.8619 (mp) REVERT: C 241 ASN cc_start: 0.8469 (m-40) cc_final: 0.8204 (t0) REVERT: C 242 ARG cc_start: 0.8844 (mtt90) cc_final: 0.8325 (mtt90) REVERT: C 306 GLN cc_start: 0.8629 (tp40) cc_final: 0.8325 (mm110) REVERT: C 333 GLN cc_start: 0.8775 (tp40) cc_final: 0.8445 (tp40) REVERT: A 76 LYS cc_start: 0.9525 (OUTLIER) cc_final: 0.9289 (mmmt) REVERT: A 164 GLN cc_start: 0.8855 (mt0) cc_final: 0.8484 (mt0) REVERT: A 176 ASP cc_start: 0.8445 (m-30) cc_final: 0.8034 (m-30) REVERT: A 181 MET cc_start: 0.9000 (tpt) cc_final: 0.8691 (tpp) REVERT: A 192 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.6865 (mt) REVERT: A 193 GLN cc_start: 0.8362 (mm-40) cc_final: 0.7920 (mm-40) outliers start: 30 outliers final: 10 residues processed: 207 average time/residue: 0.6211 time to fit residues: 136.8617 Evaluate side-chains 190 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 174 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 D residue 22 ARG 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 25 GLU Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 249 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 32 optimal weight: 0.0170 chunk 29 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 ASN G 44 HIS A 304 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.110565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.076951 restraints weight = 18201.975| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.19 r_work: 0.2967 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10040 Z= 0.228 Angle : 0.749 11.662 13666 Z= 0.372 Chirality : 0.046 0.355 1654 Planarity : 0.005 0.064 1612 Dihedral : 15.302 159.804 2240 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.94 % Allowed : 25.30 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.24), residues: 1218 helix: 2.28 (0.20), residues: 610 sheet: 0.45 (0.34), residues: 210 loop : -1.25 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 219 TYR 0.015 0.002 TYR D 59 PHE 0.023 0.002 PHE B 215 TRP 0.040 0.002 TRP A 315 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00521 (10037) covalent geometry : angle 0.74682 (13662) SS BOND : bond 0.00964 ( 2) SS BOND : angle 3.21557 ( 4) hydrogen bonds : bond 0.04480 ( 582) hydrogen bonds : angle 4.50731 ( 1707) Misc. bond : bond 0.00023 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 103 TYR cc_start: 0.8373 (m-80) cc_final: 0.8040 (m-80) REVERT: B 193 GLN cc_start: 0.8863 (tp40) cc_final: 0.8513 (mm110) REVERT: B 313 LYS cc_start: 0.8616 (mtpp) cc_final: 0.8249 (mtmm) REVERT: B 314 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.7528 (mp10) REVERT: D 22 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8403 (mmt-90) REVERT: D 172 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8357 (mp0) REVERT: D 258 ASP cc_start: 0.7939 (t0) cc_final: 0.7676 (t0) REVERT: G 48 ASP cc_start: 0.8385 (t0) cc_final: 0.7955 (m-30) REVERT: C 20 ASP cc_start: 0.8501 (m-30) cc_final: 0.8086 (m-30) REVERT: C 21 ARG cc_start: 0.8563 (ttm-80) cc_final: 0.7950 (ttp-110) REVERT: C 25 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: C 242 ARG cc_start: 0.8831 (mtt90) cc_final: 0.8199 (mtt90) REVERT: C 306 GLN cc_start: 0.8755 (tp40) cc_final: 0.8098 (mp10) REVERT: C 333 GLN cc_start: 0.8738 (tp40) cc_final: 0.8392 (tp40) REVERT: A 76 LYS cc_start: 0.9548 (OUTLIER) cc_final: 0.9313 (mmmt) REVERT: A 164 GLN cc_start: 0.8782 (mt0) cc_final: 0.8399 (mt0) REVERT: A 176 ASP cc_start: 0.8421 (m-30) cc_final: 0.8038 (m-30) REVERT: A 181 MET cc_start: 0.8976 (tpt) cc_final: 0.8735 (tpp) REVERT: A 190 GLN cc_start: 0.8177 (mt0) cc_final: 0.7780 (pt0) REVERT: A 192 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.6843 (mt) REVERT: A 193 GLN cc_start: 0.8427 (mm-40) cc_final: 0.8052 (mm-40) outliers start: 29 outliers final: 11 residues processed: 204 average time/residue: 0.6193 time to fit residues: 134.3212 Evaluate side-chains 199 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 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 25 GLU 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 192 LEU Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 321 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 66 optimal weight: 0.4980 chunk 51 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.111922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.079120 restraints weight = 18091.362| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.13 r_work: 0.3002 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 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 0.053 10040 Z= 0.166 Angle : 0.722 13.469 13666 Z= 0.359 Chirality : 0.045 0.369 1654 Planarity : 0.005 0.064 1612 Dihedral : 15.126 158.696 2240 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.83 % Allowed : 25.51 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.24), residues: 1218 helix: 2.31 (0.20), residues: 610 sheet: 0.55 (0.35), residues: 207 loop : -1.26 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 219 TYR 0.021 0.001 TYR G 40 PHE 0.024 0.001 PHE B 215 TRP 0.040 0.001 TRP A 315 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00380 (10037) covalent geometry : angle 0.71978 (13662) SS BOND : bond 0.00564 ( 2) SS BOND : angle 3.63608 ( 4) hydrogen bonds : bond 0.04208 ( 582) hydrogen bonds : angle 4.44983 ( 1707) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 78 ARG cc_start: 0.8467 (ptm160) cc_final: 0.8205 (ptm160) REVERT: B 82 MET cc_start: 0.9002 (mtp) cc_final: 0.8560 (ptp) REVERT: B 103 TYR cc_start: 0.8315 (m-80) cc_final: 0.7934 (m-80) REVERT: B 193 GLN cc_start: 0.8855 (tp40) cc_final: 0.8653 (mm-40) REVERT: B 313 LYS cc_start: 0.8598 (mtpp) cc_final: 0.8225 (mtmm) REVERT: B 314 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.7422 (mp10) REVERT: D 22 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8423 (mmt-90) REVERT: D 172 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8383 (mp0) REVERT: G 48 ASP cc_start: 0.8333 (t0) cc_final: 0.7942 (m-30) REVERT: C 20 ASP cc_start: 0.8480 (m-30) cc_final: 0.8063 (m-30) REVERT: C 25 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7558 (mp0) REVERT: C 229 ASP cc_start: 0.8554 (m-30) cc_final: 0.7978 (m-30) REVERT: C 241 ASN cc_start: 0.8102 (m-40) cc_final: 0.7621 (t0) REVERT: C 242 ARG cc_start: 0.8815 (mtt90) cc_final: 0.8282 (mtt90) REVERT: C 306 GLN cc_start: 0.8648 (tp40) cc_final: 0.8260 (mm110) REVERT: C 333 GLN cc_start: 0.8721 (tp40) cc_final: 0.8373 (tp40) REVERT: A 76 LYS cc_start: 0.9540 (OUTLIER) cc_final: 0.9328 (mmmt) REVERT: A 89 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.9000 (mp) REVERT: A 164 GLN cc_start: 0.8802 (mt0) cc_final: 0.8413 (mt0) REVERT: A 176 ASP cc_start: 0.8413 (m-30) cc_final: 0.8025 (m-30) REVERT: A 181 MET cc_start: 0.8980 (tpt) cc_final: 0.8727 (tpp) REVERT: A 190 GLN cc_start: 0.8102 (mt0) cc_final: 0.7692 (pt0) REVERT: A 192 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.6818 (mt) REVERT: A 193 GLN cc_start: 0.8400 (mm-40) cc_final: 0.7962 (mm-40) outliers start: 28 outliers final: 13 residues processed: 203 average time/residue: 0.5916 time to fit residues: 128.1121 Evaluate side-chains 197 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 128 THR Chi-restraints excluded: chain D residue 133 VAL 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 25 GLU Chi-restraints excluded: chain A residue 76 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 72 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 0 optimal weight: 60.0000 chunk 61 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.110808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.077556 restraints weight = 18111.594| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.15 r_work: 0.2980 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10040 Z= 0.211 Angle : 0.774 13.431 13666 Z= 0.385 Chirality : 0.046 0.362 1654 Planarity : 0.006 0.072 1612 Dihedral : 15.166 156.994 2240 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.24), residues: 1218 helix: 2.13 (0.20), residues: 616 sheet: 0.46 (0.35), residues: 210 loop : -1.21 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 219 TYR 0.015 0.001 TYR D 59 PHE 0.021 0.002 PHE B 318 TRP 0.044 0.001 TRP A 315 HIS 0.006 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00484 (10037) covalent geometry : angle 0.77132 (13662) SS BOND : bond 0.00603 ( 2) SS BOND : angle 3.67759 ( 4) hydrogen bonds : bond 0.04382 ( 582) hydrogen bonds : angle 4.52037 ( 1707) Misc. bond : bond 0.00015 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.359 Fit side-chains REVERT: B 78 ARG cc_start: 0.8491 (ptm160) cc_final: 0.8244 (ptm160) REVERT: B 81 LYS cc_start: 0.8953 (mmmt) cc_final: 0.8376 (mppt) REVERT: B 82 MET cc_start: 0.8996 (mtp) cc_final: 0.8540 (ptp) REVERT: B 103 TYR cc_start: 0.8359 (m-80) cc_final: 0.8022 (m-80) REVERT: B 313 LYS cc_start: 0.8607 (mtpp) cc_final: 0.8239 (mtmm) REVERT: B 314 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.7403 (mp10) REVERT: D 172 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8381 (mp0) REVERT: G 48 ASP cc_start: 0.8366 (t0) cc_final: 0.7955 (m-30) REVERT: C 20 ASP cc_start: 0.8503 (m-30) cc_final: 0.8107 (m-30) REVERT: C 21 ARG cc_start: 0.8665 (ttm-80) cc_final: 0.8128 (ttm-80) REVERT: C 25 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7570 (mp0) REVERT: C 229 ASP cc_start: 0.8562 (m-30) cc_final: 0.8038 (m-30) REVERT: C 241 ASN cc_start: 0.8111 (m-40) cc_final: 0.7694 (t0) REVERT: C 242 ARG cc_start: 0.8821 (mtt90) cc_final: 0.8292 (mtt90) REVERT: C 306 GLN cc_start: 0.8728 (tp40) cc_final: 0.8092 (mp10) REVERT: C 333 GLN cc_start: 0.8738 (tp40) cc_final: 0.8392 (tp40) REVERT: A 76 LYS cc_start: 0.9534 (OUTLIER) cc_final: 0.9309 (mmmt) REVERT: A 89 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.9031 (mp) REVERT: A 164 GLN cc_start: 0.8736 (mt0) cc_final: 0.8337 (mt0) REVERT: A 176 ASP cc_start: 0.8434 (m-30) cc_final: 0.8052 (m-30) REVERT: A 181 MET cc_start: 0.8985 (tpt) cc_final: 0.8768 (tpp) REVERT: A 190 GLN cc_start: 0.8068 (mt0) cc_final: 0.7659 (pt0) REVERT: A 192 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.6770 (mt) REVERT: A 193 GLN cc_start: 0.8387 (mm-40) cc_final: 0.8007 (mm-40) REVERT: A 199 MET cc_start: 0.8941 (ppp) cc_final: 0.8372 (ttt) outliers start: 24 outliers final: 15 residues processed: 201 average time/residue: 0.6151 time to fit residues: 131.5328 Evaluate side-chains 199 residues out of total 1075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 128 THR 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 25 GLU 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 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 Chi-restraints excluded: chain A residue 321 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 77 optimal weight: 0.0010 chunk 73 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 111 optimal weight: 0.3980 chunk 107 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 75 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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** G 44 HIS A 151 GLN A 304 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.113065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.079559 restraints weight = 18129.612| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 3.22 r_work: 0.3031 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10040 Z= 0.144 Angle : 0.768 13.337 13666 Z= 0.380 Chirality : 0.045 0.360 1654 Planarity : 0.005 0.065 1612 Dihedral : 14.950 157.459 2240 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.23 % Allowed : 26.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.24), residues: 1218 helix: 2.13 (0.20), residues: 617 sheet: 0.62 (0.35), residues: 206 loop : -1.25 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 219 TYR 0.021 0.001 TYR G 40 PHE 0.026 0.001 PHE B 215 TRP 0.040 0.001 TRP A 315 HIS 0.011 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00323 (10037) covalent geometry : angle 0.76585 (13662) SS BOND : bond 0.00680 ( 2) SS BOND : angle 3.39114 ( 4) hydrogen bonds : bond 0.04096 ( 582) hydrogen bonds : angle 4.46650 ( 1707) Misc. bond : bond 0.00003 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4701.10 seconds wall clock time: 80 minutes 41.93 seconds (4841.93 seconds total)