Starting phenix.real_space_refine on Sun Jun 15 15:40:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ghv_40052/06_2025/8ghv_40052_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ghv_40052/06_2025/8ghv_40052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ghv_40052/06_2025/8ghv_40052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ghv_40052/06_2025/8ghv_40052.map" model { file = "/net/cci-nas-00/data/ceres_data/8ghv_40052/06_2025/8ghv_40052_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ghv_40052/06_2025/8ghv_40052_neut_trim.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 1.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1971 atoms to isotropic. 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 S 54 5.16 5 C 5308 2.51 5 N 1383 2.21 5 O 1492 1.98 5 H 7637 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15874 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3144 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 71 Chain: "B" Number of atoms: 4847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 4847 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 89 Chain: "C" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 698 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "D" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 3889 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 271} Chain breaks: 1 Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 201 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 5, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 131 Chain: "S" Number of atoms: 3269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3269 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 51 Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ZI5': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.76, per 1000 atoms: 0.55 Number of scatterers: 15874 At special positions: 0 Unit cell: (92.8789, 123.555, 132.076, 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 54 16.00 O 1492 8.00 N 1383 7.00 C 5308 6.00 H 7637 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 257 " - pdb=" SG CYS D 264 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.28 Conformation dependent library (CDL) restraints added in 1.4 seconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 13 sheets defined 35.8% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 8 through 30 removed outlier: 3.869A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.684A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.738A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.600A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 22 removed outlier: 3.671A pdb=" N ALA C 12 " --> pdb=" O SER C 8 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C 22 " --> pdb=" O GLN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.883A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 141 removed outlier: 3.978A pdb=" N LEU D 117 " --> pdb=" O PRO D 113 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 150 removed outlier: 3.586A pdb=" N ARG D 150 " --> pdb=" O SER D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 179 removed outlier: 3.927A pdb=" N ILE D 156 " --> pdb=" O SER D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 220 removed outlier: 3.767A pdb=" N ILE D 218 " --> pdb=" O ARG D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 228 Processing helix chain 'D' and resid 229 through 254 Proline residue: D 251 - end of helix removed outlier: 3.922A pdb=" N GLY D 254 " --> pdb=" O LEU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 306 removed outlier: 3.887A pdb=" N SER D 284 " --> pdb=" O ILE D 280 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL D 285 " --> pdb=" O GLY D 281 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR D 294 " --> pdb=" O ILE D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 357 removed outlier: 4.113A pdb=" N LEU D 347 " --> pdb=" O LYS D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 368 Processing helix chain 'D' and resid 372 through 400 removed outlier: 3.746A pdb=" N MET D 384 " --> pdb=" O ALA D 380 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU D 388 " --> pdb=" O MET D 384 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN D 389 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER D 390 " --> pdb=" O CYS D 386 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR D 391 " --> pdb=" O LEU D 387 " (cutoff:3.500A) Proline residue: D 394 - end of helix removed outlier: 3.869A pdb=" N ALA D 398 " --> pdb=" O PRO D 394 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 399 " --> pdb=" O ILE D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 412 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.757A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.245A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 37 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.858A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.969A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.083A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.863A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.122A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.863A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.710A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.590A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 removed outlier: 3.520A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB3, first strand: chain 'S' and resid 135 through 136 removed outlier: 6.330A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'S' and resid 182 through 183 removed outlier: 6.802A pdb=" N ASN S 182 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) 405 hydrogen bonds defined for protein. 1164 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: 5.49 Time building geometry restraints manager: 5.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7608 1.03 - 1.23: 136 1.23 - 1.43: 3448 1.43 - 1.62: 4778 1.62 - 1.82: 77 Bond restraints: 16047 Sorted by residual: bond pdb=" C20 ZI5 D 501 " pdb=" N1 ZI5 D 501 " ideal model delta sigma weight residual 1.337 1.444 -0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" N VAL D 392 " pdb=" CA VAL D 392 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.08e-02 8.57e+03 1.58e+01 bond pdb=" C LEU B 79 " pdb=" O LEU B 79 " ideal model delta sigma weight residual 1.236 1.192 0.043 1.14e-02 7.69e+03 1.45e+01 bond pdb=" N ILE D 395 " pdb=" CA ILE D 395 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.08e-02 8.57e+03 1.42e+01 bond pdb=" N VAL D 110 " pdb=" H VAL D 110 " ideal model delta sigma weight residual 0.860 0.931 -0.071 2.00e-02 2.50e+03 1.26e+01 ... (remaining 16042 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 28472 2.43 - 4.85: 295 4.85 - 7.28: 13 7.28 - 9.71: 0 9.71 - 12.13: 4 Bond angle restraints: 28784 Sorted by residual: angle pdb=" N ILE D 141 " pdb=" CA ILE D 141 " pdb=" C ILE D 141 " ideal model delta sigma weight residual 112.98 108.01 4.97 1.25e+00 6.40e-01 1.58e+01 angle pdb=" N ILE D 105 " pdb=" CA ILE D 105 " pdb=" C ILE D 105 " ideal model delta sigma weight residual 112.83 108.97 3.86 9.90e-01 1.02e+00 1.52e+01 angle pdb=" CA ASP B 76 " pdb=" C ASP B 76 " pdb=" O ASP B 76 " ideal model delta sigma weight residual 121.87 117.63 4.24 1.10e+00 8.26e-01 1.48e+01 angle pdb=" CA ASP B 76 " pdb=" C ASP B 76 " pdb=" N GLY B 77 " ideal model delta sigma weight residual 115.30 120.34 -5.04 1.33e+00 5.65e-01 1.44e+01 angle pdb=" C THR S 78 " pdb=" N LEU S 79 " pdb=" CA LEU S 79 " ideal model delta sigma weight residual 122.94 128.61 -5.67 1.50e+00 4.44e-01 1.43e+01 ... (remaining 28779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7081 17.96 - 35.92: 470 35.92 - 53.89: 130 53.89 - 71.85: 21 71.85 - 89.81: 3 Dihedral angle restraints: 7705 sinusoidal: 3836 harmonic: 3869 Sorted by residual: dihedral pdb=" CB CYS D 257 " pdb=" SG CYS D 257 " pdb=" SG CYS D 264 " pdb=" CB CYS D 264 " ideal model delta sinusoidal sigma weight residual -86.00 -120.33 34.33 1 1.00e+01 1.00e-02 1.67e+01 dihedral pdb=" SG CYS D 257 " pdb=" CB CYS D 264 " pdb=" SG CYS D 264 " pdb=" CA CYS D 264 " ideal model delta sinusoidal sigma weight residual -73.00 -13.90 -59.10 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP B 153 " pdb=" CB ASP B 153 " pdb=" CG ASP B 153 " pdb=" OD1 ASP B 153 " ideal model delta sinusoidal sigma weight residual -30.00 -88.48 58.48 1 2.00e+01 2.50e-03 1.15e+01 ... (remaining 7702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 986 0.042 - 0.084: 229 0.084 - 0.126: 100 0.126 - 0.168: 40 0.168 - 0.210: 8 Chirality restraints: 1363 Sorted by residual: chirality pdb=" C7 ZI5 D 501 " pdb=" C24 ZI5 D 501 " pdb=" C5 ZI5 D 501 " pdb=" C8 ZI5 D 501 " both_signs ideal model delta sigma weight residual False 2.65 2.86 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ILE D 396 " pdb=" N ILE D 396 " pdb=" C ILE D 396 " pdb=" CB ILE D 396 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.53e-01 chirality pdb=" CA ILE D 375 " pdb=" N ILE D 375 " pdb=" C ILE D 375 " pdb=" CB ILE D 375 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.88e-01 ... (remaining 1360 not shown) Planarity restraints: 2529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 176 " 0.218 2.00e-02 2.50e+03 2.53e-01 9.63e+02 pdb=" CD GLN B 176 " -0.013 2.00e-02 2.50e+03 pdb=" OE1 GLN B 176 " -0.211 2.00e-02 2.50e+03 pdb=" NE2 GLN B 176 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN B 176 " 0.387 2.00e-02 2.50e+03 pdb="HE22 GLN B 176 " -0.378 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 304 " -0.550 9.50e-02 1.11e+02 2.36e-01 5.29e+02 pdb=" NE ARG B 304 " -0.154 2.00e-02 2.50e+03 pdb=" CZ ARG B 304 " -0.047 2.00e-02 2.50e+03 pdb=" NH1 ARG B 304 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG B 304 " 0.029 2.00e-02 2.50e+03 pdb="HH11 ARG B 304 " 0.306 2.00e-02 2.50e+03 pdb="HH12 ARG B 304 " -0.239 2.00e-02 2.50e+03 pdb="HH21 ARG B 304 " 0.142 2.00e-02 2.50e+03 pdb="HH22 ARG B 304 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 291 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.76e+00 pdb=" C VAL D 291 " 0.051 2.00e-02 2.50e+03 pdb=" O VAL D 291 " -0.019 2.00e-02 2.50e+03 pdb=" N TYR D 292 " -0.017 2.00e-02 2.50e+03 ... (remaining 2526 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 891 2.22 - 2.81: 31607 2.81 - 3.41: 37622 3.41 - 4.00: 51742 4.00 - 4.60: 80471 Nonbonded interactions: 202333 Sorted by model distance: nonbonded pdb=" O PHE S 32 " pdb="HH22 ARG S 72 " model vdw 1.623 2.450 nonbonded pdb=" H SER D 265 " pdb=" O ILE D 271 " model vdw 1.650 2.450 nonbonded pdb=" O LYS B 280 " pdb=" HG SER B 281 " model vdw 1.679 2.450 nonbonded pdb="HD22 ASN A 347 " pdb=" O PRO D 221 " model vdw 1.683 2.450 nonbonded pdb="HH22 ARG B 256 " pdb=" OD2 ASP C 36 " model vdw 1.726 2.450 ... (remaining 202328 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.300 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 36.750 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 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:12.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.640 ------------------------------------------------------------------------------- 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 : 0.005 0.107 8411 Z= 0.337 Angle : 0.743 6.813 11463 Z= 0.504 Chirality : 0.050 0.210 1363 Planarity : 0.005 0.126 1444 Dihedral : 13.619 89.809 2784 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.76 % Allowed : 9.24 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.25), residues: 1107 helix: 1.99 (0.28), residues: 372 sheet: 0.44 (0.31), residues: 267 loop : -1.56 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 279 HIS 0.005 0.001 HIS B 225 PHE 0.017 0.001 PHE D 379 TYR 0.013 0.001 TYR B 105 ARG 0.006 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.16458 ( 405) hydrogen bonds : angle 5.22040 ( 1164) SS BOND : bond 0.00230 ( 1) SS BOND : angle 1.22744 ( 2) covalent geometry : bond 0.00487 ( 8410) covalent geometry : angle 0.74269 (11461) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue THR 295 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue ILE 175 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue ILE 247 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue MET 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue MET 371 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue MET 384 is missing expected H atoms. Skipping. Residue LYS 402 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue MET 411 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue SER 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 1.160 Fit side-chains REVERT: B 54 HIS cc_start: 0.8643 (OUTLIER) cc_final: 0.8228 (m170) REVERT: S 174 GLN cc_start: 0.8289 (tt0) cc_final: 0.8075 (pt0) outliers start: 6 outliers final: 4 residues processed: 107 average time/residue: 1.5650 time to fit residues: 184.2883 Evaluate side-chains 83 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 266 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.166135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.133937 restraints weight = 27872.631| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.04 r_work: 0.3493 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8411 Z= 0.124 Angle : 0.499 5.078 11463 Z= 0.271 Chirality : 0.040 0.136 1363 Planarity : 0.003 0.037 1444 Dihedral : 5.575 52.049 1220 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.14 % Allowed : 12.03 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.25), residues: 1107 helix: 2.29 (0.28), residues: 385 sheet: 0.47 (0.31), residues: 272 loop : -1.55 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 279 HIS 0.004 0.001 HIS S 35 PHE 0.013 0.001 PHE D 237 TYR 0.017 0.001 TYR S 178 ARG 0.002 0.000 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.05996 ( 405) hydrogen bonds : angle 4.19512 ( 1164) SS BOND : bond 0.00220 ( 1) SS BOND : angle 1.10818 ( 2) covalent geometry : bond 0.00256 ( 8410) covalent geometry : angle 0.49884 (11461) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue THR 295 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue ILE 175 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue ILE 247 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue MET 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue MET 371 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue MET 384 is missing expected H atoms. Skipping. Residue LYS 402 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue MET 411 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue SER 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 1.280 Fit side-chains REVERT: B 137 ARG cc_start: 0.7949 (tpp-160) cc_final: 0.7487 (tpt90) REVERT: B 243 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8308 (m) outliers start: 9 outliers final: 6 residues processed: 91 average time/residue: 1.7032 time to fit residues: 170.7846 Evaluate side-chains 83 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain S residue 143 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 9 optimal weight: 0.1980 chunk 106 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 16 ASN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.163159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.129552 restraints weight = 27549.639| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.95 r_work: 0.3435 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8411 Z= 0.136 Angle : 0.510 6.175 11463 Z= 0.278 Chirality : 0.040 0.143 1363 Planarity : 0.003 0.041 1444 Dihedral : 5.162 48.534 1214 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.39 % Allowed : 12.91 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.25), residues: 1107 helix: 2.45 (0.28), residues: 386 sheet: 0.48 (0.31), residues: 272 loop : -1.57 (0.25), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 279 HIS 0.006 0.001 HIS S 35 PHE 0.013 0.001 PHE B 151 TYR 0.016 0.001 TYR S 178 ARG 0.002 0.000 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.06114 ( 405) hydrogen bonds : angle 4.07050 ( 1164) SS BOND : bond 0.00137 ( 1) SS BOND : angle 1.00879 ( 2) covalent geometry : bond 0.00294 ( 8410) covalent geometry : angle 0.51011 (11461) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue THR 295 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue ILE 175 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue ILE 247 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue MET 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue MET 371 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue MET 384 is missing expected H atoms. Skipping. Residue LYS 402 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue MET 411 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue SER 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 1.206 Fit side-chains REVERT: A 14 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7489 (mt-10) REVERT: B 23 LYS cc_start: 0.7739 (ttpt) cc_final: 0.7504 (ttpp) REVERT: B 137 ARG cc_start: 0.8015 (tpp-160) cc_final: 0.7586 (tpt90) REVERT: B 243 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8337 (m) outliers start: 11 outliers final: 7 residues processed: 90 average time/residue: 1.7533 time to fit residues: 171.9895 Evaluate side-chains 87 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 143 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 12 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 75 optimal weight: 0.0570 chunk 79 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 16 ASN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.164839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.131551 restraints weight = 27771.308| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.95 r_work: 0.3446 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8411 Z= 0.107 Angle : 0.471 5.982 11463 Z= 0.254 Chirality : 0.039 0.139 1363 Planarity : 0.003 0.039 1444 Dihedral : 4.876 45.589 1212 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.65 % Allowed : 14.56 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.25), residues: 1107 helix: 2.60 (0.27), residues: 388 sheet: 0.55 (0.31), residues: 270 loop : -1.58 (0.25), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 279 HIS 0.003 0.001 HIS S 35 PHE 0.011 0.001 PHE D 237 TYR 0.014 0.001 TYR S 178 ARG 0.002 0.000 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.05143 ( 405) hydrogen bonds : angle 3.87898 ( 1164) SS BOND : bond 0.00185 ( 1) SS BOND : angle 0.93465 ( 2) covalent geometry : bond 0.00226 ( 8410) covalent geometry : angle 0.47057 (11461) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue THR 295 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue ILE 175 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue ILE 247 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue MET 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue MET 371 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue MET 384 is missing expected H atoms. Skipping. Residue LYS 402 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue MET 411 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue SER 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Evaluate side-chains 91 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 1.344 Fit side-chains REVERT: B 23 LYS cc_start: 0.7639 (ttpt) cc_final: 0.7393 (ttpp) REVERT: B 137 ARG cc_start: 0.7979 (tpp-160) cc_final: 0.7566 (tpt90) REVERT: B 243 THR cc_start: 0.8542 (OUTLIER) cc_final: 0.8317 (m) outliers start: 13 outliers final: 8 residues processed: 88 average time/residue: 1.8215 time to fit residues: 176.5933 Evaluate side-chains 79 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 143 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 255 ASN A 306 GLN B 16 ASN B 293 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.160353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.126942 restraints weight = 27967.716| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.97 r_work: 0.3338 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8411 Z= 0.185 Angle : 0.573 7.310 11463 Z= 0.311 Chirality : 0.041 0.163 1363 Planarity : 0.004 0.046 1444 Dihedral : 5.407 49.523 1212 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.90 % Allowed : 14.81 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.25), residues: 1107 helix: 2.36 (0.27), residues: 388 sheet: 0.62 (0.31), residues: 261 loop : -1.67 (0.25), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 279 HIS 0.008 0.001 HIS S 35 PHE 0.015 0.002 PHE B 151 TYR 0.019 0.002 TYR S 178 ARG 0.003 0.000 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.06840 ( 405) hydrogen bonds : angle 4.15110 ( 1164) SS BOND : bond 0.00116 ( 1) SS BOND : angle 0.89249 ( 2) covalent geometry : bond 0.00434 ( 8410) covalent geometry : angle 0.57301 (11461) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue THR 295 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue ILE 175 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue ILE 247 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue MET 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue MET 371 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue MET 384 is missing expected H atoms. Skipping. Residue LYS 402 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue MET 411 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue SER 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Evaluate side-chains 99 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 1.487 Fit side-chains REVERT: B 23 LYS cc_start: 0.7915 (ttpt) cc_final: 0.7679 (ttpp) REVERT: B 137 ARG cc_start: 0.8142 (tpp-160) cc_final: 0.7770 (tpt90) REVERT: B 243 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8365 (m) outliers start: 15 outliers final: 9 residues processed: 96 average time/residue: 1.8811 time to fit residues: 199.3490 Evaluate side-chains 89 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 147 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 16 ASN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.161548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.127736 restraints weight = 27468.541| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.95 r_work: 0.3369 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8411 Z= 0.144 Angle : 0.525 6.600 11463 Z= 0.285 Chirality : 0.040 0.156 1363 Planarity : 0.003 0.045 1444 Dihedral : 5.298 46.855 1212 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.90 % Allowed : 15.19 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.25), residues: 1107 helix: 2.48 (0.27), residues: 387 sheet: 0.63 (0.31), residues: 259 loop : -1.68 (0.24), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 279 HIS 0.005 0.001 HIS S 35 PHE 0.013 0.001 PHE B 151 TYR 0.016 0.001 TYR S 178 ARG 0.002 0.000 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.06131 ( 405) hydrogen bonds : angle 4.04283 ( 1164) SS BOND : bond 0.00145 ( 1) SS BOND : angle 0.81627 ( 2) covalent geometry : bond 0.00320 ( 8410) covalent geometry : angle 0.52494 (11461) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue THR 295 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue ILE 175 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue ILE 247 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue MET 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue MET 371 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue MET 384 is missing expected H atoms. Skipping. Residue LYS 402 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue MET 411 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue SER 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Evaluate side-chains 96 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 1.163 Fit side-chains REVERT: B 23 LYS cc_start: 0.7834 (ttpt) cc_final: 0.7631 (ttpp) REVERT: B 79 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8607 (mp) REVERT: B 137 ARG cc_start: 0.8098 (tpp-160) cc_final: 0.7704 (tpt90) REVERT: B 243 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8334 (m) REVERT: D 134 ASN cc_start: 0.7511 (m-40) cc_final: 0.7293 (m-40) outliers start: 15 outliers final: 9 residues processed: 92 average time/residue: 1.6521 time to fit residues: 167.5244 Evaluate side-chains 91 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 147 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 97 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 74 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 16 ASN B 293 ASN D 134 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.161833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.128583 restraints weight = 27689.026| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.96 r_work: 0.3378 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8411 Z= 0.135 Angle : 0.512 6.252 11463 Z= 0.278 Chirality : 0.040 0.147 1363 Planarity : 0.003 0.044 1444 Dihedral : 5.226 47.285 1212 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.03 % Allowed : 15.82 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.25), residues: 1107 helix: 2.60 (0.27), residues: 386 sheet: 0.64 (0.31), residues: 259 loop : -1.67 (0.24), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 279 HIS 0.005 0.001 HIS S 35 PHE 0.013 0.001 PHE B 151 TYR 0.016 0.001 TYR S 178 ARG 0.002 0.000 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.05857 ( 405) hydrogen bonds : angle 3.97223 ( 1164) SS BOND : bond 0.00140 ( 1) SS BOND : angle 0.77908 ( 2) covalent geometry : bond 0.00299 ( 8410) covalent geometry : angle 0.51186 (11461) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue THR 295 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue ILE 175 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue ILE 247 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue MET 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue MET 371 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue MET 384 is missing expected H atoms. Skipping. Residue LYS 402 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue MET 411 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue SER 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 1.913 Fit side-chains REVERT: B 79 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8631 (mp) REVERT: B 137 ARG cc_start: 0.8108 (tpp-160) cc_final: 0.7728 (tpt90) REVERT: B 243 THR cc_start: 0.8547 (OUTLIER) cc_final: 0.8311 (m) REVERT: D 134 ASN cc_start: 0.7427 (m110) cc_final: 0.7174 (m-40) outliers start: 16 outliers final: 9 residues processed: 92 average time/residue: 1.9507 time to fit residues: 200.3854 Evaluate side-chains 88 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 147 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 83 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 16 ASN B 293 ASN D 181 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.161488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.127457 restraints weight = 27433.527| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.97 r_work: 0.3357 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8411 Z= 0.141 Angle : 0.522 6.457 11463 Z= 0.283 Chirality : 0.040 0.150 1363 Planarity : 0.003 0.045 1444 Dihedral : 5.263 46.944 1212 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.65 % Allowed : 15.70 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.25), residues: 1107 helix: 2.64 (0.27), residues: 386 sheet: 0.64 (0.31), residues: 259 loop : -1.68 (0.24), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 279 HIS 0.005 0.001 HIS S 35 PHE 0.013 0.001 PHE B 151 TYR 0.016 0.001 TYR S 178 ARG 0.002 0.000 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.05968 ( 405) hydrogen bonds : angle 3.97599 ( 1164) SS BOND : bond 0.00147 ( 1) SS BOND : angle 0.77302 ( 2) covalent geometry : bond 0.00315 ( 8410) covalent geometry : angle 0.52191 (11461) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue THR 295 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue ILE 175 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue ILE 247 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue MET 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue MET 371 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue MET 384 is missing expected H atoms. Skipping. Residue LYS 402 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue MET 411 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue SER 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 1.222 Fit side-chains REVERT: B 79 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8648 (mp) REVERT: B 137 ARG cc_start: 0.8124 (tpp-160) cc_final: 0.7770 (tpt90) REVERT: B 243 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8319 (m) REVERT: D 134 ASN cc_start: 0.7343 (m110) cc_final: 0.7100 (m-40) outliers start: 13 outliers final: 9 residues processed: 89 average time/residue: 1.6157 time to fit residues: 158.5560 Evaluate side-chains 89 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 147 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 43 optimal weight: 0.0870 chunk 60 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 306 GLN B 16 ASN B 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.164084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.130335 restraints weight = 27475.674| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.97 r_work: 0.3427 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8411 Z= 0.106 Angle : 0.473 5.017 11463 Z= 0.256 Chirality : 0.039 0.140 1363 Planarity : 0.003 0.040 1444 Dihedral : 4.948 44.254 1212 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.77 % Allowed : 15.82 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.25), residues: 1107 helix: 2.92 (0.27), residues: 387 sheet: 0.61 (0.30), residues: 279 loop : -1.64 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 279 HIS 0.003 0.001 HIS B 91 PHE 0.010 0.001 PHE B 151 TYR 0.012 0.001 TYR S 178 ARG 0.002 0.000 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.04975 ( 405) hydrogen bonds : angle 3.78200 ( 1164) SS BOND : bond 0.00173 ( 1) SS BOND : angle 0.75136 ( 2) covalent geometry : bond 0.00225 ( 8410) covalent geometry : angle 0.47321 (11461) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue THR 295 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue ILE 175 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue ILE 247 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue MET 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue MET 371 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue MET 384 is missing expected H atoms. Skipping. Residue LYS 402 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue MET 411 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue SER 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Evaluate side-chains 95 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 1.367 Fit side-chains REVERT: B 23 LYS cc_start: 0.7548 (ttpp) cc_final: 0.7340 (ttmm) REVERT: B 137 ARG cc_start: 0.8020 (tpp-160) cc_final: 0.7611 (tpt90) REVERT: B 243 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8352 (m) REVERT: D 134 ASN cc_start: 0.7004 (m110) cc_final: 0.6548 (m110) outliers start: 14 outliers final: 9 residues processed: 91 average time/residue: 1.5970 time to fit residues: 160.4818 Evaluate side-chains 87 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 147 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 96 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 101 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 306 GLN B 16 ASN B 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.164532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.130847 restraints weight = 27660.082| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 1.97 r_work: 0.3431 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8411 Z= 0.103 Angle : 0.469 4.978 11463 Z= 0.253 Chirality : 0.039 0.142 1363 Planarity : 0.003 0.039 1444 Dihedral : 4.851 43.614 1212 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.52 % Allowed : 16.08 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.25), residues: 1107 helix: 3.07 (0.27), residues: 387 sheet: 0.59 (0.30), residues: 281 loop : -1.57 (0.26), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 279 HIS 0.003 0.001 HIS S 35 PHE 0.010 0.001 PHE B 151 TYR 0.013 0.001 TYR S 178 ARG 0.002 0.000 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.04807 ( 405) hydrogen bonds : angle 3.71228 ( 1164) SS BOND : bond 0.00161 ( 1) SS BOND : angle 0.71041 ( 2) covalent geometry : bond 0.00219 ( 8410) covalent geometry : angle 0.46880 (11461) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 4 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 51 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue THR 190 is missing expected H atoms. Skipping. Residue MET 240 is missing expected H atoms. Skipping. Residue LYS 248 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 280 is missing expected H atoms. Skipping. Residue SER 281 is missing expected H atoms. Skipping. Residue THR 284 is missing expected H atoms. Skipping. Residue THR 295 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue THR 329 is missing expected H atoms. Skipping. Residue LYS 330 is missing expected H atoms. Skipping. Residue LYS 349 is missing expected H atoms. Skipping. Residue THR 164 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue SER 8 is missing expected H atoms. Skipping. Residue ILE 9 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue MET 21 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue SER 57 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue SER 114 is missing expected H atoms. Skipping. Residue LEU 117 is missing expected H atoms. Skipping. Residue SER 123 is missing expected H atoms. Skipping. Residue LEU 124 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue THR 128 is missing expected H atoms. Skipping. Residue LEU 142 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue ILE 175 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LYS 183 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 225 is missing expected H atoms. Skipping. Residue THR 229 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Residue ILE 243 is missing expected H atoms. Skipping. Residue ILE 247 is missing expected H atoms. Skipping. Residue VAL 249 is missing expected H atoms. Skipping. Residue LYS 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue SER 262 is missing expected H atoms. Skipping. Residue MET 277 is missing expected H atoms. Skipping. Residue THR 283 is missing expected H atoms. Skipping. Residue VAL 285 is missing expected H atoms. Skipping. Residue LYS 343 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue MET 371 is missing expected H atoms. Skipping. Residue LYS 373 is missing expected H atoms. Skipping. Residue MET 384 is missing expected H atoms. Skipping. Residue LYS 402 is missing expected H atoms. Skipping. Residue SER 410 is missing expected H atoms. Skipping. Residue MET 411 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue SER 55 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue SER 88 is missing expected H atoms. Skipping. Residue SER 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue THR 132 is missing expected H atoms. Skipping. Residue SER 133 is missing expected H atoms. Skipping. Residue SER 134 is missing expected H atoms. Skipping. Residue VAL 135 is missing expected H atoms. Skipping. Residue SER 142 is missing expected H atoms. Skipping. Residue SER 144 is missing expected H atoms. Skipping. Residue SER 146 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue SER 192 is missing expected H atoms. Skipping. Residue SER 194 is missing expected H atoms. Skipping. Residue SER 205 is missing expected H atoms. Skipping. Residue LYS 232 is missing expected H atoms. Skipping. Evaluate side-chains 90 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 1.238 Fit side-chains REVERT: B 45 MET cc_start: 0.8571 (mtp) cc_final: 0.8368 (mtm) REVERT: B 79 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8516 (mp) REVERT: B 137 ARG cc_start: 0.8021 (tpp-160) cc_final: 0.7617 (tpt90) REVERT: B 243 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.8323 (m) REVERT: D 134 ASN cc_start: 0.6893 (m110) cc_final: 0.6457 (m110) outliers start: 12 outliers final: 9 residues processed: 87 average time/residue: 1.5913 time to fit residues: 152.1425 Evaluate side-chains 87 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 147 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 101 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS B 16 ASN B 293 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.163903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.130148 restraints weight = 27513.482| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.96 r_work: 0.3427 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8411 Z= 0.113 Angle : 0.482 5.426 11463 Z= 0.259 Chirality : 0.039 0.142 1363 Planarity : 0.003 0.041 1444 Dihedral : 4.881 43.110 1212 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.65 % Allowed : 15.95 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.26), residues: 1107 helix: 3.15 (0.27), residues: 389 sheet: 0.59 (0.30), residues: 281 loop : -1.54 (0.26), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 279 HIS 0.004 0.001 HIS S 35 PHE 0.011 0.001 PHE B 151 TYR 0.014 0.001 TYR S 178 ARG 0.002 0.000 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.05008 ( 405) hydrogen bonds : angle 3.73221 ( 1164) SS BOND : bond 0.00161 ( 1) SS BOND : angle 0.71041 ( 2) covalent geometry : bond 0.00245 ( 8410) covalent geometry : angle 0.48163 (11461) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11594.09 seconds wall clock time: 203 minutes 49.57 seconds (12229.57 seconds total)