Starting phenix.real_space_refine on Tue Aug 26 21:18:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iox_60748/08_2025/9iox_60748_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iox_60748/08_2025/9iox_60748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9iox_60748/08_2025/9iox_60748_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iox_60748/08_2025/9iox_60748_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iox_60748/08_2025/9iox_60748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iox_60748/08_2025/9iox_60748.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 14 5.49 5 Mg 70 5.21 5 S 144 5.16 5 C 28910 2.51 5 N 5986 2.21 5 O 6726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41854 Number of models: 1 Model: "" Number of chains: 50 Chain: "A" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2388 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} Chain breaks: 1 Chain: "B" Number of atoms: 3755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3755 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 25, 'TRANS': 454} Chain: "C" Number of atoms: 3444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3444 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 24, 'TRANS': 416} Chain breaks: 1 Chain: "D" Number of atoms: 2686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2686 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 13, 'TRANS': 323} Chain breaks: 1 Chain: "E" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 602 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "F" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 251 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "G" Number of atoms: 1368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1368 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 4, 'TRANS': 164} Chain breaks: 2 Chain: "H" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 546 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 4, 'TRANS': 66} Chain: "I" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 275 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Chain: "K" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 297 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 31} Chain: "L" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 314 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "M" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 210 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "T" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 231 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 2, 'TRANS': 25} Chain: "V" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 216 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "X" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 214 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "Z" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 458 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "a" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2388 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 13, 'TRANS': 292} Chain breaks: 1 Chain: "b" Number of atoms: 3755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3755 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 25, 'TRANS': 454} Chain: "c" Number of atoms: 3444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3444 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 24, 'TRANS': 416} Chain breaks: 1 Chain: "d" Number of atoms: 2686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2686 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 13, 'TRANS': 323} Chain breaks: 1 Chain: "e" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 602 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "f" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 251 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "g" Number of atoms: 1368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1368 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 4, 'TRANS': 164} Chain breaks: 2 Chain: "h" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 546 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 4, 'TRANS': 66} Chain: "i" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 275 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 2, 'TRANS': 31} Chain: "k" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 297 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 31} Chain: "l" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 314 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "m" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 210 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "t" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 231 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 2, 'TRANS': 25} Chain: "v" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 216 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "x" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 214 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "z" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 458 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "A" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 452 Unusual residues: {'BCR': 2, 'CLA': 3, 'FE2': 1, 'LHG': 2, 'LMG': 1, 'PHO': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 1275 Unusual residues: {'BCR': 3, 'CLA': 16, 'LHG': 2, 'LMG': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 1263 Unusual residues: {'BCR': 3, 'CLA': 13, 'DGD': 3, 'LMG': 1, 'LMU': 1, 'SQD': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 44 Chain: "D" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 501 Unusual residues: {'BCR': 1, 'BCT': 1, 'CLA': 3, 'LHG': 1, 'LMG': 2, 'PHO': 1, 'PL9': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'BCR': 1, 'LHG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 366 Unusual residues: {'BCR': 1, 'CLA': 3, 'FE2': 1, 'LHG': 2, 'PHO': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 1235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 1235 Unusual residues: {'BCR': 2, 'CLA': 16, 'LHG': 2, 'LMG': 1} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 5 Chain: "c" Number of atoms: 1269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 1269 Unusual residues: {'BCR': 2, 'CLA': 13, 'DGD': 3, 'LMG': 2, 'LMU': 1, 'SQD': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 53 Chain: "d" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 453 Unusual residues: {'BCR': 1, 'BCT': 1, 'CLA': 3, 'LHG': 1, 'LMG': 1, 'PHO': 1, 'PL9': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "e" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'LMG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "k" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'BCR': 1, 'LHG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "z" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.43, per 1000 atoms: 0.23 Number of scatterers: 41854 At special positions: 0 Unit cell: (156.88, 204.58, 132.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 144 16.00 P 14 15.00 Mg 70 11.99 O 6726 8.00 N 5986 7.00 C 28910 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=58, symmetry=0 Number of additional bonds: simple=58, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.62 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7936 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 15 sheets defined 69.4% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 Processing helix chain 'A' and resid 30 through 54 removed outlier: 3.538A pdb=" N VAL A 35 " --> pdb=" O GLY A 31 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE A 36 " --> pdb=" O TRP A 32 " (cutoff:3.500A) Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.695A pdb=" N GLY A 74 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 removed outlier: 3.612A pdb=" N GLU A 98 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 109 Processing helix chain 'A' and resid 109 through 138 removed outlier: 4.249A pdb=" N GLN A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 138 " --> pdb=" O SER A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 159 removed outlier: 4.307A pdb=" N ALA A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Proline residue: A 150 - end of helix Processing helix chain 'A' and resid 159 through 166 Processing helix chain 'A' and resid 167 through 171 removed outlier: 3.736A pdb=" N ASP A 170 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 Processing helix chain 'A' and resid 195 through 223 Processing helix chain 'A' and resid 248 through 259 Processing helix chain 'A' and resid 267 through 295 Proline residue: A 279 - end of helix removed outlier: 3.791A pdb=" N PHE A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 333 removed outlier: 3.553A pdb=" N GLU A 333 " --> pdb=" O GLU A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 14 removed outlier: 3.874A pdb=" N VAL B 8 " --> pdb=" O TRP B 5 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N HIS B 9 " --> pdb=" O TYR B 6 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL B 11 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 12 " --> pdb=" O HIS B 9 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASN B 14 " --> pdb=" O VAL B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 45 Processing helix chain 'B' and resid 54 through 59 removed outlier: 3.960A pdb=" N GLY B 59 " --> pdb=" O TRP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 69 removed outlier: 3.608A pdb=" N MET B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B 69 " --> pdb=" O PHE B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 117 Processing helix chain 'B' and resid 134 through 156 Processing helix chain 'B' and resid 186 through 191 removed outlier: 3.696A pdb=" N ASP B 191 " --> pdb=" O ASP B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 219 removed outlier: 3.616A pdb=" N ILE B 198 " --> pdb=" O ASN B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 234 through 259 Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 271 through 277 removed outlier: 3.661A pdb=" N TRP B 275 " --> pdb=" O THR B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 294 Processing helix chain 'B' and resid 297 through 304 removed outlier: 3.558A pdb=" N ARG B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 313 removed outlier: 3.513A pdb=" N ASP B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 322 removed outlier: 3.976A pdb=" N GLY B 322 " --> pdb=" O PRO B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 335 removed outlier: 3.752A pdb=" N ASP B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 396 Processing helix chain 'B' and resid 413 through 426 removed outlier: 4.028A pdb=" N LEU B 426 " --> pdb=" O ARG B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 475 removed outlier: 3.522A pdb=" N TRP B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 481 Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 22 through 31 removed outlier: 5.714A pdb=" N ASN C 27 " --> pdb=" O TRP C 24 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C 31 " --> pdb=" O ALA C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 62 Processing helix chain 'C' and resid 68 through 72 Processing helix chain 'C' and resid 76 through 84 removed outlier: 3.570A pdb=" N ILE C 80 " --> pdb=" O LEU C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 92 removed outlier: 3.661A pdb=" N GLU C 92 " --> pdb=" O PRO C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 123 Processing helix chain 'C' and resid 142 through 169 Processing helix chain 'C' and resid 193 through 203 removed outlier: 3.645A pdb=" N TYR C 200 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU C 201 " --> pdb=" O ILE C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 215 removed outlier: 3.600A pdb=" N SER C 214 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL C 215 " --> pdb=" O ILE C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 241 removed outlier: 3.574A pdb=" N ILE C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR C 241 " --> pdb=" O ILE C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 252 removed outlier: 3.506A pdb=" N PHE C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 281 Processing helix chain 'C' and resid 286 through 291 Processing helix chain 'C' and resid 293 through 314 Processing helix chain 'C' and resid 341 through 347 removed outlier: 3.624A pdb=" N ARG C 345 " --> pdb=" O GLU C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.810A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 386 Processing helix chain 'C' and resid 409 through 442 Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 30 through 54 removed outlier: 4.067A pdb=" N LEU D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU D 36 " --> pdb=" O TRP D 32 " (cutoff:3.500A) Proline residue: D 39 - end of helix Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 82 through 86 Processing helix chain 'D' and resid 100 through 108 Processing helix chain 'D' and resid 108 through 137 removed outlier: 4.155A pdb=" N ALA D 112 " --> pdb=" O GLY D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 158 removed outlier: 3.583A pdb=" N ILE D 144 " --> pdb=" O PRO D 140 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA D 148 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Proline residue: D 149 - end of helix Processing helix chain 'D' and resid 158 through 164 Processing helix chain 'D' and resid 166 through 170 removed outlier: 3.548A pdb=" N PHE D 169 " --> pdb=" O GLY D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 188 Processing helix chain 'D' and resid 190 through 193 Processing helix chain 'D' and resid 194 through 220 Processing helix chain 'D' and resid 245 through 257 Processing helix chain 'D' and resid 263 through 291 Proline residue: D 275 - end of helix removed outlier: 3.669A pdb=" N LEU D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'D' and resid 313 through 334 removed outlier: 4.537A pdb=" N ALA D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLN D 332 " --> pdb=" O TRP D 328 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN D 334 " --> pdb=" O ALA D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 338 Processing helix chain 'E' and resid 9 through 16 removed outlier: 3.942A pdb=" N ILE E 13 " --> pdb=" O PRO E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 40 Proline residue: E 28 - end of helix Processing helix chain 'E' and resid 41 through 48 Processing helix chain 'E' and resid 72 through 80 Processing helix chain 'F' and resid 16 through 41 Proline residue: F 28 - end of helix removed outlier: 3.771A pdb=" N PHE F 41 " --> pdb=" O THR F 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 140 Processing helix chain 'G' and resid 168 through 173 removed outlier: 4.263A pdb=" N TRP G 172 " --> pdb=" O ALA G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 177 No H-bonds generated for 'chain 'G' and resid 175 through 177' Processing helix chain 'G' and resid 183 through 216 Processing helix chain 'G' and resid 218 through 232 Processing helix chain 'G' and resid 247 through 263 removed outlier: 4.174A pdb=" N VAL G 251 " --> pdb=" O PRO G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 280 removed outlier: 4.126A pdb=" N LYS G 271 " --> pdb=" O GLU G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 290 removed outlier: 3.625A pdb=" N ARG G 288 " --> pdb=" O TYR G 284 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 298 removed outlier: 3.513A pdb=" N ALA G 298 " --> pdb=" O SER G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 310 removed outlier: 3.921A pdb=" N GLN G 303 " --> pdb=" O ASN G 299 " (cutoff:3.500A) Processing helix chain 'G' and resid 315 through 325 Processing helix chain 'H' and resid 24 through 31 Processing helix chain 'H' and resid 32 through 36 removed outlier: 3.833A pdb=" N SER H 35 " --> pdb=" O PRO H 32 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLU H 36 " --> pdb=" O LEU H 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 32 through 36' Processing helix chain 'H' and resid 46 through 70 Processing helix chain 'H' and resid 80 through 85 removed outlier: 3.716A pdb=" N ALA H 85 " --> pdb=" O GLU H 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 26 removed outlier: 3.547A pdb=" N ASN I 26 " --> pdb=" O GLY I 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 17 Proline residue: K 17 - end of helix Processing helix chain 'K' and resid 18 through 25 removed outlier: 3.649A pdb=" N VAL K 22 " --> pdb=" O PHE K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 27 through 43 removed outlier: 4.071A pdb=" N PHE K 31 " --> pdb=" O VAL K 27 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE K 32 " --> pdb=" O ILE K 28 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE K 33 " --> pdb=" O PRO K 29 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU K 34 " --> pdb=" O VAL K 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 38 removed outlier: 4.565A pdb=" N SER L 34 " --> pdb=" O VAL L 30 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR L 35 " --> pdb=" O LEU L 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 30 Proline residue: M 18 - end of helix Processing helix chain 'T' and resid 2 through 23 Processing helix chain 'V' and resid 4 through 29 Proline residue: V 20 - end of helix removed outlier: 4.687A pdb=" N VAL V 23 " --> pdb=" O GLY V 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 66 through 95 Processing helix chain 'Z' and resid 2 through 29 Proline residue: Z 24 - end of helix Processing helix chain 'Z' and resid 36 through 61 removed outlier: 3.735A pdb=" N VAL Z 40 " --> pdb=" O ASN Z 36 " (cutoff:3.500A) Processing helix chain 'a' and resid 12 through 23 Processing helix chain 'a' and resid 30 through 54 removed outlier: 4.029A pdb=" N ILE a 36 " --> pdb=" O TRP a 32 " (cutoff:3.500A) Proline residue: a 39 - end of helix Processing helix chain 'a' and resid 70 through 74 removed outlier: 3.795A pdb=" N GLY a 74 " --> pdb=" O LEU a 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 101 through 109 Processing helix chain 'a' and resid 109 through 138 removed outlier: 4.275A pdb=" N GLN a 113 " --> pdb=" O GLY a 109 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP a 131 " --> pdb=" O MET a 127 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER a 134 " --> pdb=" O GLU a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 143 through 159 removed outlier: 4.266A pdb=" N ALA a 149 " --> pdb=" O VAL a 145 " (cutoff:3.500A) Proline residue: a 150 - end of helix Processing helix chain 'a' and resid 159 through 166 Processing helix chain 'a' and resid 167 through 171 removed outlier: 3.849A pdb=" N ASP a 170 " --> pdb=" O SER a 167 " (cutoff:3.500A) Processing helix chain 'a' and resid 176 through 190 Processing helix chain 'a' and resid 195 through 223 Processing helix chain 'a' and resid 248 through 259 removed outlier: 3.593A pdb=" N ILE a 259 " --> pdb=" O PHE a 255 " (cutoff:3.500A) Processing helix chain 'a' and resid 267 through 295 removed outlier: 3.595A pdb=" N ALA a 276 " --> pdb=" O HIS a 272 " (cutoff:3.500A) Proline residue: a 279 - end of helix removed outlier: 3.810A pdb=" N PHE a 295 " --> pdb=" O SER a 291 " (cutoff:3.500A) Processing helix chain 'a' and resid 316 through 333 Processing helix chain 'b' and resid 4 through 14 removed outlier: 3.881A pdb=" N VAL b 8 " --> pdb=" O TRP b 5 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N HIS b 9 " --> pdb=" O TYR b 6 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL b 11 " --> pdb=" O VAL b 8 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL b 12 " --> pdb=" O HIS b 9 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASN b 14 " --> pdb=" O VAL b 11 " (cutoff:3.500A) Processing helix chain 'b' and resid 15 through 45 removed outlier: 3.503A pdb=" N VAL b 44 " --> pdb=" O PHE b 40 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE b 45 " --> pdb=" O GLU b 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 54 through 59 removed outlier: 4.050A pdb=" N GLY b 59 " --> pdb=" O TRP b 56 " (cutoff:3.500A) Processing helix chain 'b' and resid 62 through 68 Processing helix chain 'b' and resid 92 through 117 Processing helix chain 'b' and resid 120 through 124 Processing helix chain 'b' and resid 134 through 156 removed outlier: 3.583A pdb=" N GLY b 140 " --> pdb=" O PRO b 136 " (cutoff:3.500A) Processing helix chain 'b' and resid 186 through 190 Processing helix chain 'b' and resid 194 through 219 removed outlier: 4.170A pdb=" N ILE b 198 " --> pdb=" O ASN b 194 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA b 199 " --> pdb=" O PRO b 195 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY b 209 " --> pdb=" O ALA b 205 " (cutoff:3.500A) Processing helix chain 'b' and resid 222 through 230 Processing helix chain 'b' and resid 234 through 259 Processing helix chain 'b' and resid 264 through 269 Processing helix chain 'b' and resid 271 through 277 removed outlier: 3.647A pdb=" N TRP b 275 " --> pdb=" O THR b 271 " (cutoff:3.500A) Processing helix chain 'b' and resid 278 through 294 Processing helix chain 'b' and resid 297 through 304 removed outlier: 3.577A pdb=" N ARG b 304 " --> pdb=" O ASP b 300 " (cutoff:3.500A) Processing helix chain 'b' and resid 306 through 313 removed outlier: 3.526A pdb=" N ASP b 313 " --> pdb=" O LEU b 309 " (cutoff:3.500A) Processing helix chain 'b' and resid 318 through 322 removed outlier: 3.993A pdb=" N GLY b 322 " --> pdb=" O PRO b 319 " (cutoff:3.500A) Processing helix chain 'b' and resid 330 through 335 removed outlier: 3.765A pdb=" N ASP b 334 " --> pdb=" O MET b 330 " (cutoff:3.500A) Processing helix chain 'b' and resid 391 through 396 Processing helix chain 'b' and resid 413 through 426 removed outlier: 4.022A pdb=" N LEU b 426 " --> pdb=" O ARG b 422 " (cutoff:3.500A) Processing helix chain 'b' and resid 446 through 475 Processing helix chain 'b' and resid 475 through 481 Processing helix chain 'c' and resid 15 through 20 Processing helix chain 'c' and resid 22 through 31 removed outlier: 5.717A pdb=" N ASN c 27 " --> pdb=" O TRP c 24 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE c 31 " --> pdb=" O ALA c 28 " (cutoff:3.500A) Processing helix chain 'c' and resid 34 through 62 Processing helix chain 'c' and resid 68 through 72 Processing helix chain 'c' and resid 76 through 84 removed outlier: 3.588A pdb=" N ILE c 80 " --> pdb=" O LEU c 76 " (cutoff:3.500A) Processing helix chain 'c' and resid 88 through 92 removed outlier: 3.665A pdb=" N GLU c 92 " --> pdb=" O PRO c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 96 through 123 removed outlier: 3.664A pdb=" N ALA c 111 " --> pdb=" O LEU c 107 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL c 112 " --> pdb=" O ILE c 108 " (cutoff:3.500A) Processing helix chain 'c' and resid 142 through 169 Processing helix chain 'c' and resid 193 through 203 removed outlier: 3.607A pdb=" N TYR c 200 " --> pdb=" O VAL c 196 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU c 201 " --> pdb=" O ILE c 197 " (cutoff:3.500A) Processing helix chain 'c' and resid 210 through 215 removed outlier: 3.575A pdb=" N SER c 214 " --> pdb=" O TRP c 211 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL c 215 " --> pdb=" O ILE c 212 " (cutoff:3.500A) Processing helix chain 'c' and resid 217 through 241 removed outlier: 3.556A pdb=" N ILE c 221 " --> pdb=" O ASN c 217 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR c 241 " --> pdb=" O ILE c 237 " (cutoff:3.500A) Processing helix chain 'c' and resid 245 through 252 Processing helix chain 'c' and resid 255 through 281 removed outlier: 3.689A pdb=" N LEU c 260 " --> pdb=" O GLY c 256 " (cutoff:3.500A) Processing helix chain 'c' and resid 286 through 291 Processing helix chain 'c' and resid 293 through 314 removed outlier: 3.626A pdb=" N ALA c 302 " --> pdb=" O SER c 298 " (cutoff:3.500A) Processing helix chain 'c' and resid 341 through 347 removed outlier: 3.632A pdb=" N ARG c 345 " --> pdb=" O GLU c 342 " (cutoff:3.500A) Processing helix chain 'c' and resid 364 through 371 removed outlier: 3.812A pdb=" N LEU c 368 " --> pdb=" O ASP c 364 " (cutoff:3.500A) Processing helix chain 'c' and resid 373 through 386 removed outlier: 3.734A pdb=" N THR c 385 " --> pdb=" O ALA c 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS c 386 " --> pdb=" O GLU c 382 " (cutoff:3.500A) Processing helix chain 'c' and resid 409 through 442 removed outlier: 3.532A pdb=" N TRP c 413 " --> pdb=" O SER c 409 " (cutoff:3.500A) Processing helix chain 'd' and resid 13 through 23 Processing helix chain 'd' and resid 30 through 54 removed outlier: 4.111A pdb=" N LEU d 35 " --> pdb=" O GLY d 31 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU d 36 " --> pdb=" O TRP d 32 " (cutoff:3.500A) Proline residue: d 39 - end of helix removed outlier: 3.820A pdb=" N TRP d 48 " --> pdb=" O ALA d 44 " (cutoff:3.500A) Processing helix chain 'd' and resid 82 through 86 Processing helix chain 'd' and resid 100 through 108 Processing helix chain 'd' and resid 108 through 136 removed outlier: 4.301A pdb=" N ALA d 112 " --> pdb=" O GLY d 108 " (cutoff:3.500A) Processing helix chain 'd' and resid 140 through 158 removed outlier: 3.512A pdb=" N ILE d 144 " --> pdb=" O PRO d 140 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA d 148 " --> pdb=" O ILE d 144 " (cutoff:3.500A) Proline residue: d 149 - end of helix Processing helix chain 'd' and resid 158 through 164 Processing helix chain 'd' and resid 166 through 170 removed outlier: 3.553A pdb=" N PHE d 169 " --> pdb=" O GLY d 166 " (cutoff:3.500A) Processing helix chain 'd' and resid 175 through 188 Processing helix chain 'd' and resid 190 through 193 Processing helix chain 'd' and resid 194 through 220 removed outlier: 3.638A pdb=" N GLY d 203 " --> pdb=" O MET d 199 " (cutoff:3.500A) Processing helix chain 'd' and resid 245 through 257 Processing helix chain 'd' and resid 263 through 291 removed outlier: 3.849A pdb=" N LEU d 272 " --> pdb=" O HIS d 268 " (cutoff:3.500A) Proline residue: d 275 - end of helix removed outlier: 3.870A pdb=" N LEU d 291 " --> pdb=" O VAL d 287 " (cutoff:3.500A) Processing helix chain 'd' and resid 298 through 308 Processing helix chain 'd' and resid 313 through 334 removed outlier: 4.494A pdb=" N ALA d 331 " --> pdb=" O ALA d 327 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N GLN d 332 " --> pdb=" O TRP d 328 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN d 334 " --> pdb=" O ALA d 330 " (cutoff:3.500A) Processing helix chain 'd' and resid 335 through 338 Processing helix chain 'e' and resid 9 through 16 removed outlier: 3.953A pdb=" N ILE e 13 " --> pdb=" O PRO e 9 " (cutoff:3.500A) Processing helix chain 'e' and resid 16 through 40 Proline residue: e 28 - end of helix Processing helix chain 'e' and resid 41 through 48 Processing helix chain 'e' and resid 72 through 80 Processing helix chain 'f' and resid 16 through 42 Proline residue: f 28 - end of helix removed outlier: 3.873A pdb=" N ALA f 38 " --> pdb=" O GLY f 34 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 140 Processing helix chain 'g' and resid 168 through 173 removed outlier: 4.253A pdb=" N TRP g 172 " --> pdb=" O ALA g 168 " (cutoff:3.500A) Processing helix chain 'g' and resid 175 through 177 No H-bonds generated for 'chain 'g' and resid 175 through 177' Processing helix chain 'g' and resid 183 through 215 Processing helix chain 'g' and resid 218 through 230 Processing helix chain 'g' and resid 246 through 263 removed outlier: 4.118A pdb=" N LYS g 250 " --> pdb=" O THR g 246 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL g 251 " --> pdb=" O PRO g 247 " (cutoff:3.500A) Processing helix chain 'g' and resid 265 through 279 removed outlier: 3.832A pdb=" N LYS g 271 " --> pdb=" O GLU g 267 " (cutoff:3.500A) Processing helix chain 'g' and resid 284 through 290 removed outlier: 3.699A pdb=" N ARG g 288 " --> pdb=" O TYR g 284 " (cutoff:3.500A) Processing helix chain 'g' and resid 293 through 298 Processing helix chain 'g' and resid 299 through 310 removed outlier: 3.945A pdb=" N GLN g 303 " --> pdb=" O ASN g 299 " (cutoff:3.500A) Processing helix chain 'g' and resid 315 through 325 Processing helix chain 'h' and resid 24 through 31 Processing helix chain 'h' and resid 32 through 36 removed outlier: 3.561A pdb=" N SER h 35 " --> pdb=" O PRO h 32 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU h 36 " --> pdb=" O LEU h 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 32 through 36' Processing helix chain 'h' and resid 46 through 70 Processing helix chain 'h' and resid 80 through 85 removed outlier: 3.681A pdb=" N ALA h 85 " --> pdb=" O GLU h 82 " (cutoff:3.500A) Processing helix chain 'i' and resid 2 through 26 removed outlier: 3.754A pdb=" N PHE i 23 " --> pdb=" O PHE i 19 " (cutoff:3.500A) Processing helix chain 'k' and resid 12 through 17 Proline residue: k 17 - end of helix Processing helix chain 'k' and resid 18 through 25 removed outlier: 3.610A pdb=" N VAL k 22 " --> pdb=" O PHE k 18 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL k 24 " --> pdb=" O PRO k 20 " (cutoff:3.500A) Processing helix chain 'k' and resid 26 through 28 No H-bonds generated for 'chain 'k' and resid 26 through 28' Processing helix chain 'k' and resid 29 through 43 removed outlier: 4.211A pdb=" N ILE k 33 " --> pdb=" O PRO k 29 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU k 34 " --> pdb=" O VAL k 30 " (cutoff:3.500A) Processing helix chain 'l' and resid 14 through 38 removed outlier: 4.502A pdb=" N SER l 34 " --> pdb=" O VAL l 30 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N TYR l 35 " --> pdb=" O LEU l 31 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN l 38 " --> pdb=" O SER l 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 30 Proline residue: m 18 - end of helix Processing helix chain 't' and resid 2 through 23 Processing helix chain 'v' and resid 4 through 29 Proline residue: v 20 - end of helix removed outlier: 4.625A pdb=" N VAL v 23 " --> pdb=" O GLY v 19 " (cutoff:3.500A) Processing helix chain 'x' and resid 66 through 95 Processing helix chain 'z' and resid 2 through 29 removed outlier: 3.532A pdb=" N LEU z 12 " --> pdb=" O ALA z 8 " (cutoff:3.500A) Proline residue: z 24 - end of helix removed outlier: 3.514A pdb=" N THR z 29 " --> pdb=" O VAL z 25 " (cutoff:3.500A) Processing helix chain 'z' and resid 36 through 61 removed outlier: 3.736A pdb=" N VAL z 40 " --> pdb=" O ASN z 36 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL z 61 " --> pdb=" O LEU z 57 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 82 removed outlier: 3.589A pdb=" N VAL A 82 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 166 through 169 Processing sheet with id=AA3, first strand: chain 'B' and resid 337 through 340 removed outlier: 4.174A pdb=" N GLU B 431 " --> pdb=" O VAL B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 377 through 380 removed outlier: 6.573A pdb=" N VAL B 377 " --> pdb=" O ASP B 372 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASP B 372 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA B 379 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE B 346 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL B 356 " --> pdb=" O ALA B 344 " (cutoff:3.500A) removed outlier: 10.589A pdb=" N ALA B 344 " --> pdb=" O VAL B 356 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 173 through 175 Processing sheet with id=AA6, first strand: chain 'C' and resid 329 through 331 Processing sheet with id=AA7, first strand: chain 'C' and resid 358 through 359 Processing sheet with id=AA8, first strand: chain 'a' and resid 81 through 82 removed outlier: 3.555A pdb=" N VAL a 82 " --> pdb=" O LEU a 174 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 166 through 169 Processing sheet with id=AB1, first strand: chain 'b' and resid 336 through 340 removed outlier: 4.070A pdb=" N ILE b 336 " --> pdb=" O ASP b 433 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU b 431 " --> pdb=" O VAL b 338 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'b' and resid 377 through 380 removed outlier: 6.571A pdb=" N VAL b 377 " --> pdb=" O ASP b 372 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASP b 372 " --> pdb=" O VAL b 377 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA b 379 " --> pdb=" O LEU b 370 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE b 346 " --> pdb=" O LEU b 354 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL b 356 " --> pdb=" O ALA b 344 " (cutoff:3.500A) removed outlier: 10.633A pdb=" N ALA b 344 " --> pdb=" O VAL b 356 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 173 through 175 Processing sheet with id=AB4, first strand: chain 'c' and resid 329 through 331 Processing sheet with id=AB5, first strand: chain 'c' and resid 358 through 359 Processing sheet with id=AB6, first strand: chain 'd' and resid 77 through 78 2106 hydrogen bonds defined for protein. 6072 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: 7.21 Time building geometry restraints manager: 5.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 16555 1.39 - 1.57: 26379 1.57 - 1.75: 36 1.75 - 1.92: 246 1.92 - 2.10: 288 Bond restraints: 43504 Sorted by residual: bond pdb=" C6 SQD C 501 " pdb=" S SQD C 501 " ideal model delta sigma weight residual 1.840 1.667 0.173 2.00e-02 2.50e+03 7.50e+01 bond pdb=" C6 SQD c 501 " pdb=" S SQD c 501 " ideal model delta sigma weight residual 1.840 1.667 0.173 2.00e-02 2.50e+03 7.47e+01 bond pdb=" C7 LHG B 521 " pdb=" O7 LHG B 521 " ideal model delta sigma weight residual 1.329 1.461 -0.132 2.00e-02 2.50e+03 4.33e+01 bond pdb=" C7 LHG b 520 " pdb=" O7 LHG b 520 " ideal model delta sigma weight residual 1.329 1.459 -0.130 2.00e-02 2.50e+03 4.22e+01 bond pdb=" C7 LHG b 521 " pdb=" O7 LHG b 521 " ideal model delta sigma weight residual 1.329 1.458 -0.129 2.00e-02 2.50e+03 4.14e+01 ... (remaining 43499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.55: 58707 3.55 - 7.09: 976 7.09 - 10.64: 115 10.64 - 14.19: 67 14.19 - 17.74: 73 Bond angle restraints: 59938 Sorted by residual: angle pdb=" NB CLA b 504 " pdb="MG CLA b 504 " pdb=" ND CLA b 504 " ideal model delta sigma weight residual 176.90 159.16 17.74 3.00e+00 1.11e-01 3.49e+01 angle pdb=" NB CLA B 504 " pdb="MG CLA B 504 " pdb=" ND CLA B 504 " ideal model delta sigma weight residual 176.90 159.35 17.55 3.00e+00 1.11e-01 3.42e+01 angle pdb=" NB CLA B 509 " pdb="MG CLA B 509 " pdb=" ND CLA B 509 " ideal model delta sigma weight residual 176.90 159.48 17.42 3.00e+00 1.11e-01 3.37e+01 angle pdb=" NB CLA C 504 " pdb="MG CLA C 504 " pdb=" ND CLA C 504 " ideal model delta sigma weight residual 176.90 159.93 16.97 3.00e+00 1.11e-01 3.20e+01 angle pdb=" NB CLA c 513 " pdb="MG CLA c 513 " pdb=" ND CLA c 513 " ideal model delta sigma weight residual 176.90 160.00 16.90 3.00e+00 1.11e-01 3.17e+01 ... (remaining 59933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.68: 21876 27.68 - 55.37: 1386 55.37 - 83.05: 217 83.05 - 110.73: 41 110.73 - 138.41: 50 Dihedral angle restraints: 23570 sinusoidal: 11144 harmonic: 12426 Sorted by residual: dihedral pdb=" C3A DGD C 518 " pdb=" C1A DGD C 518 " pdb=" C2A DGD C 518 " pdb=" O1A DGD C 518 " ideal model delta sinusoidal sigma weight residual -24.22 114.19 -138.41 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" C3A DGD c 518 " pdb=" C1A DGD c 518 " pdb=" C2A DGD c 518 " pdb=" O1A DGD c 518 " ideal model delta sinusoidal sigma weight residual -24.22 113.32 -137.54 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" C4D PHO D 402 " pdb=" CBD PHO D 402 " pdb=" CHA PHO D 402 " pdb=" CGD PHO D 402 " ideal model delta sinusoidal sigma weight residual 243.52 116.66 126.86 1 3.00e+01 1.11e-03 1.71e+01 ... (remaining 23567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 4424 0.043 - 0.086: 1063 0.086 - 0.129: 280 0.129 - 0.173: 38 0.173 - 0.216: 17 Chirality restraints: 5822 Sorted by residual: chirality pdb=" C2 LHG a 407 " pdb=" C1 LHG a 407 " pdb=" C3 LHG a 407 " pdb=" O2 LHG a 407 " both_signs ideal model delta sigma weight residual False -2.33 -2.55 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C2 LHG A 408 " pdb=" C1 LHG A 408 " pdb=" C3 LHG A 408 " pdb=" O2 LHG A 408 " both_signs ideal model delta sigma weight residual False -2.33 -2.54 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" C2 LHG l 101 " pdb=" C1 LHG l 101 " pdb=" C3 LHG l 101 " pdb=" O2 LHG l 101 " both_signs ideal model delta sigma weight residual False -2.33 -2.54 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 5819 not shown) Planarity restraints: 7426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB PHO A 404 " 0.130 2.00e-02 2.50e+03 1.22e-01 1.19e+03 pdb=" ND PHO A 404 " 0.079 2.00e-02 2.50e+03 pdb=" C1A PHO A 404 " 0.024 2.00e-02 2.50e+03 pdb=" C1B PHO A 404 " 0.053 2.00e-02 2.50e+03 pdb=" C1C PHO A 404 " 0.027 2.00e-02 2.50e+03 pdb=" C1D PHO A 404 " -0.026 2.00e-02 2.50e+03 pdb=" C2A PHO A 404 " -0.047 2.00e-02 2.50e+03 pdb=" C2B PHO A 404 " -0.128 2.00e-02 2.50e+03 pdb=" C2C PHO A 404 " 0.081 2.00e-02 2.50e+03 pdb=" C2D PHO A 404 " -0.078 2.00e-02 2.50e+03 pdb=" C3A PHO A 404 " 0.282 2.00e-02 2.50e+03 pdb=" C3B PHO A 404 " -0.147 2.00e-02 2.50e+03 pdb=" C3C PHO A 404 " 0.063 2.00e-02 2.50e+03 pdb=" C3D PHO A 404 " -0.056 2.00e-02 2.50e+03 pdb=" C4A PHO A 404 " 0.185 2.00e-02 2.50e+03 pdb=" C4B PHO A 404 " 0.020 2.00e-02 2.50e+03 pdb=" C4C PHO A 404 " -0.015 2.00e-02 2.50e+03 pdb=" C4D PHO A 404 " 0.007 2.00e-02 2.50e+03 pdb=" CAB PHO A 404 " -0.293 2.00e-02 2.50e+03 pdb=" CAC PHO A 404 " 0.102 2.00e-02 2.50e+03 pdb=" CAD PHO A 404 " -0.073 2.00e-02 2.50e+03 pdb=" CBD PHO A 404 " -0.114 2.00e-02 2.50e+03 pdb=" CHA PHO A 404 " -0.025 2.00e-02 2.50e+03 pdb=" CHB PHO A 404 " 0.132 2.00e-02 2.50e+03 pdb=" CHC PHO A 404 " 0.059 2.00e-02 2.50e+03 pdb=" CHD PHO A 404 " -0.067 2.00e-02 2.50e+03 pdb=" CMB PHO A 404 " -0.247 2.00e-02 2.50e+03 pdb=" CMC PHO A 404 " 0.153 2.00e-02 2.50e+03 pdb=" CMD PHO A 404 " -0.140 2.00e-02 2.50e+03 pdb=" NA PHO A 404 " 0.159 2.00e-02 2.50e+03 pdb=" NC PHO A 404 " -0.040 2.00e-02 2.50e+03 pdb=" OBD PHO A 404 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB PHO a 404 " -0.121 2.00e-02 2.50e+03 1.16e-01 1.07e+03 pdb=" ND PHO a 404 " -0.094 2.00e-02 2.50e+03 pdb=" C1A PHO a 404 " -0.015 2.00e-02 2.50e+03 pdb=" C1B PHO a 404 " -0.048 2.00e-02 2.50e+03 pdb=" C1C PHO a 404 " -0.025 2.00e-02 2.50e+03 pdb=" C1D PHO a 404 " 0.020 2.00e-02 2.50e+03 pdb=" C2A PHO a 404 " 0.065 2.00e-02 2.50e+03 pdb=" C2B PHO a 404 " 0.120 2.00e-02 2.50e+03 pdb=" C2C PHO a 404 " -0.074 2.00e-02 2.50e+03 pdb=" C2D PHO a 404 " 0.070 2.00e-02 2.50e+03 pdb=" C3A PHO a 404 " -0.272 2.00e-02 2.50e+03 pdb=" C3B PHO a 404 " 0.137 2.00e-02 2.50e+03 pdb=" C3C PHO a 404 " -0.054 2.00e-02 2.50e+03 pdb=" C3D PHO a 404 " 0.049 2.00e-02 2.50e+03 pdb=" C4A PHO a 404 " -0.178 2.00e-02 2.50e+03 pdb=" C4B PHO a 404 " -0.018 2.00e-02 2.50e+03 pdb=" C4C PHO a 404 " 0.019 2.00e-02 2.50e+03 pdb=" C4D PHO a 404 " -0.012 2.00e-02 2.50e+03 pdb=" CAB PHO a 404 " 0.271 2.00e-02 2.50e+03 pdb=" CAC PHO a 404 " -0.089 2.00e-02 2.50e+03 pdb=" CAD PHO a 404 " 0.066 2.00e-02 2.50e+03 pdb=" CBD PHO a 404 " 0.126 2.00e-02 2.50e+03 pdb=" CHA PHO a 404 " 0.030 2.00e-02 2.50e+03 pdb=" CHB PHO a 404 " -0.124 2.00e-02 2.50e+03 pdb=" CHC PHO a 404 " -0.055 2.00e-02 2.50e+03 pdb=" CHD PHO a 404 " 0.070 2.00e-02 2.50e+03 pdb=" CMB PHO a 404 " 0.228 2.00e-02 2.50e+03 pdb=" CMC PHO a 404 " -0.144 2.00e-02 2.50e+03 pdb=" CMD PHO a 404 " 0.129 2.00e-02 2.50e+03 pdb=" NA PHO a 404 " -0.158 2.00e-02 2.50e+03 pdb=" NC PHO a 404 " 0.039 2.00e-02 2.50e+03 pdb=" OBD PHO a 404 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB PHO D 402 " 0.039 2.00e-02 2.50e+03 7.32e-02 4.29e+02 pdb=" ND PHO D 402 " 0.140 2.00e-02 2.50e+03 pdb=" C1A PHO D 402 " -0.001 2.00e-02 2.50e+03 pdb=" C1B PHO D 402 " 0.013 2.00e-02 2.50e+03 pdb=" C1C PHO D 402 " 0.012 2.00e-02 2.50e+03 pdb=" C1D PHO D 402 " 0.027 2.00e-02 2.50e+03 pdb=" C2A PHO D 402 " 0.223 2.00e-02 2.50e+03 pdb=" C2B PHO D 402 " 0.019 2.00e-02 2.50e+03 pdb=" C2C PHO D 402 " -0.004 2.00e-02 2.50e+03 pdb=" C2D PHO D 402 " 0.006 2.00e-02 2.50e+03 pdb=" C3A PHO D 402 " -0.137 2.00e-02 2.50e+03 pdb=" C3B PHO D 402 " 0.036 2.00e-02 2.50e+03 pdb=" C3C PHO D 402 " -0.029 2.00e-02 2.50e+03 pdb=" C3D PHO D 402 " 0.019 2.00e-02 2.50e+03 pdb=" C4A PHO D 402 " -0.113 2.00e-02 2.50e+03 pdb=" C4B PHO D 402 " 0.045 2.00e-02 2.50e+03 pdb=" C4C PHO D 402 " -0.026 2.00e-02 2.50e+03 pdb=" C4D PHO D 402 " 0.049 2.00e-02 2.50e+03 pdb=" CAB PHO D 402 " 0.031 2.00e-02 2.50e+03 pdb=" CAC PHO D 402 " -0.063 2.00e-02 2.50e+03 pdb=" CAD PHO D 402 " 0.012 2.00e-02 2.50e+03 pdb=" CBD PHO D 402 " -0.095 2.00e-02 2.50e+03 pdb=" CHA PHO D 402 " -0.023 2.00e-02 2.50e+03 pdb=" CHB PHO D 402 " -0.016 2.00e-02 2.50e+03 pdb=" CHC PHO D 402 " 0.043 2.00e-02 2.50e+03 pdb=" CHD PHO D 402 " -0.048 2.00e-02 2.50e+03 pdb=" CMB PHO D 402 " -0.010 2.00e-02 2.50e+03 pdb=" CMC PHO D 402 " -0.008 2.00e-02 2.50e+03 pdb=" CMD PHO D 402 " -0.027 2.00e-02 2.50e+03 pdb=" NA PHO D 402 " -0.185 2.00e-02 2.50e+03 pdb=" NC PHO D 402 " -0.005 2.00e-02 2.50e+03 pdb=" OBD PHO D 402 " 0.075 2.00e-02 2.50e+03 ... (remaining 7423 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.20: 14 2.20 - 2.87: 14203 2.87 - 3.55: 60235 3.55 - 4.22: 96512 4.22 - 4.90: 173057 Nonbonded interactions: 344021 Sorted by model distance: nonbonded pdb=" NH2 ARG G 140 " pdb=" NE2 GLN G 265 " model vdw 1.525 3.200 nonbonded pdb=" OG1 THR A 286 " pdb=" O1D CLA A 402 " model vdw 2.045 3.040 nonbonded pdb=" O4 LMG D 410 " pdb=" O5 LMG D 410 " model vdw 2.140 3.040 nonbonded pdb=" NE2 HIS e 23 " pdb="FE HEM e 101 " model vdw 2.152 3.080 nonbonded pdb=" OG1 THR H 46 " pdb=" OBD CLA B 509 " model vdw 2.156 3.040 ... (remaining 344016 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 406 or resid 408)) selection = (chain 'a' and (resid 10 through 406 or (resid 408 and (name C1 or name C10 or n \ ame C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 \ or name C2 or name C23 or name C24 or name C25 or name C26 or name C27 or name C \ 28 or name C29 or name C3 or name C30 or name C31 or name C32 or name C33 or nam \ e C34 or name C35 or name C36 or name C37 or name C4 or name C5 or name C6 or na \ me C7 or name C8 or name C9 or name O1 or name O10 or name O2 or name O3 or name \ O4 or name O5 or name O6 or name O7 or name O8 or name O9 or name P )))) } ncs_group { reference = (chain 'B' and (resid 2 through 518 or resid 521)) selection = (chain 'b' and (resid 2 through 518 or (resid 521 and (name C1 or name C10 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 o \ r name C2 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C3 or name C30 or name C31 or name C32 or name C33 or name \ C34 or name C35 or name C36 or name C37 or name C38 or name C4 or name C5 or na \ me C6 or name C7 or name C8 or name C9 or name O1 or name O10 or name O2 or name \ O3 or name O4 or name O5 or name O6 or name O7 or name O8 or name O9 or name P \ )))) } ncs_group { reference = (chain 'C' and (resid 12 through 501 or resid 503 through 514 or resid 516 throu \ gh 522)) selection = (chain 'c' and (resid 12 through 501 or resid 503 through 514 or resid 516 throu \ gh 522)) } ncs_group { reference = (chain 'D' and resid 2 through 409) selection = chain 'd' } ncs_group { reference = chain 'E' selection = (chain 'e' and resid 8 through 81) } ncs_group { reference = (chain 'F' and resid 14 through 44) selection = chain 'f' } ncs_group { reference = chain 'G' selection = chain 'g' } ncs_group { reference = chain 'H' selection = (chain 'h' and resid 17 through 87) } ncs_group { reference = chain 'I' selection = chain 'i' } ncs_group { reference = chain 'K' selection = chain 'k' } ncs_group { reference = chain 'L' selection = chain 'l' } ncs_group { reference = chain 'M' selection = chain 'm' } ncs_group { reference = chain 'T' selection = chain 't' } ncs_group { reference = chain 'V' selection = chain 'v' } ncs_group { reference = chain 'X' selection = chain 'x' } ncs_group { reference = chain 'Z' selection = (chain 'z' and resid 1 through 61) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 35.330 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.200 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:1.380 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.173 43562 Z= 0.454 Angle : 1.200 17.735 59938 Z= 0.454 Chirality : 0.042 0.216 5822 Planarity : 0.014 0.236 7426 Dihedral : 18.535 138.414 15634 Min Nonbonded Distance : 1.525 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.13), residues: 4310 helix: 1.56 (0.10), residues: 2690 sheet: -0.87 (0.63), residues: 70 loop : -0.22 (0.17), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 30 TYR 0.023 0.001 TYR C 262 PHE 0.024 0.001 PHE Z 14 TRP 0.018 0.001 TRP A 131 HIS 0.008 0.001 HIS e 23 Details of bonding type rmsd covalent geometry : bond 0.00704 (43504) covalent geometry : angle 1.20033 (59938) hydrogen bonds : bond 0.13622 ( 2106) hydrogen bonds : angle 5.80861 ( 6072) Misc. bond : bond 0.08328 ( 58) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 659 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLU cc_start: 0.8096 (tp30) cc_final: 0.7789 (tp30) REVERT: A 257 ARG cc_start: 0.7930 (mtt90) cc_final: 0.7402 (mtm-85) REVERT: A 290 LEU cc_start: 0.8852 (tp) cc_final: 0.8640 (tp) REVERT: B 60 MET cc_start: 0.8553 (mmp) cc_final: 0.8266 (mmp) REVERT: C 137 TYR cc_start: 0.9114 (p90) cc_final: 0.8728 (p90) REVERT: C 301 GLN cc_start: 0.8322 (tp40) cc_final: 0.7365 (tp40) REVERT: G 136 MET cc_start: 0.6599 (mmp) cc_final: 0.6338 (mmt) REVERT: G 270 ILE cc_start: 0.7420 (pt) cc_final: 0.7162 (mm) REVERT: I 21 PHE cc_start: 0.8826 (m-80) cc_final: 0.8464 (m-80) REVERT: a 290 LEU cc_start: 0.8840 (tp) cc_final: 0.8538 (tp) REVERT: a 329 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8167 (tp30) REVERT: a 331 MET cc_start: 0.8368 (mmm) cc_final: 0.8095 (mmm) REVERT: c 74 LEU cc_start: 0.8183 (mp) cc_final: 0.7726 (mt) REVERT: c 137 TYR cc_start: 0.9114 (p90) cc_final: 0.8753 (p90) REVERT: d 255 GLN cc_start: 0.8374 (mt0) cc_final: 0.8043 (mt0) REVERT: z 6 GLN cc_start: 0.7995 (tt0) cc_final: 0.7775 (tp40) outliers start: 0 outliers final: 0 residues processed: 659 average time/residue: 0.2184 time to fit residues: 243.0051 Evaluate side-chains 525 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 525 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 4.9990 chunk 424 optimal weight: 8.9990 chunk 155 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 HIS A 303 ASN ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** G 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN Z 6 GLN a 26 ASN a 187 GLN a 261 GLN a 315 ASN a 325 ASN ** b 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 147 ASN d 142 ASN e 75 GLN g 189 GLN g 253 GLN l 5 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.134184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.102010 restraints weight = 79432.050| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 3.19 r_work: 0.3093 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.370 43562 Z= 0.215 Angle : 0.679 9.012 59938 Z= 0.313 Chirality : 0.045 0.294 5822 Planarity : 0.005 0.048 7426 Dihedral : 17.057 120.021 8176 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.52 % Allowed : 8.34 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.13), residues: 4310 helix: 1.67 (0.10), residues: 2688 sheet: -1.12 (0.59), residues: 70 loop : -0.20 (0.17), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 140 TYR 0.027 0.002 TYR c 262 PHE 0.029 0.002 PHE B 215 TRP 0.016 0.001 TRP A 131 HIS 0.012 0.002 HIS d 214 Details of bonding type rmsd covalent geometry : bond 0.00499 (43504) covalent geometry : angle 0.67929 (59938) hydrogen bonds : bond 0.05088 ( 2106) hydrogen bonds : angle 4.70934 ( 6072) Misc. bond : bond 0.07791 ( 58) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 577 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 GLU cc_start: 0.8736 (tp30) cc_final: 0.8163 (tp30) REVERT: A 257 ARG cc_start: 0.7796 (mtt90) cc_final: 0.7392 (mtm-85) REVERT: A 290 LEU cc_start: 0.9089 (tp) cc_final: 0.8802 (tp) REVERT: A 304 GLN cc_start: 0.9305 (mp10) cc_final: 0.8636 (mp10) REVERT: A 329 GLU cc_start: 0.9154 (tm-30) cc_final: 0.8872 (tp30) REVERT: B 256 MET cc_start: 0.9460 (tpp) cc_final: 0.9237 (mmm) REVERT: C 452 GLU cc_start: 0.7980 (mp0) cc_final: 0.7664 (mp0) REVERT: G 136 MET cc_start: 0.8424 (mmp) cc_final: 0.7911 (mmm) REVERT: G 270 ILE cc_start: 0.7234 (pt) cc_final: 0.6864 (mm) REVERT: G 279 SER cc_start: 0.8520 (m) cc_final: 0.8023 (p) REVERT: H 50 MET cc_start: 0.7778 (mmp) cc_final: 0.7141 (mmp) REVERT: I 30 ARG cc_start: 0.6816 (ttp-110) cc_final: 0.6203 (ptm-80) REVERT: T 18 PHE cc_start: 0.8742 (t80) cc_final: 0.8506 (t80) REVERT: Z 58 ASN cc_start: 0.9103 (t0) cc_final: 0.8666 (t0) REVERT: a 290 LEU cc_start: 0.9101 (tp) cc_final: 0.8755 (tp) REVERT: a 304 GLN cc_start: 0.9287 (mp10) cc_final: 0.8685 (mp10) REVERT: a 329 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8703 (tm-30) REVERT: b 60 MET cc_start: 0.9305 (mmp) cc_final: 0.8851 (mmp) REVERT: b 256 MET cc_start: 0.9467 (tpp) cc_final: 0.9212 (mmm) REVERT: c 452 GLU cc_start: 0.7958 (mp0) cc_final: 0.7606 (mp0) REVERT: d 255 GLN cc_start: 0.8815 (mt0) cc_final: 0.8588 (mt0) REVERT: e 18 ARG cc_start: 0.8369 (ptm-80) cc_final: 0.8049 (ttp-170) REVERT: g 136 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7468 (tpt) REVERT: g 223 LEU cc_start: 0.8399 (tp) cc_final: 0.8081 (tt) REVERT: g 232 MET cc_start: 0.7550 (mpp) cc_final: 0.7169 (mtm) REVERT: g 235 ARG cc_start: 0.8459 (tpp80) cc_final: 0.8233 (tpt170) REVERT: h 19 GLU cc_start: 0.6582 (pm20) cc_final: 0.6258 (pm20) REVERT: h 31 ARG cc_start: 0.8921 (tpt-90) cc_final: 0.8686 (tpp80) REVERT: i 30 ARG cc_start: 0.6836 (ttp-110) cc_final: 0.6303 (ptm-80) REVERT: t 18 PHE cc_start: 0.8662 (t80) cc_final: 0.8443 (t80) outliers start: 54 outliers final: 38 residues processed: 604 average time/residue: 0.2248 time to fit residues: 230.3219 Evaluate side-chains 565 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 526 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain V residue 23 VAL Chi-restraints excluded: chain a residue 291 SER Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain c residue 371 ASP Chi-restraints excluded: chain d residue 213 ILE Chi-restraints excluded: chain f residue 17 VAL Chi-restraints excluded: chain f residue 42 ILE Chi-restraints excluded: chain g residue 136 MET Chi-restraints excluded: chain g residue 211 LEU Chi-restraints excluded: chain g residue 314 VAL Chi-restraints excluded: chain h residue 83 THR Chi-restraints excluded: chain i residue 8 VAL Chi-restraints excluded: chain k residue 22 VAL Chi-restraints excluded: chain k residue 25 LEU Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 8 LEU Chi-restraints excluded: chain t residue 5 VAL Chi-restraints excluded: chain t residue 14 LEU Chi-restraints excluded: chain v residue 5 LEU Chi-restraints excluded: chain v residue 23 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 142 optimal weight: 0.6980 chunk 240 optimal weight: 6.9990 chunk 375 optimal weight: 9.9990 chunk 408 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 263 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 342 optimal weight: 4.9990 chunk 358 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 HIS ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN G 189 GLN ** G 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 252 HIS ** b 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 75 GLN g 189 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.131598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.100560 restraints weight = 80246.964| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 3.24 r_work: 0.3033 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.309 43562 Z= 0.272 Angle : 0.687 10.722 59938 Z= 0.319 Chirality : 0.045 0.307 5822 Planarity : 0.005 0.048 7426 Dihedral : 16.114 119.794 8176 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.36 % Allowed : 11.80 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.13), residues: 4310 helix: 1.55 (0.10), residues: 2684 sheet: -1.27 (0.57), residues: 74 loop : -0.30 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 311 TYR 0.028 0.002 TYR c 262 PHE 0.021 0.002 PHE B 215 TRP 0.019 0.001 TRP A 131 HIS 0.012 0.002 HIS d 214 Details of bonding type rmsd covalent geometry : bond 0.00632 (43504) covalent geometry : angle 0.68714 (59938) hydrogen bonds : bond 0.05217 ( 2106) hydrogen bonds : angle 4.71927 ( 6072) Misc. bond : bond 0.06383 ( 58) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 568 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8502 (mm-30) REVERT: A 104 GLU cc_start: 0.8817 (tp30) cc_final: 0.8286 (tp30) REVERT: A 290 LEU cc_start: 0.9135 (tp) cc_final: 0.8807 (tp) REVERT: A 304 GLN cc_start: 0.9274 (mp10) cc_final: 0.8605 (mp10) REVERT: A 328 MET cc_start: 0.8995 (mtm) cc_final: 0.8696 (mtm) REVERT: B 111 SER cc_start: 0.8863 (t) cc_final: 0.8354 (p) REVERT: B 334 ASP cc_start: 0.8436 (t0) cc_final: 0.8066 (t0) REVERT: C 452 GLU cc_start: 0.8061 (mp0) cc_final: 0.7740 (mp0) REVERT: G 136 MET cc_start: 0.8470 (mmp) cc_final: 0.7854 (mmm) REVERT: G 279 SER cc_start: 0.8695 (m) cc_final: 0.8226 (p) REVERT: H 31 ARG cc_start: 0.9034 (tpp80) cc_final: 0.8625 (tpp-160) REVERT: I 30 ARG cc_start: 0.7250 (ttp-110) cc_final: 0.6700 (ptm-80) REVERT: a 290 LEU cc_start: 0.9128 (tp) cc_final: 0.8772 (tp) REVERT: a 329 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8832 (tm-30) REVERT: b 111 SER cc_start: 0.8860 (t) cc_final: 0.8355 (p) REVERT: b 258 TYR cc_start: 0.8913 (m-80) cc_final: 0.8642 (m-80) REVERT: b 334 ASP cc_start: 0.8448 (t0) cc_final: 0.8131 (t0) REVERT: c 452 GLU cc_start: 0.8100 (mp0) cc_final: 0.7768 (mp0) REVERT: d 11 LYS cc_start: 0.7841 (mmmm) cc_final: 0.7463 (mmtt) REVERT: e 18 ARG cc_start: 0.8358 (ptm-80) cc_final: 0.8093 (ttp-170) REVERT: e 71 ASN cc_start: 0.8582 (t0) cc_final: 0.8353 (t0) REVERT: g 136 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7561 (mmm) REVERT: g 223 LEU cc_start: 0.8612 (tp) cc_final: 0.8291 (tt) REVERT: g 232 MET cc_start: 0.7609 (mpp) cc_final: 0.7260 (mtm) REVERT: g 235 ARG cc_start: 0.8486 (tpp80) cc_final: 0.8278 (tpt170) REVERT: h 50 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7854 (ttm) REVERT: i 30 ARG cc_start: 0.7319 (ttp-110) cc_final: 0.6752 (ptm-80) REVERT: t 18 PHE cc_start: 0.8729 (t80) cc_final: 0.8457 (t80) outliers start: 84 outliers final: 66 residues processed: 606 average time/residue: 0.2234 time to fit residues: 228.5320 Evaluate side-chains 586 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 518 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 72 ASN Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain G residue 260 TYR Chi-restraints excluded: chain G residue 306 LEU Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain T residue 5 VAL Chi-restraints excluded: chain V residue 5 LEU Chi-restraints excluded: chain a residue 291 SER Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain c residue 74 LEU Chi-restraints excluded: chain c residue 371 ASP Chi-restraints excluded: chain d residue 72 ASN Chi-restraints excluded: chain d residue 213 ILE Chi-restraints excluded: chain e residue 11 SER Chi-restraints excluded: chain e residue 17 ILE Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain f residue 17 VAL Chi-restraints excluded: chain f residue 39 MET Chi-restraints excluded: chain f residue 41 PHE Chi-restraints excluded: chain f residue 42 ILE Chi-restraints excluded: chain g residue 136 MET Chi-restraints excluded: chain g residue 211 LEU Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain g residue 306 LEU Chi-restraints excluded: chain g residue 314 VAL Chi-restraints excluded: chain h residue 50 MET Chi-restraints excluded: chain h residue 70 SER Chi-restraints excluded: chain h residue 83 THR Chi-restraints excluded: chain i residue 8 VAL Chi-restraints excluded: chain i residue 17 CYS Chi-restraints excluded: chain k residue 25 LEU Chi-restraints excluded: chain l residue 22 LEU Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 8 LEU Chi-restraints excluded: chain t residue 5 VAL Chi-restraints excluded: chain t residue 14 LEU Chi-restraints excluded: chain v residue 5 LEU Chi-restraints excluded: chain z residue 3 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 217 optimal weight: 3.9990 chunk 386 optimal weight: 0.8980 chunk 424 optimal weight: 10.0000 chunk 422 optimal weight: 0.0970 chunk 187 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 250 optimal weight: 8.9990 chunk 344 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 319 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 HIS A 261 GLN ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN E 75 GLN G 189 GLN a 252 HIS ** b 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 406 ASN e 75 GLN g 189 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.133866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.103056 restraints weight = 79032.235| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.28 r_work: 0.3145 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.284 43562 Z= 0.156 Angle : 0.594 11.148 59938 Z= 0.277 Chirality : 0.042 0.263 5822 Planarity : 0.004 0.047 7426 Dihedral : 15.650 119.113 8176 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.19 % Allowed : 14.10 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.13), residues: 4310 helix: 1.69 (0.10), residues: 2676 sheet: -0.74 (0.61), residues: 64 loop : -0.14 (0.17), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 103 TYR 0.030 0.001 TYR c 262 PHE 0.025 0.001 PHE B 215 TRP 0.020 0.001 TRP A 131 HIS 0.009 0.001 HIS d 214 Details of bonding type rmsd covalent geometry : bond 0.00357 (43504) covalent geometry : angle 0.59351 (59938) hydrogen bonds : bond 0.04630 ( 2106) hydrogen bonds : angle 4.46664 ( 6072) Misc. bond : bond 0.06096 ( 58) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 576 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.9142 (tmm) cc_final: 0.8807 (tmm) REVERT: A 104 GLU cc_start: 0.8684 (tp30) cc_final: 0.8045 (tp30) REVERT: A 290 LEU cc_start: 0.8957 (tp) cc_final: 0.8685 (tp) REVERT: A 304 GLN cc_start: 0.9293 (mp10) cc_final: 0.8613 (mp10) REVERT: A 329 GLU cc_start: 0.9133 (tm-30) cc_final: 0.8919 (tp30) REVERT: B 111 SER cc_start: 0.8941 (t) cc_final: 0.8344 (p) REVERT: B 334 ASP cc_start: 0.8473 (t0) cc_final: 0.7961 (t0) REVERT: C 452 GLU cc_start: 0.8170 (mp0) cc_final: 0.7925 (mp0) REVERT: E 71 ASN cc_start: 0.8587 (t0) cc_final: 0.8276 (t0) REVERT: G 279 SER cc_start: 0.8777 (m) cc_final: 0.8401 (p) REVERT: G 302 PHE cc_start: 0.8721 (t80) cc_final: 0.8367 (t80) REVERT: H 50 MET cc_start: 0.7621 (mmp) cc_final: 0.7003 (mmp) REVERT: I 30 ARG cc_start: 0.7059 (ttp-110) cc_final: 0.6477 (ptm-80) REVERT: a 37 MET cc_start: 0.9211 (tmm) cc_final: 0.8774 (tmm) REVERT: a 290 LEU cc_start: 0.8972 (tp) cc_final: 0.8587 (tp) REVERT: a 304 GLN cc_start: 0.9303 (mp10) cc_final: 0.8623 (mp10) REVERT: a 329 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8780 (tm-30) REVERT: b 111 SER cc_start: 0.8936 (t) cc_final: 0.8337 (p) REVERT: b 334 ASP cc_start: 0.8467 (t0) cc_final: 0.7999 (t0) REVERT: c 452 GLU cc_start: 0.8200 (mp0) cc_final: 0.7814 (mp0) REVERT: d 255 GLN cc_start: 0.8801 (mt0) cc_final: 0.8530 (mt0) REVERT: e 18 ARG cc_start: 0.8319 (ptm-80) cc_final: 0.8059 (ttp-170) REVERT: e 71 ASN cc_start: 0.8665 (t0) cc_final: 0.8256 (t0) REVERT: g 136 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7555 (mmm) REVERT: g 232 MET cc_start: 0.7656 (mpp) cc_final: 0.7243 (mtm) REVERT: g 235 ARG cc_start: 0.8560 (tpp80) cc_final: 0.8243 (tpt170) REVERT: h 50 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7823 (ttm) REVERT: i 30 ARG cc_start: 0.7159 (ttp-110) cc_final: 0.6569 (ptm-80) REVERT: t 18 PHE cc_start: 0.8685 (t80) cc_final: 0.8425 (t80) outliers start: 78 outliers final: 57 residues processed: 610 average time/residue: 0.2231 time to fit residues: 230.1494 Evaluate side-chains 586 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 527 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain G residue 260 TYR Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain a residue 291 SER Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 246 PHE Chi-restraints excluded: chain c residue 74 LEU Chi-restraints excluded: chain c residue 371 ASP Chi-restraints excluded: chain d residue 25 ASP Chi-restraints excluded: chain d residue 213 ILE Chi-restraints excluded: chain d residue 287 VAL Chi-restraints excluded: chain e residue 11 SER Chi-restraints excluded: chain e residue 17 ILE Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain f residue 17 VAL Chi-restraints excluded: chain f residue 39 MET Chi-restraints excluded: chain f residue 41 PHE Chi-restraints excluded: chain f residue 42 ILE Chi-restraints excluded: chain g residue 136 MET Chi-restraints excluded: chain g residue 211 LEU Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain g residue 291 LYS Chi-restraints excluded: chain g residue 314 VAL Chi-restraints excluded: chain h residue 50 MET Chi-restraints excluded: chain h residue 83 THR Chi-restraints excluded: chain i residue 17 CYS Chi-restraints excluded: chain k residue 25 LEU Chi-restraints excluded: chain l residue 22 LEU Chi-restraints excluded: chain m residue 8 LEU Chi-restraints excluded: chain t residue 5 VAL Chi-restraints excluded: chain t residue 14 LEU Chi-restraints excluded: chain v residue 5 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 284 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 360 optimal weight: 0.9980 chunk 226 optimal weight: 0.9980 chunk 280 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 325 optimal weight: 8.9990 chunk 329 optimal weight: 5.9990 chunk 188 optimal weight: 8.9990 chunk 195 optimal weight: 2.9990 chunk 408 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 GLN E 75 GLN G 189 GLN ** G 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 252 HIS ** b 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 75 GLN g 189 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.134984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.103176 restraints weight = 78616.380| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 3.27 r_work: 0.3133 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.262 43562 Z= 0.140 Angle : 0.582 14.896 59938 Z= 0.271 Chirality : 0.041 0.260 5822 Planarity : 0.004 0.046 7426 Dihedral : 15.316 118.815 8176 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.44 % Allowed : 14.86 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.13), residues: 4310 helix: 1.78 (0.10), residues: 2674 sheet: -0.98 (0.56), residues: 74 loop : -0.07 (0.17), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 472 TYR 0.013 0.001 TYR G 309 PHE 0.024 0.001 PHE M 21 TRP 0.018 0.001 TRP A 131 HIS 0.007 0.001 HIS d 214 Details of bonding type rmsd covalent geometry : bond 0.00317 (43504) covalent geometry : angle 0.58215 (59938) hydrogen bonds : bond 0.04350 ( 2106) hydrogen bonds : angle 4.36241 ( 6072) Misc. bond : bond 0.05682 ( 58) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 571 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.9075 (tmm) cc_final: 0.8683 (tmm) REVERT: A 104 GLU cc_start: 0.8779 (tp30) cc_final: 0.8253 (tp30) REVERT: A 290 LEU cc_start: 0.8983 (tp) cc_final: 0.8655 (tp) REVERT: A 304 GLN cc_start: 0.9285 (mp10) cc_final: 0.8648 (mp10) REVERT: B 111 SER cc_start: 0.8869 (t) cc_final: 0.8330 (p) REVERT: C 262 TYR cc_start: 0.8933 (m-80) cc_final: 0.8502 (m-80) REVERT: E 71 ASN cc_start: 0.8598 (t0) cc_final: 0.8280 (t0) REVERT: F 37 THR cc_start: 0.9180 (t) cc_final: 0.8966 (t) REVERT: G 136 MET cc_start: 0.8716 (mmp) cc_final: 0.8191 (mmm) REVERT: G 253 GLN cc_start: 0.8507 (tm-30) cc_final: 0.8258 (tm-30) REVERT: G 278 LEU cc_start: 0.8776 (mm) cc_final: 0.8569 (mm) REVERT: G 279 SER cc_start: 0.8877 (m) cc_final: 0.8470 (p) REVERT: I 30 ARG cc_start: 0.7151 (ttp-110) cc_final: 0.6589 (ptm-80) REVERT: X 73 LEU cc_start: 0.8822 (mt) cc_final: 0.8103 (pp) REVERT: a 37 MET cc_start: 0.9224 (tmm) cc_final: 0.8577 (tmm) REVERT: a 290 LEU cc_start: 0.9000 (tp) cc_final: 0.8604 (tp) REVERT: a 304 GLN cc_start: 0.9293 (mp10) cc_final: 0.8634 (mp10) REVERT: b 111 SER cc_start: 0.8835 (t) cc_final: 0.8267 (p) REVERT: b 334 ASP cc_start: 0.8464 (t0) cc_final: 0.8094 (t0) REVERT: c 55 MET cc_start: 0.8940 (tpp) cc_final: 0.8013 (tpt) REVERT: c 452 GLU cc_start: 0.8096 (mp0) cc_final: 0.7761 (mp0) REVERT: d 11 LYS cc_start: 0.7713 (mmmm) cc_final: 0.7370 (mmtt) REVERT: d 255 GLN cc_start: 0.8725 (mt0) cc_final: 0.8455 (mt0) REVERT: e 71 ASN cc_start: 0.8669 (t0) cc_final: 0.8218 (t0) REVERT: g 136 MET cc_start: 0.7731 (mtp) cc_final: 0.7502 (mmm) REVERT: g 137 TYR cc_start: 0.6465 (t80) cc_final: 0.6158 (t80) REVERT: g 232 MET cc_start: 0.7667 (mpp) cc_final: 0.6918 (mtm) REVERT: h 50 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7746 (ttt) REVERT: i 30 ARG cc_start: 0.7295 (ttp-110) cc_final: 0.6755 (ptm-80) REVERT: t 18 PHE cc_start: 0.8609 (t80) cc_final: 0.8277 (t80) outliers start: 87 outliers final: 64 residues processed: 609 average time/residue: 0.2121 time to fit residues: 220.3923 Evaluate side-chains 604 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 539 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain G residue 260 TYR Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain Z residue 3 SER Chi-restraints excluded: chain a residue 42 LEU Chi-restraints excluded: chain a residue 291 SER Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 148 LEU Chi-restraints excluded: chain b residue 246 PHE Chi-restraints excluded: chain b residue 368 VAL Chi-restraints excluded: chain c residue 74 LEU Chi-restraints excluded: chain c residue 371 ASP Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 213 ILE Chi-restraints excluded: chain d residue 287 VAL Chi-restraints excluded: chain e residue 11 SER Chi-restraints excluded: chain e residue 17 ILE Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain f residue 17 VAL Chi-restraints excluded: chain f residue 39 MET Chi-restraints excluded: chain f residue 41 PHE Chi-restraints excluded: chain f residue 42 ILE Chi-restraints excluded: chain g residue 211 LEU Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain g residue 291 LYS Chi-restraints excluded: chain g residue 314 VAL Chi-restraints excluded: chain h residue 50 MET Chi-restraints excluded: chain h residue 70 SER Chi-restraints excluded: chain h residue 83 THR Chi-restraints excluded: chain i residue 17 CYS Chi-restraints excluded: chain k residue 25 LEU Chi-restraints excluded: chain l residue 22 LEU Chi-restraints excluded: chain m residue 8 LEU Chi-restraints excluded: chain t residue 14 LEU Chi-restraints excluded: chain z residue 3 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 409 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 302 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 356 optimal weight: 7.9990 chunk 170 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 92 optimal weight: 9.9990 chunk 191 optimal weight: 1.9990 chunk 182 optimal weight: 4.9990 chunk 406 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 HIS A 261 GLN ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN G 189 GLN ** G 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 252 HIS ** b 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 75 GLN g 189 GLN g 303 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.134022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.101707 restraints weight = 79252.258| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 3.32 r_work: 0.3084 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.262 43562 Z= 0.165 Angle : 0.602 15.021 59938 Z= 0.277 Chirality : 0.041 0.267 5822 Planarity : 0.004 0.045 7426 Dihedral : 15.108 118.882 8176 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.81 % Allowed : 15.25 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.13), residues: 4310 helix: 1.78 (0.10), residues: 2672 sheet: -0.99 (0.57), residues: 74 loop : -0.07 (0.17), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 472 TYR 0.024 0.001 TYR c 262 PHE 0.020 0.001 PHE b 246 TRP 0.017 0.001 TRP A 131 HIS 0.009 0.001 HIS b 201 Details of bonding type rmsd covalent geometry : bond 0.00382 (43504) covalent geometry : angle 0.60215 (59938) hydrogen bonds : bond 0.04385 ( 2106) hydrogen bonds : angle 4.36888 ( 6072) Misc. bond : bond 0.05659 ( 58) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 547 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.9095 (tmm) cc_final: 0.8691 (tmm) REVERT: A 104 GLU cc_start: 0.8788 (tp30) cc_final: 0.8286 (tp30) REVERT: A 290 LEU cc_start: 0.9064 (tp) cc_final: 0.8706 (tp) REVERT: A 304 GLN cc_start: 0.9305 (mp10) cc_final: 0.8643 (mp10) REVERT: A 320 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8887 (mp) REVERT: B 111 SER cc_start: 0.8936 (t) cc_final: 0.8414 (p) REVERT: C 452 GLU cc_start: 0.7920 (mp0) cc_final: 0.7712 (mp0) REVERT: D 11 LYS cc_start: 0.7622 (mmtp) cc_final: 0.7348 (mmtt) REVERT: E 71 ASN cc_start: 0.8568 (t0) cc_final: 0.8167 (t0) REVERT: G 253 GLN cc_start: 0.8543 (tm-30) cc_final: 0.8309 (tm-30) REVERT: G 309 TYR cc_start: 0.8435 (m-10) cc_final: 0.8232 (m-80) REVERT: I 30 ARG cc_start: 0.7234 (ttp-110) cc_final: 0.6654 (ptm-80) REVERT: X 73 LEU cc_start: 0.8823 (mt) cc_final: 0.8103 (pp) REVERT: Z 1 MET cc_start: 0.8191 (mmp) cc_final: 0.7763 (mmm) REVERT: a 37 MET cc_start: 0.9166 (tmm) cc_final: 0.8579 (tmm) REVERT: a 290 LEU cc_start: 0.9047 (tp) cc_final: 0.8664 (tp) REVERT: a 304 GLN cc_start: 0.9293 (mp10) cc_final: 0.8617 (mp10) REVERT: b 111 SER cc_start: 0.8910 (t) cc_final: 0.8344 (p) REVERT: b 334 ASP cc_start: 0.8499 (t0) cc_final: 0.8175 (t0) REVERT: c 452 GLU cc_start: 0.8212 (mp0) cc_final: 0.7801 (mp0) REVERT: d 11 LYS cc_start: 0.7721 (mmmm) cc_final: 0.7411 (mmtt) REVERT: d 45 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8570 (mm) REVERT: d 255 GLN cc_start: 0.8784 (mt0) cc_final: 0.8543 (mt0) REVERT: e 71 ASN cc_start: 0.8777 (t0) cc_final: 0.8298 (t0) REVERT: g 136 MET cc_start: 0.7648 (mtp) cc_final: 0.7432 (mmm) REVERT: g 223 LEU cc_start: 0.8310 (tp) cc_final: 0.7953 (tt) REVERT: g 232 MET cc_start: 0.7718 (mpp) cc_final: 0.6975 (mtm) REVERT: h 50 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7692 (ttt) REVERT: i 30 ARG cc_start: 0.7412 (ttp-110) cc_final: 0.6868 (ptm-80) REVERT: t 18 PHE cc_start: 0.8468 (t80) cc_final: 0.8226 (t80) REVERT: v 5 LEU cc_start: 0.7155 (pt) cc_final: 0.6511 (mp) outliers start: 100 outliers final: 77 residues processed: 599 average time/residue: 0.2201 time to fit residues: 224.5343 Evaluate side-chains 609 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 529 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain G residue 260 TYR Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain K residue 25 LEU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain Z residue 3 SER Chi-restraints excluded: chain a residue 42 LEU Chi-restraints excluded: chain a residue 205 VAL Chi-restraints excluded: chain a residue 291 SER Chi-restraints excluded: chain b residue 13 ILE Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 148 LEU Chi-restraints excluded: chain b residue 246 PHE Chi-restraints excluded: chain b residue 368 VAL Chi-restraints excluded: chain c residue 57 LEU Chi-restraints excluded: chain c residue 371 ASP Chi-restraints excluded: chain c residue 384 MET Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 45 LEU Chi-restraints excluded: chain d residue 213 ILE Chi-restraints excluded: chain d residue 287 VAL Chi-restraints excluded: chain e residue 11 SER Chi-restraints excluded: chain e residue 17 ILE Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain f residue 17 VAL Chi-restraints excluded: chain f residue 39 MET Chi-restraints excluded: chain f residue 41 PHE Chi-restraints excluded: chain f residue 42 ILE Chi-restraints excluded: chain g residue 211 LEU Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain g residue 291 LYS Chi-restraints excluded: chain g residue 314 VAL Chi-restraints excluded: chain h residue 50 MET Chi-restraints excluded: chain h residue 70 SER Chi-restraints excluded: chain h residue 83 THR Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain i residue 17 CYS Chi-restraints excluded: chain k residue 25 LEU Chi-restraints excluded: chain l residue 22 LEU Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain m residue 8 LEU Chi-restraints excluded: chain t residue 14 LEU Chi-restraints excluded: chain z residue 3 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 183 optimal weight: 1.9990 chunk 277 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 137 optimal weight: 0.8980 chunk 298 optimal weight: 9.9990 chunk 315 optimal weight: 0.9990 chunk 254 optimal weight: 8.9990 chunk 221 optimal weight: 0.9990 chunk 296 optimal weight: 4.9990 chunk 236 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 HIS ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN G 189 GLN ** G 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 252 HIS ** b 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 75 GLN g 189 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.135834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.104541 restraints weight = 78694.236| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 3.55 r_work: 0.3139 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.235 43562 Z= 0.124 Angle : 0.576 12.736 59938 Z= 0.266 Chirality : 0.040 0.242 5822 Planarity : 0.004 0.046 7426 Dihedral : 14.869 118.813 8176 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.44 % Allowed : 15.84 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.13), residues: 4310 helix: 1.85 (0.10), residues: 2672 sheet: -0.87 (0.57), residues: 74 loop : -0.01 (0.17), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 64 TYR 0.021 0.001 TYR g 137 PHE 0.033 0.001 PHE M 21 TRP 0.018 0.001 TRP A 131 HIS 0.006 0.001 HIS d 214 Details of bonding type rmsd covalent geometry : bond 0.00277 (43504) covalent geometry : angle 0.57595 (59938) hydrogen bonds : bond 0.04125 ( 2106) hydrogen bonds : angle 4.28301 ( 6072) Misc. bond : bond 0.05359 ( 58) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 568 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.9122 (tmm) cc_final: 0.8759 (tmm) REVERT: A 104 GLU cc_start: 0.8782 (tp30) cc_final: 0.8381 (tp30) REVERT: A 290 LEU cc_start: 0.8998 (tp) cc_final: 0.8671 (tp) REVERT: A 304 GLN cc_start: 0.9302 (mp10) cc_final: 0.8656 (mp10) REVERT: A 320 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8872 (mp) REVERT: B 111 SER cc_start: 0.8884 (t) cc_final: 0.8365 (p) REVERT: C 262 TYR cc_start: 0.8891 (m-80) cc_final: 0.8495 (m-80) REVERT: D 11 LYS cc_start: 0.7574 (mmtp) cc_final: 0.7325 (mmtt) REVERT: D 45 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8648 (mm) REVERT: E 71 ASN cc_start: 0.8564 (t0) cc_final: 0.8198 (t0) REVERT: G 253 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8380 (tm-30) REVERT: I 30 ARG cc_start: 0.7202 (ttp-110) cc_final: 0.6653 (ptm-80) REVERT: V 4 GLU cc_start: 0.8899 (pt0) cc_final: 0.8515 (pp20) REVERT: X 73 LEU cc_start: 0.8817 (mt) cc_final: 0.8094 (pp) REVERT: Z 1 MET cc_start: 0.8227 (mmp) cc_final: 0.7808 (mmm) REVERT: a 37 MET cc_start: 0.9166 (tmm) cc_final: 0.8548 (tmm) REVERT: a 290 LEU cc_start: 0.8972 (tp) cc_final: 0.8591 (tp) REVERT: a 304 GLN cc_start: 0.9292 (mp10) cc_final: 0.8615 (mp10) REVERT: b 111 SER cc_start: 0.8851 (t) cc_final: 0.8299 (p) REVERT: b 334 ASP cc_start: 0.8460 (t0) cc_final: 0.8172 (t0) REVERT: c 55 MET cc_start: 0.8870 (tpp) cc_final: 0.7991 (tpt) REVERT: c 452 GLU cc_start: 0.8173 (mp0) cc_final: 0.7825 (mp0) REVERT: d 11 LYS cc_start: 0.7702 (mmmm) cc_final: 0.7421 (mmtt) REVERT: d 45 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8641 (mm) REVERT: d 255 GLN cc_start: 0.8724 (mt0) cc_final: 0.8486 (mt0) REVERT: e 71 ASN cc_start: 0.8689 (t0) cc_final: 0.8207 (t0) REVERT: g 136 MET cc_start: 0.7632 (mtp) cc_final: 0.7412 (mmm) REVERT: g 223 LEU cc_start: 0.8386 (tp) cc_final: 0.8015 (tt) REVERT: g 232 MET cc_start: 0.7768 (mpp) cc_final: 0.7037 (mtm) REVERT: h 50 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7635 (ttt) REVERT: i 30 ARG cc_start: 0.7355 (ttp-110) cc_final: 0.6836 (ptm-80) REVERT: t 18 PHE cc_start: 0.8447 (t80) cc_final: 0.8146 (t80) REVERT: v 5 LEU cc_start: 0.7042 (pt) cc_final: 0.6462 (mp) outliers start: 87 outliers final: 69 residues processed: 610 average time/residue: 0.2062 time to fit residues: 214.2264 Evaluate side-chains 613 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 540 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain G residue 260 TYR Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain a residue 291 SER Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 148 LEU Chi-restraints excluded: chain b residue 246 PHE Chi-restraints excluded: chain b residue 368 VAL Chi-restraints excluded: chain c residue 57 LEU Chi-restraints excluded: chain c residue 384 MET Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 25 ASP Chi-restraints excluded: chain d residue 45 LEU Chi-restraints excluded: chain d residue 213 ILE Chi-restraints excluded: chain d residue 272 LEU Chi-restraints excluded: chain d residue 287 VAL Chi-restraints excluded: chain e residue 11 SER Chi-restraints excluded: chain e residue 17 ILE Chi-restraints excluded: chain f residue 17 VAL Chi-restraints excluded: chain f residue 39 MET Chi-restraints excluded: chain f residue 41 PHE Chi-restraints excluded: chain f residue 42 ILE Chi-restraints excluded: chain g residue 211 LEU Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain g residue 291 LYS Chi-restraints excluded: chain g residue 314 VAL Chi-restraints excluded: chain h residue 50 MET Chi-restraints excluded: chain h residue 70 SER Chi-restraints excluded: chain h residue 83 THR Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain i residue 17 CYS Chi-restraints excluded: chain k residue 25 LEU Chi-restraints excluded: chain l residue 22 LEU Chi-restraints excluded: chain m residue 8 LEU Chi-restraints excluded: chain t residue 5 VAL Chi-restraints excluded: chain t residue 14 LEU Chi-restraints excluded: chain x residue 86 ILE Chi-restraints excluded: chain z residue 3 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 165 optimal weight: 10.0000 chunk 201 optimal weight: 30.0000 chunk 228 optimal weight: 0.4980 chunk 121 optimal weight: 1.9990 chunk 167 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 chunk 3 optimal weight: 0.8980 chunk 282 optimal weight: 10.0000 chunk 255 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 143 optimal weight: 7.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 HIS A 261 GLN ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 GLN E 75 GLN G 189 GLN G 220 GLN ** G 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 252 HIS a 261 GLN ** b 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 75 GLN g 189 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.126501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.096783 restraints weight = 79328.068| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.85 r_work: 0.3030 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.282 43562 Z= 0.247 Angle : 0.669 14.894 59938 Z= 0.309 Chirality : 0.043 0.291 5822 Planarity : 0.005 0.046 7426 Dihedral : 15.142 118.851 8176 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.03 % Allowed : 16.24 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.13), residues: 4310 helix: 1.67 (0.10), residues: 2672 sheet: -1.12 (0.56), residues: 74 loop : -0.18 (0.17), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 472 TYR 0.025 0.002 TYR a 254 PHE 0.038 0.002 PHE m 21 TRP 0.013 0.001 TRP A 131 HIS 0.008 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00577 (43504) covalent geometry : angle 0.66862 (59938) hydrogen bonds : bond 0.04764 ( 2106) hydrogen bonds : angle 4.50821 ( 6072) Misc. bond : bond 0.05904 ( 58) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 546 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLU cc_start: 0.8746 (tp30) cc_final: 0.8243 (tp30) REVERT: A 189 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8804 (mm-30) REVERT: A 290 LEU cc_start: 0.9094 (tp) cc_final: 0.8751 (tp) REVERT: A 304 GLN cc_start: 0.9314 (mp10) cc_final: 0.8640 (mp10) REVERT: A 320 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8840 (mp) REVERT: B 111 SER cc_start: 0.8964 (t) cc_final: 0.8548 (p) REVERT: B 334 ASP cc_start: 0.8502 (t0) cc_final: 0.8056 (t0) REVERT: D 11 LYS cc_start: 0.7619 (mmtp) cc_final: 0.7369 (mmtt) REVERT: D 45 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8731 (mm) REVERT: E 71 ASN cc_start: 0.8471 (t0) cc_final: 0.8094 (t0) REVERT: G 206 MET cc_start: 0.8246 (ttt) cc_final: 0.7967 (ttt) REVERT: G 291 LYS cc_start: 0.8581 (tmtt) cc_final: 0.8012 (tppt) REVERT: I 30 ARG cc_start: 0.7399 (ttp-110) cc_final: 0.6916 (ptm-80) REVERT: Z 1 MET cc_start: 0.8251 (mmp) cc_final: 0.7870 (mmm) REVERT: a 37 MET cc_start: 0.9171 (tmm) cc_final: 0.8498 (tmm) REVERT: a 290 LEU cc_start: 0.9097 (tp) cc_final: 0.8731 (tp) REVERT: a 304 GLN cc_start: 0.9303 (mp10) cc_final: 0.8635 (mp10) REVERT: b 111 SER cc_start: 0.8965 (t) cc_final: 0.8574 (p) REVERT: b 179 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8219 (mp10) REVERT: b 334 ASP cc_start: 0.8526 (t0) cc_final: 0.8228 (t0) REVERT: c 452 GLU cc_start: 0.8214 (mp0) cc_final: 0.7866 (mp0) REVERT: d 11 LYS cc_start: 0.7774 (mmmm) cc_final: 0.7493 (mmtt) REVERT: d 45 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.8737 (mm) REVERT: d 255 GLN cc_start: 0.8870 (mt0) cc_final: 0.8580 (mt0) REVERT: e 71 ASN cc_start: 0.8639 (t0) cc_final: 0.8082 (t0) REVERT: g 136 MET cc_start: 0.7696 (mtp) cc_final: 0.7396 (mmm) REVERT: g 223 LEU cc_start: 0.8431 (tp) cc_final: 0.8098 (tt) REVERT: g 232 MET cc_start: 0.7718 (mpp) cc_final: 0.7200 (mmt) REVERT: h 46 THR cc_start: 0.8672 (p) cc_final: 0.8432 (p) REVERT: i 30 ARG cc_start: 0.7538 (ttp-110) cc_final: 0.6891 (ptt90) REVERT: t 18 PHE cc_start: 0.8430 (t80) cc_final: 0.8093 (t80) outliers start: 108 outliers final: 88 residues processed: 610 average time/residue: 0.2282 time to fit residues: 238.6783 Evaluate side-chains 622 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 530 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 371 ASP Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 220 GLN Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain G residue 258 CYS Chi-restraints excluded: chain G residue 260 TYR Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain V residue 5 LEU Chi-restraints excluded: chain Z residue 3 SER Chi-restraints excluded: chain a residue 205 VAL Chi-restraints excluded: chain a residue 291 SER Chi-restraints excluded: chain b residue 13 ILE Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 179 GLN Chi-restraints excluded: chain b residue 246 PHE Chi-restraints excluded: chain b residue 368 VAL Chi-restraints excluded: chain c residue 74 LEU Chi-restraints excluded: chain c residue 371 ASP Chi-restraints excluded: chain c residue 384 MET Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 25 ASP Chi-restraints excluded: chain d residue 45 LEU Chi-restraints excluded: chain d residue 213 ILE Chi-restraints excluded: chain d residue 287 VAL Chi-restraints excluded: chain e residue 11 SER Chi-restraints excluded: chain e residue 17 ILE Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain f residue 17 VAL Chi-restraints excluded: chain f residue 39 MET Chi-restraints excluded: chain f residue 41 PHE Chi-restraints excluded: chain f residue 42 ILE Chi-restraints excluded: chain g residue 211 LEU Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain g residue 256 ILE Chi-restraints excluded: chain g residue 291 LYS Chi-restraints excluded: chain g residue 314 VAL Chi-restraints excluded: chain h residue 70 SER Chi-restraints excluded: chain h residue 83 THR Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 17 CYS Chi-restraints excluded: chain k residue 25 LEU Chi-restraints excluded: chain l residue 22 LEU Chi-restraints excluded: chain l residue 27 VAL Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain m residue 8 LEU Chi-restraints excluded: chain t residue 5 VAL Chi-restraints excluded: chain t residue 14 LEU Chi-restraints excluded: chain x residue 86 ILE Chi-restraints excluded: chain z residue 3 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 247 optimal weight: 5.9990 chunk 400 optimal weight: 7.9990 chunk 232 optimal weight: 0.6980 chunk 67 optimal weight: 0.0980 chunk 130 optimal weight: 2.9990 chunk 384 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 370 optimal weight: 0.0050 chunk 63 optimal weight: 10.0000 chunk 228 optimal weight: 0.8980 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 HIS ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN G 189 GLN G 220 GLN a 252 HIS ** b 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 75 GLN g 189 GLN g 220 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.130510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.100696 restraints weight = 78867.488| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.82 r_work: 0.3131 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.241 43562 Z= 0.122 Angle : 0.603 15.611 59938 Z= 0.279 Chirality : 0.041 0.227 5822 Planarity : 0.004 0.047 7426 Dihedral : 14.860 118.830 8176 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.44 % Allowed : 16.80 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.13), residues: 4310 helix: 1.79 (0.10), residues: 2674 sheet: -0.53 (0.61), residues: 64 loop : -0.03 (0.17), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 434 TYR 0.022 0.001 TYR a 254 PHE 0.027 0.001 PHE B 215 TRP 0.019 0.001 TRP A 131 HIS 0.007 0.001 HIS D 268 Details of bonding type rmsd covalent geometry : bond 0.00269 (43504) covalent geometry : angle 0.60321 (59938) hydrogen bonds : bond 0.04205 ( 2106) hydrogen bonds : angle 4.32135 ( 6072) Misc. bond : bond 0.05491 ( 58) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 561 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLU cc_start: 0.8709 (tp30) cc_final: 0.8274 (tp30) REVERT: A 189 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8793 (mm-30) REVERT: A 290 LEU cc_start: 0.8974 (tp) cc_final: 0.8663 (tp) REVERT: A 304 GLN cc_start: 0.9318 (mp10) cc_final: 0.8653 (mp10) REVERT: A 320 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8776 (mp) REVERT: B 111 SER cc_start: 0.8857 (t) cc_final: 0.8337 (p) REVERT: B 179 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8107 (mp10) REVERT: B 283 GLU cc_start: 0.8433 (tp30) cc_final: 0.8146 (tp30) REVERT: C 262 TYR cc_start: 0.8897 (m-80) cc_final: 0.8479 (m-80) REVERT: D 11 LYS cc_start: 0.7594 (mmtp) cc_final: 0.7344 (mmtt) REVERT: D 45 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8677 (mm) REVERT: E 71 ASN cc_start: 0.8469 (t0) cc_final: 0.8123 (t0) REVERT: G 279 SER cc_start: 0.8937 (m) cc_final: 0.8492 (p) REVERT: G 291 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.7992 (tppt) REVERT: I 30 ARG cc_start: 0.7319 (ttp-110) cc_final: 0.6854 (ptm-80) REVERT: Z 1 MET cc_start: 0.8266 (mmp) cc_final: 0.7915 (mmm) REVERT: a 37 MET cc_start: 0.9148 (tmm) cc_final: 0.8468 (tmm) REVERT: a 290 LEU cc_start: 0.8988 (tp) cc_final: 0.8631 (tp) REVERT: a 304 GLN cc_start: 0.9307 (mp10) cc_final: 0.8606 (mp10) REVERT: b 111 SER cc_start: 0.8887 (t) cc_final: 0.8370 (p) REVERT: b 179 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8142 (mp10) REVERT: b 334 ASP cc_start: 0.8514 (t0) cc_final: 0.8225 (t0) REVERT: c 55 MET cc_start: 0.8849 (tpp) cc_final: 0.7974 (tpt) REVERT: c 262 TYR cc_start: 0.8911 (m-80) cc_final: 0.8612 (m-80) REVERT: c 452 GLU cc_start: 0.8183 (mp0) cc_final: 0.7844 (mp0) REVERT: d 11 LYS cc_start: 0.7740 (mmmm) cc_final: 0.7474 (mmtt) REVERT: d 45 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8572 (mm) REVERT: d 255 GLN cc_start: 0.8802 (mt0) cc_final: 0.8541 (mt0) REVERT: e 71 ASN cc_start: 0.8545 (t0) cc_final: 0.8051 (t0) REVERT: g 136 MET cc_start: 0.7670 (mtp) cc_final: 0.7456 (mmm) REVERT: g 223 LEU cc_start: 0.8497 (tp) cc_final: 0.8193 (tt) REVERT: g 232 MET cc_start: 0.7783 (mpp) cc_final: 0.7084 (mtm) REVERT: i 30 ARG cc_start: 0.7325 (ttp-110) cc_final: 0.6807 (ptm-80) REVERT: t 18 PHE cc_start: 0.8425 (t80) cc_final: 0.8148 (t80) REVERT: v 5 LEU cc_start: 0.7043 (pt) cc_final: 0.6456 (mp) outliers start: 87 outliers final: 75 residues processed: 606 average time/residue: 0.2478 time to fit residues: 256.0063 Evaluate side-chains 621 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 540 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 179 GLN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 220 GLN Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain G residue 258 CYS Chi-restraints excluded: chain G residue 260 TYR Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 291 LYS Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain V residue 5 LEU Chi-restraints excluded: chain Z residue 3 SER Chi-restraints excluded: chain a residue 190 HIS Chi-restraints excluded: chain a residue 291 SER Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 148 LEU Chi-restraints excluded: chain b residue 179 GLN Chi-restraints excluded: chain b residue 246 PHE Chi-restraints excluded: chain b residue 368 VAL Chi-restraints excluded: chain c residue 57 LEU Chi-restraints excluded: chain c residue 74 LEU Chi-restraints excluded: chain c residue 384 MET Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 25 ASP Chi-restraints excluded: chain d residue 45 LEU Chi-restraints excluded: chain d residue 213 ILE Chi-restraints excluded: chain d residue 272 LEU Chi-restraints excluded: chain d residue 287 VAL Chi-restraints excluded: chain e residue 17 ILE Chi-restraints excluded: chain f residue 17 VAL Chi-restraints excluded: chain f residue 39 MET Chi-restraints excluded: chain f residue 41 PHE Chi-restraints excluded: chain f residue 42 ILE Chi-restraints excluded: chain g residue 211 LEU Chi-restraints excluded: chain g residue 220 GLN Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain g residue 291 LYS Chi-restraints excluded: chain g residue 314 VAL Chi-restraints excluded: chain h residue 70 SER Chi-restraints excluded: chain h residue 83 THR Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain i residue 17 CYS Chi-restraints excluded: chain k residue 25 LEU Chi-restraints excluded: chain l residue 22 LEU Chi-restraints excluded: chain m residue 8 LEU Chi-restraints excluded: chain t residue 5 VAL Chi-restraints excluded: chain x residue 86 ILE Chi-restraints excluded: chain z residue 3 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 375 optimal weight: 9.9990 chunk 378 optimal weight: 6.9990 chunk 178 optimal weight: 9.9990 chunk 295 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 345 optimal weight: 3.9990 chunk 417 optimal weight: 5.9990 chunk 260 optimal weight: 2.9990 chunk 327 optimal weight: 0.0870 overall best weight: 2.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 HIS A 261 GLN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN G 189 GLN G 220 GLN ** G 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 252 HIS ** b 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 75 GLN g 189 GLN g 220 GLN ** g 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 303 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.128463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.098915 restraints weight = 78977.026| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.86 r_work: 0.3069 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.254 43562 Z= 0.178 Angle : 0.631 14.460 59938 Z= 0.293 Chirality : 0.042 0.268 5822 Planarity : 0.004 0.046 7426 Dihedral : 14.843 118.838 8176 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.39 % Allowed : 17.05 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.13), residues: 4310 helix: 1.77 (0.10), residues: 2676 sheet: -1.01 (0.56), residues: 74 loop : -0.05 (0.17), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 472 TYR 0.019 0.001 TYR a 254 PHE 0.028 0.001 PHE B 215 TRP 0.016 0.001 TRP A 131 HIS 0.007 0.001 HIS d 214 Details of bonding type rmsd covalent geometry : bond 0.00416 (43504) covalent geometry : angle 0.63062 (59938) hydrogen bonds : bond 0.04407 ( 2106) hydrogen bonds : angle 4.39291 ( 6072) Misc. bond : bond 0.05497 ( 58) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8620 Ramachandran restraints generated. 4310 Oldfield, 0 Emsley, 4310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 537 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLU cc_start: 0.8714 (tp30) cc_final: 0.8236 (tp30) REVERT: A 261 GLN cc_start: 0.3540 (OUTLIER) cc_final: 0.3146 (tp-100) REVERT: A 290 LEU cc_start: 0.9063 (tp) cc_final: 0.8728 (tp) REVERT: A 304 GLN cc_start: 0.9329 (mp10) cc_final: 0.8661 (mp10) REVERT: A 320 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8811 (mp) REVERT: B 111 SER cc_start: 0.8917 (t) cc_final: 0.8408 (p) REVERT: B 179 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8146 (mp10) REVERT: C 262 TYR cc_start: 0.8937 (m-80) cc_final: 0.8461 (m-80) REVERT: D 11 LYS cc_start: 0.7585 (mmtp) cc_final: 0.7344 (mmtt) REVERT: D 45 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8686 (mm) REVERT: E 71 ASN cc_start: 0.8490 (t0) cc_final: 0.8119 (t0) REVERT: G 263 LEU cc_start: 0.8162 (tp) cc_final: 0.7915 (tt) REVERT: G 291 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8014 (tppt) REVERT: I 30 ARG cc_start: 0.7380 (ttp-110) cc_final: 0.6871 (ptm-80) REVERT: Z 1 MET cc_start: 0.8365 (mmp) cc_final: 0.8071 (mmm) REVERT: a 37 MET cc_start: 0.9163 (tmm) cc_final: 0.8482 (tmm) REVERT: a 290 LEU cc_start: 0.9037 (tp) cc_final: 0.8673 (tp) REVERT: a 304 GLN cc_start: 0.9320 (mp10) cc_final: 0.8614 (mp10) REVERT: b 111 SER cc_start: 0.8943 (t) cc_final: 0.8514 (p) REVERT: b 179 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8149 (mp10) REVERT: b 334 ASP cc_start: 0.8592 (t0) cc_final: 0.8279 (t0) REVERT: c 262 TYR cc_start: 0.8955 (m-80) cc_final: 0.8623 (m-80) REVERT: c 452 GLU cc_start: 0.8217 (mp0) cc_final: 0.7820 (mp0) REVERT: d 11 LYS cc_start: 0.7735 (mmmm) cc_final: 0.7457 (mmtt) REVERT: d 45 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8691 (mm) REVERT: d 255 GLN cc_start: 0.8826 (mt0) cc_final: 0.8551 (mt0) REVERT: g 136 MET cc_start: 0.7685 (mtp) cc_final: 0.7412 (mmm) REVERT: g 223 LEU cc_start: 0.8401 (tp) cc_final: 0.8198 (tt) REVERT: g 232 MET cc_start: 0.7782 (mpp) cc_final: 0.7083 (mtm) REVERT: i 30 ARG cc_start: 0.7384 (ttp-110) cc_final: 0.6704 (ptt90) REVERT: t 18 PHE cc_start: 0.8428 (t80) cc_final: 0.8125 (t80) REVERT: v 5 LEU cc_start: 0.7046 (pt) cc_final: 0.6469 (mp) outliers start: 85 outliers final: 75 residues processed: 585 average time/residue: 0.2178 time to fit residues: 217.3588 Evaluate side-chains 614 residues out of total 3560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 532 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 MET Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 332 HIS Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 179 GLN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 246 PHE Chi-restraints excluded: chain B residue 368 VAL Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 384 MET Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain F residue 17 VAL Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain G residue 211 LEU Chi-restraints excluded: chain G residue 220 GLN Chi-restraints excluded: chain G residue 223 LEU Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain G residue 258 CYS Chi-restraints excluded: chain G residue 260 TYR Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 291 LYS Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain I residue 23 PHE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain V residue 5 LEU Chi-restraints excluded: chain Z residue 3 SER Chi-restraints excluded: chain a residue 127 MET Chi-restraints excluded: chain a residue 291 SER Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 148 LEU Chi-restraints excluded: chain b residue 179 GLN Chi-restraints excluded: chain b residue 246 PHE Chi-restraints excluded: chain b residue 368 VAL Chi-restraints excluded: chain c residue 57 LEU Chi-restraints excluded: chain c residue 74 LEU Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 25 ASP Chi-restraints excluded: chain d residue 45 LEU Chi-restraints excluded: chain d residue 213 ILE Chi-restraints excluded: chain d residue 272 LEU Chi-restraints excluded: chain d residue 287 VAL Chi-restraints excluded: chain e residue 17 ILE Chi-restraints excluded: chain f residue 17 VAL Chi-restraints excluded: chain f residue 39 MET Chi-restraints excluded: chain f residue 41 PHE Chi-restraints excluded: chain f residue 42 ILE Chi-restraints excluded: chain g residue 211 LEU Chi-restraints excluded: chain g residue 220 GLN Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain g residue 256 ILE Chi-restraints excluded: chain g residue 291 LYS Chi-restraints excluded: chain g residue 314 VAL Chi-restraints excluded: chain h residue 70 SER Chi-restraints excluded: chain h residue 83 THR Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain k residue 25 LEU Chi-restraints excluded: chain l residue 22 LEU Chi-restraints excluded: chain m residue 8 LEU Chi-restraints excluded: chain t residue 5 VAL Chi-restraints excluded: chain x residue 86 ILE Chi-restraints excluded: chain z residue 3 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 12 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 170 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 397 optimal weight: 4.9990 chunk 243 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 233 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 HIS A 261 GLN ** B 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN G 189 GLN G 220 GLN ** G 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 252 HIS ** b 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 189 GLN g 220 GLN ** g 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.127790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.098656 restraints weight = 79263.527| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.97 r_work: 0.3071 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.269 43562 Z= 0.198 Angle : 0.644 14.605 59938 Z= 0.298 Chirality : 0.042 0.266 5822 Planarity : 0.004 0.046 7426 Dihedral : 14.897 118.946 8176 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.67 % Allowed : 16.74 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.13), residues: 4310 helix: 1.73 (0.10), residues: 2674 sheet: -1.04 (0.56), residues: 74 loop : -0.10 (0.17), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 472 TYR 0.020 0.001 TYR A 262 PHE 0.023 0.001 PHE B 215 TRP 0.015 0.001 TRP A 131 HIS 0.007 0.001 HIS d 214 Details of bonding type rmsd covalent geometry : bond 0.00463 (43504) covalent geometry : angle 0.64365 (59938) hydrogen bonds : bond 0.04483 ( 2106) hydrogen bonds : angle 4.42964 ( 6072) Misc. bond : bond 0.05772 ( 58) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9393.85 seconds wall clock time: 161 minutes 39.90 seconds (9699.90 seconds total)