Starting phenix.real_space_refine on Thu Mar 5 00:05:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qko_14048/03_2026/7qko_14048.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qko_14048/03_2026/7qko_14048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7qko_14048/03_2026/7qko_14048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qko_14048/03_2026/7qko_14048.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qko_14048/03_2026/7qko_14048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qko_14048/03_2026/7qko_14048.map" } resolution = 2.9 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= 0.000 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 85 5.16 5 C 11150 2.51 5 N 2615 2.21 5 O 3184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17042 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3210 Classifications: {'peptide': 396} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 375} Chain breaks: 1 Chain: "B" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3218 Classifications: {'peptide': 396} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 373} Chain breaks: 1 Chain: "C" Number of atoms: 3408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3408 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 392} Chain breaks: 1 Chain: "D" Number of atoms: 3089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3089 Classifications: {'peptide': 380} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 360} Chain breaks: 1 Chain: "E" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3278 Classifications: {'peptide': 404} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 382} Chain breaks: 1 Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "L" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 142 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "D" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 73 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Time building chain proxies: 3.80, per 1000 atoms: 0.22 Number of scatterers: 17042 At special positions: 0 Unit cell: (103.05, 106.485, 172.895, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 P 8 15.00 O 3184 8.00 N 2615 7.00 C 11150 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 144 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN I 4 " - " MAN I 5 " ALPHA1-3 " BMA F 3 " - " MAN F 7 " " MAN F 4 " - " MAN F 5 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 7 " " MAN K 4 " - " MAN K 5 " " BMA L 3 " - " MAN L 7 " " MAN L 4 " - " MAN L 5 " ALPHA1-6 " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 6 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 6 " " BMA K 3 " - " MAN K 4 " " MAN K 4 " - " MAN K 6 " " BMA L 3 " - " MAN L 4 " " MAN L 4 " - " MAN L 6 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG F 1 " - " ASN A 141 " " NAG G 1 " - " ASN B 141 " " NAG H 1 " - " ASN C 143 " " NAG I 1 " - " ASN C 70 " " NAG J 1 " - " ASN C 208 " " NAG K 1 " - " ASN D 141 " " NAG L 1 " - " ASN E 141 " Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 687.4 milliseconds 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3854 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 20 sheets defined 42.3% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 63 through 66 removed outlier: 3.588A pdb=" N ARG A 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 66' Processing helix chain 'A' and resid 68 through 73 removed outlier: 4.125A pdb=" N GLY A 73 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 211 through 231 removed outlier: 4.302A pdb=" N ILE A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Proline residue: A 221 - end of helix removed outlier: 3.793A pdb=" N GLY A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A 231 " --> pdb=" O PHE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 235 Processing helix chain 'A' and resid 241 through 264 Processing helix chain 'A' and resid 272 through 300 Processing helix chain 'A' and resid 309 through 318 removed outlier: 4.181A pdb=" N ASP A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 324 Processing helix chain 'A' and resid 371 through 434 removed outlier: 4.087A pdb=" N ILE A 376 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLY A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ARG A 429 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU A 430 " --> pdb=" O PHE A 426 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 12 removed outlier: 3.889A pdb=" N THR B 6 " --> pdb=" O VAL B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 72 Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 217 through 238 removed outlier: 4.940A pdb=" N ILE B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Proline residue: B 227 - end of helix Processing helix chain 'B' and resid 239 through 241 No H-bonds generated for 'chain 'B' and resid 239 through 241' Processing helix chain 'B' and resid 242 through 246 Processing helix chain 'B' and resid 247 through 267 removed outlier: 4.094A pdb=" N SER B 254 " --> pdb=" O SER B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 306 Processing helix chain 'B' and resid 315 through 325 removed outlier: 3.888A pdb=" N ILE B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 331 removed outlier: 3.836A pdb=" N PHE B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 461 removed outlier: 3.579A pdb=" N ASN B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 13 removed outlier: 4.276A pdb=" N ARG C 6 " --> pdb=" O ASN C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 232 through 244 removed outlier: 3.567A pdb=" N CYS C 236 " --> pdb=" O PHE C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 248 Processing helix chain 'C' and resid 255 through 276 removed outlier: 3.941A pdb=" N ALA C 260 " --> pdb=" O LYS C 256 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 314 Processing helix chain 'C' and resid 323 through 338 Proline residue: C 335 - end of helix Processing helix chain 'C' and resid 423 through 478 Proline residue: C 463 - end of helix Processing helix chain 'D' and resid 2 through 12 Processing helix chain 'D' and resid 68 through 73 removed outlier: 4.049A pdb=" N GLY D 73 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'D' and resid 211 through 230 removed outlier: 4.960A pdb=" N ILE D 220 " --> pdb=" O VAL D 216 " (cutoff:3.500A) Proline residue: D 221 - end of helix removed outlier: 4.078A pdb=" N GLY D 230 " --> pdb=" O SER D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 241 through 264 Processing helix chain 'D' and resid 272 through 300 Processing helix chain 'D' and resid 309 through 324 Proline residue: D 321 - end of helix Processing helix chain 'D' and resid 382 through 431 removed outlier: 3.710A pdb=" N PHE D 426 " --> pdb=" O THR D 422 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY D 428 " --> pdb=" O SER D 424 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ARG D 429 " --> pdb=" O VAL D 425 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE D 431 " --> pdb=" O ALA D 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 12 Processing helix chain 'E' and resid 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 131 through 135 removed outlier: 4.317A pdb=" N TYR E 134 " --> pdb=" O ALA E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 226 Processing helix chain 'E' and resid 226 through 235 Processing helix chain 'E' and resid 236 through 242 removed outlier: 3.588A pdb=" N VAL E 240 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR E 241 " --> pdb=" O VAL E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 272 removed outlier: 3.767A pdb=" N LYS E 272 " --> pdb=" O LEU E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 308 Processing helix chain 'E' and resid 318 through 328 removed outlier: 3.633A pdb=" N LYS E 322 " --> pdb=" O SER E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 470 removed outlier: 3.590A pdb=" N ASN E 439 " --> pdb=" O SER E 435 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TRP E 440 " --> pdb=" O GLU E 436 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY E 470 " --> pdb=" O ILE E 466 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 81 removed outlier: 4.421A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 81 removed outlier: 4.421A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASN A 53 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LEU A 40 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N ARG A 55 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE A 38 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ARG A 57 " --> pdb=" O GLN A 36 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N GLN A 36 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLN A 59 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLY A 34 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N ILE A 61 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 9.805A pdb=" N THR A 32 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 4.452A pdb=" N ILE A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 199 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP A 180 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLN A 208 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N MET A 178 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 77 through 80 removed outlier: 3.597A pdb=" N GLN B 111 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA B 115 " --> pdb=" O GLN B 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 77 through 80 removed outlier: 3.597A pdb=" N GLN B 111 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA B 115 " --> pdb=" O GLN B 111 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLU B 49 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU B 43 " --> pdb=" O GLU B 49 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THR B 51 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N PHE B 55 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LEU B 37 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASN B 57 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU B 35 " --> pdb=" O ASN B 57 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ALA B 59 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL B 33 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N THR B 61 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N VAL B 31 " --> pdb=" O THR B 61 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.805A pdb=" N ILE B 212 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA8, first strand: chain 'C' and resid 80 through 82 Processing sheet with id=AA9, first strand: chain 'C' and resid 80 through 82 removed outlier: 6.816A pdb=" N THR C 51 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER C 44 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N THR C 53 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LEU C 42 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ASN C 55 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR C 63 " --> pdb=" O ASN C 32 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN C 32 " --> pdb=" O TYR C 63 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 92 through 94 removed outlier: 4.945A pdb=" N ALA C 150 " --> pdb=" O GLN C 213 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLN C 213 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 92 through 94 removed outlier: 4.945A pdb=" N ALA C 150 " --> pdb=" O GLN C 213 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLN C 213 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 164 through 166 Processing sheet with id=AB4, first strand: chain 'D' and resid 77 through 80 removed outlier: 4.313A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLY D 114 " --> pdb=" O ASP D 62 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 77 through 80 removed outlier: 4.313A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLY D 114 " --> pdb=" O ASP D 62 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE D 49 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL D 43 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLU D 51 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG D 55 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LEU D 37 " --> pdb=" O ARG D 55 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ARG D 57 " --> pdb=" O LEU D 35 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LEU D 35 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N GLN D 59 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL D 33 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N ILE D 61 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE D 31 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 10.829A pdb=" N VAL D 63 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 12.961A pdb=" N VAL D 29 " --> pdb=" O VAL D 63 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 90 through 92 removed outlier: 4.694A pdb=" N ILE D 148 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU D 199 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N TYR D 198 " --> pdb=" O TRP D 187 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TRP D 187 " --> pdb=" O TYR D 198 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASP D 200 " --> pdb=" O LYS D 185 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS D 185 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR D 202 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLY D 183 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N HIS D 204 " --> pdb=" O TYR D 181 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TYR D 181 " --> pdb=" O HIS D 204 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE D 206 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 115 through 118 Processing sheet with id=AB8, first strand: chain 'E' and resid 115 through 118 removed outlier: 6.741A pdb=" N ASN E 53 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU E 40 " --> pdb=" O ASN E 53 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N TRP E 55 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR E 38 " --> pdb=" O TRP E 55 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N GLU E 57 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N THR E 36 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N GLN E 59 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LYS E 34 " --> pdb=" O GLN E 59 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N ASN E 61 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 9.961A pdb=" N THR E 32 " --> pdb=" O ASN E 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 77 through 81 Processing sheet with id=AC1, first strand: chain 'E' and resid 90 through 92 removed outlier: 3.828A pdb=" N CYS E 142 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE E 214 " --> pdb=" O ARG E 187 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 90 through 92 removed outlier: 3.828A pdb=" N CYS E 142 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) 884 hydrogen bonds defined for protein. 2547 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.89 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2610 1.31 - 1.43: 4824 1.43 - 1.56: 9872 1.56 - 1.68: 27 1.68 - 1.81: 138 Bond restraints: 17471 Sorted by residual: bond pdb=" C31 POV C 601 " pdb=" O31 POV C 601 " ideal model delta sigma weight residual 1.327 1.430 -0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C31 POV A 502 " pdb=" O31 POV A 502 " ideal model delta sigma weight residual 1.327 1.430 -0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C31 POV C 603 " pdb=" O31 POV C 603 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" C31 POV C 602 " pdb=" O31 POV C 602 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C31 POV A 501 " pdb=" O31 POV A 501 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.33e+01 ... (remaining 17466 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 23275 2.36 - 4.73: 346 4.73 - 7.09: 103 7.09 - 9.46: 38 9.46 - 11.82: 20 Bond angle restraints: 23782 Sorted by residual: angle pdb=" O13 POV C 602 " pdb=" P POV C 602 " pdb=" O14 POV C 602 " ideal model delta sigma weight residual 121.11 109.29 11.82 3.00e+00 1.11e-01 1.55e+01 angle pdb=" O13 POV D 501 " pdb=" P POV D 501 " pdb=" O14 POV D 501 " ideal model delta sigma weight residual 121.11 109.31 11.80 3.00e+00 1.11e-01 1.55e+01 angle pdb=" O11 POV D 501 " pdb=" P POV D 501 " pdb=" O12 POV D 501 " ideal model delta sigma weight residual 97.67 109.44 -11.77 3.00e+00 1.11e-01 1.54e+01 angle pdb=" O13 POV A 501 " pdb=" P POV A 501 " pdb=" O14 POV A 501 " ideal model delta sigma weight residual 121.11 109.43 11.68 3.00e+00 1.11e-01 1.52e+01 angle pdb=" O11 POV A 501 " pdb=" P POV A 501 " pdb=" O12 POV A 501 " ideal model delta sigma weight residual 97.67 109.32 -11.65 3.00e+00 1.11e-01 1.51e+01 ... (remaining 23777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.27: 10456 31.27 - 62.53: 334 62.53 - 93.80: 77 93.80 - 125.07: 54 125.07 - 156.34: 7 Dihedral angle restraints: 10928 sinusoidal: 5007 harmonic: 5921 Sorted by residual: dihedral pdb=" C3 POV C 603 " pdb=" C31 POV C 603 " pdb=" O31 POV C 603 " pdb=" C32 POV C 603 " ideal model delta sinusoidal sigma weight residual 172.61 16.27 156.34 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" C3 POV A 501 " pdb=" C31 POV A 501 " pdb=" O31 POV A 501 " pdb=" C32 POV A 501 " ideal model delta sinusoidal sigma weight residual 172.61 -40.50 -146.89 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" C3 POV B 501 " pdb=" C31 POV B 501 " pdb=" O31 POV B 501 " pdb=" C32 POV B 501 " ideal model delta sinusoidal sigma weight residual 172.61 -41.14 -146.25 1 3.00e+01 1.11e-03 1.95e+01 ... (remaining 10925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2387 0.060 - 0.119: 400 0.119 - 0.179: 46 0.179 - 0.239: 4 0.239 - 0.299: 6 Chirality restraints: 2843 Sorted by residual: chirality pdb=" C5 BMA L 3 " pdb=" C4 BMA L 3 " pdb=" C6 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 2840 not shown) Planarity restraints: 2863 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 119 " 0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO E 120 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO E 120 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 120 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET E 291 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C MET E 291 " 0.029 2.00e-02 2.50e+03 pdb=" O MET E 291 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE E 292 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 316 " 0.007 2.00e-02 2.50e+03 1.50e-02 2.26e+00 pdb=" C PHE D 316 " -0.026 2.00e-02 2.50e+03 pdb=" O PHE D 316 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE D 317 " 0.009 2.00e-02 2.50e+03 ... (remaining 2860 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3094 2.77 - 3.31: 16462 3.31 - 3.84: 28638 3.84 - 4.37: 33511 4.37 - 4.90: 57926 Nonbonded interactions: 139631 Sorted by model distance: nonbonded pdb=" OD1 ASN E 68 " pdb=" OG SER E 70 " model vdw 2.242 3.040 nonbonded pdb=" O LEU E 92 " pdb=" ND2 ASN E 95 " model vdw 2.254 3.120 nonbonded pdb=" O ILE A 315 " pdb=" OG1 THR A 319 " model vdw 2.257 3.040 nonbonded pdb=" OD1 ASN B 107 " pdb=" ND2 ASN C 152 " model vdw 2.268 3.120 nonbonded pdb=" O GLY A 153 " pdb=" OG1 THR A 154 " model vdw 2.278 3.040 ... (remaining 139626 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 1 through 328 or resid 381 through 432 or (resid 501 and ( \ name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or \ name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 \ or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name \ C33 or name C34 or name C35 or name C36 or name O11 or name O12 or name O13 or n \ ame O14 or name O21 or name O22 or name O31 or name O32 or name P )) or (resid 5 \ 02 and (name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or n \ ame C26 or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name O21 or name O22 or name O \ 31 or name O32)))) selection = (chain 'D' and (resid 1 through 501 or (resid 502 and (name C2 or name C21 or na \ me C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 o \ r name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name C3 \ 5 or name C36 or name O21 or name O22 or name O31 or name O32)))) } ncs_group { reference = (chain 'F' and (resid 2 or resid 5 through 7)) selection = (chain 'I' and (resid 1 or resid 4 through 6)) selection = (chain 'K' and (resid 2 or resid 5 through 7)) selection = (chain 'L' and (resid 2 or resid 5 through 7)) } ncs_group { reference = chain 'G' selection = chain 'H' } 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=0.45 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.840 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 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 : 0.006 0.103 17516 Z= 0.311 Angle : 0.853 11.825 23912 Z= 0.350 Chirality : 0.047 0.299 2843 Planarity : 0.004 0.045 2856 Dihedral : 18.352 156.336 7059 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.25 % Allowed : 5.42 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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 are not related in a simple way. whole: 0.18 (0.19), residues: 1976 helix: 1.85 (0.19), residues: 745 sheet: -0.76 (0.25), residues: 408 loop : -1.01 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 81 TYR 0.008 0.001 TYR C 439 PHE 0.010 0.001 PHE A 284 TRP 0.012 0.001 TRP D 187 HIS 0.004 0.001 HIS E 471 Details of bonding type rmsd covalent geometry : bond 0.00627 (17471) covalent geometry : angle 0.84479 (23782) SS BOND : bond 0.00233 ( 5) SS BOND : angle 0.77949 ( 10) hydrogen bonds : bond 0.10968 ( 808) hydrogen bonds : angle 5.12137 ( 2547) link_ALPHA1-2 : bond 0.00928 ( 1) link_ALPHA1-2 : angle 1.72369 ( 3) link_ALPHA1-3 : bond 0.00418 ( 9) link_ALPHA1-3 : angle 1.80385 ( 27) link_ALPHA1-6 : bond 0.00635 ( 9) link_ALPHA1-6 : angle 1.74213 ( 27) link_BETA1-4 : bond 0.00835 ( 14) link_BETA1-4 : angle 2.10986 ( 42) link_NAG-ASN : bond 0.00149 ( 7) link_NAG-ASN : angle 1.57553 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 311 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: A 36 GLN cc_start: 0.7824 (pt0) cc_final: 0.7529 (pt0) REVERT: A 324 MET cc_start: 0.8341 (mtm) cc_final: 0.7944 (mtm) REVERT: B 48 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7879 (mt-10) REVERT: B 93 MET cc_start: 0.8248 (mmm) cc_final: 0.7804 (mmt) REVERT: B 177 LYS cc_start: 0.8099 (tmtt) cc_final: 0.7796 (tmtp) REVERT: B 268 ASP cc_start: 0.7838 (m-30) cc_final: 0.7114 (m-30) REVERT: B 275 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8131 (mt) REVERT: B 285 MET cc_start: 0.7745 (mmt) cc_final: 0.7343 (mmt) REVERT: C 5 GLU cc_start: 0.7199 (pt0) cc_final: 0.6742 (tt0) REVERT: C 46 LYS cc_start: 0.7172 (tttp) cc_final: 0.6695 (mtpt) REVERT: C 49 ASP cc_start: 0.7831 (m-30) cc_final: 0.7403 (m-30) REVERT: C 186 GLU cc_start: 0.7809 (tt0) cc_final: 0.7544 (tp30) REVERT: C 280 GLU cc_start: 0.7752 (mp0) cc_final: 0.7140 (mt-10) REVERT: D 13 GLU cc_start: 0.8141 (tp30) cc_final: 0.7374 (pm20) REVERT: D 45 GLU cc_start: 0.8205 (mp0) cc_final: 0.7956 (mp0) REVERT: D 94 ASN cc_start: 0.7990 (m110) cc_final: 0.7517 (m110) REVERT: D 105 MET cc_start: 0.8637 (mmt) cc_final: 0.8305 (mmt) REVERT: D 163 ASP cc_start: 0.7105 (t0) cc_final: 0.6731 (t0) REVERT: D 171 MET cc_start: 0.7413 (mtm) cc_final: 0.7131 (mtt) REVERT: D 172 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7784 (mp0) REVERT: D 320 ILE cc_start: 0.6325 (mm) cc_final: 0.6061 (mm) REVERT: D 398 GLU cc_start: 0.6830 (mm-30) cc_final: 0.6489 (tp30) REVERT: E 44 ASN cc_start: 0.7183 (t0) cc_final: 0.6541 (t0) REVERT: E 48 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7750 (mt-10) REVERT: E 93 GLU cc_start: 0.7426 (tp30) cc_final: 0.6980 (tp30) REVERT: E 166 GLU cc_start: 0.7121 (pt0) cc_final: 0.6807 (pt0) REVERT: E 225 ASN cc_start: 0.8138 (m-40) cc_final: 0.7931 (m110) REVERT: E 469 THR cc_start: 0.8270 (m) cc_final: 0.8025 (p) REVERT: E 474 GLN cc_start: 0.7323 (pt0) cc_final: 0.7010 (mt0) outliers start: 23 outliers final: 4 residues processed: 329 average time/residue: 0.5017 time to fit residues: 187.5476 Evaluate side-chains 202 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 197 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 280 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.0670 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN C 152 ASN D 14 ASN D 36 GLN D 58 GLN E 53 ASN E 107 ASN E 196 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.135432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.109214 restraints weight = 22900.775| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.08 r_work: 0.3136 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17516 Z= 0.120 Angle : 0.591 8.487 23912 Z= 0.277 Chirality : 0.045 0.245 2843 Planarity : 0.004 0.038 2856 Dihedral : 18.828 138.976 3208 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.87 % Allowed : 12.15 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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 are not related in a simple way. whole: 0.35 (0.19), residues: 1976 helix: 2.04 (0.19), residues: 752 sheet: -0.66 (0.25), residues: 417 loop : -1.00 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 113 TYR 0.013 0.001 TYR C 117 PHE 0.012 0.001 PHE C 473 TRP 0.012 0.001 TRP A 60 HIS 0.004 0.001 HIS A 104 Details of bonding type rmsd covalent geometry : bond 0.00257 (17471) covalent geometry : angle 0.57037 (23782) SS BOND : bond 0.00167 ( 5) SS BOND : angle 1.84836 ( 10) hydrogen bonds : bond 0.04016 ( 808) hydrogen bonds : angle 4.33555 ( 2547) link_ALPHA1-2 : bond 0.01889 ( 1) link_ALPHA1-2 : angle 3.50747 ( 3) link_ALPHA1-3 : bond 0.00765 ( 9) link_ALPHA1-3 : angle 2.11398 ( 27) link_ALPHA1-6 : bond 0.00968 ( 9) link_ALPHA1-6 : angle 2.03433 ( 27) link_BETA1-4 : bond 0.00823 ( 14) link_BETA1-4 : angle 2.36973 ( 42) link_NAG-ASN : bond 0.00163 ( 7) link_NAG-ASN : angle 1.76717 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 227 time to evaluate : 0.627 Fit side-chains REVERT: A 407 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7335 (m-30) REVERT: B 48 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8214 (mt-10) REVERT: B 93 MET cc_start: 0.8597 (mmm) cc_final: 0.8333 (mmm) REVERT: B 167 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.6322 (pm20) REVERT: B 168 ARG cc_start: 0.7798 (tpp-160) cc_final: 0.7108 (mmt180) REVERT: B 177 LYS cc_start: 0.8160 (tmtt) cc_final: 0.7917 (tmtp) REVERT: B 268 ASP cc_start: 0.8245 (m-30) cc_final: 0.7834 (m-30) REVERT: B 275 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8281 (mt) REVERT: B 285 MET cc_start: 0.8175 (mmt) cc_final: 0.7840 (mmt) REVERT: C 5 GLU cc_start: 0.7630 (pt0) cc_final: 0.7035 (tt0) REVERT: C 186 GLU cc_start: 0.8227 (tt0) cc_final: 0.7812 (tp30) REVERT: D 94 ASN cc_start: 0.8140 (m110) cc_final: 0.7907 (m110) REVERT: D 105 MET cc_start: 0.8821 (mmt) cc_final: 0.8525 (mmt) REVERT: D 117 MET cc_start: 0.8157 (tpp) cc_final: 0.7914 (tpt) REVERT: D 163 ASP cc_start: 0.7713 (t0) cc_final: 0.7290 (t0) REVERT: D 172 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7963 (mp0) REVERT: D 262 GLU cc_start: 0.8083 (tt0) cc_final: 0.7519 (pt0) REVERT: D 398 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6669 (tp30) REVERT: D 407 ASP cc_start: 0.7898 (t0) cc_final: 0.7630 (t0) REVERT: D 426 PHE cc_start: 0.7947 (m-80) cc_final: 0.7636 (m-80) REVERT: E 44 ASN cc_start: 0.7623 (t0) cc_final: 0.6881 (t0) REVERT: E 93 GLU cc_start: 0.7904 (tp30) cc_final: 0.7498 (tp30) REVERT: E 186 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8741 (mm) REVERT: E 225 ASN cc_start: 0.8521 (m-40) cc_final: 0.8307 (m110) REVERT: E 266 LEU cc_start: 0.7712 (tp) cc_final: 0.7324 (tp) REVERT: E 271 GLN cc_start: 0.7922 (tt0) cc_final: 0.7576 (mt0) REVERT: E 469 THR cc_start: 0.8374 (m) cc_final: 0.8142 (p) REVERT: E 474 GLN cc_start: 0.7601 (pt0) cc_final: 0.7334 (mt0) outliers start: 53 outliers final: 21 residues processed: 261 average time/residue: 0.4736 time to fit residues: 141.5923 Evaluate side-chains 214 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 454 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 48 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 181 optimal weight: 5.9990 chunk 180 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 58 GLN A 140 GLN B 87 GLN B 107 ASN D 58 GLN D 140 GLN E 39 ASN E 68 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.134072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.107749 restraints weight = 23079.996| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.12 r_work: 0.3114 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17516 Z= 0.129 Angle : 0.580 12.263 23912 Z= 0.272 Chirality : 0.044 0.231 2843 Planarity : 0.003 0.037 2856 Dihedral : 17.313 138.815 3207 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.63 % Allowed : 13.39 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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 are not related in a simple way. whole: 0.43 (0.19), residues: 1976 helix: 2.10 (0.19), residues: 753 sheet: -0.60 (0.25), residues: 414 loop : -0.95 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 66 TYR 0.010 0.001 TYR B 223 PHE 0.015 0.001 PHE A 256 TRP 0.011 0.001 TRP D 187 HIS 0.004 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00288 (17471) covalent geometry : angle 0.55951 (23782) SS BOND : bond 0.00928 ( 5) SS BOND : angle 3.10699 ( 10) hydrogen bonds : bond 0.03945 ( 808) hydrogen bonds : angle 4.25793 ( 2547) link_ALPHA1-2 : bond 0.01824 ( 1) link_ALPHA1-2 : angle 3.01435 ( 3) link_ALPHA1-3 : bond 0.00924 ( 9) link_ALPHA1-3 : angle 1.70448 ( 27) link_ALPHA1-6 : bond 0.01017 ( 9) link_ALPHA1-6 : angle 2.13127 ( 27) link_BETA1-4 : bond 0.00822 ( 14) link_BETA1-4 : angle 2.20272 ( 42) link_NAG-ASN : bond 0.00182 ( 7) link_NAG-ASN : angle 1.81229 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 198 time to evaluate : 0.620 Fit side-chains REVERT: A 407 ASP cc_start: 0.7777 (m-30) cc_final: 0.7508 (m-30) REVERT: B 48 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8441 (mt-10) REVERT: B 93 MET cc_start: 0.8615 (mmm) cc_final: 0.8135 (mmt) REVERT: B 167 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6335 (pm20) REVERT: B 168 ARG cc_start: 0.7785 (tpp-160) cc_final: 0.7111 (mmt180) REVERT: B 177 LYS cc_start: 0.8183 (tmtt) cc_final: 0.7941 (tmtp) REVERT: B 268 ASP cc_start: 0.8229 (m-30) cc_final: 0.7927 (m-30) REVERT: B 275 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8288 (mt) REVERT: B 284 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8085 (mp) REVERT: C 5 GLU cc_start: 0.7619 (pt0) cc_final: 0.6992 (tt0) REVERT: C 46 LYS cc_start: 0.7897 (mtpp) cc_final: 0.7662 (mtpt) REVERT: C 186 GLU cc_start: 0.8230 (tt0) cc_final: 0.7819 (tp30) REVERT: D 13 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.7656 (pm20) REVERT: D 94 ASN cc_start: 0.8104 (m110) cc_final: 0.7871 (m110) REVERT: D 105 MET cc_start: 0.8831 (mmt) cc_final: 0.8539 (mmt) REVERT: D 262 GLU cc_start: 0.8113 (tt0) cc_final: 0.7569 (pt0) REVERT: D 398 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6723 (tp30) REVERT: D 407 ASP cc_start: 0.7942 (t0) cc_final: 0.7605 (t0) REVERT: E 14 ASP cc_start: 0.8417 (t70) cc_final: 0.8114 (t0) REVERT: E 93 GLU cc_start: 0.7964 (tp30) cc_final: 0.7542 (tp30) REVERT: E 186 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8758 (mm) REVERT: E 225 ASN cc_start: 0.8541 (m-40) cc_final: 0.8329 (m110) REVERT: E 235 SER cc_start: 0.8718 (OUTLIER) cc_final: 0.8349 (p) REVERT: E 266 LEU cc_start: 0.7638 (tp) cc_final: 0.7250 (tp) REVERT: E 460 SER cc_start: 0.8163 (p) cc_final: 0.7941 (m) REVERT: E 469 THR cc_start: 0.8412 (m) cc_final: 0.8163 (p) REVERT: E 474 GLN cc_start: 0.7638 (pt0) cc_final: 0.7367 (mt0) outliers start: 67 outliers final: 28 residues processed: 239 average time/residue: 0.4566 time to fit residues: 125.4323 Evaluate side-chains 219 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLN Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 454 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 190 optimal weight: 4.9990 chunk 72 optimal weight: 0.4980 chunk 137 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 185 optimal weight: 6.9990 chunk 8 optimal weight: 0.0370 chunk 75 optimal weight: 4.9990 overall best weight: 1.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN C 26 HIS C 187 ASN D 58 GLN E 53 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.132789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.106448 restraints weight = 23141.824| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.10 r_work: 0.3092 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17516 Z= 0.147 Angle : 0.584 10.963 23912 Z= 0.273 Chirality : 0.045 0.255 2843 Planarity : 0.004 0.036 2856 Dihedral : 16.282 136.575 3207 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.34 % Allowed : 13.88 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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 are not related in a simple way. whole: 0.46 (0.19), residues: 1976 helix: 2.10 (0.19), residues: 760 sheet: -0.58 (0.25), residues: 413 loop : -0.95 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 57 TYR 0.010 0.001 TYR B 223 PHE 0.014 0.001 PHE A 256 TRP 0.010 0.001 TRP D 60 HIS 0.004 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00342 (17471) covalent geometry : angle 0.56293 (23782) SS BOND : bond 0.00365 ( 5) SS BOND : angle 3.10166 ( 10) hydrogen bonds : bond 0.03933 ( 808) hydrogen bonds : angle 4.25981 ( 2547) link_ALPHA1-2 : bond 0.01797 ( 1) link_ALPHA1-2 : angle 3.04529 ( 3) link_ALPHA1-3 : bond 0.00916 ( 9) link_ALPHA1-3 : angle 1.76995 ( 27) link_ALPHA1-6 : bond 0.01021 ( 9) link_ALPHA1-6 : angle 2.17631 ( 27) link_BETA1-4 : bond 0.00782 ( 14) link_BETA1-4 : angle 2.23927 ( 42) link_NAG-ASN : bond 0.00218 ( 7) link_NAG-ASN : angle 1.74459 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 200 time to evaluate : 0.594 Fit side-chains REVERT: A 200 ASP cc_start: 0.8426 (p0) cc_final: 0.8148 (p0) REVERT: A 407 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7468 (m-30) REVERT: B 48 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8331 (mt-10) REVERT: B 93 MET cc_start: 0.8646 (mmm) cc_final: 0.8359 (mmt) REVERT: B 167 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.6350 (pm20) REVERT: B 168 ARG cc_start: 0.7789 (tpp-160) cc_final: 0.7131 (mmt180) REVERT: B 177 LYS cc_start: 0.8201 (tmtt) cc_final: 0.7947 (tmtp) REVERT: B 182 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7563 (tm-30) REVERT: B 268 ASP cc_start: 0.8219 (m-30) cc_final: 0.7936 (m-30) REVERT: B 284 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8137 (mp) REVERT: B 314 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7477 (ttp) REVERT: C 5 GLU cc_start: 0.7709 (pt0) cc_final: 0.7104 (tt0) REVERT: C 46 LYS cc_start: 0.7949 (mtpp) cc_final: 0.7615 (mtpt) REVERT: C 49 ASP cc_start: 0.8143 (m-30) cc_final: 0.7895 (m-30) REVERT: C 186 GLU cc_start: 0.8210 (tt0) cc_final: 0.7826 (tp30) REVERT: C 280 GLU cc_start: 0.7893 (mp0) cc_final: 0.7302 (mt-10) REVERT: C 489 ASP cc_start: 0.7946 (t70) cc_final: 0.7648 (t0) REVERT: D 94 ASN cc_start: 0.8121 (m110) cc_final: 0.7835 (m110) REVERT: D 105 MET cc_start: 0.8822 (mmt) cc_final: 0.8540 (mmt) REVERT: D 407 ASP cc_start: 0.7830 (t0) cc_final: 0.7473 (t0) REVERT: E 93 GLU cc_start: 0.7926 (tp30) cc_final: 0.7539 (tp30) REVERT: E 225 ASN cc_start: 0.8577 (m-40) cc_final: 0.8343 (m110) REVERT: E 235 SER cc_start: 0.8717 (OUTLIER) cc_final: 0.8349 (p) REVERT: E 266 LEU cc_start: 0.7746 (tp) cc_final: 0.7345 (tp) REVERT: E 460 SER cc_start: 0.8196 (p) cc_final: 0.7927 (m) REVERT: E 469 THR cc_start: 0.8421 (m) cc_final: 0.8172 (p) REVERT: E 474 GLN cc_start: 0.7688 (pt0) cc_final: 0.7427 (mt0) outliers start: 80 outliers final: 35 residues processed: 249 average time/residue: 0.4573 time to fit residues: 130.9170 Evaluate side-chains 234 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 193 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 454 ILE Chi-restraints excluded: chain E residue 488 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 124 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 10 optimal weight: 0.0050 chunk 183 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 22 optimal weight: 0.1980 chunk 1 optimal weight: 0.0270 overall best weight: 0.8454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 58 GLN A 140 GLN D 58 GLN D 140 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.133947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.107023 restraints weight = 22767.630| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.16 r_work: 0.3102 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17516 Z= 0.122 Angle : 0.570 10.696 23912 Z= 0.266 Chirality : 0.044 0.271 2843 Planarity : 0.003 0.035 2856 Dihedral : 15.266 134.445 3205 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.18 % Allowed : 14.75 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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 are not related in a simple way. whole: 0.57 (0.19), residues: 1976 helix: 2.22 (0.19), residues: 754 sheet: -0.53 (0.25), residues: 413 loop : -0.89 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 485 TYR 0.010 0.001 TYR A 277 PHE 0.013 0.001 PHE C 473 TRP 0.011 0.001 TRP D 187 HIS 0.004 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00269 (17471) covalent geometry : angle 0.55050 (23782) SS BOND : bond 0.00202 ( 5) SS BOND : angle 2.79997 ( 10) hydrogen bonds : bond 0.03767 ( 808) hydrogen bonds : angle 4.15887 ( 2547) link_ALPHA1-2 : bond 0.01825 ( 1) link_ALPHA1-2 : angle 3.13663 ( 3) link_ALPHA1-3 : bond 0.00921 ( 9) link_ALPHA1-3 : angle 1.73737 ( 27) link_ALPHA1-6 : bond 0.01087 ( 9) link_ALPHA1-6 : angle 2.18940 ( 27) link_BETA1-4 : bond 0.00774 ( 14) link_BETA1-4 : angle 2.16806 ( 42) link_NAG-ASN : bond 0.00166 ( 7) link_NAG-ASN : angle 1.59783 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 194 time to evaluate : 0.645 Fit side-chains REVERT: A 200 ASP cc_start: 0.8369 (p0) cc_final: 0.8147 (p0) REVERT: A 258 LEU cc_start: 0.7327 (mt) cc_final: 0.7100 (mp) REVERT: A 407 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7490 (m-30) REVERT: B 48 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8460 (mt-10) REVERT: B 93 MET cc_start: 0.8620 (mmm) cc_final: 0.8334 (mmm) REVERT: B 167 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.6327 (pm20) REVERT: B 168 ARG cc_start: 0.7755 (tpp-160) cc_final: 0.7076 (mmt180) REVERT: B 177 LYS cc_start: 0.8166 (tmtt) cc_final: 0.7912 (tmtp) REVERT: B 268 ASP cc_start: 0.8216 (m-30) cc_final: 0.7941 (m-30) REVERT: B 284 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8158 (mp) REVERT: B 314 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7440 (ttp) REVERT: B 424 LEU cc_start: 0.6390 (OUTLIER) cc_final: 0.5614 (mm) REVERT: C 5 GLU cc_start: 0.7620 (pt0) cc_final: 0.7001 (tt0) REVERT: C 46 LYS cc_start: 0.7937 (mtpp) cc_final: 0.7610 (mtpt) REVERT: C 85 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8486 (pt0) REVERT: C 186 GLU cc_start: 0.8212 (tt0) cc_final: 0.7832 (tp30) REVERT: D 94 ASN cc_start: 0.8077 (m110) cc_final: 0.7824 (m110) REVERT: D 105 MET cc_start: 0.8789 (mmt) cc_final: 0.8518 (mmt) REVERT: D 171 MET cc_start: 0.8373 (mtm) cc_final: 0.7921 (mtt) REVERT: D 262 GLU cc_start: 0.8133 (tt0) cc_final: 0.7750 (pt0) REVERT: D 398 GLU cc_start: 0.7295 (tp30) cc_final: 0.6500 (tp30) REVERT: D 407 ASP cc_start: 0.7958 (t0) cc_final: 0.7539 (t0) REVERT: E 14 ASP cc_start: 0.8421 (t70) cc_final: 0.8208 (t0) REVERT: E 186 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8723 (mm) REVERT: E 200 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7985 (p) REVERT: E 225 ASN cc_start: 0.8645 (m-40) cc_final: 0.8384 (m110) REVERT: E 235 SER cc_start: 0.8711 (OUTLIER) cc_final: 0.8363 (p) REVERT: E 266 LEU cc_start: 0.7728 (tp) cc_final: 0.7355 (tp) REVERT: E 460 SER cc_start: 0.8173 (OUTLIER) cc_final: 0.7920 (m) REVERT: E 469 THR cc_start: 0.8494 (m) cc_final: 0.8245 (p) REVERT: E 474 GLN cc_start: 0.7688 (pt0) cc_final: 0.7460 (mt0) outliers start: 77 outliers final: 34 residues processed: 246 average time/residue: 0.4533 time to fit residues: 128.3509 Evaluate side-chains 232 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 188 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 454 ILE Chi-restraints excluded: chain E residue 460 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 86 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 140 optimal weight: 6.9990 chunk 129 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 197 optimal weight: 0.6980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 58 GLN D 58 GLN E 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.132648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.105555 restraints weight = 22838.057| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.16 r_work: 0.3081 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17516 Z= 0.149 Angle : 0.597 10.645 23912 Z= 0.278 Chirality : 0.045 0.258 2843 Planarity : 0.004 0.036 2856 Dihedral : 14.514 129.220 3205 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.18 % Allowed : 14.70 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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 are not related in a simple way. whole: 0.56 (0.19), residues: 1976 helix: 2.22 (0.19), residues: 747 sheet: -0.46 (0.25), residues: 417 loop : -0.92 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 57 TYR 0.011 0.001 TYR A 277 PHE 0.013 0.001 PHE A 256 TRP 0.010 0.001 TRP D 187 HIS 0.004 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00346 (17471) covalent geometry : angle 0.57735 (23782) SS BOND : bond 0.00360 ( 5) SS BOND : angle 2.88180 ( 10) hydrogen bonds : bond 0.03888 ( 808) hydrogen bonds : angle 4.21665 ( 2547) link_ALPHA1-2 : bond 0.01798 ( 1) link_ALPHA1-2 : angle 3.12426 ( 3) link_ALPHA1-3 : bond 0.00885 ( 9) link_ALPHA1-3 : angle 1.74959 ( 27) link_ALPHA1-6 : bond 0.01113 ( 9) link_ALPHA1-6 : angle 2.23366 ( 27) link_BETA1-4 : bond 0.00764 ( 14) link_BETA1-4 : angle 2.19959 ( 42) link_NAG-ASN : bond 0.00234 ( 7) link_NAG-ASN : angle 1.65374 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 193 time to evaluate : 0.615 Fit side-chains REVERT: A 36 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.8121 (mt0) REVERT: A 200 ASP cc_start: 0.8401 (p0) cc_final: 0.8159 (p0) REVERT: A 407 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7479 (m-30) REVERT: B 48 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8336 (mt-10) REVERT: B 167 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.5961 (tp30) REVERT: B 177 LYS cc_start: 0.8186 (tmtt) cc_final: 0.7932 (tmtp) REVERT: B 182 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7539 (tm-30) REVERT: B 268 ASP cc_start: 0.8201 (m-30) cc_final: 0.7957 (m-30) REVERT: B 284 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8171 (mp) REVERT: B 314 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7438 (ttp) REVERT: B 424 LEU cc_start: 0.6517 (OUTLIER) cc_final: 0.5787 (mm) REVERT: C 5 GLU cc_start: 0.7713 (pt0) cc_final: 0.7115 (tt0) REVERT: C 46 LYS cc_start: 0.7969 (mtpp) cc_final: 0.7596 (mtpt) REVERT: C 49 ASP cc_start: 0.8365 (m-30) cc_final: 0.8087 (m-30) REVERT: C 186 GLU cc_start: 0.8167 (tt0) cc_final: 0.7791 (tp30) REVERT: C 280 GLU cc_start: 0.7894 (mp0) cc_final: 0.7238 (mt-10) REVERT: C 489 ASP cc_start: 0.7838 (t70) cc_final: 0.7541 (t0) REVERT: D 94 ASN cc_start: 0.8076 (m110) cc_final: 0.7827 (m110) REVERT: D 105 MET cc_start: 0.8704 (mmt) cc_final: 0.8445 (mmt) REVERT: D 171 MET cc_start: 0.8401 (mtm) cc_final: 0.7963 (mtt) REVERT: D 262 GLU cc_start: 0.8228 (tt0) cc_final: 0.7852 (pt0) REVERT: D 398 GLU cc_start: 0.7263 (tp30) cc_final: 0.6498 (tp30) REVERT: D 407 ASP cc_start: 0.7938 (t0) cc_final: 0.7531 (t0) REVERT: E 186 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8791 (mm) REVERT: E 200 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.8022 (p) REVERT: E 225 ASN cc_start: 0.8698 (m-40) cc_final: 0.8422 (m110) REVERT: E 235 SER cc_start: 0.8712 (OUTLIER) cc_final: 0.8331 (p) REVERT: E 266 LEU cc_start: 0.7734 (tp) cc_final: 0.7371 (tp) REVERT: E 469 THR cc_start: 0.8524 (m) cc_final: 0.8266 (p) REVERT: E 474 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7445 (mt0) outliers start: 77 outliers final: 41 residues processed: 239 average time/residue: 0.4704 time to fit residues: 128.8261 Evaluate side-chains 235 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 183 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 454 ILE Chi-restraints excluded: chain E residue 460 SER Chi-restraints excluded: chain E residue 474 GLN Chi-restraints excluded: chain E residue 488 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 78 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 94 optimal weight: 0.1980 chunk 88 optimal weight: 0.7980 chunk 69 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 58 GLN A 140 GLN D 58 GLN E 271 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.133893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.106858 restraints weight = 22706.391| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.17 r_work: 0.3104 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17516 Z= 0.118 Angle : 0.575 10.581 23912 Z= 0.266 Chirality : 0.044 0.257 2843 Planarity : 0.003 0.036 2856 Dihedral : 13.959 126.375 3205 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.69 % Allowed : 15.18 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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 are not related in a simple way. whole: 0.60 (0.19), residues: 1976 helix: 2.28 (0.19), residues: 749 sheet: -0.53 (0.25), residues: 416 loop : -0.89 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 57 TYR 0.010 0.001 TYR A 277 PHE 0.011 0.001 PHE A 256 TRP 0.011 0.001 TRP D 60 HIS 0.003 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00259 (17471) covalent geometry : angle 0.55560 (23782) SS BOND : bond 0.00455 ( 5) SS BOND : angle 2.62614 ( 10) hydrogen bonds : bond 0.03708 ( 808) hydrogen bonds : angle 4.14639 ( 2547) link_ALPHA1-2 : bond 0.01920 ( 1) link_ALPHA1-2 : angle 3.30005 ( 3) link_ALPHA1-3 : bond 0.00873 ( 9) link_ALPHA1-3 : angle 1.71589 ( 27) link_ALPHA1-6 : bond 0.01213 ( 9) link_ALPHA1-6 : angle 2.22127 ( 27) link_BETA1-4 : bond 0.00790 ( 14) link_BETA1-4 : angle 2.14807 ( 42) link_NAG-ASN : bond 0.00177 ( 7) link_NAG-ASN : angle 1.58528 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 185 time to evaluate : 0.606 Fit side-chains REVERT: A 200 ASP cc_start: 0.8391 (p0) cc_final: 0.8167 (p0) REVERT: A 407 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7488 (m-30) REVERT: B 48 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8448 (mt-10) REVERT: B 167 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6427 (pm20) REVERT: B 177 LYS cc_start: 0.8162 (tmtt) cc_final: 0.7903 (tmtp) REVERT: B 284 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8151 (mp) REVERT: B 314 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7418 (ttp) REVERT: B 424 LEU cc_start: 0.6512 (OUTLIER) cc_final: 0.5741 (mm) REVERT: C 5 GLU cc_start: 0.7672 (pt0) cc_final: 0.7071 (tt0) REVERT: C 46 LYS cc_start: 0.7838 (mtpp) cc_final: 0.7513 (mtpt) REVERT: C 168 ASP cc_start: 0.7124 (m-30) cc_final: 0.6615 (t0) REVERT: C 186 GLU cc_start: 0.8141 (tt0) cc_final: 0.7766 (tp30) REVERT: D 94 ASN cc_start: 0.7985 (m110) cc_final: 0.7726 (m110) REVERT: D 105 MET cc_start: 0.8689 (mmt) cc_final: 0.8422 (mmt) REVERT: D 171 MET cc_start: 0.8364 (mtm) cc_final: 0.7937 (mtt) REVERT: D 262 GLU cc_start: 0.8179 (tt0) cc_final: 0.7785 (pt0) REVERT: D 398 GLU cc_start: 0.7298 (tp30) cc_final: 0.6505 (tp30) REVERT: D 407 ASP cc_start: 0.7880 (t0) cc_final: 0.7474 (t0) REVERT: E 164 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7163 (mt-10) REVERT: E 186 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8730 (mm) REVERT: E 200 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.7995 (p) REVERT: E 225 ASN cc_start: 0.8680 (m-40) cc_final: 0.8428 (m110) REVERT: E 235 SER cc_start: 0.8681 (OUTLIER) cc_final: 0.8322 (p) REVERT: E 266 LEU cc_start: 0.7673 (tp) cc_final: 0.7283 (tp) REVERT: E 460 SER cc_start: 0.8160 (OUTLIER) cc_final: 0.7899 (m) REVERT: E 469 THR cc_start: 0.8518 (m) cc_final: 0.8265 (p) REVERT: E 474 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7426 (mt0) outliers start: 68 outliers final: 38 residues processed: 227 average time/residue: 0.4437 time to fit residues: 116.1196 Evaluate side-chains 231 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 183 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 454 ILE Chi-restraints excluded: chain E residue 460 SER Chi-restraints excluded: chain E residue 474 GLN Chi-restraints excluded: chain E residue 488 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 35 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 173 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 133 optimal weight: 0.1980 chunk 4 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 58 GLN D 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.134757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.107796 restraints weight = 22910.767| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.17 r_work: 0.3118 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17516 Z= 0.117 Angle : 0.565 10.525 23912 Z= 0.262 Chirality : 0.044 0.277 2843 Planarity : 0.003 0.036 2856 Dihedral : 13.016 118.608 3205 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.31 % Allowed : 15.62 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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 are not related in a simple way. whole: 0.62 (0.19), residues: 1976 helix: 2.27 (0.19), residues: 757 sheet: -0.46 (0.25), residues: 416 loop : -0.91 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 57 TYR 0.009 0.001 TYR A 277 PHE 0.016 0.001 PHE D 227 TRP 0.012 0.001 TRP A 187 HIS 0.003 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00253 (17471) covalent geometry : angle 0.54666 (23782) SS BOND : bond 0.00368 ( 5) SS BOND : angle 2.38272 ( 10) hydrogen bonds : bond 0.03635 ( 808) hydrogen bonds : angle 4.09210 ( 2547) link_ALPHA1-2 : bond 0.02084 ( 1) link_ALPHA1-2 : angle 3.47673 ( 3) link_ALPHA1-3 : bond 0.00852 ( 9) link_ALPHA1-3 : angle 1.65044 ( 27) link_ALPHA1-6 : bond 0.01336 ( 9) link_ALPHA1-6 : angle 2.06288 ( 27) link_BETA1-4 : bond 0.00819 ( 14) link_BETA1-4 : angle 2.16157 ( 42) link_NAG-ASN : bond 0.00172 ( 7) link_NAG-ASN : angle 1.54260 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 204 time to evaluate : 0.619 Fit side-chains REVERT: A 200 ASP cc_start: 0.8377 (p0) cc_final: 0.8162 (p0) REVERT: A 400 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7308 (mptm) REVERT: A 407 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7429 (m-30) REVERT: B 48 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8415 (mt-10) REVERT: B 167 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.6391 (pm20) REVERT: B 177 LYS cc_start: 0.8150 (tmtt) cc_final: 0.7897 (tmtp) REVERT: B 182 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7584 (tm-30) REVERT: B 284 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8161 (mp) REVERT: B 424 LEU cc_start: 0.6519 (OUTLIER) cc_final: 0.5748 (mm) REVERT: C 5 GLU cc_start: 0.7599 (pt0) cc_final: 0.6979 (tt0) REVERT: C 46 LYS cc_start: 0.7768 (mtpp) cc_final: 0.7448 (mtpt) REVERT: C 168 ASP cc_start: 0.7094 (m-30) cc_final: 0.6594 (t0) REVERT: C 186 GLU cc_start: 0.8141 (tt0) cc_final: 0.7760 (tp30) REVERT: D 94 ASN cc_start: 0.7928 (m110) cc_final: 0.7702 (m110) REVERT: D 105 MET cc_start: 0.8643 (mmt) cc_final: 0.8372 (mmt) REVERT: D 171 MET cc_start: 0.8367 (mtm) cc_final: 0.7943 (mtt) REVERT: D 262 GLU cc_start: 0.8160 (tt0) cc_final: 0.7758 (pt0) REVERT: D 398 GLU cc_start: 0.7261 (tp30) cc_final: 0.6539 (tp30) REVERT: D 407 ASP cc_start: 0.7890 (t0) cc_final: 0.7463 (t0) REVERT: E 164 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7094 (mt-10) REVERT: E 186 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8766 (mm) REVERT: E 200 THR cc_start: 0.8331 (OUTLIER) cc_final: 0.8008 (p) REVERT: E 225 ASN cc_start: 0.8683 (m-40) cc_final: 0.8431 (m110) REVERT: E 235 SER cc_start: 0.8689 (OUTLIER) cc_final: 0.8335 (p) REVERT: E 266 LEU cc_start: 0.7702 (tp) cc_final: 0.7366 (tp) REVERT: E 460 SER cc_start: 0.8114 (OUTLIER) cc_final: 0.7881 (m) REVERT: E 469 THR cc_start: 0.8527 (m) cc_final: 0.8278 (p) REVERT: E 474 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.7427 (mt0) outliers start: 61 outliers final: 33 residues processed: 242 average time/residue: 0.4517 time to fit residues: 126.3078 Evaluate side-chains 233 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 189 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 460 SER Chi-restraints excluded: chain E residue 474 GLN Chi-restraints excluded: chain E residue 488 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 150 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 19 optimal weight: 0.0370 chunk 147 optimal weight: 0.0470 chunk 96 optimal weight: 0.0030 chunk 109 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 26 optimal weight: 0.0070 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 58 GLN ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 313 HIS D 58 GLN ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.136221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.109369 restraints weight = 22775.770| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.17 r_work: 0.3140 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 17516 Z= 0.107 Angle : 0.553 10.426 23912 Z= 0.259 Chirality : 0.043 0.243 2843 Planarity : 0.003 0.037 2856 Dihedral : 12.428 110.068 3205 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.93 % Allowed : 16.27 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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 are not related in a simple way. whole: 0.70 (0.19), residues: 1976 helix: 2.38 (0.19), residues: 753 sheet: -0.42 (0.25), residues: 416 loop : -0.90 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 57 TYR 0.011 0.001 TYR A 277 PHE 0.013 0.001 PHE C 473 TRP 0.013 0.001 TRP A 187 HIS 0.004 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00225 (17471) covalent geometry : angle 0.53523 (23782) SS BOND : bond 0.00298 ( 5) SS BOND : angle 2.16223 ( 10) hydrogen bonds : bond 0.03516 ( 808) hydrogen bonds : angle 4.02745 ( 2547) link_ALPHA1-2 : bond 0.02311 ( 1) link_ALPHA1-2 : angle 3.73720 ( 3) link_ALPHA1-3 : bond 0.00800 ( 9) link_ALPHA1-3 : angle 1.67010 ( 27) link_ALPHA1-6 : bond 0.01382 ( 9) link_ALPHA1-6 : angle 1.93829 ( 27) link_BETA1-4 : bond 0.00827 ( 14) link_BETA1-4 : angle 2.15578 ( 42) link_NAG-ASN : bond 0.00164 ( 7) link_NAG-ASN : angle 1.48542 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 203 time to evaluate : 0.561 Fit side-chains REVERT: A 407 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7398 (m-30) REVERT: B 48 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8440 (mt-10) REVERT: B 167 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.6374 (pm20) REVERT: B 177 LYS cc_start: 0.8111 (tmtt) cc_final: 0.7866 (tmtp) REVERT: B 268 ASP cc_start: 0.8274 (m-30) cc_final: 0.7989 (m-30) REVERT: B 284 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8216 (mp) REVERT: B 424 LEU cc_start: 0.6515 (OUTLIER) cc_final: 0.5751 (mm) REVERT: C 5 GLU cc_start: 0.7591 (pt0) cc_final: 0.6966 (tt0) REVERT: C 46 LYS cc_start: 0.7798 (mtpp) cc_final: 0.7479 (mtpt) REVERT: C 168 ASP cc_start: 0.7077 (m-30) cc_final: 0.6463 (t0) REVERT: C 186 GLU cc_start: 0.8202 (tt0) cc_final: 0.7962 (mm-30) REVERT: D 105 MET cc_start: 0.8642 (mmt) cc_final: 0.8357 (mmt) REVERT: D 171 MET cc_start: 0.8322 (mtm) cc_final: 0.7900 (mtt) REVERT: D 262 GLU cc_start: 0.8163 (tt0) cc_final: 0.7759 (pt0) REVERT: D 398 GLU cc_start: 0.7214 (tp30) cc_final: 0.6509 (tp30) REVERT: D 407 ASP cc_start: 0.7869 (t0) cc_final: 0.7420 (t0) REVERT: E 164 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7103 (mt-10) REVERT: E 186 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8743 (mm) REVERT: E 200 THR cc_start: 0.8281 (OUTLIER) cc_final: 0.7962 (p) REVERT: E 225 ASN cc_start: 0.8631 (m-40) cc_final: 0.8406 (m110) REVERT: E 266 LEU cc_start: 0.7646 (tp) cc_final: 0.7271 (tp) REVERT: E 469 THR cc_start: 0.8508 (m) cc_final: 0.8274 (p) REVERT: E 474 GLN cc_start: 0.7651 (pt0) cc_final: 0.7413 (mt0) outliers start: 54 outliers final: 32 residues processed: 240 average time/residue: 0.4453 time to fit residues: 123.4037 Evaluate side-chains 225 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 488 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 132 optimal weight: 0.9990 chunk 116 optimal weight: 0.2980 chunk 42 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 142 optimal weight: 0.5980 chunk 110 optimal weight: 0.0570 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 GLN ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN D 58 GLN D 140 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.136123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.109246 restraints weight = 22705.598| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.17 r_work: 0.3138 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17516 Z= 0.112 Angle : 0.564 10.565 23912 Z= 0.264 Chirality : 0.043 0.259 2843 Planarity : 0.003 0.036 2856 Dihedral : 12.230 104.815 3205 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.44 % Allowed : 17.08 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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 are not related in a simple way. whole: 0.73 (0.19), residues: 1976 helix: 2.35 (0.19), residues: 759 sheet: -0.38 (0.25), residues: 415 loop : -0.87 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 57 TYR 0.011 0.001 TYR A 277 PHE 0.015 0.001 PHE D 284 TRP 0.014 0.001 TRP D 60 HIS 0.004 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00241 (17471) covalent geometry : angle 0.54633 (23782) SS BOND : bond 0.00300 ( 5) SS BOND : angle 2.16890 ( 10) hydrogen bonds : bond 0.03535 ( 808) hydrogen bonds : angle 4.04035 ( 2547) link_ALPHA1-2 : bond 0.02387 ( 1) link_ALPHA1-2 : angle 3.78181 ( 3) link_ALPHA1-3 : bond 0.00790 ( 9) link_ALPHA1-3 : angle 1.64564 ( 27) link_ALPHA1-6 : bond 0.01370 ( 9) link_ALPHA1-6 : angle 1.88763 ( 27) link_BETA1-4 : bond 0.00819 ( 14) link_BETA1-4 : angle 2.14797 ( 42) link_NAG-ASN : bond 0.00156 ( 7) link_NAG-ASN : angle 1.49173 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 193 time to evaluate : 0.559 Fit side-chains REVERT: A 407 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7395 (m-30) REVERT: B 48 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8420 (mt-10) REVERT: B 167 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.6361 (pm20) REVERT: B 177 LYS cc_start: 0.8098 (tmtt) cc_final: 0.7857 (tmtp) REVERT: B 284 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8211 (mp) REVERT: B 314 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7415 (ttp) REVERT: B 424 LEU cc_start: 0.6493 (OUTLIER) cc_final: 0.5734 (mm) REVERT: C 5 GLU cc_start: 0.7593 (pt0) cc_final: 0.6964 (tt0) REVERT: C 46 LYS cc_start: 0.7795 (mtpp) cc_final: 0.7477 (mtpt) REVERT: C 168 ASP cc_start: 0.7067 (m-30) cc_final: 0.6455 (t0) REVERT: C 186 GLU cc_start: 0.8195 (tt0) cc_final: 0.7953 (mm-30) REVERT: D 105 MET cc_start: 0.8632 (mmt) cc_final: 0.8346 (mmt) REVERT: D 171 MET cc_start: 0.8336 (mtm) cc_final: 0.7912 (mtt) REVERT: D 262 GLU cc_start: 0.8190 (tt0) cc_final: 0.7786 (pt0) REVERT: D 308 MET cc_start: 0.7505 (ttp) cc_final: 0.6806 (tmt) REVERT: D 313 ARG cc_start: 0.7540 (ttm110) cc_final: 0.7334 (mtp-110) REVERT: D 407 ASP cc_start: 0.7866 (t0) cc_final: 0.7395 (t0) REVERT: E 164 GLU cc_start: 0.7353 (mm-30) cc_final: 0.7100 (mt-10) REVERT: E 186 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8743 (mm) REVERT: E 200 THR cc_start: 0.8287 (OUTLIER) cc_final: 0.7958 (p) REVERT: E 225 ASN cc_start: 0.8634 (m-40) cc_final: 0.8406 (m110) REVERT: E 266 LEU cc_start: 0.7633 (tp) cc_final: 0.7240 (tp) REVERT: E 469 THR cc_start: 0.8516 (m) cc_final: 0.8278 (p) REVERT: E 474 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7387 (mt0) outliers start: 45 outliers final: 34 residues processed: 224 average time/residue: 0.4516 time to fit residues: 116.7205 Evaluate side-chains 233 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 191 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 454 ILE Chi-restraints excluded: chain E residue 474 GLN Chi-restraints excluded: chain E residue 488 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 0 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 79 optimal weight: 0.0030 chunk 176 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 26 optimal weight: 0.0370 overall best weight: 0.7672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 GLN D 58 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.135378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.108418 restraints weight = 22841.815| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.18 r_work: 0.3128 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17516 Z= 0.118 Angle : 0.558 10.580 23912 Z= 0.263 Chirality : 0.044 0.269 2843 Planarity : 0.003 0.036 2856 Dihedral : 11.955 93.862 3205 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.49 % Allowed : 17.19 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % 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 are not related in a simple way. whole: 0.69 (0.19), residues: 1976 helix: 2.27 (0.19), residues: 763 sheet: -0.35 (0.25), residues: 416 loop : -0.88 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 113 TYR 0.011 0.001 TYR A 277 PHE 0.013 0.001 PHE D 284 TRP 0.010 0.001 TRP D 60 HIS 0.003 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00262 (17471) covalent geometry : angle 0.54055 (23782) SS BOND : bond 0.00337 ( 5) SS BOND : angle 2.24905 ( 10) hydrogen bonds : bond 0.03569 ( 808) hydrogen bonds : angle 4.07080 ( 2547) link_ALPHA1-2 : bond 0.02620 ( 1) link_ALPHA1-2 : angle 3.97630 ( 3) link_ALPHA1-3 : bond 0.00759 ( 9) link_ALPHA1-3 : angle 1.63848 ( 27) link_ALPHA1-6 : bond 0.01357 ( 9) link_ALPHA1-6 : angle 1.81515 ( 27) link_BETA1-4 : bond 0.00789 ( 14) link_BETA1-4 : angle 2.13720 ( 42) link_NAG-ASN : bond 0.00149 ( 7) link_NAG-ASN : angle 1.53369 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5430.81 seconds wall clock time: 93 minutes 11.93 seconds (5591.93 seconds total)