Starting phenix.real_space_refine on Sun Jun 15 15:27:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qko_14048/06_2025/7qko_14048.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qko_14048/06_2025/7qko_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7qko_14048/06_2025/7qko_14048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qko_14048/06_2025/7qko_14048.map" model { file = "/net/cci-nas-00/data/ceres_data/7qko_14048/06_2025/7qko_14048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qko_14048/06_2025/7qko_14048.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.73, per 1000 atoms: 0.63 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: 5.68 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.08 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: 5.61 Time building geometry restraints manager: 6.20 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 432 or resid 501 or (resid 502 and (name C2 or n \ ame 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 C \ 34 or name C35 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: 1.210 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: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 42.090 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.080 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:15.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.380 ------------------------------------------------------------------------------- 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 : 8.07 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (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 TRP 0.012 0.001 TRP D 187 HIS 0.004 0.001 HIS E 471 PHE 0.010 0.001 PHE A 284 TYR 0.008 0.001 TYR C 439 ARG 0.002 0.000 ARG C 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00149 ( 7) link_NAG-ASN : angle 1.57553 ( 21) 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_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) hydrogen bonds : bond 0.10968 ( 808) hydrogen bonds : angle 5.12137 ( 2547) SS BOND : bond 0.00233 ( 5) SS BOND : angle 0.77949 ( 10) covalent geometry : bond 0.00627 (17471) covalent geometry : angle 0.84479 (23782) *********************** 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 : 1.935 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: 0.8130 (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 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: 0.7130 (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: 0.7182 (t0) cc_final: 0.6540 (t0) REVERT: E 48 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7751 (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: 1.0796 time to fit residues: 404.0172 Evaluate side-chains 201 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 196 time to evaluate : 2.035 ------------------------------------------------------------------------------- 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 167 optimal weight: 0.0970 chunk 150 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 80 optimal weight: 0.3980 chunk 155 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 94 optimal weight: 0.4980 chunk 115 optimal weight: 0.7980 chunk 179 optimal weight: 5.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN D 14 ASN D 36 GLN D 58 GLN E 53 ASN E 107 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.135356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.109179 restraints weight = 22823.602| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.07 r_work: 0.3136 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.20 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 = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17516 Z= 0.120 Angle : 0.584 8.318 23912 Z= 0.276 Chirality : 0.044 0.221 2843 Planarity : 0.004 0.038 2856 Dihedral : 19.171 138.519 3208 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.93 % Allowed : 12.20 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.19), residues: 1976 helix: 2.03 (0.19), residues: 756 sheet: -0.64 (0.25), residues: 418 loop : -1.00 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 60 HIS 0.003 0.001 HIS A 104 PHE 0.012 0.001 PHE C 473 TYR 0.013 0.001 TYR C 117 ARG 0.004 0.000 ARG E 125 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 7) link_NAG-ASN : angle 1.65685 ( 21) link_ALPHA1-6 : bond 0.00936 ( 9) link_ALPHA1-6 : angle 2.00923 ( 27) link_BETA1-4 : bond 0.00883 ( 14) link_BETA1-4 : angle 2.30009 ( 42) link_ALPHA1-2 : bond 0.02036 ( 1) link_ALPHA1-2 : angle 3.65650 ( 3) link_ALPHA1-3 : bond 0.00737 ( 9) link_ALPHA1-3 : angle 1.99903 ( 27) hydrogen bonds : bond 0.04107 ( 808) hydrogen bonds : angle 4.35848 ( 2547) SS BOND : bond 0.00309 ( 5) SS BOND : angle 2.55940 ( 10) covalent geometry : bond 0.00258 (17471) covalent geometry : angle 0.56375 (23782) *********************** 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 275 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 221 time to evaluate : 2.086 Fit side-chains REVERT: A 407 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7305 (m-30) REVERT: B 48 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8310 (mt-10) REVERT: B 93 MET cc_start: 0.8610 (mmm) cc_final: 0.8351 (mmm) REVERT: B 167 GLU cc_start: 0.6700 (OUTLIER) cc_final: 0.6311 (pm20) REVERT: B 168 ARG cc_start: 0.7794 (tpp-160) cc_final: 0.7105 (mmt180) REVERT: B 177 LYS cc_start: 0.8158 (tmtt) cc_final: 0.7914 (tmtp) REVERT: B 268 ASP cc_start: 0.8202 (m-30) cc_final: 0.7797 (m-30) REVERT: B 275 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8277 (mt) REVERT: B 285 MET cc_start: 0.8162 (mmt) cc_final: 0.7832 (mmt) REVERT: C 5 GLU cc_start: 0.7623 (pt0) cc_final: 0.7029 (tt0) REVERT: C 186 GLU cc_start: 0.8224 (tt0) cc_final: 0.7810 (tp30) REVERT: C 242 LEU cc_start: 0.7534 (tp) cc_final: 0.7327 (mp) REVERT: D 94 ASN cc_start: 0.8145 (m110) cc_final: 0.7903 (m110) REVERT: D 105 MET cc_start: 0.8814 (mmt) cc_final: 0.8515 (mmt) REVERT: D 117 MET cc_start: 0.8151 (tpp) cc_final: 0.7915 (tpt) REVERT: D 163 ASP cc_start: 0.7719 (t0) cc_final: 0.7285 (t0) REVERT: D 172 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7963 (mp0) REVERT: D 262 GLU cc_start: 0.8084 (tt0) cc_final: 0.7493 (pt0) REVERT: D 398 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6679 (tp30) REVERT: D 407 ASP cc_start: 0.7892 (t0) cc_final: 0.7627 (t0) REVERT: D 426 PHE cc_start: 0.7956 (m-80) cc_final: 0.7646 (m-80) REVERT: E 93 GLU cc_start: 0.7895 (tp30) cc_final: 0.7483 (tp30) REVERT: E 186 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8725 (mm) REVERT: E 225 ASN cc_start: 0.8512 (m-40) cc_final: 0.8295 (m110) REVERT: E 266 LEU cc_start: 0.7743 (tp) cc_final: 0.7362 (tp) REVERT: E 271 GLN cc_start: 0.7881 (tt0) cc_final: 0.7519 (mt0) REVERT: E 469 THR cc_start: 0.8368 (m) cc_final: 0.8137 (p) REVERT: E 474 GLN cc_start: 0.7586 (pt0) cc_final: 0.7313 (mt0) outliers start: 54 outliers final: 22 residues processed: 255 average time/residue: 1.2443 time to fit residues: 363.8760 Evaluate side-chains 214 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 1.995 ------------------------------------------------------------------------------- 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 126 SER 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 178 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 193 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 39 GLN A 58 GLN A 140 GLN B 87 GLN B 107 ASN C 26 HIS C 152 ASN C 187 ASN D 58 GLN E 39 ASN E 68 ASN E 196 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.130388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.103970 restraints weight = 23011.313| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.08 r_work: 0.3059 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17516 Z= 0.200 Angle : 0.639 12.774 23912 Z= 0.303 Chirality : 0.047 0.228 2843 Planarity : 0.004 0.039 2856 Dihedral : 17.552 138.008 3207 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.61 % Allowed : 12.47 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.19), residues: 1976 helix: 1.89 (0.19), residues: 752 sheet: -0.62 (0.25), residues: 406 loop : -1.03 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 86 HIS 0.005 0.001 HIS A 104 PHE 0.019 0.002 PHE A 256 TYR 0.015 0.002 TYR B 223 ARG 0.005 0.001 ARG C 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 7) link_NAG-ASN : angle 1.89083 ( 21) link_ALPHA1-6 : bond 0.01011 ( 9) link_ALPHA1-6 : angle 2.17985 ( 27) link_BETA1-4 : bond 0.00794 ( 14) link_BETA1-4 : angle 2.35531 ( 42) link_ALPHA1-2 : bond 0.02158 ( 1) link_ALPHA1-2 : angle 3.15616 ( 3) link_ALPHA1-3 : bond 0.00898 ( 9) link_ALPHA1-3 : angle 1.77261 ( 27) hydrogen bonds : bond 0.04358 ( 808) hydrogen bonds : angle 4.46130 ( 2547) SS BOND : bond 0.00413 ( 5) SS BOND : angle 3.59609 ( 10) covalent geometry : bond 0.00476 (17471) covalent geometry : angle 0.61840 (23782) *********************** 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 278 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 193 time to evaluate : 1.975 Fit side-chains revert: symmetry clash REVERT: A 36 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.8133 (pt0) REVERT: A 171 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7627 (ttt) REVERT: A 407 ASP cc_start: 0.7830 (m-30) cc_final: 0.7592 (m-30) REVERT: B 48 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8358 (mt-10) REVERT: B 93 MET cc_start: 0.8649 (mmm) cc_final: 0.8356 (mmt) REVERT: B 167 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.5942 (tp30) REVERT: B 182 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7591 (tm-30) REVERT: B 268 ASP cc_start: 0.8289 (m-30) cc_final: 0.7999 (m-30) REVERT: B 275 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8345 (mt) REVERT: B 284 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8180 (mp) REVERT: B 285 MET cc_start: 0.8188 (mmt) cc_final: 0.7857 (mmt) REVERT: C 5 GLU cc_start: 0.7712 (pt0) cc_final: 0.7125 (tt0) REVERT: C 186 GLU cc_start: 0.8222 (tt0) cc_final: 0.7845 (tp30) REVERT: C 280 GLU cc_start: 0.8078 (mp0) cc_final: 0.7427 (mt-10) REVERT: C 489 ASP cc_start: 0.7902 (t70) cc_final: 0.7651 (t0) REVERT: D 13 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8250 (tp30) REVERT: D 94 ASN cc_start: 0.8212 (m110) cc_final: 0.7922 (m110) REVERT: D 105 MET cc_start: 0.8802 (mmt) cc_final: 0.8582 (mmt) REVERT: D 207 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8312 (mtt) REVERT: D 262 GLU cc_start: 0.8143 (tt0) cc_final: 0.7615 (pt0) REVERT: D 407 ASP cc_start: 0.7941 (t0) cc_final: 0.7647 (t0) REVERT: E 14 ASP cc_start: 0.8412 (t70) cc_final: 0.8164 (t0) REVERT: E 93 GLU cc_start: 0.7973 (tp30) cc_final: 0.7572 (tp30) REVERT: E 186 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8744 (mm) REVERT: E 225 ASN cc_start: 0.8655 (m-40) cc_final: 0.8414 (m110) REVERT: E 266 LEU cc_start: 0.7840 (tp) cc_final: 0.7488 (tp) REVERT: E 469 THR cc_start: 0.8486 (m) cc_final: 0.8211 (p) REVERT: E 474 GLN cc_start: 0.7707 (pt0) cc_final: 0.7463 (mt0) outliers start: 85 outliers final: 31 residues processed: 246 average time/residue: 1.4109 time to fit residues: 396.8087 Evaluate side-chains 227 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 328 THR 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 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 321 VAL Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 207 MET 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 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 488 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 133 optimal weight: 0.8980 chunk 152 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 118 optimal weight: 0.0170 overall best weight: 0.6620 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.133415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.107168 restraints weight = 22924.980| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.09 r_work: 0.3102 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- 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: 6 | |-----------------------------------------------------------------------------| |-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: 6 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17516 Z= 0.117 Angle : 0.574 10.992 23912 Z= 0.269 Chirality : 0.044 0.268 2843 Planarity : 0.003 0.037 2856 Dihedral : 16.312 137.471 3207 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.63 % Allowed : 14.37 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.19), residues: 1976 helix: 2.11 (0.19), residues: 754 sheet: -0.59 (0.25), residues: 413 loop : -0.94 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 187 HIS 0.003 0.001 HIS A 299 PHE 0.014 0.001 PHE D 284 TYR 0.010 0.001 TYR C 117 ARG 0.003 0.000 ARG A 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00170 ( 7) link_NAG-ASN : angle 1.72258 ( 21) link_ALPHA1-6 : bond 0.01046 ( 9) link_ALPHA1-6 : angle 2.16050 ( 27) link_BETA1-4 : bond 0.00802 ( 14) link_BETA1-4 : angle 2.20817 ( 42) link_ALPHA1-2 : bond 0.01871 ( 1) link_ALPHA1-2 : angle 3.20051 ( 3) link_ALPHA1-3 : bond 0.00922 ( 9) link_ALPHA1-3 : angle 1.74729 ( 27) hydrogen bonds : bond 0.03876 ( 808) hydrogen bonds : angle 4.23800 ( 2547) SS BOND : bond 0.00394 ( 5) SS BOND : angle 2.98525 ( 10) covalent geometry : bond 0.00252 (17471) covalent geometry : angle 0.55390 (23782) *********************** 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 270 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 203 time to evaluate : 1.953 Fit side-chains REVERT: A 200 ASP cc_start: 0.8446 (p0) cc_final: 0.8140 (p0) REVERT: A 407 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7471 (m-30) REVERT: B 48 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8427 (mt-10) REVERT: B 93 MET cc_start: 0.8536 (mmm) cc_final: 0.8254 (mmt) REVERT: B 167 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6347 (pm20) REVERT: B 168 ARG cc_start: 0.7745 (tpp-160) cc_final: 0.7056 (mmt180) REVERT: B 268 ASP cc_start: 0.8240 (m-30) cc_final: 0.7976 (m-30) REVERT: B 275 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8312 (mt) REVERT: B 284 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8168 (mp) REVERT: B 314 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7436 (ttp) REVERT: C 5 GLU cc_start: 0.7681 (pt0) cc_final: 0.7073 (tt0) REVERT: C 186 GLU cc_start: 0.8185 (tt0) cc_final: 0.7816 (tp30) REVERT: C 489 ASP cc_start: 0.7922 (t70) cc_final: 0.7626 (t0) REVERT: D 13 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8264 (tp30) REVERT: D 94 ASN cc_start: 0.8094 (m110) cc_final: 0.7813 (m110) REVERT: D 105 MET cc_start: 0.8780 (mmt) cc_final: 0.8502 (mmt) REVERT: D 171 MET cc_start: 0.8290 (mtm) cc_final: 0.7844 (mtt) REVERT: D 262 GLU cc_start: 0.8099 (tt0) cc_final: 0.7568 (pt0) REVERT: D 398 GLU cc_start: 0.7264 (mm-30) cc_final: 0.6925 (tp30) REVERT: D 407 ASP cc_start: 0.7802 (t0) cc_final: 0.7474 (t0) REVERT: E 14 ASP cc_start: 0.8443 (t70) cc_final: 0.8176 (t0) REVERT: E 186 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8720 (mm) REVERT: E 225 ASN cc_start: 0.8565 (m-40) cc_final: 0.8344 (m110) REVERT: E 235 SER cc_start: 0.8722 (OUTLIER) cc_final: 0.8342 (p) REVERT: E 266 LEU cc_start: 0.7769 (tp) cc_final: 0.7373 (tp) REVERT: E 469 THR cc_start: 0.8488 (m) cc_final: 0.8232 (p) REVERT: E 474 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7443 (mt0) outliers start: 67 outliers final: 26 residues processed: 245 average time/residue: 0.9837 time to fit residues: 278.5462 Evaluate side-chains 224 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 189 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 231 LEU 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 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 314 MET 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 321 VAL Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 13 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 111 ASP Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 56 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 417 VAL Chi-restraints excluded: chain E residue 454 ILE Chi-restraints excluded: chain E residue 474 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 79 optimal weight: 0.0770 chunk 44 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 193 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- 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 E 53 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.130703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.103252 restraints weight = 23179.281| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.20 r_work: 0.3049 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17516 Z= 0.184 Angle : 0.619 11.322 23912 Z= 0.291 Chirality : 0.046 0.255 2843 Planarity : 0.004 0.035 2856 Dihedral : 15.637 134.288 3207 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.56 % Allowed : 14.10 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.19), residues: 1976 helix: 2.01 (0.19), residues: 753 sheet: -0.55 (0.25), residues: 414 loop : -0.95 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 187 HIS 0.004 0.001 HIS D 104 PHE 0.015 0.001 PHE C 473 TYR 0.012 0.001 TYR E 117 ARG 0.005 0.001 ARG C 81 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 7) link_NAG-ASN : angle 1.72181 ( 21) link_ALPHA1-6 : bond 0.01054 ( 9) link_ALPHA1-6 : angle 2.25392 ( 27) link_BETA1-4 : bond 0.00755 ( 14) link_BETA1-4 : angle 2.30229 ( 42) link_ALPHA1-2 : bond 0.01690 ( 1) link_ALPHA1-2 : angle 2.98059 ( 3) link_ALPHA1-3 : bond 0.00901 ( 9) link_ALPHA1-3 : angle 1.79810 ( 27) hydrogen bonds : bond 0.04128 ( 808) hydrogen bonds : angle 4.33904 ( 2547) SS BOND : bond 0.00565 ( 5) SS BOND : angle 3.27944 ( 10) covalent geometry : bond 0.00440 (17471) covalent geometry : angle 0.59842 (23782) *********************** 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 279 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 195 time to evaluate : 2.723 Fit side-chains REVERT: A 36 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8131 (mt0) REVERT: A 171 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7615 (ttt) REVERT: A 200 ASP cc_start: 0.8453 (p0) cc_final: 0.8142 (p0) REVERT: A 407 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7588 (m-30) REVERT: B 48 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8354 (mt-10) REVERT: B 167 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.5925 (tp30) REVERT: B 168 ARG cc_start: 0.7724 (tpp-160) cc_final: 0.6721 (mmt180) REVERT: B 268 ASP cc_start: 0.8234 (m-30) cc_final: 0.8026 (m-30) REVERT: B 284 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8223 (mp) REVERT: B 314 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7508 (ttp) REVERT: B 424 LEU cc_start: 0.6476 (OUTLIER) cc_final: 0.5816 (mm) REVERT: C 5 GLU cc_start: 0.7721 (pt0) cc_final: 0.7141 (tt0) REVERT: C 46 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7849 (ttpt) REVERT: C 186 GLU cc_start: 0.8159 (tt0) cc_final: 0.7802 (tp30) REVERT: C 277 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.6875 (mtp180) REVERT: C 280 GLU cc_start: 0.8044 (mp0) cc_final: 0.7415 (mt-10) REVERT: C 489 ASP cc_start: 0.7968 (t70) cc_final: 0.7671 (t0) REVERT: D 13 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8296 (tp30) REVERT: D 57 ARG cc_start: 0.8286 (ttm-80) cc_final: 0.8043 (mtp-110) REVERT: D 94 ASN cc_start: 0.8208 (m110) cc_final: 0.7871 (m110) REVERT: D 105 MET cc_start: 0.8725 (mmt) cc_final: 0.8453 (mmt) REVERT: D 108 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8311 (pp) REVERT: D 171 MET cc_start: 0.8412 (mtm) cc_final: 0.7976 (mtt) REVERT: D 262 GLU cc_start: 0.8146 (tt0) cc_final: 0.7591 (pt0) REVERT: D 398 GLU cc_start: 0.7348 (mm-30) cc_final: 0.6983 (tp30) REVERT: D 407 ASP cc_start: 0.7972 (t0) cc_final: 0.7621 (t0) REVERT: E 164 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7233 (mt-10) REVERT: E 186 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8746 (mm) REVERT: E 200 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8084 (p) REVERT: E 225 ASN cc_start: 0.8632 (m-40) cc_final: 0.8397 (m110) REVERT: E 235 SER cc_start: 0.8800 (OUTLIER) cc_final: 0.8433 (p) REVERT: E 266 LEU cc_start: 0.7826 (tp) cc_final: 0.7463 (tp) REVERT: E 469 THR cc_start: 0.8537 (m) cc_final: 0.8266 (p) REVERT: E 474 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7460 (mt0) outliers start: 84 outliers final: 41 residues processed: 248 average time/residue: 1.3046 time to fit residues: 373.4827 Evaluate side-chains 248 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 193 time to evaluate : 4.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 307 THR 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 416 LEU 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 199 SER 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 158 ILE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 277 ARG 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 23 GLU Chi-restraints excluded: chain D residue 40 LEU 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 108 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 111 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 chunk 152 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 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 D 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.132568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.105353 restraints weight = 22973.849| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.19 r_work: 0.3080 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- 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: 6 | |-----------------------------------------------------------------------------| |-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: 6 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17516 Z= 0.127 Angle : 0.583 11.017 23912 Z= 0.273 Chirality : 0.044 0.270 2843 Planarity : 0.003 0.036 2856 Dihedral : 14.915 132.835 3205 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.90 % Allowed : 15.18 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.19), residues: 1976 helix: 2.12 (0.19), residues: 753 sheet: -0.55 (0.25), residues: 414 loop : -0.92 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 60 HIS 0.004 0.001 HIS A 299 PHE 0.012 0.001 PHE C 473 TYR 0.009 0.001 TYR A 277 ARG 0.003 0.000 ARG A 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00186 ( 7) link_NAG-ASN : angle 1.66645 ( 21) link_ALPHA1-6 : bond 0.01115 ( 9) link_ALPHA1-6 : angle 2.23373 ( 27) link_BETA1-4 : bond 0.00790 ( 14) link_BETA1-4 : angle 2.19066 ( 42) link_ALPHA1-2 : bond 0.01888 ( 1) link_ALPHA1-2 : angle 3.23584 ( 3) link_ALPHA1-3 : bond 0.00902 ( 9) link_ALPHA1-3 : angle 1.73964 ( 27) hydrogen bonds : bond 0.03869 ( 808) hydrogen bonds : angle 4.23317 ( 2547) SS BOND : bond 0.00345 ( 5) SS BOND : angle 2.81903 ( 10) covalent geometry : bond 0.00284 (17471) covalent geometry : angle 0.56321 (23782) *********************** 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 272 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 200 time to evaluate : 1.802 Fit side-chains REVERT: A 200 ASP cc_start: 0.8509 (p0) cc_final: 0.8256 (p0) REVERT: A 407 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7558 (m-30) REVERT: B 48 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8392 (mt-10) REVERT: B 167 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.5912 (tp30) REVERT: B 168 ARG cc_start: 0.7732 (tpp-160) cc_final: 0.6747 (mmt180) REVERT: B 268 ASP cc_start: 0.8185 (m-30) cc_final: 0.7978 (m-30) REVERT: B 284 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8182 (mp) REVERT: B 314 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7437 (ttp) REVERT: B 424 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.5692 (mm) REVERT: C 5 GLU cc_start: 0.7699 (pt0) cc_final: 0.7100 (tt0) REVERT: C 186 GLU cc_start: 0.8140 (tt0) cc_final: 0.7782 (tp30) REVERT: C 277 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8444 (mtp-110) REVERT: C 489 ASP cc_start: 0.7807 (t70) cc_final: 0.7516 (t0) REVERT: D 57 ARG cc_start: 0.8263 (ttm-80) cc_final: 0.8031 (mtm110) REVERT: D 94 ASN cc_start: 0.8118 (m110) cc_final: 0.7817 (m110) REVERT: D 105 MET cc_start: 0.8690 (mmt) cc_final: 0.8435 (mmt) REVERT: D 108 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8305 (pp) REVERT: D 171 MET cc_start: 0.8360 (mtm) cc_final: 0.7932 (mtt) REVERT: D 208 GLN cc_start: 0.8538 (mm-40) cc_final: 0.8290 (mm110) REVERT: D 262 GLU cc_start: 0.8170 (tt0) cc_final: 0.7712 (pt0) REVERT: D 398 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6957 (tp30) REVERT: D 407 ASP cc_start: 0.7939 (t0) cc_final: 0.7585 (t0) REVERT: E 164 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7220 (mt-10) REVERT: E 200 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.8051 (p) REVERT: E 225 ASN cc_start: 0.8693 (m-40) cc_final: 0.8432 (m110) REVERT: E 266 LEU cc_start: 0.7747 (tp) cc_final: 0.7370 (tp) REVERT: E 469 THR cc_start: 0.8544 (m) cc_final: 0.8278 (p) REVERT: E 474 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7469 (mt0) outliers start: 72 outliers final: 36 residues processed: 246 average time/residue: 1.1988 time to fit residues: 338.5994 Evaluate side-chains 232 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 187 time to evaluate : 2.213 ------------------------------------------------------------------------------- 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 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 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 12 LEU 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 242 LEU Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain C residue 283 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 108 LEU 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 E residue 47 GLU 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 417 VAL Chi-restraints excluded: chain E residue 454 ILE Chi-restraints excluded: chain E residue 460 SER Chi-restraints excluded: chain E residue 474 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 195 optimal weight: 5.9990 chunk 177 optimal weight: 0.3980 chunk 114 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 78 optimal weight: 0.4980 chunk 174 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 141 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3574 r_free = 0.3574 target = 0.134625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.107536 restraints weight = 22842.192| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.18 r_work: 0.3111 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 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 = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17516 Z= 0.113 Angle : 0.566 10.586 23912 Z= 0.262 Chirality : 0.044 0.254 2843 Planarity : 0.003 0.036 2856 Dihedral : 13.785 128.754 3205 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.31 % Allowed : 15.73 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.19), residues: 1976 helix: 2.28 (0.19), residues: 749 sheet: -0.48 (0.25), residues: 415 loop : -0.89 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 60 HIS 0.004 0.001 HIS A 299 PHE 0.015 0.001 PHE D 227 TYR 0.010 0.001 TYR A 277 ARG 0.002 0.000 ARG A 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00177 ( 7) link_NAG-ASN : angle 1.50574 ( 21) link_ALPHA1-6 : bond 0.01261 ( 9) link_ALPHA1-6 : angle 2.19338 ( 27) link_BETA1-4 : bond 0.00819 ( 14) link_BETA1-4 : angle 2.15168 ( 42) link_ALPHA1-2 : bond 0.01953 ( 1) link_ALPHA1-2 : angle 3.35519 ( 3) link_ALPHA1-3 : bond 0.00894 ( 9) link_ALPHA1-3 : angle 1.68612 ( 27) hydrogen bonds : bond 0.03668 ( 808) hydrogen bonds : angle 4.10688 ( 2547) SS BOND : bond 0.00226 ( 5) SS BOND : angle 2.44084 ( 10) covalent geometry : bond 0.00240 (17471) covalent geometry : angle 0.54746 (23782) *********************** 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 266 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 205 time to evaluate : 2.152 Fit side-chains REVERT: A 200 ASP cc_start: 0.8375 (p0) cc_final: 0.8155 (p0) REVERT: A 400 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7233 (mptm) REVERT: A 407 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7491 (m-30) REVERT: B 48 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8413 (mt-10) REVERT: B 167 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.5956 (tp30) REVERT: B 182 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7584 (tm-30) REVERT: B 268 ASP cc_start: 0.8167 (m-30) cc_final: 0.7907 (m-30) REVERT: B 284 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8190 (mp) REVERT: B 424 LEU cc_start: 0.6506 (OUTLIER) cc_final: 0.5738 (mm) REVERT: C 5 GLU cc_start: 0.7606 (pt0) cc_final: 0.6984 (tt0) REVERT: C 168 ASP cc_start: 0.7116 (m-30) cc_final: 0.6611 (t0) REVERT: C 186 GLU cc_start: 0.8145 (tt0) cc_final: 0.7770 (tp30) REVERT: D 94 ASN cc_start: 0.7983 (m110) cc_final: 0.7708 (m110) REVERT: D 105 MET cc_start: 0.8651 (mmt) cc_final: 0.8383 (mmt) REVERT: D 171 MET cc_start: 0.8323 (mtm) cc_final: 0.7899 (mtt) REVERT: D 207 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8348 (mtt) REVERT: D 262 GLU cc_start: 0.8222 (tt0) cc_final: 0.7727 (pt0) REVERT: D 398 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6834 (tp30) REVERT: D 407 ASP cc_start: 0.7939 (t0) cc_final: 0.7518 (t0) REVERT: E 14 ASP cc_start: 0.8439 (t70) cc_final: 0.8217 (t0) REVERT: E 164 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7130 (mt-10) REVERT: E 200 THR cc_start: 0.8357 (OUTLIER) cc_final: 0.8050 (p) REVERT: E 225 ASN cc_start: 0.8648 (m-40) cc_final: 0.8416 (m110) REVERT: E 235 SER cc_start: 0.8717 (OUTLIER) cc_final: 0.8339 (p) REVERT: E 266 LEU cc_start: 0.7692 (tp) cc_final: 0.7369 (tp) REVERT: E 460 SER cc_start: 0.8160 (OUTLIER) cc_final: 0.7896 (m) REVERT: E 469 THR cc_start: 0.8519 (m) cc_final: 0.8266 (p) REVERT: E 474 GLN cc_start: 0.7628 (pt0) cc_final: 0.7391 (mt0) outliers start: 61 outliers final: 31 residues processed: 247 average time/residue: 1.3049 time to fit residues: 371.9610 Evaluate side-chains 236 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 195 time to evaluate : 2.211 ------------------------------------------------------------------------------- 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 400 LYS Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 416 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 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 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 178 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 207 MET 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 E residue 47 GLU 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 460 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 66 optimal weight: 0.2980 chunk 18 optimal weight: 2.9990 chunk 173 optimal weight: 0.9990 chunk 167 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 152 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 58 GLN A 140 GLN 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 = 0.3570 r_free = 0.3570 target = 0.134258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107288 restraints weight = 22751.071| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.17 r_work: 0.3111 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 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 = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17516 Z= 0.119 Angle : 0.572 10.424 23912 Z= 0.266 Chirality : 0.044 0.259 2843 Planarity : 0.003 0.036 2856 Dihedral : 13.145 122.297 3205 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.36 % Allowed : 16.27 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.19), residues: 1976 helix: 2.24 (0.19), residues: 758 sheet: -0.45 (0.25), residues: 414 loop : -0.93 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 187 HIS 0.004 0.001 HIS A 299 PHE 0.018 0.001 PHE D 284 TYR 0.011 0.001 TYR A 277 ARG 0.002 0.000 ARG A 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00162 ( 7) link_NAG-ASN : angle 1.50328 ( 21) link_ALPHA1-6 : bond 0.01289 ( 9) link_ALPHA1-6 : angle 2.06809 ( 27) link_BETA1-4 : bond 0.00807 ( 14) link_BETA1-4 : angle 2.16308 ( 42) link_ALPHA1-2 : bond 0.02096 ( 1) link_ALPHA1-2 : angle 3.49187 ( 3) link_ALPHA1-3 : bond 0.00847 ( 9) link_ALPHA1-3 : angle 1.67976 ( 27) hydrogen bonds : bond 0.03641 ( 808) hydrogen bonds : angle 4.10081 ( 2547) SS BOND : bond 0.00420 ( 5) SS BOND : angle 2.47237 ( 10) covalent geometry : bond 0.00261 (17471) covalent geometry : angle 0.55346 (23782) *********************** 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 258 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 196 time to evaluate : 1.830 Fit side-chains REVERT: A 36 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8308 (mt0) REVERT: A 200 ASP cc_start: 0.8399 (p0) cc_final: 0.8176 (p0) REVERT: A 400 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7570 (mptt) REVERT: A 407 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7471 (m-30) REVERT: B 48 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8412 (mt-10) REVERT: B 167 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.6386 (pm20) REVERT: B 182 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7585 (tm-30) REVERT: B 284 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8199 (mp) REVERT: B 424 LEU cc_start: 0.6517 (OUTLIER) cc_final: 0.5742 (mm) REVERT: C 5 GLU cc_start: 0.7683 (pt0) cc_final: 0.7076 (tt0) REVERT: C 168 ASP cc_start: 0.7093 (m-30) cc_final: 0.6582 (t0) REVERT: C 186 GLU cc_start: 0.8139 (tt0) cc_final: 0.7759 (tp30) REVERT: D 94 ASN cc_start: 0.7966 (m110) cc_final: 0.7731 (m110) REVERT: D 105 MET cc_start: 0.8656 (mmt) cc_final: 0.8385 (mmt) REVERT: D 117 MET cc_start: 0.8143 (tpt) cc_final: 0.7731 (tpt) REVERT: D 171 MET cc_start: 0.8344 (mtm) cc_final: 0.7923 (mtt) REVERT: D 207 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8376 (mtt) REVERT: D 398 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6808 (tp30) REVERT: D 407 ASP cc_start: 0.7970 (t0) cc_final: 0.7553 (t0) REVERT: E 164 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7146 (mt-10) REVERT: E 186 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8776 (mm) REVERT: E 200 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.8034 (p) REVERT: E 225 ASN cc_start: 0.8676 (m-40) cc_final: 0.8433 (m110) REVERT: E 266 LEU cc_start: 0.7755 (tp) cc_final: 0.7390 (tp) REVERT: E 460 SER cc_start: 0.8135 (OUTLIER) cc_final: 0.7881 (m) REVERT: E 469 THR cc_start: 0.8541 (m) cc_final: 0.8288 (p) REVERT: E 474 GLN cc_start: 0.7639 (pt0) cc_final: 0.7398 (mt0) outliers start: 62 outliers final: 33 residues processed: 234 average time/residue: 1.0403 time to fit residues: 279.5211 Evaluate side-chains 230 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 186 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 324 MET 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 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 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 158 ILE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 456 LEU 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 207 MET 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 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 287 LEU Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 460 SER 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 31 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 168 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 146 optimal weight: 0.4980 chunk 112 optimal weight: 9.9990 chunk 23 optimal weight: 0.1980 chunk 83 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 C 313 HIS D 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.134719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.107670 restraints weight = 22755.464| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.18 r_work: 0.3115 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2083 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= 0.116 Angle : 0.566 10.603 23912 Z= 0.264 Chirality : 0.044 0.228 2843 Planarity : 0.003 0.036 2856 Dihedral : 12.812 117.394 3205 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.93 % Allowed : 16.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.19), residues: 1976 helix: 2.25 (0.19), residues: 761 sheet: -0.45 (0.25), residues: 420 loop : -0.90 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 60 HIS 0.004 0.001 HIS A 299 PHE 0.015 0.001 PHE D 227 TYR 0.010 0.001 TYR A 277 ARG 0.002 0.000 ARG A 20 Details of bonding type rmsd link_NAG-ASN : bond 0.00168 ( 7) link_NAG-ASN : angle 1.50158 ( 21) link_ALPHA1-6 : bond 0.01332 ( 9) link_ALPHA1-6 : angle 2.02902 ( 27) link_BETA1-4 : bond 0.00818 ( 14) link_BETA1-4 : angle 2.15887 ( 42) link_ALPHA1-2 : bond 0.02196 ( 1) link_ALPHA1-2 : angle 3.58420 ( 3) link_ALPHA1-3 : bond 0.00825 ( 9) link_ALPHA1-3 : angle 1.66935 ( 27) hydrogen bonds : bond 0.03631 ( 808) hydrogen bonds : angle 4.08375 ( 2547) SS BOND : bond 0.00343 ( 5) SS BOND : angle 2.37742 ( 10) covalent geometry : bond 0.00252 (17471) covalent geometry : angle 0.54813 (23782) *********************** 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 246 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 192 time to evaluate : 1.848 Fit side-chains REVERT: A 36 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8049 (mt0) REVERT: A 200 ASP cc_start: 0.8398 (p0) cc_final: 0.8171 (p0) REVERT: A 400 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7333 (mptm) REVERT: A 407 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7438 (m-30) REVERT: B 48 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8420 (mt-10) REVERT: B 167 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6404 (pm20) REVERT: B 182 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7573 (tm-30) REVERT: B 284 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8225 (mp) REVERT: B 314 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7415 (ttp) REVERT: B 424 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.5747 (mm) REVERT: C 5 GLU cc_start: 0.7608 (pt0) cc_final: 0.6984 (tt0) REVERT: C 46 LYS cc_start: 0.8306 (ttpp) cc_final: 0.7739 (ptmt) REVERT: C 168 ASP cc_start: 0.7085 (m-30) cc_final: 0.6626 (t0) REVERT: C 186 GLU cc_start: 0.8180 (tt0) cc_final: 0.7760 (tp30) REVERT: D 94 ASN cc_start: 0.7921 (m110) cc_final: 0.7708 (m110) REVERT: D 105 MET cc_start: 0.8651 (mmt) cc_final: 0.8382 (mmt) REVERT: D 171 MET cc_start: 0.8352 (mtm) cc_final: 0.7935 (mtt) REVERT: D 207 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8425 (mtt) REVERT: D 208 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8535 (mm110) REVERT: D 262 GLU cc_start: 0.8151 (tt0) cc_final: 0.7808 (pt0) REVERT: D 398 GLU cc_start: 0.7217 (mm-30) cc_final: 0.6809 (tp30) REVERT: D 407 ASP cc_start: 0.7968 (t0) cc_final: 0.7549 (t0) REVERT: E 164 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7166 (mt-10) REVERT: E 186 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8767 (mm) REVERT: E 200 THR cc_start: 0.8375 (OUTLIER) cc_final: 0.8062 (p) REVERT: E 225 ASN cc_start: 0.8669 (m-40) cc_final: 0.8431 (m110) REVERT: E 266 LEU cc_start: 0.7735 (tp) cc_final: 0.7368 (tp) REVERT: E 460 SER cc_start: 0.8119 (OUTLIER) cc_final: 0.7876 (m) REVERT: E 469 THR cc_start: 0.8543 (m) cc_final: 0.8290 (p) REVERT: E 474 GLN cc_start: 0.7647 (pt0) cc_final: 0.7405 (mt0) outliers start: 54 outliers final: 32 residues processed: 229 average time/residue: 1.0077 time to fit residues: 265.8988 Evaluate side-chains 233 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 188 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 324 MET 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 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 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 178 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 58 GLN 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 207 MET Chi-restraints excluded: chain D residue 208 GLN 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 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 287 LEU Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 460 SER 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 159 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 C 451 GLN D 58 GLN ** D 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.134577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.107535 restraints weight = 22742.444| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.17 r_work: 0.3114 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 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 = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17516 Z= 0.121 Angle : 0.568 10.474 23912 Z= 0.266 Chirality : 0.044 0.240 2843 Planarity : 0.003 0.038 2856 Dihedral : 12.607 113.096 3205 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.66 % Allowed : 17.08 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.19), residues: 1976 helix: 2.24 (0.19), residues: 761 sheet: -0.43 (0.25), residues: 420 loop : -0.90 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 187 HIS 0.004 0.001 HIS A 299 PHE 0.013 0.001 PHE C 473 TYR 0.012 0.001 TYR A 277 ARG 0.006 0.000 ARG D 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00159 ( 7) link_NAG-ASN : angle 1.50234 ( 21) link_ALPHA1-6 : bond 0.01335 ( 9) link_ALPHA1-6 : angle 1.98344 ( 27) link_BETA1-4 : bond 0.00811 ( 14) link_BETA1-4 : angle 2.16485 ( 42) link_ALPHA1-2 : bond 0.02299 ( 1) link_ALPHA1-2 : angle 3.67645 ( 3) link_ALPHA1-3 : bond 0.00807 ( 9) link_ALPHA1-3 : angle 1.65844 ( 27) hydrogen bonds : bond 0.03638 ( 808) hydrogen bonds : angle 4.08980 ( 2547) SS BOND : bond 0.00321 ( 5) SS BOND : angle 2.37758 ( 10) covalent geometry : bond 0.00268 (17471) covalent geometry : angle 0.55028 (23782) ********************** 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: 49 poor density : 189 time to evaluate : 1.552 Fit side-chains REVERT: A 36 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8139 (mt0) REVERT: A 200 ASP cc_start: 0.8401 (p0) cc_final: 0.8171 (p0) REVERT: A 400 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7584 (mptt) REVERT: A 407 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7435 (m-30) REVERT: B 48 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8422 (mt-10) REVERT: B 167 GLU cc_start: 0.6625 (OUTLIER) cc_final: 0.6415 (pm20) REVERT: B 182 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7581 (tm-30) REVERT: B 284 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8228 (mp) REVERT: B 314 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7410 (ttp) REVERT: B 424 LEU cc_start: 0.6527 (OUTLIER) cc_final: 0.5769 (mm) REVERT: C 5 GLU cc_start: 0.7613 (pt0) cc_final: 0.6990 (tt0) REVERT: C 46 LYS cc_start: 0.8272 (ttpp) cc_final: 0.7660 (ptmt) REVERT: C 168 ASP cc_start: 0.7083 (m-30) cc_final: 0.6633 (t0) REVERT: C 186 GLU cc_start: 0.8171 (tt0) cc_final: 0.7753 (tp30) REVERT: D 94 ASN cc_start: 0.7911 (m110) cc_final: 0.7699 (m110) REVERT: D 105 MET cc_start: 0.8639 (mmt) cc_final: 0.8368 (mmt) REVERT: D 117 MET cc_start: 0.8000 (tpt) cc_final: 0.7612 (tpt) REVERT: D 171 MET cc_start: 0.8348 (mtm) cc_final: 0.7925 (mtt) REVERT: D 262 GLU cc_start: 0.8176 (tt0) cc_final: 0.7823 (pt0) REVERT: D 398 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6805 (tp30) REVERT: D 407 ASP cc_start: 0.7970 (t0) cc_final: 0.7549 (t0) REVERT: E 164 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7156 (mt-10) REVERT: E 186 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8771 (mm) REVERT: E 200 THR cc_start: 0.8372 (OUTLIER) cc_final: 0.8045 (p) REVERT: E 225 ASN cc_start: 0.8678 (m-40) cc_final: 0.8437 (m110) REVERT: E 266 LEU cc_start: 0.7746 (tp) cc_final: 0.7352 (tp) REVERT: E 460 SER cc_start: 0.8108 (OUTLIER) cc_final: 0.7871 (m) REVERT: E 469 THR cc_start: 0.8545 (m) cc_final: 0.8288 (p) REVERT: E 474 GLN cc_start: 0.7649 (pt0) cc_final: 0.7406 (mt0) outliers start: 49 outliers final: 34 residues processed: 223 average time/residue: 1.0525 time to fit residues: 268.6389 Evaluate side-chains 229 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 184 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 324 MET 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 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 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 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 178 ILE Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 58 GLN 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 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 287 LEU Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 460 SER 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 172 optimal weight: 3.9990 chunk 41 optimal weight: 0.0050 chunk 30 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 191 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- 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 D 140 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.134160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.107169 restraints weight = 22750.772| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.16 r_work: 0.3108 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 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 = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2117 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= 0.129 Angle : 0.572 10.480 23912 Z= 0.267 Chirality : 0.044 0.257 2843 Planarity : 0.003 0.037 2856 Dihedral : 12.457 108.811 3205 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.82 % Allowed : 16.81 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.19), residues: 1976 helix: 2.24 (0.19), residues: 760 sheet: -0.44 (0.25), residues: 416 loop : -0.92 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 60 HIS 0.004 0.001 HIS A 299 PHE 0.013 0.001 PHE E 267 TYR 0.012 0.001 TYR A 277 ARG 0.006 0.000 ARG D 57 Details of bonding type rmsd link_NAG-ASN : bond 0.00160 ( 7) link_NAG-ASN : angle 1.52076 ( 21) link_ALPHA1-6 : bond 0.01337 ( 9) link_ALPHA1-6 : angle 1.93914 ( 27) link_BETA1-4 : bond 0.00801 ( 14) link_BETA1-4 : angle 2.17458 ( 42) link_ALPHA1-2 : bond 0.02382 ( 1) link_ALPHA1-2 : angle 3.72719 ( 3) link_ALPHA1-3 : bond 0.00794 ( 9) link_ALPHA1-3 : angle 1.64897 ( 27) hydrogen bonds : bond 0.03664 ( 808) hydrogen bonds : angle 4.10641 ( 2547) SS BOND : bond 0.00325 ( 5) SS BOND : angle 2.44024 ( 10) covalent geometry : bond 0.00293 (17471) covalent geometry : angle 0.55444 (23782) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12312.43 seconds wall clock time: 217 minutes 29.75 seconds (13049.75 seconds total)