Starting phenix.real_space_refine on Sat Jul 4 01:33:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7qko_14048/07_2026/7qko_14048.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qko_14048/07_2026/7qko_14048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qko_14048/07_2026/7qko_14048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qko_14048/07_2026/7qko_14048.map" model { file = "/net/cci-nas-00/data/ceres_data/7qko_14048/07_2026/7qko_14048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qko_14048/07_2026/7qko_14048.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7qko_14048/07_2026/7qko_14048.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7qko_14048/07_2026/7qko_14048.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 85 5.16 5 C 11150 2.51 5 N 2615 2.21 5 O 3184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17042 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3210 Classifications: {'peptide': 396} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 375} Chain breaks: 1 Chain: "B" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3218 Classifications: {'peptide': 396} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 373} Chain breaks: 1 Chain: "C" Number of atoms: 3408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3408 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 392} Chain breaks: 1 Chain: "D" Number of atoms: 3089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3089 Classifications: {'peptide': 380} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 360} Chain breaks: 1 Chain: "E" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3278 Classifications: {'peptide': 404} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 382} Chain breaks: 1 Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen 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 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 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 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 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 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 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: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Time building chain proxies: 3.22, per 1000 atoms: 0.19 Number of scatterers: 17042 At special positions: 0 Unit cell: (103.05, 106.485, 172.895, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 85 16.00 P 8 15.00 O 3184 8.00 N 2615 7.00 C 11150 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS C 144 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN I 4 " - " MAN I 5 " ALPHA1-3 " BMA F 3 " - " MAN F 7 " " MAN F 4 " - " MAN F 5 " " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 7 " " MAN K 4 " - " MAN K 5 " " BMA L 3 " - " MAN L 7 " " MAN L 4 " - " MAN L 5 " ALPHA1-6 " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 6 " " BMA G 3 " - " MAN G 5 " " BMA H 3 " - " MAN H 5 " " BMA I 3 " - " MAN I 6 " " BMA K 3 " - " MAN K 4 " " MAN K 4 " - " MAN K 6 " " BMA L 3 " - " MAN L 4 " " MAN L 4 " - " MAN L 6 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG F 1 " - " ASN A 141 " " NAG G 1 " - " ASN B 141 " " NAG H 1 " - " ASN C 143 " " NAG I 1 " - " ASN C 70 " " NAG J 1 " - " ASN C 208 " " NAG K 1 " - " ASN D 141 " " NAG L 1 " - " ASN E 141 " Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 784.2 milliseconds 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3854 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 20 sheets defined 42.3% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 63 through 66 removed outlier: 3.588A pdb=" N ARG A 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 66' Processing helix chain 'A' and resid 68 through 73 removed outlier: 4.125A pdb=" N GLY A 73 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 211 through 231 removed outlier: 4.302A pdb=" N ILE A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Proline residue: A 221 - end of helix removed outlier: 3.793A pdb=" N GLY A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A 231 " --> pdb=" O PHE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 235 Processing helix chain 'A' and resid 241 through 264 Processing helix chain 'A' and resid 272 through 300 Processing helix chain 'A' and resid 309 through 318 removed outlier: 4.181A pdb=" N ASP A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 324 Processing helix chain 'A' and resid 371 through 434 removed outlier: 4.087A pdb=" N ILE A 376 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLY A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ARG A 429 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU A 430 " --> pdb=" O PHE A 426 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 12 removed outlier: 3.889A pdb=" N THR B 6 " --> pdb=" O VAL B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 72 Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 217 through 238 removed outlier: 4.940A pdb=" N ILE B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) Proline residue: B 227 - end of helix Processing helix chain 'B' and resid 239 through 241 No H-bonds generated for 'chain 'B' and resid 239 through 241' Processing helix chain 'B' and resid 242 through 246 Processing helix chain 'B' and resid 247 through 267 removed outlier: 4.094A pdb=" N SER B 254 " --> pdb=" O SER B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 306 Processing helix chain 'B' and resid 315 through 325 removed outlier: 3.888A pdb=" N ILE B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 331 removed outlier: 3.836A pdb=" N PHE B 329 " --> pdb=" O THR B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 461 removed outlier: 3.579A pdb=" N ASN B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 13 removed outlier: 4.276A pdb=" N ARG C 6 " --> pdb=" O ASN C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 232 through 244 removed outlier: 3.567A pdb=" N CYS C 236 " --> pdb=" O PHE C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 248 Processing helix chain 'C' and resid 255 through 276 removed outlier: 3.941A pdb=" N ALA C 260 " --> pdb=" O LYS C 256 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 314 Processing helix chain 'C' and resid 323 through 338 Proline residue: C 335 - end of helix Processing helix chain 'C' and resid 423 through 478 Proline residue: C 463 - end of helix Processing helix chain 'D' and resid 2 through 12 Processing helix chain 'D' and resid 68 through 73 removed outlier: 4.049A pdb=" N GLY D 73 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'D' and resid 211 through 230 removed outlier: 4.960A pdb=" N ILE D 220 " --> pdb=" O VAL D 216 " (cutoff:3.500A) Proline residue: D 221 - end of helix removed outlier: 4.078A pdb=" N GLY D 230 " --> pdb=" O SER D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 241 through 264 Processing helix chain 'D' and resid 272 through 300 Processing helix chain 'D' and resid 309 through 324 Proline residue: D 321 - end of helix Processing helix chain 'D' and resid 382 through 431 removed outlier: 3.710A pdb=" N PHE D 426 " --> pdb=" O THR D 422 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY D 428 " --> pdb=" O SER D 424 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ARG D 429 " --> pdb=" O VAL D 425 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE D 431 " --> pdb=" O ALA D 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 12 Processing helix chain 'E' and resid 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 131 through 135 removed outlier: 4.317A pdb=" N TYR E 134 " --> pdb=" O ALA E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 226 Processing helix chain 'E' and resid 226 through 235 Processing helix chain 'E' and resid 236 through 242 removed outlier: 3.588A pdb=" N VAL E 240 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR E 241 " --> pdb=" O VAL E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 272 removed outlier: 3.767A pdb=" N LYS E 272 " --> pdb=" O LEU E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 308 Processing helix chain 'E' and resid 318 through 328 removed outlier: 3.633A pdb=" N LYS E 322 " --> pdb=" O SER E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 470 removed outlier: 3.590A pdb=" N ASN E 439 " --> pdb=" O SER E 435 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TRP E 440 " --> pdb=" O GLU E 436 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY E 470 " --> pdb=" O ILE E 466 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 81 removed outlier: 4.421A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 81 removed outlier: 4.421A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASN A 53 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LEU A 40 " --> pdb=" O ASN A 53 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N ARG A 55 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE A 38 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ARG A 57 " --> pdb=" O GLN A 36 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N GLN A 36 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLN A 59 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLY A 34 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N ILE A 61 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 9.805A pdb=" N THR A 32 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 4.452A pdb=" N ILE A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 199 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP A 180 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLN A 208 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N MET A 178 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 77 through 80 removed outlier: 3.597A pdb=" N GLN B 111 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA B 115 " --> pdb=" O GLN B 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 77 through 80 removed outlier: 3.597A pdb=" N GLN B 111 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA B 115 " --> pdb=" O GLN B 111 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLU B 49 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU B 43 " --> pdb=" O GLU B 49 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THR B 51 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N PHE B 55 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LEU B 37 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASN B 57 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU B 35 " --> pdb=" O ASN B 57 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N ALA B 59 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL B 33 " --> pdb=" O ALA B 59 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N THR B 61 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N VAL B 31 " --> pdb=" O THR B 61 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.805A pdb=" N ILE B 212 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA8, first strand: chain 'C' and resid 80 through 82 Processing sheet with id=AA9, first strand: chain 'C' and resid 80 through 82 removed outlier: 6.816A pdb=" N THR C 51 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER C 44 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N THR C 53 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LEU C 42 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ASN C 55 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR C 63 " --> pdb=" O ASN C 32 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN C 32 " --> pdb=" O TYR C 63 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 92 through 94 removed outlier: 4.945A pdb=" N ALA C 150 " --> pdb=" O GLN C 213 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLN C 213 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 92 through 94 removed outlier: 4.945A pdb=" N ALA C 150 " --> pdb=" O GLN C 213 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLN C 213 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 164 through 166 Processing sheet with id=AB4, first strand: chain 'D' and resid 77 through 80 removed outlier: 4.313A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLY D 114 " --> pdb=" O ASP D 62 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 77 through 80 removed outlier: 4.313A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLY D 114 " --> pdb=" O ASP D 62 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE D 49 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL D 43 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLU D 51 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG D 55 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LEU D 37 " --> pdb=" O ARG D 55 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ARG D 57 " --> pdb=" O LEU D 35 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LEU D 35 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N GLN D 59 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL D 33 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N ILE D 61 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE D 31 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 10.829A pdb=" N VAL D 63 " --> pdb=" O VAL D 29 " (cutoff:3.500A) removed outlier: 12.961A pdb=" N VAL D 29 " --> pdb=" O VAL D 63 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 90 through 92 removed outlier: 4.694A pdb=" N ILE D 148 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU D 199 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N TYR D 198 " --> pdb=" O TRP D 187 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TRP D 187 " --> pdb=" O TYR D 198 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASP D 200 " --> pdb=" O LYS D 185 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS D 185 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR D 202 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLY D 183 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N HIS D 204 " --> pdb=" O TYR D 181 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TYR D 181 " --> pdb=" O HIS D 204 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE D 206 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 115 through 118 Processing sheet with id=AB8, first strand: chain 'E' and resid 115 through 118 removed outlier: 6.741A pdb=" N ASN E 53 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU E 40 " --> pdb=" O ASN E 53 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N TRP E 55 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR E 38 " --> pdb=" O TRP E 55 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N GLU E 57 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N THR E 36 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N GLN E 59 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N LYS E 34 " --> pdb=" O GLN E 59 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N ASN E 61 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 9.961A pdb=" N THR E 32 " --> pdb=" O ASN E 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 77 through 81 Processing sheet with id=AC1, first strand: chain 'E' and resid 90 through 92 removed outlier: 3.828A pdb=" N CYS E 142 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE E 214 " --> pdb=" O ARG E 187 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 90 through 92 removed outlier: 3.828A pdb=" N CYS E 142 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) 884 hydrogen bonds defined for protein. 2547 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.85 Time building geometry restraints manager: 2.30 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: 9805 31.27 - 62.53: 258 62.53 - 93.80: 17 93.80 - 125.07: 3 125.07 - 156.34: 7 Dihedral angle restraints: 10090 sinusoidal: 4169 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 10087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2387 0.060 - 0.119: 400 0.119 - 0.179: 46 0.179 - 0.239: 4 0.239 - 0.299: 6 Chirality restraints: 2843 Sorted by residual: chirality pdb=" C5 BMA L 3 " pdb=" C4 BMA L 3 " pdb=" C6 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 2840 not shown) Planarity restraints: 2863 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 119 " 0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO E 120 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO E 120 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 120 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET E 291 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C MET E 291 " 0.029 2.00e-02 2.50e+03 pdb=" O MET E 291 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE E 292 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 316 " 0.007 2.00e-02 2.50e+03 1.50e-02 2.26e+00 pdb=" C PHE D 316 " -0.026 2.00e-02 2.50e+03 pdb=" O PHE D 316 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE D 317 " 0.009 2.00e-02 2.50e+03 ... (remaining 2860 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3094 2.77 - 3.31: 16462 3.31 - 3.84: 28638 3.84 - 4.37: 33511 4.37 - 4.90: 57926 Nonbonded interactions: 139631 Sorted by model distance: nonbonded pdb=" OD1 ASN E 68 " pdb=" OG SER E 70 " model vdw 2.242 3.040 nonbonded pdb=" O LEU E 92 " pdb=" ND2 ASN E 95 " model vdw 2.254 3.120 nonbonded pdb=" O ILE A 315 " pdb=" OG1 THR A 319 " model vdw 2.257 3.040 nonbonded pdb=" OD1 ASN B 107 " pdb=" ND2 ASN C 152 " model vdw 2.268 3.120 nonbonded pdb=" O GLY A 153 " pdb=" OG1 THR A 154 " model vdw 2.278 3.040 ... (remaining 139626 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 328 or resid 381 through 432 or (resid 501 and ( \ name N or name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or \ name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 \ or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 or name \ C33 or name C34 or name C35 or name C36 or name O11 or name O12 or name O13 or n \ ame O14 or name O21 or name O22 or name O31 or name O32 or name P )) or (resid 5 \ 02 and (name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or n \ ame C26 or name C27 or name C28 or name C29 or name C3 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name O21 or name O22 or name O \ 31 or name O32)))) selection = (chain 'D' and (resid 1 through 501 or (resid 502 and (name C2 or name C21 or na \ me C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 o \ r name C29 or name C3 or name C31 or name C32 or name C33 or name C34 or name C3 \ 5 or name C36 or name O21 or name O22 or name O31 or name O32)))) } ncs_group { reference = (chain 'F' and (resid 2 or resid 5 through 7)) selection = (chain 'I' and (resid 1 or resid 4 through 6)) selection = (chain 'K' and (resid 2 or resid 5 through 7)) selection = (chain 'L' and (resid 2 or resid 5 through 7)) } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.790 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 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 : 14.224 156.336 6221 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.25 % Allowed : 5.42 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.19), residues: 1976 helix: 1.85 (0.19), residues: 745 sheet: -0.76 (0.25), residues: 408 loop : -1.01 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 81 TYR 0.008 0.001 TYR C 439 PHE 0.010 0.001 PHE A 284 TRP 0.012 0.001 TRP D 187 HIS 0.004 0.001 HIS E 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.31 (17471) covalent geometry : angle 0.84479 / 0.35 (23782) SS BOND : bond 0.00233 / 0.12 ( 5) SS BOND : angle 0.77949 / 0.49 ( 10) hydrogen bonds : bond 0.10968 / 7.54 ( 808) hydrogen bonds : angle 5.12137 / 3.62 ( 2547) link_ALPHA1-2 : bond 0.00928 / 0.49 ( 1) link_ALPHA1-2 : angle 1.72369 / 0.95 ( 3) link_ALPHA1-3 : bond 0.00418 / 0.24 ( 9) link_ALPHA1-3 : angle 1.80385 / 1.16 ( 27) link_ALPHA1-6 : bond 0.00635 / 0.39 ( 9) link_ALPHA1-6 : angle 1.74213 / 1.21 ( 27) link_BETA1-4 : bond 0.00835 / 0.61 ( 14) link_BETA1-4 : angle 2.10986 / 1.30 ( 42) link_NAG-ASN : bond 0.00149 / 0.08 ( 7) link_NAG-ASN : angle 1.57553 / 0.90 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 311 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: A 36 GLN cc_start: 0.7824 (pt0) cc_final: 0.7529 (pt0) REVERT: A 324 MET cc_start: 0.8341 (mtm) cc_final: 0.7944 (mtm) REVERT: B 48 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7879 (mt-10) REVERT: B 93 MET cc_start: 0.8248 (mmm) cc_final: 0.7804 (mmt) REVERT: B 177 LYS cc_start: 0.8099 (tmtt) cc_final: 0.7796 (tmtp) REVERT: B 268 ASP cc_start: 0.7838 (m-30) cc_final: 0.7114 (m-30) REVERT: B 275 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8131 (mt) REVERT: B 285 MET cc_start: 0.7745 (mmt) cc_final: 0.7343 (mmt) REVERT: C 5 GLU cc_start: 0.7199 (pt0) cc_final: 0.6742 (tt0) REVERT: C 46 LYS cc_start: 0.7172 (tttp) cc_final: 0.6695 (mtpt) REVERT: C 49 ASP cc_start: 0.7831 (m-30) cc_final: 0.7403 (m-30) REVERT: C 186 GLU cc_start: 0.7809 (tt0) cc_final: 0.7544 (tp30) REVERT: C 280 GLU cc_start: 0.7752 (mp0) cc_final: 0.7140 (mt-10) REVERT: D 13 GLU cc_start: 0.8141 (tp30) cc_final: 0.7374 (pm20) REVERT: D 45 GLU cc_start: 0.8205 (mp0) cc_final: 0.7956 (mp0) REVERT: D 94 ASN cc_start: 0.7990 (m110) cc_final: 0.7517 (m110) REVERT: D 105 MET cc_start: 0.8637 (mmt) cc_final: 0.8305 (mmt) REVERT: D 163 ASP cc_start: 0.7105 (t0) cc_final: 0.6731 (t0) REVERT: D 171 MET cc_start: 0.7413 (mtm) cc_final: 0.7131 (mtt) REVERT: D 172 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7784 (mp0) REVERT: D 320 ILE cc_start: 0.6325 (mm) cc_final: 0.6061 (mm) REVERT: D 398 GLU cc_start: 0.6830 (mm-30) cc_final: 0.6489 (tp30) REVERT: E 44 ASN cc_start: 0.7183 (t0) cc_final: 0.6541 (t0) REVERT: E 48 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7750 (mt-10) REVERT: E 93 GLU cc_start: 0.7426 (tp30) cc_final: 0.6980 (tp30) REVERT: E 166 GLU cc_start: 0.7121 (pt0) cc_final: 0.6807 (pt0) REVERT: E 225 ASN cc_start: 0.8138 (m-40) cc_final: 0.7931 (m110) REVERT: E 469 THR cc_start: 0.8270 (m) cc_final: 0.8025 (p) REVERT: E 474 GLN cc_start: 0.7323 (pt0) cc_final: 0.7010 (mt0) outliers start: 23 outliers final: 4 residues processed: 329 average time/residue: 0.4913 time to fit residues: 184.0936 Evaluate side-chains 202 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 197 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 280 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.0670 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3581 r_free = 0.3581 target = 0.135137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.108872 restraints weight = 22941.000| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.08 r_work: 0.3132 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 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 = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 17516 Z= 0.115 Angle : 0.554 8.186 23912 Z= 0.269 Chirality : 0.043 0.158 2843 Planarity : 0.004 0.038 2856 Dihedral : 14.496 137.563 2370 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.71 % Allowed : 12.53 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.19), residues: 1976 helix: 2.02 (0.19), residues: 755 sheet: -0.64 (0.25), residues: 418 loop : -1.01 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 113 TYR 0.012 0.001 TYR C 117 PHE 0.012 0.001 PHE C 473 TRP 0.011 0.001 TRP A 60 HIS 0.004 0.001 HIS A 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (17471) covalent geometry : angle 0.53795 / 0.27 (23782) SS BOND : bond 0.00180 / 0.09 ( 5) SS BOND : angle 2.95184 / 1.83 ( 10) hydrogen bonds : bond 0.04111 / 2.63 ( 808) hydrogen bonds : angle 4.37152 / 3.12 ( 2547) link_ALPHA1-2 : bond 0.01286 / 0.68 ( 1) link_ALPHA1-2 : angle 2.42723 / 1.33 ( 3) link_ALPHA1-3 : bond 0.00454 / 0.26 ( 9) link_ALPHA1-3 : angle 1.64448 / 1.11 ( 27) link_ALPHA1-6 : bond 0.00755 / 0.48 ( 9) link_ALPHA1-6 : angle 1.60523 / 1.11 ( 27) link_BETA1-4 : bond 0.00812 / 0.59 ( 14) link_BETA1-4 : angle 1.98289 / 1.27 ( 42) link_NAG-ASN : bond 0.00186 / 0.10 ( 7) link_NAG-ASN : angle 1.61914 / 0.99 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 225 time to evaluate : 0.644 Fit side-chains REVERT: A 407 ASP cc_start: 0.7662 (OUTLIER) cc_final: 0.7275 (m-30) REVERT: B 48 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8308 (mt-10) REVERT: B 93 MET cc_start: 0.8616 (mmm) cc_final: 0.8354 (mmm) REVERT: B 167 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.5860 (tp30) REVERT: B 168 ARG cc_start: 0.7774 (tpp-160) cc_final: 0.6873 (mmt180) REVERT: B 177 LYS cc_start: 0.8163 (tmtt) cc_final: 0.7923 (tmtp) REVERT: B 268 ASP cc_start: 0.8173 (m-30) cc_final: 0.7783 (m-30) REVERT: B 275 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8298 (mt) REVERT: B 285 MET cc_start: 0.8172 (mmt) cc_final: 0.7840 (mmt) REVERT: C 5 GLU cc_start: 0.7623 (pt0) cc_final: 0.7030 (tt0) REVERT: C 186 GLU cc_start: 0.8239 (tt0) cc_final: 0.7815 (tp30) REVERT: C 242 LEU cc_start: 0.7539 (tp) cc_final: 0.7328 (mp) REVERT: D 94 ASN cc_start: 0.8150 (m110) cc_final: 0.7911 (m110) REVERT: D 105 MET cc_start: 0.8814 (mmt) cc_final: 0.8515 (mmt) REVERT: D 117 MET cc_start: 0.8125 (tpp) cc_final: 0.7892 (tpt) REVERT: D 163 ASP cc_start: 0.7717 (t0) cc_final: 0.7279 (t0) REVERT: D 171 MET cc_start: 0.7863 (mtm) cc_final: 0.7574 (mtt) REVERT: D 172 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7947 (mp0) REVERT: D 262 GLU cc_start: 0.8117 (tt0) cc_final: 0.7493 (pt0) REVERT: D 398 GLU cc_start: 0.7191 (mm-30) cc_final: 0.6670 (tp30) REVERT: D 407 ASP cc_start: 0.7891 (t0) cc_final: 0.7611 (t0) REVERT: D 426 PHE cc_start: 0.7989 (m-80) cc_final: 0.7691 (m-80) REVERT: E 44 ASN cc_start: 0.7608 (t0) cc_final: 0.6867 (t0) REVERT: E 93 GLU cc_start: 0.7906 (tp30) cc_final: 0.7493 (tp30) REVERT: E 186 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8730 (mm) REVERT: E 266 LEU cc_start: 0.7671 (tp) cc_final: 0.7292 (tp) REVERT: E 271 GLN cc_start: 0.7882 (tt0) cc_final: 0.7528 (mt0) REVERT: E 469 THR cc_start: 0.8373 (m) cc_final: 0.8143 (p) REVERT: E 474 GLN cc_start: 0.7585 (pt0) cc_final: 0.7315 (mt0) outliers start: 50 outliers final: 25 residues processed: 256 average time/residue: 0.4440 time to fit residues: 130.8996 Evaluate side-chains 218 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLN Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 207 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 85 LEU Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 454 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 48 optimal weight: 0.0050 chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 181 optimal weight: 0.7980 chunk 180 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 GLN A 140 GLN B 87 GLN B 107 ASN C 152 ASN D 58 GLN E 39 ASN E 68 ASN E 196 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.133156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.106919 restraints weight = 23163.390| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.11 r_work: 0.3099 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 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 = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1287 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= 0.139 Angle : 0.560 12.017 23912 Z= 0.271 Chirality : 0.043 0.221 2843 Planarity : 0.004 0.037 2856 Dihedral : 13.711 139.067 2369 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.85 % Allowed : 12.64 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.19), residues: 1976 helix: 2.05 (0.19), residues: 752 sheet: -0.62 (0.25), residues: 412 loop : -0.98 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 57 TYR 0.011 0.001 TYR B 223 PHE 0.015 0.001 PHE A 256 TRP 0.011 0.001 TRP D 187 HIS 0.004 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (17471) covalent geometry : angle 0.54281 / 0.27 (23782) SS BOND : bond 0.00593 / 0.30 ( 5) SS BOND : angle 3.31577 / 2.03 ( 10) hydrogen bonds : bond 0.04026 / 2.56 ( 808) hydrogen bonds : angle 4.32707 / 3.10 ( 2547) link_ALPHA1-2 : bond 0.01234 / 0.65 ( 1) link_ALPHA1-2 : angle 1.84269 / 1.00 ( 3) link_ALPHA1-3 : bond 0.00501 / 0.29 ( 9) link_ALPHA1-3 : angle 1.52447 / 0.99 ( 27) link_ALPHA1-6 : bond 0.00804 / 0.51 ( 9) link_ALPHA1-6 : angle 1.56485 / 1.06 ( 27) link_BETA1-4 : bond 0.00762 / 0.56 ( 14) link_BETA1-4 : angle 2.01431 / 1.26 ( 42) link_NAG-ASN : bond 0.00171 / 0.08 ( 7) link_NAG-ASN : angle 1.79218 / 1.10 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 199 time to evaluate : 0.668 Fit side-chains REVERT: A 407 ASP cc_start: 0.7792 (m-30) cc_final: 0.7504 (m-30) REVERT: B 48 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8342 (mt-10) REVERT: B 93 MET cc_start: 0.8623 (mmm) cc_final: 0.8194 (mmt) REVERT: B 167 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.6296 (pm20) REVERT: B 168 ARG cc_start: 0.7797 (tpp-160) cc_final: 0.7114 (mmt180) REVERT: B 177 LYS cc_start: 0.8179 (tmtt) cc_final: 0.7929 (tmtp) REVERT: B 268 ASP cc_start: 0.8223 (m-30) cc_final: 0.7929 (m-30) REVERT: B 275 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8310 (mt) REVERT: B 284 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8111 (mp) REVERT: C 5 GLU cc_start: 0.7674 (pt0) cc_final: 0.7082 (tt0) REVERT: C 46 LYS cc_start: 0.7851 (mtpp) cc_final: 0.7609 (ttpt) REVERT: C 186 GLU cc_start: 0.8236 (tt0) cc_final: 0.7825 (tp30) REVERT: C 242 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7409 (mp) REVERT: C 280 GLU cc_start: 0.7992 (mp0) cc_final: 0.7377 (mt-10) REVERT: D 13 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.7670 (pm20) REVERT: D 94 ASN cc_start: 0.8167 (m110) cc_final: 0.7923 (m110) REVERT: D 105 MET cc_start: 0.8834 (mmt) cc_final: 0.8557 (mmt) REVERT: D 171 MET cc_start: 0.7979 (mtm) cc_final: 0.7676 (mtt) REVERT: D 172 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7984 (mp0) REVERT: D 262 GLU cc_start: 0.8113 (tt0) cc_final: 0.7594 (pt0) REVERT: D 398 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6850 (tp30) REVERT: D 407 ASP cc_start: 0.7949 (t0) cc_final: 0.7638 (t0) REVERT: E 14 ASP cc_start: 0.8416 (t70) cc_final: 0.8131 (t0) REVERT: E 93 GLU cc_start: 0.7983 (tp30) cc_final: 0.7562 (tp30) REVERT: E 186 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8777 (mm) REVERT: E 225 ASN cc_start: 0.8272 (m110) cc_final: 0.7924 (m-40) REVERT: E 266 LEU cc_start: 0.7690 (tp) cc_final: 0.7284 (tp) REVERT: E 469 THR cc_start: 0.8419 (m) cc_final: 0.8165 (p) REVERT: E 474 GLN cc_start: 0.7642 (pt0) cc_final: 0.7377 (mt0) outliers start: 71 outliers final: 27 residues processed: 245 average time/residue: 0.4786 time to fit residues: 135.3360 Evaluate side-chains 222 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 423 VAL Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 242 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 89 ASP Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 416 LEU Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 108 VAL 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 454 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 190 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 185 optimal weight: 7.9990 chunk 8 optimal weight: 0.0000 chunk 75 optimal weight: 2.9990 overall best weight: 1.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 GLN A 39 GLN A 58 GLN C 26 HIS C 187 ASN D 58 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.131396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.105014 restraints weight = 23164.168| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.09 r_work: 0.3072 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17516 Z= 0.163 Angle : 0.574 11.082 23912 Z= 0.277 Chirality : 0.044 0.161 2843 Planarity : 0.004 0.035 2856 Dihedral : 12.955 137.612 2369 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.45 % Allowed : 13.39 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.19), residues: 1976 helix: 2.04 (0.19), residues: 752 sheet: -0.60 (0.25), residues: 408 loop : -0.99 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 81 TYR 0.011 0.001 TYR B 223 PHE 0.015 0.001 PHE A 256 TRP 0.011 0.001 TRP D 187 HIS 0.004 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (17471) covalent geometry : angle 0.55753 / 0.27 (23782) SS BOND : bond 0.00355 / 0.18 ( 5) SS BOND : angle 3.34753 / 2.06 ( 10) hydrogen bonds : bond 0.04060 / 2.57 ( 808) hydrogen bonds : angle 4.33116 / 3.09 ( 2547) link_ALPHA1-2 : bond 0.01060 / 0.56 ( 1) link_ALPHA1-2 : angle 1.58287 / 0.86 ( 3) link_ALPHA1-3 : bond 0.00498 / 0.29 ( 9) link_ALPHA1-3 : angle 1.49208 / 0.98 ( 27) link_ALPHA1-6 : bond 0.00795 / 0.51 ( 9) link_ALPHA1-6 : angle 1.61774 / 1.09 ( 27) link_BETA1-4 : bond 0.00744 / 0.55 ( 14) link_BETA1-4 : angle 2.06625 / 1.30 ( 42) link_NAG-ASN : bond 0.00269 / 0.15 ( 7) link_NAG-ASN : angle 1.78342 / 1.11 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 202 time to evaluate : 0.703 Fit side-chains REVERT: A 200 ASP cc_start: 0.8398 (p0) cc_final: 0.8062 (p0) REVERT: A 407 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7549 (m-30) REVERT: B 48 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8352 (mt-10) REVERT: B 93 MET cc_start: 0.8643 (mmm) cc_final: 0.8262 (mmt) REVERT: B 167 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6297 (pm20) REVERT: B 168 ARG cc_start: 0.7801 (tpp-160) cc_final: 0.7150 (mmt180) REVERT: B 182 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7553 (tm-30) REVERT: B 268 ASP cc_start: 0.8259 (m-30) cc_final: 0.7969 (m-30) REVERT: B 275 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8317 (mt) REVERT: B 284 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8168 (mp) REVERT: B 314 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.7494 (ttp) REVERT: C 5 GLU cc_start: 0.7707 (pt0) cc_final: 0.7108 (tt0) REVERT: C 46 LYS cc_start: 0.7876 (mtpp) cc_final: 0.7592 (mtpt) REVERT: C 186 GLU cc_start: 0.8211 (tt0) cc_final: 0.7837 (tp30) REVERT: C 280 GLU cc_start: 0.8006 (mp0) cc_final: 0.7353 (mt-10) REVERT: C 489 ASP cc_start: 0.7955 (t70) cc_final: 0.7670 (t0) REVERT: D 13 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8275 (tp30) REVERT: D 94 ASN cc_start: 0.8175 (m110) cc_final: 0.7879 (m110) REVERT: D 105 MET cc_start: 0.8796 (mmt) cc_final: 0.8508 (mmt) REVERT: D 171 MET cc_start: 0.8095 (mtm) cc_final: 0.7762 (mtt) REVERT: D 172 GLU cc_start: 0.8240 (mm-30) cc_final: 0.8025 (mp0) REVERT: D 262 GLU cc_start: 0.8122 (tt0) cc_final: 0.7526 (pt0) REVERT: D 398 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6940 (tp30) REVERT: D 407 ASP cc_start: 0.7822 (t0) cc_final: 0.7498 (t0) REVERT: E 93 GLU cc_start: 0.7960 (tp30) cc_final: 0.7558 (tp30) REVERT: E 225 ASN cc_start: 0.8357 (m110) cc_final: 0.8011 (m-40) REVERT: E 266 LEU cc_start: 0.7786 (tp) cc_final: 0.7416 (tp) REVERT: E 271 GLN cc_start: 0.7936 (tt0) cc_final: 0.7708 (mt0) REVERT: E 469 THR cc_start: 0.8501 (m) cc_final: 0.8238 (p) REVERT: E 474 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7465 (mt0) outliers start: 82 outliers final: 37 residues processed: 251 average time/residue: 0.4828 time to fit residues: 139.8844 Evaluate side-chains 239 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 194 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 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 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 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 111 ASP Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 282 MET 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 133 THR Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 474 GLN Chi-restraints excluded: chain E residue 488 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 124 optimal weight: 0.0670 chunk 133 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 137 optimal weight: 0.0470 chunk 10 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 22 optimal weight: 0.0970 chunk 1 optimal weight: 0.5980 overall best weight: 0.7616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3560 r_free = 0.3560 target = 0.133426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.107079 restraints weight = 22923.640| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.12 r_work: 0.3102 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 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 = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1652 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= 0.114 Angle : 0.532 10.701 23912 Z= 0.257 Chirality : 0.042 0.156 2843 Planarity : 0.003 0.036 2856 Dihedral : 12.358 136.632 2369 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.63 % Allowed : 15.24 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.19), residues: 1976 helix: 2.13 (0.19), residues: 761 sheet: -0.54 (0.25), residues: 413 loop : -0.93 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 20 TYR 0.009 0.001 TYR A 277 PHE 0.010 0.001 PHE A 256 TRP 0.012 0.001 TRP D 187 HIS 0.004 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (17471) covalent geometry : angle 0.51650 / 0.25 (23782) SS BOND : bond 0.00448 / 0.23 ( 5) SS BOND : angle 2.81723 / 1.72 ( 10) hydrogen bonds : bond 0.03780 / 2.41 ( 808) hydrogen bonds : angle 4.17938 / 2.98 ( 2547) link_ALPHA1-2 : bond 0.01057 / 0.56 ( 1) link_ALPHA1-2 : angle 1.58202 / 0.85 ( 3) link_ALPHA1-3 : bond 0.00491 / 0.28 ( 9) link_ALPHA1-3 : angle 1.45360 / 0.95 ( 27) link_ALPHA1-6 : bond 0.00769 / 0.49 ( 9) link_ALPHA1-6 : angle 1.54886 / 1.07 ( 27) link_BETA1-4 : bond 0.00744 / 0.55 ( 14) link_BETA1-4 : angle 1.93571 / 1.22 ( 42) link_NAG-ASN : bond 0.00147 / 0.07 ( 7) link_NAG-ASN : angle 1.63945 / 1.00 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 201 time to evaluate : 0.708 Fit side-chains REVERT: A 36 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8201 (mt0) REVERT: A 200 ASP cc_start: 0.8500 (p0) cc_final: 0.8272 (p0) REVERT: A 258 LEU cc_start: 0.7338 (mt) cc_final: 0.7115 (mp) REVERT: A 407 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7528 (m-30) REVERT: B 48 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8266 (mt-10) REVERT: B 93 MET cc_start: 0.8621 (mmm) cc_final: 0.8195 (mmt) REVERT: B 167 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.6262 (pm20) REVERT: B 168 ARG cc_start: 0.7764 (tpp-160) cc_final: 0.7087 (mmt180) REVERT: B 268 ASP cc_start: 0.8195 (m-30) cc_final: 0.7952 (m-30) REVERT: B 284 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8173 (mp) REVERT: B 424 LEU cc_start: 0.6416 (OUTLIER) cc_final: 0.5649 (mm) REVERT: C 5 GLU cc_start: 0.7681 (pt0) cc_final: 0.7080 (tt0) REVERT: C 46 LYS cc_start: 0.7956 (mtpp) cc_final: 0.7649 (mtpt) REVERT: C 85 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8486 (pt0) REVERT: C 186 GLU cc_start: 0.8185 (tt0) cc_final: 0.7824 (tp30) REVERT: D 94 ASN cc_start: 0.8089 (m110) cc_final: 0.7840 (m110) REVERT: D 105 MET cc_start: 0.8738 (mmt) cc_final: 0.8473 (mmt) REVERT: D 171 MET cc_start: 0.8053 (mtm) cc_final: 0.7739 (mtt) REVERT: D 172 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7973 (mp0) REVERT: D 262 GLU cc_start: 0.8140 (tt0) cc_final: 0.7639 (pt0) REVERT: D 398 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6939 (tp30) REVERT: D 407 ASP cc_start: 0.7937 (t0) cc_final: 0.7556 (t0) REVERT: E 186 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8738 (mm) REVERT: E 200 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.7972 (p) REVERT: E 225 ASN cc_start: 0.8300 (m110) cc_final: 0.7956 (m-40) REVERT: E 235 SER cc_start: 0.8681 (OUTLIER) cc_final: 0.8337 (p) REVERT: E 266 LEU cc_start: 0.7785 (tp) cc_final: 0.7390 (tp) REVERT: E 469 THR cc_start: 0.8497 (m) cc_final: 0.8252 (p) REVERT: E 474 GLN cc_start: 0.7692 (pt0) cc_final: 0.7444 (mt0) outliers start: 67 outliers final: 28 residues processed: 244 average time/residue: 0.4956 time to fit residues: 139.3077 Evaluate side-chains 226 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 189 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLN Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 154 THR 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 56 ILE Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 454 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 86 optimal weight: 0.0020 chunk 155 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 140 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 197 optimal weight: 0.0770 overall best weight: 0.5546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 GLN A 58 GLN A 140 GLN ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3572 r_free = 0.3572 target = 0.134448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.107476 restraints weight = 22733.108| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.17 r_work: 0.3111 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 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 = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17516 Z= 0.105 Angle : 0.526 10.410 23912 Z= 0.254 Chirality : 0.042 0.155 2843 Planarity : 0.003 0.036 2856 Dihedral : 11.948 134.922 2367 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.74 % Allowed : 14.97 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.19), residues: 1976 helix: 2.28 (0.19), residues: 750 sheet: -0.54 (0.25), residues: 416 loop : -0.90 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 57 TYR 0.009 0.001 TYR A 277 PHE 0.012 0.001 PHE C 473 TRP 0.012 0.001 TRP D 187 HIS 0.003 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (17471) covalent geometry : angle 0.51165 / 0.25 (23782) SS BOND : bond 0.00315 / 0.16 ( 5) SS BOND : angle 2.59646 / 1.58 ( 10) hydrogen bonds : bond 0.03667 / 2.33 ( 808) hydrogen bonds : angle 4.11831 / 2.94 ( 2547) link_ALPHA1-2 : bond 0.01011 / 0.53 ( 1) link_ALPHA1-2 : angle 1.53368 / 0.82 ( 3) link_ALPHA1-3 : bond 0.00482 / 0.28 ( 9) link_ALPHA1-3 : angle 1.45047 / 0.95 ( 27) link_ALPHA1-6 : bond 0.00770 / 0.49 ( 9) link_ALPHA1-6 : angle 1.52946 / 1.05 ( 27) link_BETA1-4 : bond 0.00743 / 0.54 ( 14) link_BETA1-4 : angle 1.88877 / 1.18 ( 42) link_NAG-ASN : bond 0.00137 / 0.07 ( 7) link_NAG-ASN : angle 1.57000 / 0.94 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 199 time to evaluate : 0.701 Fit side-chains REVERT: A 200 ASP cc_start: 0.8400 (p0) cc_final: 0.8172 (p0) REVERT: A 407 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7484 (m-30) REVERT: B 48 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8432 (mt-10) REVERT: B 93 MET cc_start: 0.8595 (mmm) cc_final: 0.8313 (mmm) REVERT: B 167 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.6281 (pm20) REVERT: B 268 ASP cc_start: 0.8105 (m-30) cc_final: 0.7878 (m-30) REVERT: B 284 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8152 (mp) REVERT: B 314 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7397 (ttp) REVERT: B 424 LEU cc_start: 0.6361 (OUTLIER) cc_final: 0.5579 (mm) REVERT: C 5 GLU cc_start: 0.7588 (pt0) cc_final: 0.6965 (tt0) REVERT: C 46 LYS cc_start: 0.7835 (mtpp) cc_final: 0.7509 (mtpt) REVERT: C 85 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8476 (pt0) REVERT: C 168 ASP cc_start: 0.7127 (m-30) cc_final: 0.6615 (t0) REVERT: C 186 GLU cc_start: 0.8190 (tt0) cc_final: 0.7798 (tp30) REVERT: D 94 ASN cc_start: 0.8009 (m110) cc_final: 0.7780 (m110) REVERT: D 105 MET cc_start: 0.8720 (mmt) cc_final: 0.8455 (mmt) REVERT: D 171 MET cc_start: 0.8036 (mtm) cc_final: 0.7742 (mtt) REVERT: D 172 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7919 (mp0) REVERT: D 262 GLU cc_start: 0.8195 (tt0) cc_final: 0.7733 (pt0) REVERT: D 398 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6829 (tp30) REVERT: D 407 ASP cc_start: 0.7887 (t0) cc_final: 0.7480 (t0) REVERT: E 164 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7189 (mt-10) REVERT: E 186 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8789 (mm) REVERT: E 200 THR cc_start: 0.8256 (OUTLIER) cc_final: 0.7947 (p) REVERT: E 225 ASN cc_start: 0.8273 (m110) cc_final: 0.7935 (m-40) REVERT: E 235 SER cc_start: 0.8685 (OUTLIER) cc_final: 0.8350 (p) REVERT: E 266 LEU cc_start: 0.7636 (tp) cc_final: 0.7332 (tp) REVERT: E 469 THR cc_start: 0.8479 (m) cc_final: 0.8241 (p) REVERT: E 474 GLN cc_start: 0.7669 (pt0) cc_final: 0.7421 (mt0) outliers start: 69 outliers final: 34 residues processed: 245 average time/residue: 0.4974 time to fit residues: 140.0131 Evaluate side-chains 233 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 190 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 321 VAL 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 89 ASP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 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 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 488 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 78 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 GLN A 58 GLN ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.134177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.108025 restraints weight = 22875.953| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.08 r_work: 0.3116 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 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 = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17516 Z= 0.115 Angle : 0.526 10.209 23912 Z= 0.254 Chirality : 0.042 0.156 2843 Planarity : 0.003 0.036 2856 Dihedral : 11.652 131.079 2367 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.63 % Allowed : 15.18 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.19), residues: 1976 helix: 2.31 (0.19), residues: 750 sheet: -0.49 (0.25), residues: 416 loop : -0.89 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 57 TYR 0.009 0.001 TYR A 277 PHE 0.015 0.001 PHE D 227 TRP 0.011 0.001 TRP A 187 HIS 0.003 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (17471) covalent geometry : angle 0.51172 / 0.25 (23782) SS BOND : bond 0.00217 / 0.11 ( 5) SS BOND : angle 2.57572 / 1.56 ( 10) hydrogen bonds : bond 0.03671 / 2.34 ( 808) hydrogen bonds : angle 4.10524 / 2.93 ( 2547) link_ALPHA1-2 : bond 0.00966 / 0.51 ( 1) link_ALPHA1-2 : angle 1.45746 / 0.78 ( 3) link_ALPHA1-3 : bond 0.00476 / 0.27 ( 9) link_ALPHA1-3 : angle 1.45081 / 0.95 ( 27) link_ALPHA1-6 : bond 0.00753 / 0.48 ( 9) link_ALPHA1-6 : angle 1.53855 / 1.06 ( 27) link_BETA1-4 : bond 0.00729 / 0.53 ( 14) link_BETA1-4 : angle 1.90454 / 1.19 ( 42) link_NAG-ASN : bond 0.00143 / 0.07 ( 7) link_NAG-ASN : angle 1.55060 / 0.93 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 194 time to evaluate : 0.670 Fit side-chains REVERT: A 200 ASP cc_start: 0.8396 (p0) cc_final: 0.8172 (p0) REVERT: A 407 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7462 (m-30) REVERT: B 48 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8407 (mt-10) REVERT: B 93 MET cc_start: 0.8550 (mmm) cc_final: 0.8146 (mmt) REVERT: B 167 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.6274 (pm20) REVERT: B 268 ASP cc_start: 0.8084 (m-30) cc_final: 0.7842 (m-30) REVERT: B 284 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8145 (mp) REVERT: B 314 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7394 (ttp) REVERT: B 424 LEU cc_start: 0.6474 (OUTLIER) cc_final: 0.5700 (mm) REVERT: C 5 GLU cc_start: 0.7588 (pt0) cc_final: 0.6969 (tt0) REVERT: C 46 LYS cc_start: 0.7836 (mtpp) cc_final: 0.7521 (mtpt) REVERT: C 85 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8465 (pt0) REVERT: C 168 ASP cc_start: 0.7133 (m-30) cc_final: 0.6601 (t0) REVERT: C 186 GLU cc_start: 0.8183 (tt0) cc_final: 0.7806 (tp30) REVERT: D 94 ASN cc_start: 0.7979 (m110) cc_final: 0.7748 (m110) REVERT: D 105 MET cc_start: 0.8678 (mmt) cc_final: 0.8406 (mmt) REVERT: D 171 MET cc_start: 0.8022 (mtm) cc_final: 0.7711 (mtt) REVERT: D 262 GLU cc_start: 0.8213 (tt0) cc_final: 0.7773 (pt0) REVERT: D 398 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6801 (tp30) REVERT: D 407 ASP cc_start: 0.7968 (t0) cc_final: 0.7547 (t0) REVERT: E 164 GLU cc_start: 0.7410 (mm-30) cc_final: 0.7180 (mt-10) REVERT: E 186 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8725 (mm) REVERT: E 200 THR cc_start: 0.8276 (OUTLIER) cc_final: 0.7968 (p) REVERT: E 225 ASN cc_start: 0.8344 (m110) cc_final: 0.8092 (m-40) REVERT: E 235 SER cc_start: 0.8719 (OUTLIER) cc_final: 0.8368 (p) REVERT: E 266 LEU cc_start: 0.7761 (tp) cc_final: 0.7396 (tp) REVERT: E 469 THR cc_start: 0.8512 (m) cc_final: 0.8267 (p) REVERT: E 474 GLN cc_start: 0.7629 (pt0) cc_final: 0.7394 (mt0) outliers start: 67 outliers final: 38 residues processed: 236 average time/residue: 0.4784 time to fit residues: 130.4851 Evaluate side-chains 234 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 187 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 282 MET 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 56 ILE Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 488 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 35 optimal weight: 5.9990 chunk 39 optimal weight: 0.0070 chunk 87 optimal weight: 0.4980 chunk 173 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.0170 chunk 56 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 GLN A 140 GLN ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3577 r_free = 0.3577 target = 0.134836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.108726 restraints weight = 23075.790| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.10 r_work: 0.3124 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 17516 Z= 0.108 Angle : 0.522 10.034 23912 Z= 0.251 Chirality : 0.042 0.155 2843 Planarity : 0.003 0.037 2856 Dihedral : 11.309 125.771 2367 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.09 % Allowed : 15.89 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.19), residues: 1976 helix: 2.28 (0.19), residues: 758 sheet: -0.46 (0.25), residues: 416 loop : -0.91 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 20 TYR 0.010 0.001 TYR A 277 PHE 0.010 0.001 PHE A 256 TRP 0.011 0.001 TRP A 187 HIS 0.003 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (17471) covalent geometry : angle 0.50828 / 0.25 (23782) SS BOND : bond 0.00260 / 0.13 ( 5) SS BOND : angle 2.37301 / 1.42 ( 10) hydrogen bonds : bond 0.03591 / 2.28 ( 808) hydrogen bonds : angle 4.06534 / 2.91 ( 2547) link_ALPHA1-2 : bond 0.00942 / 0.50 ( 1) link_ALPHA1-2 : angle 1.44213 / 0.76 ( 3) link_ALPHA1-3 : bond 0.00470 / 0.27 ( 9) link_ALPHA1-3 : angle 1.44572 / 0.95 ( 27) link_ALPHA1-6 : bond 0.00745 / 0.47 ( 9) link_ALPHA1-6 : angle 1.52544 / 1.05 ( 27) link_BETA1-4 : bond 0.00726 / 0.53 ( 14) link_BETA1-4 : angle 1.87540 / 1.17 ( 42) link_NAG-ASN : bond 0.00157 / 0.08 ( 7) link_NAG-ASN : angle 1.50789 / 0.90 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 195 time to evaluate : 0.702 Fit side-chains REVERT: A 200 ASP cc_start: 0.8387 (p0) cc_final: 0.8169 (p0) REVERT: A 407 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7460 (m-30) REVERT: B 48 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8416 (mt-10) REVERT: B 93 MET cc_start: 0.8545 (mmm) cc_final: 0.8261 (mmm) REVERT: B 167 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.6198 (pm20) REVERT: B 182 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7590 (tm-30) REVERT: B 284 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8146 (mp) REVERT: B 314 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7369 (ttp) REVERT: B 424 LEU cc_start: 0.6474 (OUTLIER) cc_final: 0.5703 (mm) REVERT: C 5 GLU cc_start: 0.7586 (pt0) cc_final: 0.6965 (tt0) REVERT: C 46 LYS cc_start: 0.7841 (mtpp) cc_final: 0.7517 (mtpt) REVERT: C 85 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8464 (pt0) REVERT: C 168 ASP cc_start: 0.7087 (m-30) cc_final: 0.6592 (t0) REVERT: C 186 GLU cc_start: 0.8181 (tt0) cc_final: 0.7801 (tp30) REVERT: D 94 ASN cc_start: 0.7937 (m110) cc_final: 0.7713 (m110) REVERT: D 105 MET cc_start: 0.8670 (mmt) cc_final: 0.8382 (mmt) REVERT: D 171 MET cc_start: 0.8003 (mtm) cc_final: 0.7693 (mtt) REVERT: D 262 GLU cc_start: 0.8201 (tt0) cc_final: 0.7758 (pt0) REVERT: D 398 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6799 (tp30) REVERT: D 407 ASP cc_start: 0.7873 (t0) cc_final: 0.7445 (t0) REVERT: E 164 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7135 (mt-10) REVERT: E 186 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8766 (mm) REVERT: E 200 THR cc_start: 0.8265 (OUTLIER) cc_final: 0.7945 (p) REVERT: E 225 ASN cc_start: 0.8341 (m110) cc_final: 0.8077 (m-40) REVERT: E 266 LEU cc_start: 0.7724 (tp) cc_final: 0.7375 (tp) REVERT: E 469 THR cc_start: 0.8503 (m) cc_final: 0.8266 (p) REVERT: E 474 GLN cc_start: 0.7633 (pt0) cc_final: 0.7396 (mt0) outliers start: 57 outliers final: 35 residues processed: 232 average time/residue: 0.4670 time to fit residues: 125.6714 Evaluate side-chains 231 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 187 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 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 318 ILE Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 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 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 417 VAL Chi-restraints excluded: chain E residue 454 ILE Chi-restraints excluded: chain E residue 488 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 150 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 19 optimal weight: 0.4980 chunk 147 optimal weight: 0.5980 chunk 96 optimal weight: 5.9990 chunk 109 optimal weight: 0.0980 chunk 4 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 GLN D 58 GLN D 140 GLN E 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.133392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.106390 restraints weight = 22833.518| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.15 r_work: 0.3094 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 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 = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17516 Z= 0.139 Angle : 0.546 10.517 23912 Z= 0.264 Chirality : 0.043 0.158 2843 Planarity : 0.003 0.036 2856 Dihedral : 11.136 118.996 2367 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.93 % Allowed : 16.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.19), residues: 1976 helix: 2.25 (0.19), residues: 753 sheet: -0.45 (0.25), residues: 416 loop : -0.96 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 81 TYR 0.011 0.001 TYR A 277 PHE 0.016 0.001 PHE D 227 TRP 0.009 0.001 TRP D 187 HIS 0.003 0.001 HIS A 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (17471) covalent geometry : angle 0.53159 / 0.26 (23782) SS BOND : bond 0.00461 / 0.23 ( 5) SS BOND : angle 2.67959 / 1.63 ( 10) hydrogen bonds : bond 0.03757 / 2.39 ( 808) hydrogen bonds : angle 4.14393 / 2.96 ( 2547) link_ALPHA1-2 : bond 0.00878 / 0.46 ( 1) link_ALPHA1-2 : angle 1.33631 / 0.71 ( 3) link_ALPHA1-3 : bond 0.00452 / 0.26 ( 9) link_ALPHA1-3 : angle 1.46048 / 0.96 ( 27) link_ALPHA1-6 : bond 0.00732 / 0.47 ( 9) link_ALPHA1-6 : angle 1.58001 / 1.07 ( 27) link_BETA1-4 : bond 0.00710 / 0.52 ( 14) link_BETA1-4 : angle 1.96152 / 1.22 ( 42) link_NAG-ASN : bond 0.00218 / 0.11 ( 7) link_NAG-ASN : angle 1.59429 / 0.97 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 195 time to evaluate : 0.682 Fit side-chains REVERT: A 200 ASP cc_start: 0.8415 (p0) cc_final: 0.8186 (p0) REVERT: A 407 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7487 (m-30) REVERT: B 48 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8295 (mt-10) REVERT: B 93 MET cc_start: 0.8653 (mmm) cc_final: 0.8193 (mmt) REVERT: B 167 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.6211 (pm20) REVERT: B 182 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7579 (tm-30) REVERT: B 249 MET cc_start: 0.8199 (mmp) cc_final: 0.7953 (mmm) REVERT: B 284 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8161 (mp) REVERT: B 314 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7422 (ttp) REVERT: B 424 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.5764 (mm) REVERT: C 5 GLU cc_start: 0.7682 (pt0) cc_final: 0.7083 (tt0) REVERT: C 46 LYS cc_start: 0.7847 (mtpp) cc_final: 0.7503 (mtpt) REVERT: C 85 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8500 (pt0) REVERT: C 168 ASP cc_start: 0.7107 (m-30) cc_final: 0.6468 (t0) REVERT: C 186 GLU cc_start: 0.8188 (tt0) cc_final: 0.7768 (tp30) REVERT: C 280 GLU cc_start: 0.7780 (mp0) cc_final: 0.7422 (mp0) REVERT: D 94 ASN cc_start: 0.7989 (m110) cc_final: 0.7747 (m110) REVERT: D 105 MET cc_start: 0.8681 (mmt) cc_final: 0.8425 (mmt) REVERT: D 171 MET cc_start: 0.8050 (mtm) cc_final: 0.7729 (mtt) REVERT: D 262 GLU cc_start: 0.8261 (tt0) cc_final: 0.7817 (pt0) REVERT: D 398 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6909 (tp30) REVERT: D 407 ASP cc_start: 0.7903 (t0) cc_final: 0.7465 (t0) REVERT: E 164 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7118 (mt-10) REVERT: E 186 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8789 (mm) REVERT: E 200 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.8074 (p) REVERT: E 225 ASN cc_start: 0.8531 (m110) cc_final: 0.8140 (m-40) REVERT: E 235 SER cc_start: 0.8685 (OUTLIER) cc_final: 0.8304 (p) REVERT: E 266 LEU cc_start: 0.7767 (tp) cc_final: 0.7364 (tp) REVERT: E 469 THR cc_start: 0.8541 (m) cc_final: 0.8291 (p) REVERT: E 474 GLN cc_start: 0.7673 (pt0) cc_final: 0.7445 (mt0) outliers start: 54 outliers final: 31 residues processed: 232 average time/residue: 0.4765 time to fit residues: 127.9071 Evaluate side-chains 228 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 187 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 85 GLU Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 417 ILE Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 488 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 132 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 126 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 142 optimal weight: 0.8980 chunk 110 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 GLN ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.134822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.108685 restraints weight = 22860.312| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.08 r_work: 0.3123 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 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 = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17516 Z= 0.109 Angle : 0.527 10.265 23912 Z= 0.256 Chirality : 0.042 0.156 2843 Planarity : 0.003 0.036 2856 Dihedral : 10.829 112.585 2367 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.55 % Allowed : 16.70 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.19), residues: 1976 helix: 2.28 (0.19), residues: 758 sheet: -0.43 (0.25), residues: 420 loop : -0.94 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 57 TYR 0.012 0.001 TYR A 277 PHE 0.011 0.001 PHE A 227 TRP 0.012 0.001 TRP D 60 HIS 0.004 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (17471) covalent geometry : angle 0.51288 / 0.25 (23782) SS BOND : bond 0.00362 / 0.19 ( 5) SS BOND : angle 2.34549 / 1.42 ( 10) hydrogen bonds : bond 0.03605 / 2.30 ( 808) hydrogen bonds : angle 4.07950 / 2.92 ( 2547) link_ALPHA1-2 : bond 0.00894 / 0.47 ( 1) link_ALPHA1-2 : angle 1.39453 / 0.74 ( 3) link_ALPHA1-3 : bond 0.00457 / 0.26 ( 9) link_ALPHA1-3 : angle 1.45100 / 0.95 ( 27) link_ALPHA1-6 : bond 0.00736 / 0.47 ( 9) link_ALPHA1-6 : angle 1.52795 / 1.05 ( 27) link_BETA1-4 : bond 0.00725 / 0.53 ( 14) link_BETA1-4 : angle 1.86825 / 1.17 ( 42) link_NAG-ASN : bond 0.00202 / 0.11 ( 7) link_NAG-ASN : angle 1.51963 / 0.91 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 194 time to evaluate : 0.671 Fit side-chains REVERT: A 200 ASP cc_start: 0.8377 (p0) cc_final: 0.8145 (p0) REVERT: A 407 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7410 (m-30) REVERT: A 430 LEU cc_start: 0.8385 (mp) cc_final: 0.8150 (mt) REVERT: B 48 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8405 (mt-10) REVERT: B 93 MET cc_start: 0.8549 (mmm) cc_final: 0.8149 (mmt) REVERT: B 167 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.6221 (pm20) REVERT: B 182 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7485 (tm-30) REVERT: B 249 MET cc_start: 0.7974 (mmp) cc_final: 0.7773 (mmm) REVERT: B 284 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8156 (mp) REVERT: B 314 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7381 (ttp) REVERT: B 424 LEU cc_start: 0.6516 (OUTLIER) cc_final: 0.5741 (mm) REVERT: C 5 GLU cc_start: 0.7572 (pt0) cc_final: 0.6954 (tt0) REVERT: C 46 LYS cc_start: 0.7853 (mtpp) cc_final: 0.7499 (mtpt) REVERT: C 85 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8474 (pt0) REVERT: C 168 ASP cc_start: 0.7076 (m-30) cc_final: 0.6454 (t0) REVERT: C 186 GLU cc_start: 0.8165 (tt0) cc_final: 0.7949 (mm-30) REVERT: D 94 ASN cc_start: 0.7885 (m110) cc_final: 0.7675 (m110) REVERT: D 105 MET cc_start: 0.8631 (mmt) cc_final: 0.8354 (mmt) REVERT: D 171 MET cc_start: 0.7990 (mtm) cc_final: 0.7675 (mtt) REVERT: D 262 GLU cc_start: 0.8278 (tt0) cc_final: 0.7827 (pt0) REVERT: D 398 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6803 (tp30) REVERT: D 407 ASP cc_start: 0.7865 (t0) cc_final: 0.7419 (t0) REVERT: E 186 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8763 (mm) REVERT: E 200 THR cc_start: 0.8363 (OUTLIER) cc_final: 0.8059 (p) REVERT: E 225 ASN cc_start: 0.8494 (m110) cc_final: 0.8101 (m-40) REVERT: E 266 LEU cc_start: 0.7717 (tp) cc_final: 0.7344 (tp) REVERT: E 469 THR cc_start: 0.8518 (m) cc_final: 0.8283 (p) REVERT: E 474 GLN cc_start: 0.7661 (pt0) cc_final: 0.7429 (mt0) outliers start: 47 outliers final: 30 residues processed: 228 average time/residue: 0.4586 time to fit residues: 121.2775 Evaluate side-chains 224 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 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 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 85 GLU Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 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 417 VAL Chi-restraints excluded: chain E residue 454 ILE Chi-restraints excluded: chain E residue 488 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 0 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 133 optimal weight: 0.0370 chunk 79 optimal weight: 0.0670 chunk 176 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 26 optimal weight: 0.4980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 GLN ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.134890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.108773 restraints weight = 22965.384| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.09 r_work: 0.3124 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 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 = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2037 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= 0.112 Angle : 0.528 10.188 23912 Z= 0.257 Chirality : 0.042 0.156 2843 Planarity : 0.003 0.036 2856 Dihedral : 10.586 105.106 2367 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.49 % Allowed : 16.92 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.19), residues: 1976 helix: 2.25 (0.19), residues: 761 sheet: -0.43 (0.25), residues: 415 loop : -0.92 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 20 TYR 0.012 0.001 TYR A 277 PHE 0.014 0.001 PHE C 473 TRP 0.011 0.001 TRP D 187 HIS 0.003 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (17471) covalent geometry : angle 0.51401 / 0.25 (23782) SS BOND : bond 0.00336 / 0.17 ( 5) SS BOND : angle 2.36574 / 1.43 ( 10) hydrogen bonds : bond 0.03600 / 2.29 ( 808) hydrogen bonds : angle 4.06708 / 2.91 ( 2547) link_ALPHA1-2 : bond 0.00856 / 0.45 ( 1) link_ALPHA1-2 : angle 1.35191 / 0.71 ( 3) link_ALPHA1-3 : bond 0.00445 / 0.26 ( 9) link_ALPHA1-3 : angle 1.45293 / 0.95 ( 27) link_ALPHA1-6 : bond 0.00730 / 0.47 ( 9) link_ALPHA1-6 : angle 1.53147 / 1.05 ( 27) link_BETA1-4 : bond 0.00716 / 0.52 ( 14) link_BETA1-4 : angle 1.87320 / 1.17 ( 42) link_NAG-ASN : bond 0.00173 / 0.09 ( 7) link_NAG-ASN : angle 1.50728 / 0.90 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5654.64 seconds wall clock time: 97 minutes 38.27 seconds (5858.27 seconds total)