Starting phenix.real_space_refine on Sat Feb 7 13:17:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dmh_47005/02_2026/9dmh_47005_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dmh_47005/02_2026/9dmh_47005.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dmh_47005/02_2026/9dmh_47005_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dmh_47005/02_2026/9dmh_47005_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dmh_47005/02_2026/9dmh_47005.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dmh_47005/02_2026/9dmh_47005.map" } resolution = 2.06 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= 0.024 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 S 76 5.16 5 C 11011 2.51 5 N 2698 2.21 5 O 3131 1.98 5 H 16518 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33437 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 6391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 6391 Classifications: {'peptide': 397} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 376} Chain breaks: 2 Chain: "C" Number of atoms: 6467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 6467 Classifications: {'peptide': 400} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 379} Chain breaks: 1 Chain: "E" Number of atoms: 6575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 6575 Classifications: {'peptide': 405} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 379} Chain breaks: 3 Chain: "D" Number of atoms: 7055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 7055 Classifications: {'peptide': 433} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 402} Chain breaks: 1 Chain: "B" Number of atoms: 6480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 6480 Classifications: {'peptide': 411} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 387} Chain breaks: 1 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 2, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'ACH': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'ACH': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.33, per 1000 atoms: 0.16 Number of scatterers: 33437 At special positions: 0 Unit cell: (101.915, 104.72, 172.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 76 16.00 P 3 15.00 O 3131 8.00 N 2698 7.00 C 11011 6.00 H 16518 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.15 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 142 " distance=2.04 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " distance=2.04 Simple disulfide: pdb=" SG CYS D 130 " - pdb=" SG CYS D 144 " distance=2.05 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 470 " 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 ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA H 3 " - " MAN H 4 " " BMA J 3 " - " MAN J 4 " ALPHA1-6 " BMA F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 5 " " BMA I 3 " - " MAN I 5 " " BMA J 3 " - " MAN J 5 " BETA1-3 " BMA I 3 " - " BMA I 4 " 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-ASN " NAG F 1 " - " ASN A 141 " " NAG G 1 " - " ASN C 141 " " NAG H 1 " - " ASN E 141 " " NAG I 1 " - " ASN D 143 " " NAG J 1 " - " ASN B 141 " " NAG K 1 " - " ASN B 66 " Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 937.2 milliseconds 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3914 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 19 sheets defined 45.6% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 68 through 73 removed outlier: 4.245A pdb=" N GLY A 73 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.600A pdb=" N LYS A 84 " --> pdb=" O PRO A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 218 Processing helix chain 'A' and resid 218 through 230 removed outlier: 4.190A pdb=" N GLY A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 236 through 240 Processing helix chain 'A' and resid 241 through 263 removed outlier: 3.682A pdb=" N VAL A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 300 Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 319 through 324 Processing helix chain 'A' and resid 370 through 436 removed outlier: 4.991A pdb=" N GLY A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ARG A 429 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 68 through 73 removed outlier: 4.228A pdb=" N GLY C 73 " --> pdb=" O ASP C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 211 through 218 Processing helix chain 'C' and resid 218 through 229 Processing helix chain 'C' and resid 230 through 235 Processing helix chain 'C' and resid 236 through 240 Processing helix chain 'C' and resid 241 through 264 Processing helix chain 'C' and resid 272 through 300 Processing helix chain 'C' and resid 309 through 318 removed outlier: 3.510A pdb=" N ASP C 318 " --> pdb=" O LYS C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 324 Processing helix chain 'C' and resid 369 through 436 removed outlier: 4.820A pdb=" N GLY C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ARG C 429 " --> pdb=" O VAL C 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 68 through 73 removed outlier: 4.214A pdb=" N ASP E 73 " --> pdb=" O ALA E 70 " (cutoff:3.500A) 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 222 through 229 Processing helix chain 'E' and resid 229 through 243 Processing helix chain 'E' and resid 244 through 246 No H-bonds generated for 'chain 'E' and resid 244 through 246' Processing helix chain 'E' and resid 247 through 251 Processing helix chain 'E' and resid 252 through 273 removed outlier: 3.941A pdb=" N ASP E 273 " --> pdb=" O LEU E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 311 Processing helix chain 'E' and resid 320 through 329 Processing helix chain 'E' and resid 330 through 335 removed outlier: 3.591A pdb=" N TYR E 334 " --> pdb=" O LYS E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 469 Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 65 through 68 removed outlier: 3.683A pdb=" N LYS D 68 " --> pdb=" O ASN D 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 65 through 68' Processing helix chain 'D' and resid 70 through 75 removed outlier: 4.005A pdb=" N GLY D 75 " --> pdb=" O GLU D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.570A pdb=" N VAL D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 211 No H-bonds generated for 'chain 'D' and resid 209 through 211' Processing helix chain 'D' and resid 225 through 242 removed outlier: 4.642A pdb=" N VAL D 234 " --> pdb=" O ILE D 230 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 243 through 249 Processing helix chain 'D' and resid 250 through 254 removed outlier: 3.557A pdb=" N GLY D 254 " --> pdb=" O ALA D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 276 removed outlier: 3.688A pdb=" N LYS D 276 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 314 Processing helix chain 'D' and resid 323 through 332 Processing helix chain 'D' and resid 332 through 338 removed outlier: 3.571A pdb=" N GLU D 336 " --> pdb=" O GLU D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 473 Proline residue: D 416 - end of helix Proline residue: D 458 - end of helix removed outlier: 3.769A pdb=" N GLY D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 removed outlier: 3.550A pdb=" N ARG B 6 " --> pdb=" O ASN B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 66 Processing helix chain 'B' and resid 68 through 72 Processing helix chain 'B' and resid 83 through 85 No H-bonds generated for 'chain 'B' and resid 83 through 85' Processing helix chain 'B' and resid 175 through 179 removed outlier: 3.977A pdb=" N TYR B 179 " --> pdb=" O THR B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 227 through 237 Processing helix chain 'B' and resid 238 through 244 removed outlier: 3.554A pdb=" N LEU B 244 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 272 removed outlier: 3.501A pdb=" N GLN B 272 " --> pdb=" O PHE B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 310 Processing helix chain 'B' and resid 319 through 328 Processing helix chain 'B' and resid 328 through 334 Processing helix chain 'B' and resid 398 through 459 removed outlier: 3.633A pdb=" N ALA B 457 " --> pdb=" O ILE B 453 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 80 removed outlier: 4.081A pdb=" N HIS A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 80 removed outlier: 4.081A pdb=" N HIS A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE A 49 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL A 43 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR A 51 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARG A 55 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LEU A 37 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LYS A 57 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LEU A 35 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLN A 59 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N VAL A 33 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N VAL A 61 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N VAL A 31 " --> pdb=" O VAL A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 4.353A pdb=" N THR A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LEU A 199 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLN A 208 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ILE A 178 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 81 removed outlier: 4.112A pdb=" N HIS C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 81 removed outlier: 4.112A pdb=" N HIS C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASN C 53 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU C 40 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N ARG C 55 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE C 38 " --> pdb=" O ARG C 55 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LYS C 57 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLN C 36 " --> pdb=" O LYS C 57 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N GLN C 59 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N GLY C 34 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N VAL C 61 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N THR C 32 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 90 through 92 removed outlier: 4.260A pdb=" N THR C 148 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N LEU C 199 " --> pdb=" O THR C 148 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N TYR C 198 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N SER C 187 " --> pdb=" O TYR C 198 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASP C 200 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LYS C 185 " --> pdb=" O ASP C 200 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N THR C 202 " --> pdb=" O GLY C 183 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY C 183 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N HIS C 204 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER C 181 " --> pdb=" O HIS C 204 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL C 206 " --> pdb=" O LYS C 179 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 77 through 81 removed outlier: 3.979A pdb=" N SER E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 77 through 81 removed outlier: 3.979A pdb=" N SER E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLU E 49 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU E 43 " --> pdb=" O GLU E 49 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER E 51 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TYR E 55 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LEU E 37 " --> pdb=" O TYR E 55 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASP E 57 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU E 35 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N GLU E 59 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL E 33 " --> pdb=" O GLU E 59 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N THR E 61 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N VAL E 31 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 11.201A pdb=" N TYR E 63 " --> pdb=" O VAL E 29 " (cutoff:3.500A) removed outlier: 13.239A pdb=" N VAL E 29 " --> pdb=" O TYR E 63 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 90 through 92 removed outlier: 6.857A pdb=" N ILE E 217 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 90 through 92 Processing sheet with id=AB2, first strand: chain 'D' and resid 79 through 82 removed outlier: 3.853A pdb=" N PHE D 117 " --> pdb=" O TYR D 113 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 79 through 82 removed outlier: 3.853A pdb=" N PHE D 117 " --> pdb=" O TYR D 113 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N THR D 51 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU D 45 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR D 53 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TRP D 57 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N LEU D 39 " --> pdb=" O TRP D 57 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLU D 59 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LEU D 37 " --> pdb=" O GLU D 59 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N GLY D 61 " --> pdb=" O LEU D 35 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LEU D 35 " --> pdb=" O GLY D 61 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N THR D 63 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N VAL D 33 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL D 31 " --> pdb=" O THR D 159 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N SER D 161 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL D 33 " --> pdb=" O SER D 161 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 92 through 94 removed outlier: 5.427A pdb=" N SER D 150 " --> pdb=" O GLN D 213 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N GLN D 213 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE D 220 " --> pdb=" O VAL D 193 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 92 through 94 removed outlier: 5.427A pdb=" N SER D 150 " --> pdb=" O GLN D 213 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N GLN D 213 " --> pdb=" O SER D 150 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 164 through 167 Processing sheet with id=AB7, first strand: chain 'B' and resid 77 through 81 removed outlier: 3.708A pdb=" N SER B 115 " --> pdb=" O TYR B 111 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 77 through 81 removed outlier: 3.708A pdb=" N SER B 115 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER B 53 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU B 40 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N TRP B 55 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N THR B 38 " --> pdb=" O TRP B 55 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N GLY B 57 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N THR B 36 " --> pdb=" O GLY B 57 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ASP B 59 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N LYS B 34 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 8.750A pdb=" N GLN B 61 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N SER B 32 " --> pdb=" O GLN B 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.175A pdb=" N SER B 148 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N THR B 208 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE B 215 " --> pdb=" O ASP B 188 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.175A pdb=" N SER B 148 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N THR B 208 " --> pdb=" O SER B 148 " (cutoff:3.500A) 967 hydrogen bonds defined for protein. 2766 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.72 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 16499 1.04 - 1.23: 348 1.23 - 1.43: 6844 1.43 - 1.62: 10042 1.62 - 1.82: 121 Bond restraints: 33854 Sorted by residual: bond pdb=" NZ LYS E 434 " pdb=" HZ1 LYS E 434 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" NZ LYS C 368 " pdb=" HZ1 LYS C 368 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" NZ LYS C 57 " pdb=" HZ3 LYS C 57 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" NZ LYS B 1 " pdb=" HZ2 LYS B 1 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" NZ LYS E 274 " pdb=" HZ3 LYS E 274 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 ... (remaining 33849 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.58: 61153 12.58 - 25.15: 0 25.15 - 37.73: 0 37.73 - 50.30: 2 50.30 - 62.88: 4 Bond angle restraints: 61159 Sorted by residual: angle pdb=" CA PHE A 326 " pdb=" N PHE A 326 " pdb=" H PHE A 326 " ideal model delta sigma weight residual 114.00 176.88 -62.88 3.00e+00 1.11e-01 4.39e+02 angle pdb=" CA LEU E 407 " pdb=" N LEU E 407 " pdb=" H LEU E 407 " ideal model delta sigma weight residual 114.00 173.32 -59.32 3.00e+00 1.11e-01 3.91e+02 angle pdb=" CA GLU E 206 " pdb=" N GLU E 206 " pdb=" H GLU E 206 " ideal model delta sigma weight residual 114.00 173.01 -59.01 3.00e+00 1.11e-01 3.87e+02 angle pdb=" CA ILE C 367 " pdb=" N ILE C 367 " pdb=" H ILE C 367 " ideal model delta sigma weight residual 114.00 168.54 -54.54 3.00e+00 1.11e-01 3.31e+02 angle pdb=" CA GLY E 168 " pdb=" N GLY E 168 " pdb=" H GLY E 168 " ideal model delta sigma weight residual 114.00 162.45 -48.45 3.00e+00 1.11e-01 2.61e+02 ... (remaining 61154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.23: 15854 35.23 - 70.47: 429 70.47 - 105.70: 87 105.70 - 140.94: 8 140.94 - 176.17: 1 Dihedral angle restraints: 16379 sinusoidal: 9119 harmonic: 7260 Sorted by residual: dihedral pdb=" CD ARG A 301 " pdb=" NE ARG A 301 " pdb=" CZ ARG A 301 " pdb=" NH1 ARG A 301 " ideal model delta sinusoidal sigma weight residual 0.00 78.99 -78.99 1 1.00e+01 1.00e-02 7.77e+01 dihedral pdb=" CD ARG B 461 " pdb=" NE ARG B 461 " pdb=" CZ ARG B 461 " pdb=" NH1 ARG B 461 " ideal model delta sinusoidal sigma weight residual 0.00 47.27 -47.27 1 1.00e+01 1.00e-02 3.09e+01 dihedral pdb=" C29 POV E 501 " pdb="C210 POV E 501 " pdb="C211 POV E 501 " pdb="C212 POV E 501 " ideal model delta sinusoidal sigma weight residual 112.25 -63.92 176.17 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 16376 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.948: 2801 0.948 - 1.896: 0 1.896 - 2.844: 0 2.844 - 3.792: 0 3.792 - 4.741: 1 Chirality restraints: 2802 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 2.34 -4.74 2.00e-02 2.50e+03 5.62e+04 chirality pdb=" C1 MAN F 4 " pdb=" O6 BMA F 3 " pdb=" C2 MAN F 4 " pdb=" O5 MAN F 4 " both_signs ideal model delta sigma weight residual False 2.40 1.81 0.59 2.00e-02 2.50e+03 8.63e+02 chirality pdb=" C1 MAN J 4 " pdb=" O3 BMA J 3 " pdb=" C2 MAN J 4 " pdb=" O5 MAN J 4 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-02 2.50e+03 5.26e+01 ... (remaining 2799 not shown) Planarity restraints: 4829 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.244 2.00e-02 2.50e+03 2.04e-01 5.20e+02 pdb=" C7 NAG F 1 " 0.066 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " -0.168 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.340 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 182 " 0.603 9.50e-02 1.11e+02 2.20e-01 2.22e+02 pdb=" NE ARG A 182 " 0.087 2.00e-02 2.50e+03 pdb=" CZ ARG A 182 " 0.034 2.00e-02 2.50e+03 pdb=" NH1 ARG A 182 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 182 " -0.016 2.00e-02 2.50e+03 pdb="HH11 ARG A 182 " -0.184 2.00e-02 2.50e+03 pdb="HH12 ARG A 182 " 0.131 2.00e-02 2.50e+03 pdb="HH21 ARG A 182 " -0.106 2.00e-02 2.50e+03 pdb="HH22 ARG A 182 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " 0.152 2.00e-02 2.50e+03 1.28e-01 2.05e+02 pdb=" C7 NAG K 2 " -0.034 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " -0.036 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " -0.204 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " 0.122 2.00e-02 2.50e+03 ... (remaining 4826 not shown) Histogram of nonbonded interaction distances: 1.33 - 1.98: 148 1.98 - 2.64: 41077 2.64 - 3.29: 101189 3.29 - 3.95: 134047 3.95 - 4.60: 204647 Nonbonded interactions: 481108 Sorted by model distance: nonbonded pdb="HD22 ASN B 301 " pdb=" HB3 CYS B 438 " model vdw 1.329 2.270 nonbonded pdb=" HZ1 LYS D 290 " pdb=" C12 POV D 501 " model vdw 1.476 2.750 nonbonded pdb="HG11 VAL B 305 " pdb=" OD1 ASP B 435 " model vdw 1.495 2.620 nonbonded pdb=" HZ1 LYS B 46 " pdb=" O ALA B 271 " model vdw 1.530 2.450 nonbonded pdb=" HH TYR C 15 " pdb=" H TRP C 86 " model vdw 1.681 2.100 ... (remaining 481103 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 436 or resid 501)) selection = (chain 'C' and (resid 1 through 325 or resid 327 through 329 or resid 369 throug \ h 501)) } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = (chain 'G' and (resid 1 through 3 or resid 5)) selection = (chain 'I' and (resid 1 through 3 or resid 5)) selection = (chain 'J' and (resid 1 through 3 or resid 5)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.890 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: 0.160 Extract box with map and model: 0.380 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 29.220 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 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 0.179 17367 Z= 0.290 Angle : 0.882 19.326 23712 Z= 0.450 Chirality : 0.105 4.741 2802 Planarity : 0.015 0.489 2908 Dihedral : 18.228 176.175 6719 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.08 % Favored : 97.87 % Rotamer: Outliers : 0.32 % Allowed : 9.90 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % 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: 1.23 (0.19), residues: 2020 helix: 2.20 (0.18), residues: 785 sheet: -0.30 (0.24), residues: 410 loop : 0.16 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 429 TYR 0.015 0.001 TYR B 467 PHE 0.019 0.002 PHE A 256 TRP 0.015 0.001 TRP C 311 HIS 0.011 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00520 (17336) covalent geometry : angle 0.82992 (23625) SS BOND : bond 0.04989 ( 6) SS BOND : angle 3.54532 ( 12) hydrogen bonds : bond 0.12196 ( 881) hydrogen bonds : angle 5.56160 ( 2766) link_ALPHA1-3 : bond 0.00845 ( 3) link_ALPHA1-3 : angle 3.75374 ( 9) link_ALPHA1-6 : bond 0.00300 ( 4) link_ALPHA1-6 : angle 3.24124 ( 12) link_BETA1-3 : bond 0.00360 ( 1) link_BETA1-3 : angle 5.34159 ( 3) link_BETA1-4 : bond 0.00543 ( 11) link_BETA1-4 : angle 4.28597 ( 33) link_NAG-ASN : bond 0.13299 ( 6) link_NAG-ASN : angle 7.74276 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 246 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: A 324 MET cc_start: 0.4514 (ptt) cc_final: 0.4241 (ptt) REVERT: C 367 ILE cc_start: 0.4766 (OUTLIER) cc_final: 0.4537 (pt) REVERT: C 387 LYS cc_start: 0.7975 (tptm) cc_final: 0.7527 (tptp) REVERT: B 418 GLU cc_start: 0.7326 (tp30) cc_final: 0.7047 (tp30) REVERT: B 447 SER cc_start: 0.7946 (m) cc_final: 0.7619 (m) outliers start: 6 outliers final: 3 residues processed: 249 average time/residue: 1.1672 time to fit residues: 327.1671 Evaluate side-chains 232 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 228 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 306 HIS Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain D residue 298 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN D 475 GLN B 258 ASN B 316 HIS B 432 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.150499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.112328 restraints weight = 45345.325| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.51 r_work: 0.3201 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.0795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17367 Z= 0.140 Angle : 0.587 10.208 23712 Z= 0.291 Chirality : 0.044 0.301 2802 Planarity : 0.006 0.176 2908 Dihedral : 13.040 163.831 2814 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.98 % Favored : 97.97 % Rotamer: Outliers : 1.02 % Allowed : 9.96 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % 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: 1.62 (0.19), residues: 2020 helix: 2.56 (0.18), residues: 795 sheet: -0.09 (0.25), residues: 405 loop : 0.30 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 301 TYR 0.012 0.001 TYR B 467 PHE 0.013 0.001 PHE C 414 TRP 0.011 0.001 TRP D 176 HIS 0.005 0.001 HIS E 317 Details of bonding type rmsd covalent geometry : bond 0.00300 (17336) covalent geometry : angle 0.56777 (23625) SS BOND : bond 0.00362 ( 6) SS BOND : angle 1.16312 ( 12) hydrogen bonds : bond 0.05142 ( 881) hydrogen bonds : angle 4.47887 ( 2766) link_ALPHA1-3 : bond 0.00902 ( 3) link_ALPHA1-3 : angle 2.63067 ( 9) link_ALPHA1-6 : bond 0.00751 ( 4) link_ALPHA1-6 : angle 1.84866 ( 12) link_BETA1-3 : bond 0.00604 ( 1) link_BETA1-3 : angle 2.77648 ( 3) link_BETA1-4 : bond 0.00233 ( 11) link_BETA1-4 : angle 3.09124 ( 33) link_NAG-ASN : bond 0.00486 ( 6) link_NAG-ASN : angle 2.30906 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 235 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 MET cc_start: 0.4018 (ptt) cc_final: 0.3759 (ptt) REVERT: A 407 ASP cc_start: 0.7373 (OUTLIER) cc_final: 0.6712 (m-30) REVERT: C 387 LYS cc_start: 0.7978 (tptm) cc_final: 0.7515 (tptp) REVERT: D 332 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.7103 (mp0) REVERT: D 470 GLN cc_start: 0.8241 (mm110) cc_final: 0.7953 (mm110) REVERT: B 447 SER cc_start: 0.7882 (m) cc_final: 0.7554 (m) outliers start: 19 outliers final: 9 residues processed: 244 average time/residue: 1.2311 time to fit residues: 338.1688 Evaluate side-chains 241 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 230 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 405 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 48 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 66 optimal weight: 0.2980 chunk 110 optimal weight: 1.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN E 318 GLN D 60 HIS D 475 GLN B 258 ASN B 432 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.148153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.109417 restraints weight = 44952.950| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.57 r_work: 0.3174 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17367 Z= 0.189 Angle : 0.614 8.542 23712 Z= 0.313 Chirality : 0.046 0.270 2802 Planarity : 0.005 0.050 2908 Dihedral : 11.637 159.540 2810 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.93 % Favored : 98.02 % Rotamer: Outliers : 1.71 % Allowed : 9.42 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % 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: 1.60 (0.18), residues: 2020 helix: 2.54 (0.17), residues: 795 sheet: -0.07 (0.25), residues: 394 loop : 0.27 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 55 TYR 0.016 0.002 TYR A 72 PHE 0.020 0.002 PHE A 105 TRP 0.016 0.002 TRP D 176 HIS 0.006 0.001 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00414 (17336) covalent geometry : angle 0.59605 (23625) SS BOND : bond 0.00381 ( 6) SS BOND : angle 1.38455 ( 12) hydrogen bonds : bond 0.05623 ( 881) hydrogen bonds : angle 4.55603 ( 2766) link_ALPHA1-3 : bond 0.00829 ( 3) link_ALPHA1-3 : angle 1.61688 ( 9) link_ALPHA1-6 : bond 0.00708 ( 4) link_ALPHA1-6 : angle 1.87503 ( 12) link_BETA1-3 : bond 0.00898 ( 1) link_BETA1-3 : angle 1.50331 ( 3) link_BETA1-4 : bond 0.00528 ( 11) link_BETA1-4 : angle 3.02740 ( 33) link_NAG-ASN : bond 0.00658 ( 6) link_NAG-ASN : angle 2.91393 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 234 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: A 324 MET cc_start: 0.4269 (ptt) cc_final: 0.3996 (ptt) REVERT: A 407 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.6840 (m-30) REVERT: C 387 LYS cc_start: 0.7956 (tptm) cc_final: 0.7501 (tptp) REVERT: E 295 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7796 (mm) REVERT: E 427 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7310 (tm-30) REVERT: D 252 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7195 (m-30) REVERT: D 332 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7261 (mp0) REVERT: D 470 GLN cc_start: 0.8238 (mm110) cc_final: 0.8007 (mm110) REVERT: B 447 SER cc_start: 0.7922 (m) cc_final: 0.7605 (m) outliers start: 32 outliers final: 12 residues processed: 252 average time/residue: 1.2057 time to fit residues: 341.3014 Evaluate side-chains 248 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 232 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 262 GLU Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 405 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 126 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 chunk 193 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 171 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN A 186 HIS ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN E 318 GLN D 432 ASN D 475 GLN B 258 ASN B 432 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.150740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.112475 restraints weight = 44991.046| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.57 r_work: 0.3241 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17367 Z= 0.137 Angle : 0.544 6.134 23712 Z= 0.276 Chirality : 0.044 0.215 2802 Planarity : 0.004 0.044 2908 Dihedral : 10.740 151.655 2808 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.93 % Favored : 98.02 % Rotamer: Outliers : 1.34 % Allowed : 9.53 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % 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: 1.79 (0.19), residues: 2020 helix: 2.70 (0.17), residues: 796 sheet: 0.05 (0.25), residues: 411 loop : 0.36 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 55 TYR 0.013 0.001 TYR E 134 PHE 0.015 0.001 PHE D 291 TRP 0.012 0.001 TRP D 176 HIS 0.006 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00291 (17336) covalent geometry : angle 0.52902 (23625) SS BOND : bond 0.00243 ( 6) SS BOND : angle 0.99905 ( 12) hydrogen bonds : bond 0.05023 ( 881) hydrogen bonds : angle 4.37375 ( 2766) link_ALPHA1-3 : bond 0.00915 ( 3) link_ALPHA1-3 : angle 1.93865 ( 9) link_ALPHA1-6 : bond 0.00735 ( 4) link_ALPHA1-6 : angle 1.96628 ( 12) link_BETA1-3 : bond 0.00722 ( 1) link_BETA1-3 : angle 1.63742 ( 3) link_BETA1-4 : bond 0.00370 ( 11) link_BETA1-4 : angle 2.47991 ( 33) link_NAG-ASN : bond 0.00235 ( 6) link_NAG-ASN : angle 2.39356 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 240 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 324 MET cc_start: 0.4252 (ptt) cc_final: 0.3967 (ptt) REVERT: C 387 LYS cc_start: 0.7966 (tptm) cc_final: 0.7473 (tptp) REVERT: E 208 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.6840 (mt0) REVERT: E 295 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7797 (mm) REVERT: E 427 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7341 (tm-30) REVERT: D 252 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.7112 (m-30) REVERT: D 470 GLN cc_start: 0.8150 (mm110) cc_final: 0.7946 (mm110) REVERT: B 413 SER cc_start: 0.8194 (t) cc_final: 0.7972 (m) REVERT: B 447 SER cc_start: 0.7904 (m) cc_final: 0.7596 (m) outliers start: 25 outliers final: 11 residues processed: 250 average time/residue: 1.1743 time to fit residues: 331.3582 Evaluate side-chains 243 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 229 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain C residue 262 GLU Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 208 GLN Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 426 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 200 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 185 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN E 318 GLN D 431 GLN D 475 GLN B 258 ASN B 432 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.148114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.109473 restraints weight = 45044.487| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.57 r_work: 0.3219 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17367 Z= 0.183 Angle : 0.586 6.677 23712 Z= 0.300 Chirality : 0.045 0.214 2802 Planarity : 0.005 0.046 2908 Dihedral : 10.647 149.901 2806 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.03 % Favored : 97.92 % Rotamer: Outliers : 1.45 % Allowed : 9.69 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % 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: 1.72 (0.19), residues: 2020 helix: 2.64 (0.17), residues: 795 sheet: 0.02 (0.25), residues: 405 loop : 0.32 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 125 TYR 0.015 0.002 TYR E 134 PHE 0.017 0.002 PHE A 105 TRP 0.016 0.002 TRP D 176 HIS 0.006 0.001 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00401 (17336) covalent geometry : angle 0.56935 (23625) SS BOND : bond 0.00363 ( 6) SS BOND : angle 1.30311 ( 12) hydrogen bonds : bond 0.05404 ( 881) hydrogen bonds : angle 4.47890 ( 2766) link_ALPHA1-3 : bond 0.00838 ( 3) link_ALPHA1-3 : angle 1.84262 ( 9) link_ALPHA1-6 : bond 0.00793 ( 4) link_ALPHA1-6 : angle 1.90087 ( 12) link_BETA1-3 : bond 0.00845 ( 1) link_BETA1-3 : angle 1.13152 ( 3) link_BETA1-4 : bond 0.00454 ( 11) link_BETA1-4 : angle 2.68148 ( 33) link_NAG-ASN : bond 0.00553 ( 6) link_NAG-ASN : angle 2.77145 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 229 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 ASP cc_start: 0.7333 (OUTLIER) cc_final: 0.6718 (m-30) REVERT: C 387 LYS cc_start: 0.7921 (tptm) cc_final: 0.7465 (tptp) REVERT: E 208 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.6778 (mt0) REVERT: E 295 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7785 (mm) REVERT: E 427 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7277 (tm-30) REVERT: D 252 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.7187 (m-30) REVERT: D 470 GLN cc_start: 0.8186 (mm110) cc_final: 0.7977 (mm110) REVERT: B 413 SER cc_start: 0.8166 (t) cc_final: 0.7941 (m) REVERT: B 447 SER cc_start: 0.7931 (m) cc_final: 0.7625 (m) outliers start: 27 outliers final: 11 residues processed: 244 average time/residue: 1.2128 time to fit residues: 334.1231 Evaluate side-chains 240 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 225 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 262 GLU Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 208 GLN Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 466 ASP Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain B residue 405 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 109 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 26 optimal weight: 0.0370 chunk 175 optimal weight: 0.0570 chunk 98 optimal weight: 0.2980 chunk 160 optimal weight: 0.3980 chunk 104 optimal weight: 2.9990 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 GLN ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 HIS C 393 ASN E 318 GLN D 475 GLN B 258 ASN B 432 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.152574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.114744 restraints weight = 45068.462| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.57 r_work: 0.3276 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17367 Z= 0.098 Angle : 0.499 5.897 23712 Z= 0.252 Chirality : 0.043 0.251 2802 Planarity : 0.004 0.043 2908 Dihedral : 9.462 134.801 2806 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.73 % Favored : 98.22 % Rotamer: Outliers : 0.86 % Allowed : 10.06 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % 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: 2.00 (0.19), residues: 2020 helix: 2.97 (0.17), residues: 793 sheet: 0.05 (0.25), residues: 410 loop : 0.45 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 22 TYR 0.011 0.001 TYR B 467 PHE 0.012 0.001 PHE C 414 TRP 0.009 0.001 TRP E 60 HIS 0.003 0.001 HIS A 25 Details of bonding type rmsd covalent geometry : bond 0.00198 (17336) covalent geometry : angle 0.48576 (23625) SS BOND : bond 0.00087 ( 6) SS BOND : angle 0.55054 ( 12) hydrogen bonds : bond 0.04401 ( 881) hydrogen bonds : angle 4.13823 ( 2766) link_ALPHA1-3 : bond 0.00862 ( 3) link_ALPHA1-3 : angle 1.84350 ( 9) link_ALPHA1-6 : bond 0.00828 ( 4) link_ALPHA1-6 : angle 1.81413 ( 12) link_BETA1-3 : bond 0.00731 ( 1) link_BETA1-3 : angle 2.31073 ( 3) link_BETA1-4 : bond 0.00317 ( 11) link_BETA1-4 : angle 2.16055 ( 33) link_NAG-ASN : bond 0.00229 ( 6) link_NAG-ASN : angle 2.11012 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 229 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.6780 (m-30) REVERT: C 306 HIS cc_start: 0.8120 (m90) cc_final: 0.7851 (m90) REVERT: C 385 THR cc_start: 0.8147 (m) cc_final: 0.7932 (m) REVERT: C 387 LYS cc_start: 0.7951 (tptm) cc_final: 0.7504 (tptp) REVERT: E 208 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.6795 (mt0) REVERT: D 332 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: D 470 GLN cc_start: 0.8056 (mm110) cc_final: 0.7784 (mm110) REVERT: B 413 SER cc_start: 0.8218 (t) cc_final: 0.7999 (m) REVERT: B 447 SER cc_start: 0.7900 (m) cc_final: 0.7594 (m) outliers start: 16 outliers final: 3 residues processed: 237 average time/residue: 1.2066 time to fit residues: 323.8912 Evaluate side-chains 230 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 224 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain C residue 262 GLU Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain E residue 208 GLN Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain D residue 332 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 98 optimal weight: 0.0870 chunk 88 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN E 318 GLN D 475 GLN B 258 ASN B 432 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.151750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.113717 restraints weight = 45085.616| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.58 r_work: 0.3260 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17367 Z= 0.116 Angle : 0.514 5.749 23712 Z= 0.260 Chirality : 0.043 0.245 2802 Planarity : 0.004 0.039 2908 Dihedral : 9.041 133.716 2806 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.98 % Favored : 97.97 % Rotamer: Outliers : 0.96 % Allowed : 9.85 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % 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: 2.07 (0.19), residues: 2020 helix: 3.00 (0.17), residues: 796 sheet: 0.14 (0.25), residues: 418 loop : 0.46 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 6 TYR 0.011 0.001 TYR B 467 PHE 0.012 0.001 PHE E 267 TRP 0.009 0.001 TRP D 176 HIS 0.004 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00248 (17336) covalent geometry : angle 0.49955 (23625) SS BOND : bond 0.00237 ( 6) SS BOND : angle 0.89585 ( 12) hydrogen bonds : bond 0.04576 ( 881) hydrogen bonds : angle 4.15994 ( 2766) link_ALPHA1-3 : bond 0.00796 ( 3) link_ALPHA1-3 : angle 1.82341 ( 9) link_ALPHA1-6 : bond 0.00944 ( 4) link_ALPHA1-6 : angle 1.69330 ( 12) link_BETA1-3 : bond 0.00826 ( 1) link_BETA1-3 : angle 1.85457 ( 3) link_BETA1-4 : bond 0.00336 ( 11) link_BETA1-4 : angle 2.30767 ( 33) link_NAG-ASN : bond 0.00298 ( 6) link_NAG-ASN : angle 2.35492 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 228 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 ASP cc_start: 0.7373 (OUTLIER) cc_final: 0.6777 (m-30) REVERT: C 306 HIS cc_start: 0.8131 (m90) cc_final: 0.7858 (m90) REVERT: C 387 LYS cc_start: 0.7955 (tptm) cc_final: 0.7498 (tptp) REVERT: D 332 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7209 (mp0) REVERT: D 470 GLN cc_start: 0.8078 (mm110) cc_final: 0.7814 (mm110) REVERT: B 447 SER cc_start: 0.7910 (m) cc_final: 0.7598 (m) outliers start: 18 outliers final: 7 residues processed: 237 average time/residue: 1.2020 time to fit residues: 322.3830 Evaluate side-chains 231 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 222 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain C residue 262 GLU Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 439 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 26 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 118 optimal weight: 0.0070 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN E 318 GLN D 475 GLN B 258 ASN B 432 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.151575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.113581 restraints weight = 44751.532| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.57 r_work: 0.3255 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17367 Z= 0.119 Angle : 0.514 5.377 23712 Z= 0.260 Chirality : 0.043 0.247 2802 Planarity : 0.004 0.040 2908 Dihedral : 8.672 127.891 2806 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.03 % Favored : 97.92 % Rotamer: Outliers : 0.91 % Allowed : 9.90 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % 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: 2.08 (0.19), residues: 2020 helix: 3.01 (0.17), residues: 796 sheet: 0.16 (0.25), residues: 418 loop : 0.48 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 6 TYR 0.012 0.001 TYR B 467 PHE 0.012 0.001 PHE C 414 TRP 0.011 0.001 TRP D 176 HIS 0.004 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00254 (17336) covalent geometry : angle 0.50052 (23625) SS BOND : bond 0.00224 ( 6) SS BOND : angle 0.89662 ( 12) hydrogen bonds : bond 0.04604 ( 881) hydrogen bonds : angle 4.16495 ( 2766) link_ALPHA1-3 : bond 0.00739 ( 3) link_ALPHA1-3 : angle 1.75881 ( 9) link_ALPHA1-6 : bond 0.00965 ( 4) link_ALPHA1-6 : angle 1.69978 ( 12) link_BETA1-3 : bond 0.00754 ( 1) link_BETA1-3 : angle 2.23556 ( 3) link_BETA1-4 : bond 0.00330 ( 11) link_BETA1-4 : angle 2.23771 ( 33) link_NAG-ASN : bond 0.00274 ( 6) link_NAG-ASN : angle 2.31165 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 227 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 407 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.6795 (m-30) REVERT: C 306 HIS cc_start: 0.8148 (m90) cc_final: 0.7880 (m90) REVERT: C 385 THR cc_start: 0.8078 (m) cc_final: 0.7853 (m) REVERT: C 387 LYS cc_start: 0.7937 (tptm) cc_final: 0.7495 (tptp) REVERT: D 332 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: D 470 GLN cc_start: 0.8159 (mm110) cc_final: 0.7899 (mm110) REVERT: B 447 SER cc_start: 0.7857 (m) cc_final: 0.7537 (m) outliers start: 17 outliers final: 8 residues processed: 237 average time/residue: 1.2080 time to fit residues: 322.7303 Evaluate side-chains 230 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 220 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain C residue 262 GLU Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 439 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 140 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 153 optimal weight: 0.4980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN E 208 GLN E 318 GLN D 475 GLN B 258 ASN B 432 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.150825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.112708 restraints weight = 44807.101| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.58 r_work: 0.3243 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17367 Z= 0.139 Angle : 0.535 5.335 23712 Z= 0.272 Chirality : 0.044 0.241 2802 Planarity : 0.004 0.038 2908 Dihedral : 8.616 126.471 2806 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.93 % Favored : 98.02 % Rotamer: Outliers : 1.02 % Allowed : 10.01 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % 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: 2.04 (0.19), residues: 2020 helix: 2.97 (0.17), residues: 796 sheet: 0.14 (0.25), residues: 408 loop : 0.45 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 6 TYR 0.015 0.001 TYR E 134 PHE 0.014 0.002 PHE E 267 TRP 0.012 0.001 TRP D 176 HIS 0.005 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00303 (17336) covalent geometry : angle 0.52098 (23625) SS BOND : bond 0.00288 ( 6) SS BOND : angle 1.07569 ( 12) hydrogen bonds : bond 0.04812 ( 881) hydrogen bonds : angle 4.24896 ( 2766) link_ALPHA1-3 : bond 0.00715 ( 3) link_ALPHA1-3 : angle 1.72585 ( 9) link_ALPHA1-6 : bond 0.01022 ( 4) link_ALPHA1-6 : angle 1.57565 ( 12) link_BETA1-3 : bond 0.00790 ( 1) link_BETA1-3 : angle 2.06698 ( 3) link_BETA1-4 : bond 0.00364 ( 11) link_BETA1-4 : angle 2.33875 ( 33) link_NAG-ASN : bond 0.00354 ( 6) link_NAG-ASN : angle 2.48911 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 225 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.6824 (m-30) REVERT: C 306 HIS cc_start: 0.8155 (m90) cc_final: 0.7882 (m90) REVERT: C 387 LYS cc_start: 0.7918 (tptm) cc_final: 0.7464 (tptp) REVERT: E 208 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7421 (mm110) REVERT: E 295 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7771 (mm) REVERT: D 328 LYS cc_start: 0.7110 (tttt) cc_final: 0.6798 (tptm) REVERT: D 332 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: D 470 GLN cc_start: 0.8180 (mm110) cc_final: 0.7930 (mm110) REVERT: B 447 SER cc_start: 0.7853 (m) cc_final: 0.7534 (m) outliers start: 19 outliers final: 11 residues processed: 235 average time/residue: 1.1668 time to fit residues: 310.4945 Evaluate side-chains 235 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 220 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain C residue 262 GLU Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 208 GLN Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 439 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 140 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 134 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN E 318 GLN D 475 GLN B 258 ASN B 432 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.150841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.112732 restraints weight = 45103.722| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.58 r_work: 0.3244 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17367 Z= 0.137 Angle : 0.533 5.302 23712 Z= 0.271 Chirality : 0.043 0.238 2802 Planarity : 0.004 0.039 2908 Dihedral : 8.550 124.330 2806 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.98 % Favored : 97.97 % Rotamer: Outliers : 0.91 % Allowed : 10.12 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % 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: 2.02 (0.19), residues: 2020 helix: 2.97 (0.17), residues: 796 sheet: 0.13 (0.25), residues: 408 loop : 0.43 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 6 TYR 0.013 0.001 TYR E 134 PHE 0.013 0.001 PHE D 291 TRP 0.012 0.001 TRP D 176 HIS 0.004 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00296 (17336) covalent geometry : angle 0.51932 (23625) SS BOND : bond 0.00266 ( 6) SS BOND : angle 1.01834 ( 12) hydrogen bonds : bond 0.04782 ( 881) hydrogen bonds : angle 4.24691 ( 2766) link_ALPHA1-3 : bond 0.00714 ( 3) link_ALPHA1-3 : angle 1.71687 ( 9) link_ALPHA1-6 : bond 0.01113 ( 4) link_ALPHA1-6 : angle 1.60480 ( 12) link_BETA1-3 : bond 0.00771 ( 1) link_BETA1-3 : angle 2.05196 ( 3) link_BETA1-4 : bond 0.00355 ( 11) link_BETA1-4 : angle 2.30907 ( 33) link_NAG-ASN : bond 0.00324 ( 6) link_NAG-ASN : angle 2.44053 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 222 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 ASP cc_start: 0.7387 (OUTLIER) cc_final: 0.6811 (m-30) REVERT: C 306 HIS cc_start: 0.8152 (m90) cc_final: 0.7876 (m90) REVERT: C 387 LYS cc_start: 0.7912 (tptm) cc_final: 0.7460 (tptp) REVERT: E 295 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7769 (mm) REVERT: D 328 LYS cc_start: 0.7113 (tttt) cc_final: 0.6795 (tptm) REVERT: D 332 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: D 470 GLN cc_start: 0.8191 (mm110) cc_final: 0.7951 (mm110) REVERT: B 413 SER cc_start: 0.8232 (t) cc_final: 0.8015 (m) REVERT: B 447 SER cc_start: 0.7907 (m) cc_final: 0.7596 (m) outliers start: 17 outliers final: 11 residues processed: 230 average time/residue: 1.2919 time to fit residues: 335.0970 Evaluate side-chains 234 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 220 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain C residue 262 GLU Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain E residue 77 SER Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 424 ILE Chi-restraints excluded: chain D residue 439 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 136 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 201 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 175 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 144 optimal weight: 0.5980 chunk 118 optimal weight: 0.3980 chunk 79 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 393 ASN E 318 GLN D 475 GLN B 258 ASN B 432 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.151282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.113383 restraints weight = 44818.414| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.57 r_work: 0.3254 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17367 Z= 0.122 Angle : 0.516 5.184 23712 Z= 0.263 Chirality : 0.043 0.211 2802 Planarity : 0.004 0.039 2908 Dihedral : 8.318 119.145 2806 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.03 % Favored : 97.92 % Rotamer: Outliers : 0.96 % Allowed : 10.12 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.24 % 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: 2.09 (0.19), residues: 2020 helix: 3.03 (0.17), residues: 795 sheet: 0.14 (0.25), residues: 415 loop : 0.49 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 6 TYR 0.012 0.001 TYR E 134 PHE 0.013 0.001 PHE C 227 TRP 0.011 0.001 TRP D 176 HIS 0.003 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00260 (17336) covalent geometry : angle 0.50295 (23625) SS BOND : bond 0.00219 ( 6) SS BOND : angle 0.89245 ( 12) hydrogen bonds : bond 0.04624 ( 881) hydrogen bonds : angle 4.18613 ( 2766) link_ALPHA1-3 : bond 0.00708 ( 3) link_ALPHA1-3 : angle 1.68373 ( 9) link_ALPHA1-6 : bond 0.01026 ( 4) link_ALPHA1-6 : angle 1.53379 ( 12) link_BETA1-3 : bond 0.00736 ( 1) link_BETA1-3 : angle 1.94227 ( 3) link_BETA1-4 : bond 0.00343 ( 11) link_BETA1-4 : angle 2.23238 ( 33) link_NAG-ASN : bond 0.00267 ( 6) link_NAG-ASN : angle 2.34953 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13423.82 seconds wall clock time: 227 minutes 2.84 seconds (13622.84 seconds total)