Starting phenix.real_space_refine on Tue Sep 15 01:36:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ye6_72844/09_2026/9ye6_72844_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ye6_72844/09_2026/9ye6_72844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ye6_72844/09_2026/9ye6_72844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ye6_72844/09_2026/9ye6_72844.map" model { file = "/net/cci-nas-00/data/ceres_data/9ye6_72844/09_2026/9ye6_72844_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ye6_72844/09_2026/9ye6_72844_trim.cif" } resolution = 2.47 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= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 76 5.16 5 C 10888 2.51 5 N 2694 2.21 5 O 3087 1.98 5 H 16538 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 33283 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 6394 Classifications: {'peptide': 397} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 376} Chain breaks: 2 Chain: "C" Number of atoms: 6470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 6470 Classifications: {'peptide': 400} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 379} Chain breaks: 1 Chain: "E" Number of atoms: 6578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 6578 Classifications: {'peptide': 405} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 379} Chain breaks: 3 Chain: "D" Number of atoms: 7058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 7058 Classifications: {'peptide': 433} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 402} Chain breaks: 1 Chain: "B" Number of atoms: 6489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 6489 Classifications: {'peptide': 411} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 388} Chain breaks: 1 Chain: "F" 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" 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: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'OCT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.69, per 1000 atoms: 0.14 Number of scatterers: 33283 At special positions: 0 Unit cell: (98.175, 108.46, 173.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 O 3087 8.00 N 2694 7.00 C 10888 6.00 H 16538 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=2.06 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 142 " distance=2.06 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " distance=2.05 Simple disulfide: pdb=" SG CYS D 130 " - pdb=" SG CYS D 144 " distance=2.04 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 142 " distance=2.04 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 F 3 " - " MAN F 4 " " BMA G 3 " - " MAN G 4 " " BMA I 3 " - " MAN I 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA G 3 " - " MAN G 5 " 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-ASN " NAG B 501 " - " ASN B 66 " " 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 " Time building additional restraints: 3.00 Conformation dependent library (CDL) restraints added in 807.1 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: 61 helices and 19 sheets defined 44.9% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 68 through 73 removed outlier: 4.012A pdb=" N GLY A 73 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.696A 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: 3.866A 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 260 removed outlier: 3.701A pdb=" N LEU A 258 " --> pdb=" O THR A 254 " (cutoff:3.500A) removed outlier: 3.765A 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 317 Processing helix chain 'A' and resid 319 through 324 removed outlier: 3.629A pdb=" N ILE A 323 " --> pdb=" O THR A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 435 removed outlier: 4.932A pdb=" N GLY A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ARG A 429 " --> pdb=" O VAL A 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 68 through 73 removed outlier: 4.157A 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 233 Processing helix chain 'C' and resid 236 through 240 removed outlier: 3.723A pdb=" N GLY C 240 " --> pdb=" O THR C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 262 removed outlier: 4.275A pdb=" N GLU C 262 " --> pdb=" O LEU C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 300 Processing helix chain 'C' and resid 309 through 318 removed outlier: 3.512A 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: 3.628A pdb=" N VAL C 425 " --> pdb=" O GLY C 421 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 4.869A 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: 4.223A 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 242 Processing helix chain 'E' and resid 243 through 246 Processing helix chain 'E' and resid 247 through 251 removed outlier: 3.652A pdb=" N GLY E 251 " --> pdb=" O PRO E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 272 removed outlier: 3.542A pdb=" N LEU E 261 " --> pdb=" O SER E 257 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE E 267 " --> pdb=" O THR E 263 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU E 269 " --> pdb=" O THR E 265 " (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: 3.677A 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 Processing helix chain 'D' and resid 71 through 75 removed outlier: 3.965A pdb=" N GLY D 75 " --> pdb=" O GLU D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'D' and resid 180 through 184 removed outlier: 3.603A pdb=" N PHE D 184 " --> pdb=" O PRO D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 232 Processing helix chain 'D' and resid 232 through 243 removed outlier: 3.733A pdb=" N VAL D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 249 removed outlier: 4.201A pdb=" N TYR D 248 " --> pdb=" O ASN D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 276 removed outlier: 3.874A pdb=" N VAL D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) removed outlier: 3.778A 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: 4.001A 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: 3.805A pdb=" N GLY D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 removed outlier: 3.685A pdb=" N ARG B 6 " --> pdb=" O ASN B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 66 removed outlier: 3.516A pdb=" N ASN B 66 " --> pdb=" O TYR B 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 63 through 66' Processing helix chain 'B' and resid 68 through 72 Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.666A pdb=" N VAL B 85 " --> pdb=" O SER B 82 " (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 Processing helix chain 'B' and resid 251 through 271 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 removed outlier: 3.539A pdb=" N ARG B 332 " --> pdb=" O GLU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 460 removed outlier: 3.947A pdb=" N GLY B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 4.373A 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: 4.115A 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: 4.115A pdb=" N HIS A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE A 49 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL A 43 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR A 51 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG A 55 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU A 37 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LYS A 57 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LEU A 35 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N GLN A 59 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL A 33 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N VAL A 61 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 7.840A 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: 4.338A pdb=" N THR A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU A 199 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N TYR A 198 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N SER A 187 " --> pdb=" O TYR A 198 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASP A 200 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR A 202 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLY A 183 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N HIS A 204 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER A 181 " --> pdb=" O HIS A 204 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL A 206 " --> pdb=" O LYS A 179 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 81 removed outlier: 3.793A 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: 3.793A pdb=" N HIS C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE C 49 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL C 43 " --> pdb=" O ILE C 49 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR C 51 " --> pdb=" O ILE C 41 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ARG C 55 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LEU C 37 " --> pdb=" O ARG C 55 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LYS C 57 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU C 35 " --> pdb=" O LYS C 57 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N GLN C 59 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N VAL C 33 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N VAL C 61 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N VAL C 31 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 90 through 92 removed outlier: 4.107A pdb=" N THR C 148 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LEU C 199 " --> pdb=" O THR C 148 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N TYR C 198 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N SER C 187 " --> pdb=" O TYR C 198 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASP C 200 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LYS C 185 " --> pdb=" O ASP C 200 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR C 202 " --> pdb=" O GLY C 183 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLY C 183 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N HIS C 204 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER C 181 " --> pdb=" O HIS C 204 " (cutoff:3.500A) removed outlier: 6.665A 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: 3.981A pdb=" N SER E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 4.819A 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: 3.981A pdb=" N SER E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLU E 49 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU E 43 " --> pdb=" O GLU E 49 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER E 51 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR E 55 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LEU E 37 " --> pdb=" O TYR E 55 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASP E 57 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LEU E 35 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLU E 59 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL E 33 " --> pdb=" O GLU E 59 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N THR E 61 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N VAL E 31 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 11.197A pdb=" N TYR E 63 " --> pdb=" O VAL E 29 " (cutoff:3.500A) removed outlier: 13.378A 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: 6.893A 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: 4.093A 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: 4.093A pdb=" N PHE D 117 " --> pdb=" O TYR D 113 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N THR D 51 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU D 45 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR D 53 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TRP D 57 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LEU D 39 " --> pdb=" O TRP D 57 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU D 59 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU D 37 " --> pdb=" O GLU D 59 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N GLY D 61 " --> pdb=" O LEU D 35 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N LEU D 35 " --> pdb=" O GLY D 61 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N THR D 63 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N VAL D 33 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL D 31 " --> pdb=" O THR D 159 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N SER D 161 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL D 33 " --> pdb=" O SER D 161 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 93 through 94 removed outlier: 6.893A pdb=" N ILE D 220 " --> pdb=" O VAL D 193 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 93 through 94 Processing sheet with id=AB6, first strand: chain 'D' and resid 164 through 166 Processing sheet with id=AB7, first strand: chain 'B' and resid 77 through 80 removed outlier: 3.858A 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 80 removed outlier: 3.858A pdb=" N SER B 115 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR B 49 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER B 42 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N THR B 51 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEU B 40 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N SER B 53 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLN B 61 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR B 30 " --> pdb=" O GLN B 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.112A pdb=" N SER B 148 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N THR B 208 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 6.739A 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: 5.112A pdb=" N SER B 148 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N THR B 208 " --> pdb=" O SER B 148 " (cutoff:3.500A) 942 hydrogen bonds defined for protein. 2709 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: 8.16 Time building geometry restraints manager: 4.07 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: 16519 1.04 - 1.23: 355 1.23 - 1.43: 6804 1.43 - 1.62: 9902 1.62 - 1.82: 121 Bond restraints: 33701 Sorted by residual: bond pdb=" ND2 ASN E 141 " pdb="HD21 ASN E 141 " ideal model delta sigma weight residual 0.860 0.989 -0.129 2.00e-02 2.50e+03 4.15e+01 bond pdb=" ND2 ASN B 66 " pdb="HD21 ASN B 66 " ideal model delta sigma weight residual 0.860 0.979 -0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" ND2 ASN B 141 " pdb="HD21 ASN B 141 " ideal model delta sigma weight residual 0.860 0.975 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" ND2 ASN D 143 " pdb="HD21 ASN D 143 " ideal model delta sigma weight residual 0.860 0.974 -0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" ND2 ASN A 141 " pdb="HD21 ASN A 141 " ideal model delta sigma weight residual 0.860 0.963 -0.103 2.00e-02 2.50e+03 2.66e+01 ... (remaining 33696 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.69: 60975 12.69 - 25.38: 1 25.38 - 38.07: 0 38.07 - 50.76: 0 50.76 - 63.45: 5 Bond angle restraints: 60981 Sorted by residual: angle pdb=" CA ILE C 367 " pdb=" N ILE C 367 " pdb=" H ILE C 367 " ideal model delta sigma weight residual 114.00 177.45 -63.45 3.00e+00 1.11e-01 4.47e+02 angle pdb=" CA HIS A 369 " pdb=" N HIS A 369 " pdb=" H HIS A 369 " ideal model delta sigma weight residual 114.00 174.34 -60.34 3.00e+00 1.11e-01 4.05e+02 angle pdb=" CA GLU E 206 " pdb=" N GLU E 206 " pdb=" H GLU E 206 " ideal model delta sigma weight residual 114.00 173.95 -59.95 3.00e+00 1.11e-01 3.99e+02 angle pdb=" CA LEU E 407 " pdb=" N LEU E 407 " pdb=" H LEU E 407 " ideal model delta sigma weight residual 114.00 172.28 -58.28 3.00e+00 1.11e-01 3.77e+02 angle pdb=" CA PHE A 326 " pdb=" N PHE A 326 " pdb=" H PHE A 326 " ideal model delta sigma weight residual 114.00 170.49 -56.49 3.00e+00 1.11e-01 3.55e+02 ... (remaining 60976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.20: 14992 21.20 - 42.41: 868 42.41 - 63.61: 241 63.61 - 84.81: 65 84.81 - 106.01: 25 Dihedral angle restraints: 16191 sinusoidal: 8931 harmonic: 7260 Sorted by residual: dihedral pdb=" CB CYS A 128 " pdb=" SG CYS A 128 " pdb=" SG CYS A 142 " pdb=" CB CYS A 142 " ideal model delta sinusoidal sigma weight residual 93.00 25.00 68.00 1 1.00e+01 1.00e-02 6.00e+01 dihedral pdb=" CA VAL C 425 " pdb=" C VAL C 425 " pdb=" N PHE C 426 " pdb=" CA PHE C 426 " ideal model delta harmonic sigma weight residual 180.00 -151.51 -28.49 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA VAL B 54 " pdb=" C VAL B 54 " pdb=" N TRP B 55 " pdb=" CA TRP B 55 " ideal model delta harmonic sigma weight residual 180.00 151.93 28.07 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 16188 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2517 0.083 - 0.167: 253 0.167 - 0.250: 5 0.250 - 0.334: 2 0.334 - 0.417: 3 Chirality restraints: 2780 Sorted by residual: chirality pdb=" C1 MAN G 4 " pdb=" O3 BMA G 3 " pdb=" C2 MAN G 4 " pdb=" O5 MAN G 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.69e+01 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 3.15e+01 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.36e+01 ... (remaining 2777 not shown) Planarity restraints: 4819 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 141 " 0.259 2.00e-02 2.50e+03 3.30e-01 1.63e+03 pdb=" CG ASN B 141 " 0.091 2.00e-02 2.50e+03 pdb=" OD1 ASN B 141 " -0.346 2.00e-02 2.50e+03 pdb=" ND2 ASN B 141 " 0.231 2.00e-02 2.50e+03 pdb="HD21 ASN B 141 " -0.552 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " 0.317 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 143 " -0.244 2.00e-02 2.50e+03 3.22e-01 1.56e+03 pdb=" CG ASN D 143 " -0.092 2.00e-02 2.50e+03 pdb=" OD1 ASN D 143 " 0.343 2.00e-02 2.50e+03 pdb=" ND2 ASN D 143 " -0.240 2.00e-02 2.50e+03 pdb="HD21 ASN D 143 " 0.537 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " -0.303 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 141 " 0.249 2.00e-02 2.50e+03 3.18e-01 1.52e+03 pdb=" CG ASN E 141 " 0.088 2.00e-02 2.50e+03 pdb=" OD1 ASN E 141 " -0.367 2.00e-02 2.50e+03 pdb=" ND2 ASN E 141 " 0.241 2.00e-02 2.50e+03 pdb="HD21 ASN E 141 " -0.507 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " 0.295 2.00e-02 2.50e+03 ... (remaining 4816 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 321 2.07 - 2.71: 53968 2.71 - 3.34: 95941 3.34 - 3.97: 130056 3.97 - 4.60: 200017 Nonbonded interactions: 480303 Sorted by model distance: nonbonded pdb=" HH TYR D 17 " pdb=" H TRP D 88 " model vdw 1.443 2.100 nonbonded pdb=" O ASN B 182 " pdb=" HZ1 LYS B 219 " model vdw 1.586 2.450 nonbonded pdb=" HZ3 LYS C 387 " pdb=" OE2 GLU C 391 " model vdw 1.674 2.450 nonbonded pdb=" HE1 TRP A 149 " pdb=" O LEU B 119 " model vdw 1.681 2.450 nonbonded pdb=" O TYR E 245 " pdb="HD21 ASN D 311 " model vdw 1.692 2.450 ... (remaining 480298 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 'G' } ncs_group { reference = chain 'H' selection = chain 'J' } 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: 4.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.200 Extract box with map and model: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 28.740 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 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 : 0.005 0.148 17190 Z= 0.266 Angle : 0.835 20.435 23484 Z= 0.433 Chirality : 0.051 0.417 2780 Planarity : 0.008 0.163 2897 Dihedral : 17.003 106.013 6536 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.39 % Favored : 98.56 % Rotamer: Outliers : 0.43 % Allowed : 10.28 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.18), residues: 2020 helix: 1.77 (0.18), residues: 776 sheet: -0.53 (0.24), residues: 407 loop : -0.37 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 277 TYR 0.020 0.001 TYR C 72 PHE 0.012 0.002 PHE E 224 TRP 0.016 0.002 TRP D 141 HIS 0.011 0.002 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.24 (17163) covalent geometry : angle 0.78654 / 0.42 (23409) SS BOND : bond 0.02007 / 0.99 ( 6) SS BOND : angle 3.53174 / 2.00 ( 12) hydrogen bonds : bond 0.13275 / 9.13 ( 856) hydrogen bonds : angle 5.59838 / 3.95 ( 2709) link_ALPHA1-3 : bond 0.00142 / 0.07 ( 3) link_ALPHA1-3 : angle 2.00451 / 1.18 ( 9) link_ALPHA1-6 : bond 0.00224 / 0.11 ( 2) link_ALPHA1-6 : angle 0.72605 / 0.33 ( 6) link_BETA1-4 : bond 0.00823 / 0.52 ( 10) link_BETA1-4 : angle 2.68746 / 1.88 ( 30) link_NAG-ASN : bond 0.13128 / 7.10 ( 6) link_NAG-ASN : angle 9.11903 / 5.23 ( 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 271 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 263 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 MET cc_start: 0.7951 (mmm) cc_final: 0.7699 (mmm) REVERT: A 307 VAL cc_start: 0.8845 (t) cc_final: 0.8580 (p) REVERT: C 302 SER cc_start: 0.8233 (t) cc_final: 0.8022 (p) REVERT: E 321 LEU cc_start: 0.8436 (tp) cc_final: 0.8114 (tp) REVERT: B 167 LYS cc_start: 0.7281 (ttmm) cc_final: 0.7055 (mtpm) REVERT: B 300 MET cc_start: 0.8079 (ttp) cc_final: 0.7864 (ttp) REVERT: B 323 ARG cc_start: 0.6865 (ttp-170) cc_final: 0.6648 (ttt90) outliers start: 8 outliers final: 6 residues processed: 270 average time/residue: 1.0934 time to fit residues: 336.4121 Evaluate side-chains 181 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 175 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain E residue 281 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 131 GLN D 432 ASN D 489 ASN D 491 GLN B 99 GLN B 417 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.111775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.086785 restraints weight = 59780.328| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.91 r_work: 0.2879 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 17190 Z= 0.125 Angle : 0.555 12.735 23484 Z= 0.276 Chirality : 0.044 0.257 2780 Planarity : 0.005 0.063 2897 Dihedral : 10.136 87.796 2634 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.96 % Allowed : 13.33 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % 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: 1.26 (0.19), residues: 2020 helix: 2.51 (0.18), residues: 782 sheet: -0.34 (0.24), residues: 412 loop : -0.11 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 22 TYR 0.010 0.001 TYR D 434 PHE 0.016 0.001 PHE C 414 TRP 0.010 0.001 TRP B 60 HIS 0.004 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (17163) covalent geometry : angle 0.53419 / 0.27 (23409) SS BOND : bond 0.00302 / 0.16 ( 6) SS BOND : angle 3.80464 / 2.24 ( 12) hydrogen bonds : bond 0.04823 / 3.23 ( 856) hydrogen bonds : angle 4.30511 / 3.00 ( 2709) link_ALPHA1-3 : bond 0.00691 / 0.33 ( 3) link_ALPHA1-3 : angle 2.18368 / 1.19 ( 9) link_ALPHA1-6 : bond 0.00441 / 0.21 ( 2) link_ALPHA1-6 : angle 2.12118 / 1.13 ( 6) link_BETA1-4 : bond 0.00507 / 0.32 ( 10) link_BETA1-4 : angle 2.30939 / 1.64 ( 30) link_NAG-ASN : bond 0.00409 / 0.26 ( 6) link_NAG-ASN : angle 2.80828 / 1.79 ( 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 204 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: A 278 MET cc_start: 0.8091 (mmm) cc_final: 0.7841 (mmm) REVERT: A 307 VAL cc_start: 0.8806 (t) cc_final: 0.8492 (p) REVERT: C 302 SER cc_start: 0.8094 (t) cc_final: 0.7780 (p) REVERT: B 300 MET cc_start: 0.8246 (ttp) cc_final: 0.7833 (ttp) REVERT: B 323 ARG cc_start: 0.6070 (ttp-170) cc_final: 0.5747 (ttt90) outliers start: 18 outliers final: 7 residues processed: 195 average time/residue: 1.1086 time to fit residues: 245.4620 Evaluate side-chains 177 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 169 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 449 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 65 optimal weight: 0.0980 chunk 12 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 139 optimal weight: 0.0980 chunk 81 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 185 optimal weight: 0.8980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 196 GLN B 258 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.110932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.086004 restraints weight = 59630.753| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.91 r_work: 0.2863 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 17190 Z= 0.135 Angle : 0.531 10.004 23484 Z= 0.265 Chirality : 0.043 0.226 2780 Planarity : 0.004 0.055 2897 Dihedral : 8.615 81.299 2632 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.50 % Allowed : 13.12 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.47 (0.19), residues: 2020 helix: 2.76 (0.18), residues: 783 sheet: -0.25 (0.25), residues: 407 loop : -0.06 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 22 TYR 0.010 0.001 TYR D 119 PHE 0.014 0.001 PHE C 414 TRP 0.009 0.001 TRP B 60 HIS 0.004 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (17163) covalent geometry : angle 0.51483 / 0.26 (23409) SS BOND : bond 0.01428 / 0.68 ( 6) SS BOND : angle 3.73987 / 1.70 ( 12) hydrogen bonds : bond 0.04514 / 3.03 ( 856) hydrogen bonds : angle 4.11883 / 2.87 ( 2709) link_ALPHA1-3 : bond 0.00858 / 0.42 ( 3) link_ALPHA1-3 : angle 1.79950 / 1.00 ( 9) link_ALPHA1-6 : bond 0.00513 / 0.24 ( 2) link_ALPHA1-6 : angle 2.04654 / 1.09 ( 6) link_BETA1-4 : bond 0.00405 / 0.27 ( 10) link_BETA1-4 : angle 2.03602 / 1.46 ( 30) link_NAG-ASN : bond 0.00210 / 0.11 ( 6) link_NAG-ASN : angle 1.92406 / 1.20 ( 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 207 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7048 (mp0) REVERT: A 307 VAL cc_start: 0.8804 (t) cc_final: 0.8479 (p) REVERT: C 302 SER cc_start: 0.8143 (t) cc_final: 0.7866 (p) REVERT: E 413 VAL cc_start: 0.7769 (t) cc_final: 0.7552 (m) REVERT: B 300 MET cc_start: 0.8204 (ttp) cc_final: 0.7828 (ttp) REVERT: B 323 ARG cc_start: 0.6185 (ttp-170) cc_final: 0.5757 (ttt90) outliers start: 28 outliers final: 13 residues processed: 195 average time/residue: 1.1176 time to fit residues: 248.2373 Evaluate side-chains 183 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain B residue 451 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 7 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 195 optimal weight: 10.0000 chunk 160 optimal weight: 0.8980 chunk 148 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 143 optimal weight: 0.8980 chunk 137 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 318 GLN B 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.110286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.085113 restraints weight = 59743.535| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.91 r_work: 0.2852 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17190 Z= 0.123 Angle : 0.498 6.725 23484 Z= 0.249 Chirality : 0.042 0.206 2780 Planarity : 0.004 0.051 2897 Dihedral : 7.461 69.928 2632 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.18 % Allowed : 13.17 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % 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: 1.63 (0.19), residues: 2020 helix: 2.92 (0.18), residues: 783 sheet: -0.24 (0.24), residues: 420 loop : 0.03 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 429 TYR 0.009 0.001 TYR D 119 PHE 0.014 0.001 PHE C 414 TRP 0.008 0.001 TRP B 60 HIS 0.004 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (17163) covalent geometry : angle 0.48740 / 0.25 (23409) SS BOND : bond 0.01062 / 0.51 ( 6) SS BOND : angle 1.89616 / 0.93 ( 12) hydrogen bonds : bond 0.04296 / 2.88 ( 856) hydrogen bonds : angle 3.97358 / 2.77 ( 2709) link_ALPHA1-3 : bond 0.00875 / 0.43 ( 3) link_ALPHA1-3 : angle 1.99024 / 1.07 ( 9) link_ALPHA1-6 : bond 0.00645 / 0.31 ( 2) link_ALPHA1-6 : angle 2.05345 / 1.08 ( 6) link_BETA1-4 : bond 0.00375 / 0.25 ( 10) link_BETA1-4 : angle 1.93713 / 1.35 ( 30) link_NAG-ASN : bond 0.00132 / 0.08 ( 6) link_NAG-ASN : angle 1.66622 / 1.12 ( 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 204 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7055 (mp0) REVERT: A 307 VAL cc_start: 0.8828 (t) cc_final: 0.8501 (m) REVERT: C 129 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7633 (tt0) REVERT: C 302 SER cc_start: 0.8121 (t) cc_final: 0.7888 (p) REVERT: C 415 MET cc_start: 0.7195 (mtp) cc_final: 0.6897 (ttm) REVERT: B 131 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7262 (tm-30) REVERT: B 167 LYS cc_start: 0.7054 (mtpp) cc_final: 0.6805 (mtpm) REVERT: B 300 MET cc_start: 0.8213 (ttp) cc_final: 0.7803 (ttp) REVERT: B 323 ARG cc_start: 0.6117 (ttp-170) cc_final: 0.5639 (ttt90) outliers start: 22 outliers final: 9 residues processed: 196 average time/residue: 1.0623 time to fit residues: 238.6365 Evaluate side-chains 183 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 278 MET Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain B residue 131 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 107 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN A 204 HIS E 318 GLN D 60 HIS ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.106902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.081468 restraints weight = 60166.507| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 1.92 r_work: 0.2796 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 17190 Z= 0.224 Angle : 0.560 5.757 23484 Z= 0.283 Chirality : 0.045 0.216 2780 Planarity : 0.005 0.050 2897 Dihedral : 7.683 72.845 2630 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.34 % Allowed : 13.01 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % 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: 1.45 (0.19), residues: 2020 helix: 2.73 (0.18), residues: 780 sheet: -0.17 (0.24), residues: 426 loop : -0.10 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 20 TYR 0.009 0.001 TYR D 119 PHE 0.017 0.002 PHE E 137 TRP 0.011 0.001 TRP D 176 HIS 0.007 0.001 HIS E 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.22 (17163) covalent geometry : angle 0.54803 / 0.28 (23409) SS BOND : bond 0.01113 / 0.54 ( 6) SS BOND : angle 1.95337 / 1.15 ( 12) hydrogen bonds : bond 0.04934 / 3.33 ( 856) hydrogen bonds : angle 4.13063 / 2.88 ( 2709) link_ALPHA1-3 : bond 0.00682 / 0.33 ( 3) link_ALPHA1-3 : angle 1.92039 / 1.07 ( 9) link_ALPHA1-6 : bond 0.00854 / 0.41 ( 2) link_ALPHA1-6 : angle 1.26675 / 0.69 ( 6) link_BETA1-4 : bond 0.00388 / 0.28 ( 10) link_BETA1-4 : angle 2.38287 / 1.59 ( 30) link_NAG-ASN : bond 0.00277 / 0.14 ( 6) link_NAG-ASN : angle 1.97800 / 1.26 ( 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 202 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7106 (mp0) REVERT: A 307 VAL cc_start: 0.8762 (t) cc_final: 0.8440 (m) REVERT: C 302 SER cc_start: 0.8209 (t) cc_final: 0.7982 (p) REVERT: D 431 GLN cc_start: 0.7763 (tp-100) cc_final: 0.7424 (tt0) REVERT: B 131 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7656 (tm-30) REVERT: B 270 ILE cc_start: 0.8479 (mt) cc_final: 0.8268 (pt) outliers start: 25 outliers final: 10 residues processed: 191 average time/residue: 1.0686 time to fit residues: 233.9044 Evaluate side-chains 184 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 172 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain B residue 131 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 45 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 60 optimal weight: 0.1980 chunk 79 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 146 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 393 ASN E 318 GLN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.107477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.082395 restraints weight = 60033.331| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.92 r_work: 0.2811 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17190 Z= 0.155 Angle : 0.513 5.190 23484 Z= 0.259 Chirality : 0.043 0.183 2780 Planarity : 0.004 0.050 2897 Dihedral : 7.145 66.994 2627 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.28 % Allowed : 13.06 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % 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: 1.55 (0.19), residues: 2020 helix: 2.83 (0.18), residues: 781 sheet: -0.18 (0.24), residues: 430 loop : -0.04 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 20 TYR 0.009 0.001 TYR D 119 PHE 0.013 0.001 PHE B 439 TRP 0.008 0.001 TRP C 60 HIS 0.005 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (17163) covalent geometry : angle 0.50362 / 0.26 (23409) SS BOND : bond 0.00953 / 0.46 ( 6) SS BOND : angle 1.67665 / 0.94 ( 12) hydrogen bonds : bond 0.04591 / 3.09 ( 856) hydrogen bonds : angle 4.03309 / 2.80 ( 2709) link_ALPHA1-3 : bond 0.00669 / 0.32 ( 3) link_ALPHA1-3 : angle 1.83481 / 1.00 ( 9) link_ALPHA1-6 : bond 0.00870 / 0.41 ( 2) link_ALPHA1-6 : angle 1.42613 / 0.75 ( 6) link_BETA1-4 : bond 0.00304 / 0.20 ( 10) link_BETA1-4 : angle 2.03162 / 1.35 ( 30) link_NAG-ASN : bond 0.00147 / 0.08 ( 6) link_NAG-ASN : angle 1.67439 / 1.13 ( 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 202 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: A 307 VAL cc_start: 0.8759 (t) cc_final: 0.8431 (m) REVERT: C 415 MET cc_start: 0.7256 (mtp) cc_final: 0.6951 (mtm) REVERT: D 431 GLN cc_start: 0.7765 (tp-100) cc_final: 0.7402 (tt0) REVERT: B 131 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7691 (tm-30) REVERT: B 300 MET cc_start: 0.8205 (ttp) cc_final: 0.7939 (ttp) outliers start: 24 outliers final: 14 residues processed: 191 average time/residue: 1.0776 time to fit residues: 235.3384 Evaluate side-chains 191 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 320 ILE Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 451 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 35 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 318 GLN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.106177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.080866 restraints weight = 60096.836| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.93 r_work: 0.2787 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 17190 Z= 0.229 Angle : 0.556 5.708 23484 Z= 0.281 Chirality : 0.044 0.190 2780 Planarity : 0.005 0.048 2897 Dihedral : 7.248 70.131 2627 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.45 % Allowed : 12.90 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % 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: 1.41 (0.19), residues: 2020 helix: 2.66 (0.18), residues: 781 sheet: -0.16 (0.24), residues: 426 loop : -0.12 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 429 TYR 0.009 0.001 TYR C 93 PHE 0.016 0.002 PHE E 137 TRP 0.011 0.001 TRP D 176 HIS 0.005 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.23 (17163) covalent geometry : angle 0.54453 / 0.28 (23409) SS BOND : bond 0.01115 / 0.54 ( 6) SS BOND : angle 2.08124 / 1.17 ( 12) hydrogen bonds : bond 0.04972 / 3.36 ( 856) hydrogen bonds : angle 4.13759 / 2.87 ( 2709) link_ALPHA1-3 : bond 0.00532 / 0.26 ( 3) link_ALPHA1-3 : angle 1.88493 / 1.02 ( 9) link_ALPHA1-6 : bond 0.01061 / 0.51 ( 2) link_ALPHA1-6 : angle 1.21908 / 0.64 ( 6) link_BETA1-4 : bond 0.00354 / 0.26 ( 10) link_BETA1-4 : angle 2.34251 / 1.56 ( 30) link_NAG-ASN : bond 0.00264 / 0.13 ( 6) link_NAG-ASN : angle 1.83319 / 1.19 ( 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 201 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: A 307 VAL cc_start: 0.8748 (t) cc_final: 0.8425 (m) REVERT: A 380 LYS cc_start: 0.7970 (mtpm) cc_final: 0.7729 (mtpp) REVERT: A 384 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7453 (mm-30) REVERT: C 129 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: D 156 LYS cc_start: 0.8768 (mttp) cc_final: 0.8459 (mtmt) REVERT: D 431 GLN cc_start: 0.7769 (tp-100) cc_final: 0.7432 (tt0) REVERT: B 131 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7707 (tm-30) REVERT: B 270 ILE cc_start: 0.8478 (mt) cc_final: 0.8265 (pt) outliers start: 27 outliers final: 16 residues processed: 189 average time/residue: 1.1696 time to fit residues: 250.6883 Evaluate side-chains 192 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain E residue 259 PHE Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain B residue 455 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 0.1980 chunk 33 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 81 optimal weight: 0.0970 chunk 28 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 318 GLN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.108121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.083262 restraints weight = 59777.494| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.91 r_work: 0.2824 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17190 Z= 0.115 Angle : 0.504 7.655 23484 Z= 0.254 Chirality : 0.042 0.202 2780 Planarity : 0.004 0.048 2897 Dihedral : 6.571 61.979 2627 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.91 % Allowed : 13.92 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 2.90 (0.18), residues: 782 sheet: -0.19 (0.24), residues: 428 loop : 0.02 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 22 TYR 0.009 0.001 TYR D 434 PHE 0.011 0.001 PHE B 439 TRP 0.009 0.001 TRP C 60 HIS 0.004 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (17163) covalent geometry : angle 0.49336 / 0.25 (23409) SS BOND : bond 0.00403 / 0.20 ( 6) SS BOND : angle 2.41924 / 1.40 ( 12) hydrogen bonds : bond 0.04382 / 2.94 ( 856) hydrogen bonds : angle 3.96985 / 2.76 ( 2709) link_ALPHA1-3 : bond 0.00545 / 0.26 ( 3) link_ALPHA1-3 : angle 1.75699 / 0.96 ( 9) link_ALPHA1-6 : bond 0.01218 / 0.58 ( 2) link_ALPHA1-6 : angle 1.54351 / 0.79 ( 6) link_BETA1-4 : bond 0.00288 / 0.19 ( 10) link_BETA1-4 : angle 1.80475 / 1.21 ( 30) link_NAG-ASN : bond 0.00141 / 0.09 ( 6) link_NAG-ASN : angle 1.60249 / 1.12 ( 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 197 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6998 (mp0) REVERT: A 307 VAL cc_start: 0.8674 (t) cc_final: 0.8353 (m) REVERT: A 384 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7359 (mm-30) REVERT: C 129 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7659 (tt0) REVERT: C 415 MET cc_start: 0.7274 (mtp) cc_final: 0.6968 (ttm) REVERT: D 431 GLN cc_start: 0.7767 (tp-100) cc_final: 0.7414 (tt0) REVERT: B 131 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7689 (tm-30) REVERT: B 270 ILE cc_start: 0.8390 (mt) cc_final: 0.8168 (pt) outliers start: 17 outliers final: 10 residues processed: 190 average time/residue: 1.0935 time to fit residues: 237.5839 Evaluate side-chains 189 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 176 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 324 MET Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain B residue 131 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 24 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 GLN E 318 GLN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.106998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.081845 restraints weight = 59844.649| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.92 r_work: 0.2802 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17190 Z= 0.184 Angle : 0.534 6.917 23484 Z= 0.269 Chirality : 0.043 0.178 2780 Planarity : 0.004 0.048 2897 Dihedral : 6.654 64.925 2627 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.91 % Allowed : 13.76 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.56 (0.19), residues: 2020 helix: 2.82 (0.18), residues: 782 sheet: -0.11 (0.24), residues: 419 loop : -0.05 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 429 TYR 0.009 0.001 TYR D 119 PHE 0.013 0.002 PHE A 12 TRP 0.009 0.001 TRP D 176 HIS 0.004 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (17163) covalent geometry : angle 0.52191 / 0.27 (23409) SS BOND : bond 0.00447 / 0.23 ( 6) SS BOND : angle 2.60908 / 1.49 ( 12) hydrogen bonds : bond 0.04675 / 3.16 ( 856) hydrogen bonds : angle 4.02736 / 2.80 ( 2709) link_ALPHA1-3 : bond 0.00575 / 0.28 ( 3) link_ALPHA1-3 : angle 1.83245 / 0.99 ( 9) link_ALPHA1-6 : bond 0.01289 / 0.61 ( 2) link_ALPHA1-6 : angle 1.77418 / 0.93 ( 6) link_BETA1-4 : bond 0.00303 / 0.22 ( 10) link_BETA1-4 : angle 2.13633 / 1.42 ( 30) link_NAG-ASN : bond 0.00191 / 0.10 ( 6) link_NAG-ASN : angle 1.78288 / 1.18 ( 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 193 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: A 307 VAL cc_start: 0.8734 (t) cc_final: 0.8353 (m) REVERT: A 380 LYS cc_start: 0.8028 (mtpm) cc_final: 0.7752 (mtpp) REVERT: A 384 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7470 (mm-30) REVERT: C 129 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7732 (tt0) REVERT: C 415 MET cc_start: 0.7292 (mtp) cc_final: 0.6984 (ttm) REVERT: D 431 GLN cc_start: 0.7752 (tp-100) cc_final: 0.7396 (tt0) REVERT: B 131 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7693 (tm-30) REVERT: B 198 HIS cc_start: 0.7492 (OUTLIER) cc_final: 0.7261 (m170) REVERT: B 270 ILE cc_start: 0.8407 (mt) cc_final: 0.8183 (pt) outliers start: 17 outliers final: 10 residues processed: 187 average time/residue: 1.1592 time to fit residues: 246.7212 Evaluate side-chains 190 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain B residue 131 GLU Chi-restraints excluded: chain B residue 198 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 96 optimal weight: 0.0070 chunk 4 optimal weight: 1.9990 chunk 196 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 318 GLN ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 470 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.107753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.082612 restraints weight = 59912.700| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.94 r_work: 0.2815 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17190 Z= 0.141 Angle : 0.509 5.746 23484 Z= 0.256 Chirality : 0.042 0.166 2780 Planarity : 0.004 0.048 2897 Dihedral : 6.369 61.061 2627 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.86 % Allowed : 13.92 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.63 (0.19), residues: 2020 helix: 2.90 (0.18), residues: 782 sheet: -0.12 (0.24), residues: 420 loop : -0.00 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 222 TYR 0.009 0.001 TYR D 434 PHE 0.011 0.001 PHE B 439 TRP 0.008 0.001 TRP C 60 HIS 0.004 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (17163) covalent geometry : angle 0.49958 / 0.25 (23409) SS BOND : bond 0.00791 / 0.38 ( 6) SS BOND : angle 1.21229 / 0.66 ( 12) hydrogen bonds : bond 0.04483 / 3.01 ( 856) hydrogen bonds : angle 3.98087 / 2.77 ( 2709) link_ALPHA1-3 : bond 0.00588 / 0.28 ( 3) link_ALPHA1-3 : angle 1.74392 / 0.96 ( 9) link_ALPHA1-6 : bond 0.01392 / 0.66 ( 2) link_ALPHA1-6 : angle 2.15010 / 1.12 ( 6) link_BETA1-4 : bond 0.00270 / 0.18 ( 10) link_BETA1-4 : angle 1.94741 / 1.29 ( 30) link_NAG-ASN : bond 0.00141 / 0.08 ( 6) link_NAG-ASN : angle 1.68134 / 1.14 ( 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 199 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: A 307 VAL cc_start: 0.8706 (t) cc_final: 0.8317 (m) REVERT: A 384 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7384 (mm-30) REVERT: C 129 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7679 (tt0) REVERT: C 415 MET cc_start: 0.7290 (mtp) cc_final: 0.6986 (ttm) REVERT: D 431 GLN cc_start: 0.7790 (tp-100) cc_final: 0.7407 (tt0) REVERT: B 131 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7677 (tm-30) REVERT: B 270 ILE cc_start: 0.8404 (mt) cc_final: 0.8182 (pt) outliers start: 16 outliers final: 11 residues processed: 194 average time/residue: 1.1651 time to fit residues: 257.1831 Evaluate side-chains 195 residues out of total 1868 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 181 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 126 SER Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 324 MET Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 414 PHE Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain D residue 211 SER Chi-restraints excluded: chain B residue 131 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 190 optimal weight: 1.9990 chunk 96 optimal weight: 0.0970 chunk 166 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 193 optimal weight: 3.9990 chunk 164 optimal weight: 0.9990 chunk 167 optimal weight: 0.6980 chunk 194 optimal weight: 0.7980 chunk 172 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 470 GLN B 258 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.108337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.083420 restraints weight = 60000.486| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.92 r_work: 0.2828 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17190 Z= 0.120 Angle : 0.494 5.698 23484 Z= 0.248 Chirality : 0.042 0.182 2780 Planarity : 0.004 0.047 2897 Dihedral : 6.067 58.447 2627 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.80 % Allowed : 14.19 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.71 (0.19), residues: 2020 helix: 3.01 (0.18), residues: 780 sheet: -0.14 (0.24), residues: 420 loop : 0.03 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 222 TYR 0.009 0.001 TYR D 434 PHE 0.010 0.001 PHE B 439 TRP 0.008 0.001 TRP C 311 HIS 0.004 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (17163) covalent geometry : angle 0.48572 / 0.25 (23409) SS BOND : bond 0.00463 / 0.23 ( 6) SS BOND : angle 1.07841 / 0.60 ( 12) hydrogen bonds : bond 0.04306 / 2.89 ( 856) hydrogen bonds : angle 3.91397 / 2.72 ( 2709) link_ALPHA1-3 : bond 0.00601 / 0.29 ( 3) link_ALPHA1-3 : angle 1.68321 / 0.94 ( 9) link_ALPHA1-6 : bond 0.01399 / 0.67 ( 2) link_ALPHA1-6 : angle 2.21727 / 1.15 ( 6) link_BETA1-4 : bond 0.00273 / 0.18 ( 10) link_BETA1-4 : angle 1.84853 / 1.23 ( 30) link_NAG-ASN : bond 0.00233 / 0.12 ( 6) link_NAG-ASN : angle 1.60645 / 1.11 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10103.17 seconds wall clock time: 171 minutes 21.06 seconds (10281.06 seconds total)