Starting phenix.real_space_refine on Mon Sep 14 22:59:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yf0_72868/09_2026/9yf0_72868_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yf0_72868/09_2026/9yf0_72868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yf0_72868/09_2026/9yf0_72868_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yf0_72868/09_2026/9yf0_72868_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yf0_72868/09_2026/9yf0_72868.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yf0_72868/09_2026/9yf0_72868.map" } resolution = 2.79 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= 0.019 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 74 5.16 5 C 10672 2.51 5 N 2639 2.21 5 O 3023 1.98 5 H 16210 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s 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: 32618 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 6251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 6251 Classifications: {'peptide': 388} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 368} Chain breaks: 1 Chain: "C" Number of atoms: 6311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 6311 Classifications: {'peptide': 391} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 370} Chain breaks: 1 Chain: "E" Number of atoms: 6451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 6451 Classifications: {'peptide': 398} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 373} Chain breaks: 3 Chain: "D" Number of atoms: 6938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 6938 Classifications: {'peptide': 426} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 395} Chain breaks: 1 Chain: "B" Number of atoms: 6403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 6403 Classifications: {'peptide': 406} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 383} 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: 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: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'ACH': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'ACH': 1} Classifications: {'undetermined': 1} Chain: "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: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.78, per 1000 atoms: 0.18 Number of scatterers: 32618 At special positions: 0 Unit cell: (100.045, 103.785, 159.885, 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 74 16.00 O 3023 8.00 N 2639 7.00 C 10672 6.00 H 16210 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=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " distance=2.04 Simple disulfide: pdb=" SG CYS D 130 " - pdb=" SG CYS D 144 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 470 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA H 3 " - " MAN H 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-ASN " NAG B 501 " - " ASN B 66 " " NAG F 1 " - " ASN A 141 " " NAG G 1 " - " ASN B 141 " " NAG H 1 " - " ASN C 141 " " NAG I 1 " - " ASN D 143 " " NAG J 1 " - " ASN E 141 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.37 Conformation dependent library (CDL) restraints added in 884.8 milliseconds 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 21 sheets defined 43.7% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 68 through 73 removed outlier: 3.835A pdb=" N GLY A 73 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 218 Processing helix chain 'A' and resid 218 through 232 Processing helix chain 'A' and resid 236 through 240 Processing helix chain 'A' and resid 241 through 263 Processing helix chain 'A' and resid 272 through 300 Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 319 through 323 Processing helix chain 'A' and resid 375 through 437 removed outlier: 3.575A pdb=" N VAL A 425 " --> pdb=" O GLY A 421 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLY A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG A 429 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN A 435 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN A 436 " --> pdb=" O GLU A 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 12 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 131 through 135 removed outlier: 4.296A pdb=" N HIS C 134 " --> pdb=" O ILE C 131 " (cutoff:3.500A) 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 234 Processing helix chain 'C' and resid 241 through 264 Processing helix chain 'C' and resid 272 through 300 Processing helix chain 'C' and resid 309 through 316 removed outlier: 3.617A pdb=" N VAL C 315 " --> pdb=" O TRP C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 323 Processing helix chain 'C' and resid 371 through 435 removed outlier: 4.012A pdb=" N GLY C 378 " --> pdb=" O SER C 374 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS C 380 " --> pdb=" O ILE C 376 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N TYR C 381 " --> pdb=" O GLU C 377 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA C 383 " --> pdb=" O ILE C 379 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA C 403 " --> pdb=" O TRP C 399 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE C 409 " --> pdb=" O VAL C 405 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU C 410 " --> pdb=" O MET C 406 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE C 419 " --> pdb=" O MET C 415 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR C 422 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 425 " --> pdb=" O GLY C 421 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 427 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ARG C 429 " --> pdb=" O VAL C 425 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU C 432 " --> pdb=" O GLY C 428 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 433 " --> pdb=" O ARG C 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 63 through 66 removed outlier: 4.029A pdb=" N SER E 66 " --> pdb=" O TYR E 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 63 through 66' Processing helix chain 'E' and resid 68 through 72 Processing helix chain 'E' and resid 131 through 135 removed outlier: 4.413A pdb=" N TYR E 134 " --> pdb=" O GLN E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 229 Processing helix chain 'E' and resid 229 through 246 removed outlier: 4.252A pdb=" N PHE E 244 " --> pdb=" O ALA E 240 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR E 245 " --> pdb=" O ILE E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 251 removed outlier: 3.607A pdb=" N ALA E 250 " --> pdb=" O PRO E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 275 removed outlier: 4.454A pdb=" N ILE E 258 " --> pdb=" O MET E 254 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU E 261 " --> pdb=" O SER E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 311 Processing helix chain 'E' and resid 320 through 328 removed outlier: 3.661A pdb=" N ARG E 324 " --> pdb=" O PRO E 320 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE E 326 " --> pdb=" O TRP E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 335 removed outlier: 3.539A pdb=" N TYR E 334 " --> pdb=" O LYS E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 469 Processing helix chain 'D' and resid 2 through 13 removed outlier: 3.523A pdb=" N ILE D 8 " --> pdb=" O GLU D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 75 removed outlier: 3.884A 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 225 through 232 Processing helix chain 'D' and resid 233 through 243 removed outlier: 3.513A pdb=" N VAL D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 246 No H-bonds generated for 'chain 'D' and resid 244 through 246' Processing helix chain 'D' and resid 255 through 278 Processing helix chain 'D' and resid 286 through 314 Processing helix chain 'D' and resid 323 through 330 Processing helix chain 'D' and resid 333 through 338 Processing helix chain 'D' and resid 416 through 473 removed outlier: 3.737A pdb=" N TYR D 434 " --> pdb=" O ASP D 430 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL D 455 " --> pdb=" O LEU D 451 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR D 457 " --> pdb=" O LEU D 453 " (cutoff:3.500A) Proline residue: D 458 - end of helix removed outlier: 3.984A pdb=" N GLY D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 68 through 73 removed outlier: 4.265A pdb=" N GLY B 73 " --> pdb=" O ASP B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 131 through 135 removed outlier: 4.482A pdb=" N TYR B 134 " --> pdb=" O GLU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 227 through 244 removed outlier: 3.757A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU B 239 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE B 243 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 272 Processing helix chain 'B' and resid 282 through 310 Processing helix chain 'B' and resid 319 through 324 Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 403 through 453 removed outlier: 4.025A pdb=" N VAL B 407 " --> pdb=" O CYS B 403 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TRP B 440 " --> pdb=" O ASN B 436 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B 453 " --> pdb=" O GLY B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 459 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 80 removed outlier: 4.035A pdb=" N HIS A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL A 61 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLU A 30 " --> pdb=" O VAL A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 44 removed outlier: 6.720A pdb=" N THR A 51 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VAL A 43 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE A 49 " --> pdb=" O VAL A 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.510A pdb=" N GLY A 147 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU A 199 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N THR A 196 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TYR A 190 " --> pdb=" O THR A 196 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN A 208 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ILE A 178 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 81 removed outlier: 4.399A pdb=" N HIS C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 81 removed outlier: 4.399A pdb=" N HIS C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE C 49 " --> pdb=" O ASN C 42 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ASN C 42 " --> pdb=" O ILE C 49 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR C 51 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LEU C 40 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN C 53 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL C 61 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLU C 30 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.600A pdb=" N CYS C 142 " --> pdb=" O PHE C 205 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR C 148 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU C 199 " --> pdb=" O THR C 148 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N THR C 196 " --> pdb=" O TYR C 190 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N TYR C 190 " --> pdb=" O THR C 196 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TRP C 184 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS C 204 " --> pdb=" O ARG C 182 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLN C 208 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ILE C 178 " --> pdb=" O GLN C 208 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 31 through 33 Processing sheet with id=AA8, first strand: chain 'E' and resid 35 through 44 removed outlier: 6.564A pdb=" N LYS E 53 " --> pdb=" O ALA E 38 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LEU E 40 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N SER E 51 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N SER E 42 " --> pdb=" O GLU E 49 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLU E 49 " --> pdb=" O SER E 42 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 58 through 61 removed outlier: 4.320A pdb=" N SER E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 90 through 92 removed outlier: 3.510A pdb=" N ILE E 213 " --> pdb=" O ARG E 193 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 139 through 142 removed outlier: 3.621A pdb=" N CYS E 142 " --> pdb=" O LEU E 216 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE E 217 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 123 through 129 removed outlier: 6.303A pdb=" N THR D 51 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU D 45 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR D 53 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TRP D 57 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU D 39 " --> pdb=" O TRP D 57 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU D 59 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LEU D 37 " --> pdb=" O GLU D 59 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N VAL D 31 " --> pdb=" O THR D 159 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N SER D 161 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N VAL D 33 " --> pdb=" O SER D 161 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 62 through 68 removed outlier: 4.731A pdb=" N GLY D 116 " --> pdb=" O ASP D 64 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 92 through 94 removed outlier: 5.367A pdb=" N SER D 150 " --> pdb=" O GLN D 213 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N GLN D 213 " --> pdb=" O SER D 150 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 141 through 144 removed outlier: 3.623A pdb=" N CYS D 144 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE D 220 " --> pdb=" O VAL D 193 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 164 through 166 Processing sheet with id=AB8, first strand: chain 'B' and resid 115 through 118 Processing sheet with id=AB9, first strand: chain 'B' and resid 115 through 118 removed outlier: 6.954A pdb=" N THR B 49 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N SER B 42 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N THR B 51 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LEU B 40 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N SER B 53 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLN B 61 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N THR B 30 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N VAL B 35 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA B 161 " --> pdb=" O ILE B 169 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 79 through 80 Processing sheet with id=AC2, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.053A pdb=" N SER B 148 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N THR B 208 " --> pdb=" O SER B 148 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 139 through 140 removed outlier: 7.175A pdb=" N ILE B 215 " --> pdb=" O ASP B 188 " (cutoff:3.500A) 823 hydrogen bonds defined for protein. 2364 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: 8.25 Time building geometry restraints manager: 4.55 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: 16191 1.04 - 1.23: 212 1.23 - 1.43: 6812 1.43 - 1.62: 9700 1.62 - 1.82: 117 Bond restraints: 33032 Sorted by residual: bond pdb=" NZ LYS A 145 " pdb=" HZ1 LYS A 145 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS E 253 " pdb=" HZ3 LYS E 253 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS C 380 " pdb=" HZ2 LYS C 380 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS C 185 " pdb=" HZ3 LYS C 185 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" NZ LYS B 69 " pdb=" HZ3 LYS B 69 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.62e+01 ... (remaining 33027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.43: 59780 10.43 - 20.86: 2 20.86 - 31.29: 0 31.29 - 41.72: 2 41.72 - 52.15: 1 Bond angle restraints: 59785 Sorted by residual: angle pdb=" CA SER A 374 " pdb=" N SER A 374 " pdb=" H SER A 374 " ideal model delta sigma weight residual 114.00 166.15 -52.15 3.00e+00 1.11e-01 3.02e+02 angle pdb=" CA CYS B 402 " pdb=" N CYS B 402 " pdb=" H CYS B 402 " ideal model delta sigma weight residual 114.00 155.14 -41.14 3.00e+00 1.11e-01 1.88e+02 angle pdb=" CA LYS D 415 " pdb=" N LYS D 415 " pdb=" H LYS D 415 " ideal model delta sigma weight residual 114.00 155.08 -41.08 3.00e+00 1.11e-01 1.87e+02 angle pdb=" CA GLU E 206 " pdb=" N GLU E 206 " pdb=" H GLU E 206 " ideal model delta sigma weight residual 114.00 127.88 -13.88 3.00e+00 1.11e-01 2.14e+01 angle pdb=" CA GLU E 412 " pdb=" N GLU E 412 " pdb=" H GLU E 412 " ideal model delta sigma weight residual 114.00 125.89 -11.89 3.00e+00 1.11e-01 1.57e+01 ... (remaining 59780 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.27: 14587 21.27 - 42.53: 907 42.53 - 63.80: 276 63.80 - 85.06: 68 85.06 - 106.33: 17 Dihedral angle restraints: 15855 sinusoidal: 8721 harmonic: 7134 Sorted by residual: dihedral pdb=" CA PHE C 233 " pdb=" C PHE C 233 " pdb=" N TYR C 234 " pdb=" CA TYR C 234 " ideal model delta harmonic sigma weight residual 180.00 157.86 22.14 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA LEU E 256 " pdb=" C LEU E 256 " pdb=" N SER E 257 " pdb=" CA SER E 257 " ideal model delta harmonic sigma weight residual 180.00 158.44 21.56 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA VAL E 132 " pdb=" C VAL E 132 " pdb=" N THR E 133 " pdb=" CA THR E 133 " ideal model delta harmonic sigma weight residual 180.00 -159.49 -20.51 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 15852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 2707 0.147 - 0.294: 10 0.294 - 0.440: 1 0.440 - 0.587: 2 0.587 - 0.734: 1 Chirality restraints: 2721 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.08e+01 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.78e+01 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.60e+01 ... (remaining 2718 not shown) Planarity restraints: 4733 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 143 " 0.236 2.00e-02 2.50e+03 2.28e-01 6.50e+02 pdb=" CG ASN D 143 " -0.077 2.00e-02 2.50e+03 pdb=" OD1 ASN D 143 " -0.082 2.00e-02 2.50e+03 pdb=" ND2 ASN D 143 " -0.345 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.269 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 141 " 0.202 2.00e-02 2.50e+03 2.05e-01 5.23e+02 pdb=" CG ASN C 141 " -0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN C 141 " -0.056 2.00e-02 2.50e+03 pdb=" ND2 ASN C 141 " -0.315 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " 0.245 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 66 " 0.122 2.00e-02 2.50e+03 1.23e-01 1.90e+02 pdb=" CG ASN B 66 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN B 66 " -0.026 2.00e-02 2.50e+03 pdb=" ND2 ASN B 66 " -0.197 2.00e-02 2.50e+03 pdb=" C1 NAG B 501 " 0.141 2.00e-02 2.50e+03 ... (remaining 4730 not shown) Histogram of nonbonded interaction distances: 1.13 - 1.82: 74 1.82 - 2.52: 25524 2.52 - 3.21: 102901 3.21 - 3.91: 136236 3.91 - 4.60: 214908 Nonbonded interactions: 479643 Sorted by model distance: nonbonded pdb=" HH TYR B 15 " pdb=" H TRP B 86 " model vdw 1.128 2.100 nonbonded pdb=" HE1 HIS A 186 " pdb=" C7 NAG F 2 " model vdw 1.305 2.200 nonbonded pdb=" O VAL D 490 " pdb=" HZ2 LYS D 493 " model vdw 1.436 2.450 nonbonded pdb=" O ILE E 172 " pdb=" HZ3 LYS E 190 " model vdw 1.579 2.450 nonbonded pdb=" HZ PHE C 225 " pdb="HG21 THR B 264 " model vdw 1.636 2.270 ... (remaining 479638 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 324 or resid 374 through 501)) } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'I' } 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: 2.830 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: 0.210 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 32.240 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.328 16848 Z= 0.264 Angle : 0.818 24.306 23023 Z= 0.380 Chirality : 0.051 0.734 2721 Planarity : 0.006 0.086 2844 Dihedral : 17.255 106.330 6369 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.48 % Favored : 96.47 % Rotamer: Outliers : 0.11 % Allowed : 13.81 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % 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: -1.17 (0.18), residues: 1985 helix: 0.44 (0.18), residues: 756 sheet: -2.11 (0.26), residues: 319 loop : -1.24 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 9 TYR 0.010 0.001 TYR E 334 PHE 0.017 0.001 PHE D 294 TRP 0.019 0.002 TRP D 190 HIS 0.009 0.001 HIS C 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (16822) covalent geometry : angle 0.71764 / 0.36 (22954) SS BOND : bond 0.00189 / 0.10 ( 6) SS BOND : angle 1.19592 / 0.67 ( 12) hydrogen bonds : bond 0.19440 / 13.03 ( 808) hydrogen bonds : angle 7.30533 / 5.15 ( 2364) Misc. bond : bond 0.00497 / 0.24 ( 1) link_ALPHA1-3 : bond 0.00199 / 0.09 ( 2) link_ALPHA1-3 : angle 0.89420 / 0.51 ( 6) link_ALPHA1-6 : bond 0.00182 / 0.09 ( 2) link_ALPHA1-6 : angle 1.43453 / 0.78 ( 6) link_BETA1-4 : bond 0.00401 / 0.27 ( 9) link_BETA1-4 : angle 3.53320 / 2.80 ( 27) link_NAG-ASN : bond 0.19882 / 11.64 ( 6) link_NAG-ASN : angle 13.33941 / 8.41 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 400 time to evaluate : 0.932 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 PHE cc_start: 0.7402 (m-80) cc_final: 0.6048 (OUTLIER) REVERT: C 391 GLU cc_start: 0.6559 (mt-10) cc_final: 0.6317 (mt-10) REVERT: E 451 THR cc_start: 0.7470 (m) cc_final: 0.7247 (m) REVERT: D 28 GLU cc_start: 0.6272 (pm20) cc_final: 0.6070 (pm20) outliers start: 2 outliers final: 3 residues processed: 402 average time/residue: 0.9741 time to fit residues: 456.6401 Evaluate side-chains 263 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 261 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain B residue 51 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN A 310 ASN C 48 GLN C 217 ASN C 408 HIS E 423 GLN D 60 HIS D 231 ASN B 301 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.161234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.136175 restraints weight = 61190.536| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 1.99 r_work: 0.3668 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16848 Z= 0.150 Angle : 0.603 6.101 23023 Z= 0.309 Chirality : 0.044 0.203 2721 Planarity : 0.005 0.048 2844 Dihedral : 9.459 82.180 2545 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.58 % Favored : 96.37 % Rotamer: Outliers : 2.13 % Allowed : 19.00 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % 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: -0.87 (0.18), residues: 1985 helix: 0.68 (0.18), residues: 769 sheet: -2.03 (0.25), residues: 341 loop : -1.01 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 6 TYR 0.012 0.001 TYR D 434 PHE 0.019 0.001 PHE B 446 TRP 0.008 0.001 TRP D 466 HIS 0.006 0.001 HIS A 186 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (16822) covalent geometry : angle 0.59233 / 0.31 (22954) SS BOND : bond 0.00258 / 0.13 ( 6) SS BOND : angle 0.91702 / 0.51 ( 12) hydrogen bonds : bond 0.05768 / 3.86 ( 808) hydrogen bonds : angle 5.66692 / 4.02 ( 2364) Misc. bond : bond 0.00037 / 0.02 ( 1) link_ALPHA1-3 : bond 0.00984 / 0.47 ( 2) link_ALPHA1-3 : angle 2.49421 / 1.24 ( 6) link_ALPHA1-6 : bond 0.00640 / 0.30 ( 2) link_ALPHA1-6 : angle 1.59412 / 0.87 ( 6) link_BETA1-4 : bond 0.00629 / 0.38 ( 9) link_BETA1-4 : angle 2.37034 / 1.73 ( 27) link_NAG-ASN : bond 0.00221 / 0.11 ( 6) link_NAG-ASN : angle 2.33882 / 1.36 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 267 time to evaluate : 0.937 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 PHE cc_start: 0.7740 (m-80) cc_final: 0.5700 (t80) REVERT: C 377 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.6417 (tp30) REVERT: C 391 GLU cc_start: 0.6488 (mt-10) cc_final: 0.6206 (mt-10) REVERT: E 298 PHE cc_start: 0.7657 (OUTLIER) cc_final: 0.7172 (m-80) REVERT: E 330 LYS cc_start: 0.7226 (mttt) cc_final: 0.6772 (tttt) REVERT: E 333 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7602 (mm) REVERT: E 337 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7565 (mp) REVERT: E 451 THR cc_start: 0.7972 (m) cc_final: 0.7557 (m) REVERT: D 28 GLU cc_start: 0.6596 (pm20) cc_final: 0.6130 (pm20) REVERT: D 77 ILE cc_start: 0.7483 (OUTLIER) cc_final: 0.6931 (tp) REVERT: D 296 MET cc_start: 0.8071 (mtp) cc_final: 0.7839 (mtp) REVERT: B 269 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7247 (tp) REVERT: B 292 MET cc_start: 0.7254 (mtp) cc_final: 0.7041 (mtp) REVERT: B 461 ARG cc_start: 0.7817 (ptm-80) cc_final: 0.7145 (ppt170) outliers start: 39 outliers final: 10 residues processed: 290 average time/residue: 0.9170 time to fit residues: 312.6659 Evaluate side-chains 263 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 247 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 377 GLU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 298 PHE Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 55 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.161410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.136095 restraints weight = 62055.950| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.11 r_work: 0.3689 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16848 Z= 0.145 Angle : 0.559 5.912 23023 Z= 0.285 Chirality : 0.043 0.211 2721 Planarity : 0.004 0.046 2844 Dihedral : 7.874 77.699 2544 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.53 % Favored : 96.42 % Rotamer: Outliers : 1.97 % Allowed : 19.10 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % 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: -0.66 (0.19), residues: 1985 helix: 0.92 (0.18), residues: 763 sheet: -1.85 (0.25), residues: 363 loop : -0.93 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 6 TYR 0.009 0.001 TYR D 434 PHE 0.021 0.001 PHE C 233 TRP 0.011 0.001 TRP B 427 HIS 0.003 0.001 HIS C 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (16822) covalent geometry : angle 0.54889 / 0.28 (22954) SS BOND : bond 0.00197 / 0.10 ( 6) SS BOND : angle 0.82060 / 0.45 ( 12) hydrogen bonds : bond 0.05198 / 3.47 ( 808) hydrogen bonds : angle 5.35306 / 3.79 ( 2364) Misc. bond : bond 0.00059 / 0.03 ( 1) link_ALPHA1-3 : bond 0.01003 / 0.48 ( 2) link_ALPHA1-3 : angle 1.93950 / 1.02 ( 6) link_ALPHA1-6 : bond 0.00937 / 0.45 ( 2) link_ALPHA1-6 : angle 1.50170 / 0.77 ( 6) link_BETA1-4 : bond 0.00572 / 0.31 ( 9) link_BETA1-4 : angle 2.37675 / 1.73 ( 27) link_NAG-ASN : bond 0.00153 / 0.09 ( 6) link_NAG-ASN : angle 2.09718 / 1.32 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 263 time to evaluate : 0.941 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 PHE cc_start: 0.7686 (m-80) cc_final: 0.5618 (t80) REVERT: C 377 GLU cc_start: 0.6539 (OUTLIER) cc_final: 0.6281 (tp30) REVERT: C 391 GLU cc_start: 0.6600 (mt-10) cc_final: 0.6263 (mt-10) REVERT: E 330 LYS cc_start: 0.7012 (mttt) cc_final: 0.6538 (tttt) REVERT: E 334 TYR cc_start: 0.7161 (m-10) cc_final: 0.6951 (m-10) REVERT: E 337 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7334 (mp) REVERT: E 447 LEU cc_start: 0.8151 (tp) cc_final: 0.7897 (tp) REVERT: E 451 THR cc_start: 0.7798 (m) cc_final: 0.7397 (m) REVERT: D 28 GLU cc_start: 0.6530 (pm20) cc_final: 0.6014 (pm20) REVERT: D 328 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7244 (tptp) REVERT: D 431 GLN cc_start: 0.7668 (tt0) cc_final: 0.7427 (tp-100) REVERT: B 292 MET cc_start: 0.7236 (mtp) cc_final: 0.7008 (mtp) outliers start: 36 outliers final: 16 residues processed: 281 average time/residue: 0.9652 time to fit residues: 318.9006 Evaluate side-chains 265 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 246 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 377 GLU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 492 ASP Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 415 ARG Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 86 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 178 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 GLN ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN D 244 ASN B 301 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.157063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.131238 restraints weight = 62536.767| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.11 r_work: 0.3631 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16848 Z= 0.236 Angle : 0.617 5.767 23023 Z= 0.317 Chirality : 0.045 0.256 2721 Planarity : 0.005 0.048 2844 Dihedral : 7.391 77.772 2544 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.74 % Favored : 95.21 % Rotamer: Outliers : 2.73 % Allowed : 19.16 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % 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: -0.77 (0.18), residues: 1985 helix: 0.80 (0.18), residues: 766 sheet: -1.80 (0.25), residues: 366 loop : -1.02 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 429 TYR 0.014 0.002 TYR A 381 PHE 0.029 0.002 PHE E 224 TRP 0.013 0.002 TRP B 427 HIS 0.006 0.001 HIS D 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.24 (16822) covalent geometry : angle 0.60412 / 0.31 (22954) SS BOND : bond 0.00229 / 0.12 ( 6) SS BOND : angle 1.29444 / 0.73 ( 12) hydrogen bonds : bond 0.05194 / 3.47 ( 808) hydrogen bonds : angle 5.37925 / 3.82 ( 2364) Misc. bond : bond 0.00207 / 0.10 ( 1) link_ALPHA1-3 : bond 0.01054 / 0.50 ( 2) link_ALPHA1-3 : angle 2.32100 / 1.20 ( 6) link_ALPHA1-6 : bond 0.00871 / 0.41 ( 2) link_ALPHA1-6 : angle 2.40933 / 1.27 ( 6) link_BETA1-4 : bond 0.00671 / 0.40 ( 9) link_BETA1-4 : angle 2.70621 / 1.97 ( 27) link_NAG-ASN : bond 0.00361 / 0.18 ( 6) link_NAG-ASN : angle 2.39482 / 1.61 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 246 time to evaluate : 0.925 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 PHE cc_start: 0.7795 (m-80) cc_final: 0.5687 (t80) REVERT: C 377 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.6299 (tp30) REVERT: E 256 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7782 (tt) REVERT: E 330 LYS cc_start: 0.7007 (mttt) cc_final: 0.6709 (ttpp) REVERT: E 333 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7619 (mm) REVERT: E 337 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7275 (mp) REVERT: D 28 GLU cc_start: 0.6617 (pm20) cc_final: 0.6106 (pm20) REVERT: D 198 ARG cc_start: 0.7273 (mtp180) cc_final: 0.7012 (mmm-85) REVERT: D 207 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7449 (tt) REVERT: D 328 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7246 (tptp) REVERT: D 431 GLN cc_start: 0.7709 (tt0) cc_final: 0.7454 (tp-100) REVERT: D 470 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7345 (mm-40) REVERT: B 8 TYR cc_start: 0.7143 (t80) cc_final: 0.6792 (t80) REVERT: B 34 LYS cc_start: 0.6702 (ttmm) cc_final: 0.6296 (ptmm) REVERT: B 147 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.7134 (ptm160) REVERT: B 188 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7921 (p0) REVERT: B 292 MET cc_start: 0.7285 (mtp) cc_final: 0.7070 (mtp) outliers start: 50 outliers final: 18 residues processed: 279 average time/residue: 0.9685 time to fit residues: 316.0311 Evaluate side-chains 256 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 229 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 377 GLU Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 249 ASP Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 470 GLN Chi-restraints excluded: chain D residue 492 ASP Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 162 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 195 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 191 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN A 310 ASN ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 GLN D 200 ASN B 301 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.156522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.130770 restraints weight = 62866.530| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.10 r_work: 0.3616 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 16848 Z= 0.218 Angle : 0.599 6.648 23023 Z= 0.308 Chirality : 0.044 0.221 2721 Planarity : 0.005 0.046 2844 Dihedral : 7.274 75.906 2544 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.48 % Favored : 95.47 % Rotamer: Outliers : 2.13 % Allowed : 20.63 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % 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: -0.79 (0.19), residues: 1985 helix: 0.79 (0.18), residues: 766 sheet: -1.86 (0.25), residues: 377 loop : -1.00 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 6 TYR 0.015 0.002 TYR A 381 PHE 0.024 0.002 PHE C 233 TRP 0.013 0.001 TRP B 427 HIS 0.010 0.001 HIS E 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.22 (16822) covalent geometry : angle 0.58877 / 0.31 (22954) SS BOND : bond 0.00182 / 0.09 ( 6) SS BOND : angle 1.14350 / 0.63 ( 12) hydrogen bonds : bond 0.05002 / 3.34 ( 808) hydrogen bonds : angle 5.31411 / 3.78 ( 2364) Misc. bond : bond 0.00140 / 0.07 ( 1) link_ALPHA1-3 : bond 0.00957 / 0.46 ( 2) link_ALPHA1-3 : angle 2.15437 / 1.11 ( 6) link_ALPHA1-6 : bond 0.00937 / 0.45 ( 2) link_ALPHA1-6 : angle 2.14671 / 1.14 ( 6) link_BETA1-4 : bond 0.00547 / 0.31 ( 9) link_BETA1-4 : angle 2.35971 / 1.76 ( 27) link_NAG-ASN : bond 0.00305 / 0.15 ( 6) link_NAG-ASN : angle 2.19898 / 1.46 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 240 time to evaluate : 0.909 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 PHE cc_start: 0.7760 (m-80) cc_final: 0.5658 (t80) REVERT: C 377 GLU cc_start: 0.6605 (OUTLIER) cc_final: 0.6277 (tp30) REVERT: E 330 LYS cc_start: 0.7199 (mttt) cc_final: 0.6788 (tttm) REVERT: E 337 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7279 (mp) REVERT: D 337 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7496 (tt) REVERT: D 431 GLN cc_start: 0.7722 (tt0) cc_final: 0.7454 (tp-100) REVERT: D 470 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7347 (mm-40) REVERT: B 8 TYR cc_start: 0.7234 (t80) cc_final: 0.6851 (t80) REVERT: B 34 LYS cc_start: 0.6794 (ttmm) cc_final: 0.6473 (ptmm) REVERT: B 46 LYS cc_start: 0.8435 (mmmm) cc_final: 0.7987 (mmmt) REVERT: B 147 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7106 (ptm160) REVERT: B 188 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7971 (p0) REVERT: B 268 PHE cc_start: 0.6784 (m-10) cc_final: 0.6498 (t80) outliers start: 39 outliers final: 20 residues processed: 265 average time/residue: 0.9507 time to fit residues: 295.3736 Evaluate side-chains 248 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 222 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 377 GLU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 470 GLN Chi-restraints excluded: chain D residue 492 ASP Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 427 TRP Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 101 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 174 optimal weight: 0.0870 chunk 133 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 155 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 ASN C 25 HIS D 432 ASN B 301 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.159376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.133838 restraints weight = 62504.934| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.11 r_work: 0.3659 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16848 Z= 0.128 Angle : 0.543 6.096 23023 Z= 0.279 Chirality : 0.043 0.207 2721 Planarity : 0.004 0.057 2844 Dihedral : 6.657 68.333 2544 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.23 % Favored : 95.72 % Rotamer: Outliers : 1.80 % Allowed : 20.63 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % 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: -0.52 (0.19), residues: 1985 helix: 0.98 (0.18), residues: 772 sheet: -1.69 (0.26), residues: 376 loop : -0.85 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 6 TYR 0.017 0.001 TYR C 213 PHE 0.020 0.001 PHE E 224 TRP 0.012 0.001 TRP B 427 HIS 0.004 0.001 HIS C 25 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (16822) covalent geometry : angle 0.53532 / 0.28 (22954) SS BOND : bond 0.00121 / 0.06 ( 6) SS BOND : angle 0.72655 / 0.40 ( 12) hydrogen bonds : bond 0.04594 / 3.06 ( 808) hydrogen bonds : angle 5.11065 / 3.64 ( 2364) Misc. bond : bond 0.00058 / 0.03 ( 1) link_ALPHA1-3 : bond 0.00856 / 0.41 ( 2) link_ALPHA1-3 : angle 1.96444 / 0.99 ( 6) link_ALPHA1-6 : bond 0.00982 / 0.47 ( 2) link_ALPHA1-6 : angle 1.99639 / 1.04 ( 6) link_BETA1-4 : bond 0.00434 / 0.24 ( 9) link_BETA1-4 : angle 1.83271 / 1.36 ( 27) link_NAG-ASN : bond 0.00130 / 0.09 ( 6) link_NAG-ASN : angle 1.90000 / 1.20 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 238 time to evaluate : 0.889 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 PHE cc_start: 0.7650 (m-80) cc_final: 0.5539 (t80) REVERT: C 377 GLU cc_start: 0.6477 (OUTLIER) cc_final: 0.6208 (tp30) REVERT: E 59 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6751 (mt-10) REVERT: E 330 LYS cc_start: 0.7176 (mttt) cc_final: 0.6765 (tttm) REVERT: E 333 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7625 (mm) REVERT: E 337 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7176 (mp) REVERT: E 470 HIS cc_start: 0.6950 (t70) cc_final: 0.6706 (t-170) REVERT: D 431 GLN cc_start: 0.7691 (tt0) cc_final: 0.7462 (tp-100) REVERT: D 470 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7221 (mm-40) REVERT: B 34 LYS cc_start: 0.6759 (ttmm) cc_final: 0.6379 (ptmm) REVERT: B 147 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7150 (ptm160) REVERT: B 268 PHE cc_start: 0.6688 (m-10) cc_final: 0.6441 (t80) outliers start: 33 outliers final: 13 residues processed: 257 average time/residue: 0.9252 time to fit residues: 279.0567 Evaluate side-chains 247 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 228 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 377 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 470 GLN Chi-restraints excluded: chain D residue 492 ASP Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 156 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 172 optimal weight: 0.7980 chunk 191 optimal weight: 8.9990 chunk 185 optimal weight: 0.8980 chunk 34 optimal weight: 8.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 GLN B 61 GLN ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.158478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.132820 restraints weight = 62684.937| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.12 r_work: 0.3648 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16848 Z= 0.155 Angle : 0.553 5.295 23023 Z= 0.283 Chirality : 0.043 0.208 2721 Planarity : 0.004 0.055 2844 Dihedral : 6.505 66.418 2544 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.48 % Favored : 95.47 % Rotamer: Outliers : 1.97 % Allowed : 20.63 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % 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: -0.48 (0.19), residues: 1985 helix: 1.04 (0.18), residues: 773 sheet: -1.67 (0.26), residues: 377 loop : -0.86 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 6 TYR 0.024 0.001 TYR A 381 PHE 0.022 0.001 PHE E 224 TRP 0.016 0.001 TRP B 427 HIS 0.004 0.001 HIS D 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (16822) covalent geometry : angle 0.54411 / 0.28 (22954) SS BOND : bond 0.00135 / 0.07 ( 6) SS BOND : angle 0.84973 / 0.47 ( 12) hydrogen bonds : bond 0.04579 / 3.04 ( 808) hydrogen bonds : angle 5.06706 / 3.61 ( 2364) Misc. bond : bond 0.00079 / 0.04 ( 1) link_ALPHA1-3 : bond 0.00919 / 0.44 ( 2) link_ALPHA1-3 : angle 2.04359 / 1.04 ( 6) link_ALPHA1-6 : bond 0.00869 / 0.41 ( 2) link_ALPHA1-6 : angle 2.07088 / 1.09 ( 6) link_BETA1-4 : bond 0.00497 / 0.27 ( 9) link_BETA1-4 : angle 2.04307 / 1.54 ( 27) link_NAG-ASN : bond 0.00208 / 0.10 ( 6) link_NAG-ASN : angle 2.01893 / 1.35 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 238 time to evaluate : 0.937 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 PHE cc_start: 0.7615 (m-80) cc_final: 0.5518 (t80) REVERT: C 377 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.6271 (tp30) REVERT: E 330 LYS cc_start: 0.7205 (mttt) cc_final: 0.6805 (tttm) REVERT: E 333 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7639 (mm) REVERT: E 337 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7221 (mp) REVERT: E 425 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8070 (tp40) REVERT: E 470 HIS cc_start: 0.7002 (t70) cc_final: 0.6756 (t-170) REVERT: D 337 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7514 (tt) REVERT: D 431 GLN cc_start: 0.7701 (tt0) cc_final: 0.7473 (tp-100) REVERT: D 470 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7266 (mm-40) REVERT: B 34 LYS cc_start: 0.6775 (ttmm) cc_final: 0.6410 (ptmm) REVERT: B 46 LYS cc_start: 0.8363 (mmmm) cc_final: 0.7987 (mmmt) REVERT: B 268 PHE cc_start: 0.6719 (m-10) cc_final: 0.6472 (t80) outliers start: 36 outliers final: 18 residues processed: 263 average time/residue: 0.9069 time to fit residues: 281.6458 Evaluate side-chains 253 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 229 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 377 GLU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 425 GLN Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain D residue 470 GLN Chi-restraints excluded: chain D residue 492 ASP Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 427 TRP Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 149 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 161 optimal weight: 0.9990 chunk 182 optimal weight: 0.6980 chunk 159 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN B 61 GLN ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 ASN B 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.158514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.132881 restraints weight = 62375.814| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.13 r_work: 0.3644 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16848 Z= 0.154 Angle : 0.551 5.484 23023 Z= 0.283 Chirality : 0.043 0.208 2721 Planarity : 0.004 0.059 2844 Dihedral : 6.389 64.253 2544 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.48 % Favored : 95.47 % Rotamer: Outliers : 1.91 % Allowed : 21.23 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % 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: -0.45 (0.19), residues: 1985 helix: 1.09 (0.18), residues: 767 sheet: -1.66 (0.26), residues: 377 loop : -0.84 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 6 TYR 0.020 0.001 TYR A 381 PHE 0.021 0.001 PHE E 224 TRP 0.017 0.001 TRP B 427 HIS 0.005 0.001 HIS B 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (16822) covalent geometry : angle 0.54289 / 0.28 (22954) SS BOND : bond 0.00119 / 0.06 ( 6) SS BOND : angle 0.81393 / 0.46 ( 12) hydrogen bonds : bond 0.04544 / 3.03 ( 808) hydrogen bonds : angle 5.04679 / 3.59 ( 2364) Misc. bond : bond 0.00076 / 0.04 ( 1) link_ALPHA1-3 : bond 0.00878 / 0.42 ( 2) link_ALPHA1-3 : angle 2.00062 / 1.01 ( 6) link_ALPHA1-6 : bond 0.00847 / 0.40 ( 2) link_ALPHA1-6 : angle 2.00753 / 1.05 ( 6) link_BETA1-4 : bond 0.00474 / 0.26 ( 9) link_BETA1-4 : angle 1.97326 / 1.49 ( 27) link_NAG-ASN : bond 0.00182 / 0.10 ( 6) link_NAG-ASN : angle 1.96762 / 1.31 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 226 time to evaluate : 1.001 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 PHE cc_start: 0.7608 (m-80) cc_final: 0.5507 (t80) REVERT: C 377 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.6204 (tp30) REVERT: E 330 LYS cc_start: 0.7209 (mttt) cc_final: 0.6803 (tttm) REVERT: E 333 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7647 (mm) REVERT: E 337 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7204 (mp) REVERT: E 470 HIS cc_start: 0.7026 (t70) cc_final: 0.6808 (t-170) REVERT: D 431 GLN cc_start: 0.7683 (tt0) cc_final: 0.7463 (tp-100) REVERT: D 470 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7232 (mm-40) REVERT: B 34 LYS cc_start: 0.6792 (ttmm) cc_final: 0.6445 (ptmm) REVERT: B 46 LYS cc_start: 0.8373 (mmmm) cc_final: 0.7991 (mmmt) REVERT: B 147 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7137 (ptm160) REVERT: B 268 PHE cc_start: 0.6719 (m-10) cc_final: 0.6472 (t80) outliers start: 35 outliers final: 21 residues processed: 251 average time/residue: 0.9307 time to fit residues: 274.9433 Evaluate side-chains 246 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 220 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 377 GLU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain D residue 470 GLN Chi-restraints excluded: chain D residue 492 ASP Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 73 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 193 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 ASN ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 GLN ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.157968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.132288 restraints weight = 62293.217| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.12 r_work: 0.3636 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16848 Z= 0.177 Angle : 0.569 6.099 23023 Z= 0.292 Chirality : 0.043 0.209 2721 Planarity : 0.004 0.060 2844 Dihedral : 6.400 63.738 2544 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.58 % Favored : 95.37 % Rotamer: Outliers : 1.69 % Allowed : 21.29 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % 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: -0.47 (0.19), residues: 1985 helix: 1.07 (0.18), residues: 767 sheet: -1.65 (0.26), residues: 377 loop : -0.86 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 6 TYR 0.019 0.001 TYR A 381 PHE 0.022 0.002 PHE E 224 TRP 0.025 0.001 TRP B 427 HIS 0.004 0.001 HIS D 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (16822) covalent geometry : angle 0.55981 / 0.29 (22954) SS BOND : bond 0.00140 / 0.07 ( 6) SS BOND : angle 0.91299 / 0.51 ( 12) hydrogen bonds : bond 0.04598 / 3.06 ( 808) hydrogen bonds : angle 5.06359 / 3.60 ( 2364) Misc. bond : bond 0.00088 / 0.04 ( 1) link_ALPHA1-3 : bond 0.00866 / 0.41 ( 2) link_ALPHA1-3 : angle 2.01131 / 1.02 ( 6) link_ALPHA1-6 : bond 0.00762 / 0.36 ( 2) link_ALPHA1-6 : angle 2.05290 / 1.08 ( 6) link_BETA1-4 : bond 0.00486 / 0.27 ( 9) link_BETA1-4 : angle 2.09625 / 1.59 ( 27) link_NAG-ASN : bond 0.00242 / 0.12 ( 6) link_NAG-ASN : angle 2.02520 / 1.37 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 223 time to evaluate : 0.901 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 PHE cc_start: 0.7611 (m-80) cc_final: 0.5511 (t80) REVERT: C 377 GLU cc_start: 0.6488 (OUTLIER) cc_final: 0.6208 (tp30) REVERT: E 330 LYS cc_start: 0.7216 (mttt) cc_final: 0.6806 (tttm) REVERT: E 333 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7670 (mm) REVERT: E 337 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7212 (mp) REVERT: E 470 HIS cc_start: 0.7053 (t70) cc_final: 0.6846 (t-170) REVERT: D 431 GLN cc_start: 0.7678 (tt0) cc_final: 0.7467 (tp-100) REVERT: D 449 ASP cc_start: 0.6031 (OUTLIER) cc_final: 0.5728 (t0) REVERT: D 470 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7270 (mm-40) REVERT: B 8 TYR cc_start: 0.7240 (t80) cc_final: 0.6806 (t80) REVERT: B 34 LYS cc_start: 0.6768 (ttmm) cc_final: 0.6463 (ptmm) REVERT: B 46 LYS cc_start: 0.8367 (mmmm) cc_final: 0.7887 (mmmt) REVERT: B 147 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.7144 (ptm160) REVERT: B 268 PHE cc_start: 0.6834 (m-10) cc_final: 0.6580 (t80) outliers start: 31 outliers final: 20 residues processed: 243 average time/residue: 0.9081 time to fit residues: 260.5041 Evaluate side-chains 247 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 221 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 377 GLU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 470 GLN Chi-restraints excluded: chain D residue 492 ASP Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 183 optimal weight: 3.9990 chunk 143 optimal weight: 0.3980 chunk 174 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 ASN B 408 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.157723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.131928 restraints weight = 62737.277| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.13 r_work: 0.3631 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16848 Z= 0.172 Angle : 0.566 6.396 23023 Z= 0.291 Chirality : 0.043 0.209 2721 Planarity : 0.005 0.063 2844 Dihedral : 6.359 62.012 2544 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.89 % Favored : 95.06 % Rotamer: Outliers : 1.69 % Allowed : 21.45 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % 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: -0.49 (0.19), residues: 1985 helix: 1.03 (0.18), residues: 767 sheet: -1.64 (0.26), residues: 374 loop : -0.87 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 6 TYR 0.025 0.001 TYR A 381 PHE 0.023 0.002 PHE C 233 TRP 0.029 0.001 TRP B 427 HIS 0.004 0.001 HIS D 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (16822) covalent geometry : angle 0.55747 / 0.29 (22954) SS BOND : bond 0.00135 / 0.07 ( 6) SS BOND : angle 0.90694 / 0.51 ( 12) hydrogen bonds : bond 0.04569 / 3.04 ( 808) hydrogen bonds : angle 5.06755 / 3.60 ( 2364) Misc. bond : bond 0.00085 / 0.04 ( 1) link_ALPHA1-3 : bond 0.00859 / 0.41 ( 2) link_ALPHA1-3 : angle 2.02681 / 1.02 ( 6) link_ALPHA1-6 : bond 0.00735 / 0.35 ( 2) link_ALPHA1-6 : angle 2.01528 / 1.07 ( 6) link_BETA1-4 : bond 0.00490 / 0.27 ( 9) link_BETA1-4 : angle 2.06058 / 1.56 ( 27) link_NAG-ASN : bond 0.00242 / 0.12 ( 6) link_NAG-ASN : angle 2.00714 / 1.35 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 220 time to evaluate : 0.939 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 PHE cc_start: 0.7604 (m-80) cc_final: 0.5503 (t80) REVERT: C 377 GLU cc_start: 0.6492 (OUTLIER) cc_final: 0.6214 (tp30) REVERT: E 330 LYS cc_start: 0.7214 (mttt) cc_final: 0.6803 (tttm) REVERT: E 333 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7673 (mm) REVERT: E 337 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7192 (mp) REVERT: E 470 HIS cc_start: 0.7041 (t70) cc_final: 0.6824 (t-170) REVERT: D 449 ASP cc_start: 0.6036 (OUTLIER) cc_final: 0.5730 (t0) REVERT: D 470 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7280 (mm-40) REVERT: B 8 TYR cc_start: 0.7249 (t80) cc_final: 0.6806 (t80) REVERT: B 34 LYS cc_start: 0.6813 (ttmm) cc_final: 0.6510 (ptmm) REVERT: B 46 LYS cc_start: 0.8366 (mmmm) cc_final: 0.7964 (mmmt) REVERT: B 147 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7139 (ptm160) REVERT: B 268 PHE cc_start: 0.6839 (m-10) cc_final: 0.6588 (t80) REVERT: B 427 TRP cc_start: 0.7223 (OUTLIER) cc_final: 0.6883 (m100) outliers start: 31 outliers final: 20 residues processed: 240 average time/residue: 0.9296 time to fit residues: 262.8069 Evaluate side-chains 244 residues out of total 1832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 217 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 414 PHE Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 302 SER Chi-restraints excluded: chain C residue 377 GLU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain E residue 313 SER Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 436 GLU Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 470 GLN Chi-restraints excluded: chain D residue 492 ASP Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain B residue 147 ARG Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 427 TRP Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 46 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 185 optimal weight: 0.0870 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 ASN ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 431 GLN B 61 GLN ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.157870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.132034 restraints weight = 62603.515| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.13 r_work: 0.3633 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16848 Z= 0.170 Angle : 0.569 6.529 23023 Z= 0.292 Chirality : 0.043 0.207 2721 Planarity : 0.004 0.061 2844 Dihedral : 6.286 59.985 2544 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.94 % Favored : 95.01 % Rotamer: Outliers : 1.97 % Allowed : 21.23 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.19), residues: 1985 helix: 1.04 (0.18), residues: 767 sheet: -1.70 (0.25), residues: 385 loop : -0.85 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 6 TYR 0.022 0.001 TYR C 213 PHE 0.022 0.002 PHE E 224 TRP 0.035 0.001 TRP B 427 HIS 0.004 0.001 HIS D 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (16822) covalent geometry : angle 0.56005 / 0.29 (22954) SS BOND : bond 0.00129 / 0.06 ( 6) SS BOND : angle 0.88490 / 0.49 ( 12) hydrogen bonds : bond 0.04547 / 3.03 ( 808) hydrogen bonds : angle 5.06048 / 3.60 ( 2364) Misc. bond : bond 0.00083 / 0.04 ( 1) link_ALPHA1-3 : bond 0.00832 / 0.40 ( 2) link_ALPHA1-3 : angle 2.00848 / 1.01 ( 6) link_ALPHA1-6 : bond 0.00698 / 0.33 ( 2) link_ALPHA1-6 : angle 1.99551 / 1.06 ( 6) link_BETA1-4 : bond 0.00467 / 0.26 ( 9) link_BETA1-4 : angle 2.04336 / 1.54 ( 27) link_NAG-ASN : bond 0.00240 / 0.12 ( 6) link_NAG-ASN : angle 1.99704 / 1.34 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11526.31 seconds wall clock time: 195 minutes 45.53 seconds (11745.53 seconds total)