Starting phenix.real_space_refine on Thu Mar 5 18:27:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jg2_22310/03_2026/7jg2_22310_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jg2_22310/03_2026/7jg2_22310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jg2_22310/03_2026/7jg2_22310_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jg2_22310/03_2026/7jg2_22310_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jg2_22310/03_2026/7jg2_22310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jg2_22310/03_2026/7jg2_22310.map" } resolution = 3.3 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= 0.010 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 84 5.16 5 C 7755 2.51 5 N 2068 2.21 5 O 2487 1.98 5 H 11858 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24252 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3469 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 17, 'TRANS': 213} Chain: "B" Number of atoms: 3381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3381 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 17, 'TRANS': 206} Chain: "C" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3467 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 17, 'TRANS': 213} Chain: "D" Number of atoms: 3470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3470 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 17, 'TRANS': 213} Chain: "E" Number of atoms: 8191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 8191 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 26, 'TRANS': 508} Chain breaks: 1 Chain: "J" Number of atoms: 2062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2062 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 121} 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: 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: "I" 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: 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: "C" 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: "D" 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 Time building chain proxies: 4.30, per 1000 atoms: 0.18 Number of scatterers: 24252 At special positions: 0 Unit cell: (99.756, 118.012, 173.432, 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 84 16.00 O 2487 8.00 N 2068 7.00 C 7755 6.00 H 11858 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=29, symmetry=0 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS A 296 " distance=2.03 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 318 " distance=2.03 Simple disulfide: pdb=" SG CYS A 294 " - pdb=" SG CYS B 294 " distance=2.03 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 427 " distance=2.03 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS J 68 " distance=2.03 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 296 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 318 " distance=2.62 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 427 " distance=2.03 Simple disulfide: pdb=" SG CYS C 237 " - pdb=" SG CYS C 296 " distance=2.03 Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 318 " distance=2.03 Simple disulfide: pdb=" SG CYS C 294 " - pdb=" SG CYS D 294 " distance=2.03 Simple disulfide: pdb=" SG CYS C 306 " - pdb=" SG CYS E 470 " distance=1.52 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 427 " distance=2.41 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS J 14 " distance=2.03 Simple disulfide: pdb=" SG CYS D 237 " - pdb=" SG CYS D 296 " distance=2.03 Simple disulfide: pdb=" SG CYS D 261 " - pdb=" SG CYS D 318 " distance=2.03 Simple disulfide: pdb=" SG CYS D 364 " - pdb=" SG CYS D 427 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 38 " - pdb=" SG CYS E 46 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 202 " distance=2.21 Simple disulfide: pdb=" SG CYS E 239 " - pdb=" SG CYS E 306 " distance=2.03 Simple disulfide: pdb=" SG CYS E 253 " - pdb=" SG CYS E 260 " distance=2.03 Simple disulfide: pdb=" SG CYS E 352 " - pdb=" SG CYS E 422 " distance=2.03 Simple disulfide: pdb=" SG CYS E 366 " - pdb=" SG CYS E 376 " distance=2.03 Simple disulfide: pdb=" SG CYS E 466 " - pdb=" SG CYS E 528 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 487 " distance=1.54 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 101 " distance=2.03 Simple disulfide: pdb=" SG CYS J 71 " - pdb=" SG CYS J 91 " distance=2.03 Simple disulfide: pdb=" SG CYS J 109 " - pdb=" SG CYS J 134 " 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 " MAN F 4 " - " MAN F 5 " ALPHA1-6 " BMA F 3 " - " MAN F 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 501 " - " ASN A 437 " " NAG C 501 " - " ASN C 437 " " NAG C 502 " - " ASN C 452 " " NAG D 501 " - " ASN D 452 " " NAG F 1 " - " ASN E 72 " " NAG G 1 " - " ASN E 129 " " NAG H 1 " - " ASN E 188 " " NAG I 1 " - " ASN J 48 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.29 Conformation dependent library (CDL) restraints added in 803.4 milliseconds 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2946 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 39 sheets defined 12.0% alpha, 38.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 306 through 313 Processing helix chain 'A' and resid 351 through 357 removed outlier: 3.809A pdb=" N ALA A 355 " --> pdb=" O SER A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'B' and resid 247 through 251 removed outlier: 3.599A pdb=" N LEU B 251 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 312 Processing helix chain 'B' and resid 323 through 325 No H-bonds generated for 'chain 'B' and resid 323 through 325' Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.906A pdb=" N LEU B 354 " --> pdb=" O PRO B 350 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA B 355 " --> pdb=" O SER B 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 350 through 355' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 434 through 438 removed outlier: 3.857A pdb=" N PHE B 438 " --> pdb=" O PRO B 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 305 through 312 removed outlier: 3.968A pdb=" N ARG C 309 " --> pdb=" O GLY C 305 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TRP C 310 " --> pdb=" O CYS C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 355 Processing helix chain 'C' and resid 386 through 388 No H-bonds generated for 'chain 'C' and resid 386 through 388' Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.689A pdb=" N GLY C 422 " --> pdb=" O THR C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 448 Processing helix chain 'D' and resid 247 through 252 removed outlier: 3.640A pdb=" N LEU D 251 " --> pdb=" O ALA D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 313 removed outlier: 3.557A pdb=" N TRP D 310 " --> pdb=" O CYS D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 357 removed outlier: 3.518A pdb=" N ASN D 357 " --> pdb=" O GLU D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 390 removed outlier: 3.675A pdb=" N TYR D 390 " --> pdb=" O PRO D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 434 through 438 removed outlier: 4.010A pdb=" N PHE D 438 " --> pdb=" O PRO D 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 33 Processing helix chain 'E' and resid 137 through 141 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 193 through 197 removed outlier: 3.511A pdb=" N ALA E 197 " --> pdb=" O HIS E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 246 removed outlier: 3.614A pdb=" N VAL E 245 " --> pdb=" O GLY E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 297 through 301 Processing helix chain 'E' and resid 355 through 359 removed outlier: 3.675A pdb=" N SER E 359 " --> pdb=" O PRO E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 417 Processing helix chain 'E' and resid 469 through 473 Processing helix chain 'E' and resid 519 through 523 Processing helix chain 'J' and resid 64 through 68 Processing sheet with id=AA1, first strand: chain 'A' and resid 240 through 244 removed outlier: 3.665A pdb=" N THR A 260 " --> pdb=" O GLN A 244 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ASN A 264 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL A 299 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 240 through 244 removed outlier: 3.665A pdb=" N THR A 260 " --> pdb=" O GLN A 244 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 259 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 273 through 276 Processing sheet with id=AA4, first strand: chain 'A' and resid 343 through 347 removed outlier: 3.946A pdb=" N THR A 363 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 347 removed outlier: 3.946A pdb=" N THR A 363 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 375 through 379 Processing sheet with id=AA7, first strand: chain 'B' and resid 457 through 458 removed outlier: 5.992A pdb=" N ILE A 458 " --> pdb=" O TYR J 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 240 through 244 removed outlier: 6.245A pdb=" N THR B 260 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LEU B 303 " --> pdb=" O THR B 260 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N THR B 262 " --> pdb=" O SER B 301 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N SER B 301 " --> pdb=" O THR B 262 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ASN B 264 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL B 299 " --> pdb=" O ASN B 264 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 266 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N SER B 300 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LYS B 288 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N VAL B 302 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLN B 286 " --> pdb=" O VAL B 302 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 275 through 276 Processing sheet with id=AB1, first strand: chain 'B' and resid 345 through 347 removed outlier: 3.853A pdb=" N THR B 363 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER B 410 " --> pdb=" O CYS B 364 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 375 through 379 Processing sheet with id=AB3, first strand: chain 'B' and resid 396 through 397 Processing sheet with id=AB4, first strand: chain 'C' and resid 240 through 244 removed outlier: 5.753A pdb=" N THR C 260 " --> pdb=" O LEU C 303 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU C 303 " --> pdb=" O THR C 260 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N THR C 262 " --> pdb=" O SER C 301 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER C 301 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ASN C 264 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL C 299 " --> pdb=" O ASN C 264 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER C 300 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LYS C 288 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL C 302 " --> pdb=" O GLN C 286 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLN C 286 " --> pdb=" O VAL C 302 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 273 through 275 Processing sheet with id=AB6, first strand: chain 'C' and resid 345 through 347 removed outlier: 3.714A pdb=" N THR C 363 " --> pdb=" O LEU C 347 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 410 " --> pdb=" O CYS C 364 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 345 through 347 removed outlier: 3.714A pdb=" N THR C 363 " --> pdb=" O LEU C 347 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 410 " --> pdb=" O CYS C 364 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 375 through 379 Processing sheet with id=AB9, first strand: chain 'D' and resid 457 through 458 removed outlier: 6.829A pdb=" N SER C 454 " --> pdb=" O ILE J 37 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ILE J 39 " --> pdb=" O SER C 454 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N SER C 456 " --> pdb=" O ILE J 39 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL J 41 " --> pdb=" O SER C 456 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE C 458 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR J 15 " --> pdb=" O ASP J 9 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASP J 9 " --> pdb=" O THR J 15 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL J 17 " --> pdb=" O LEU J 7 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 240 through 244 removed outlier: 3.599A pdb=" N THR D 260 " --> pdb=" O GLN D 244 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TYR D 297 " --> pdb=" O GLY D 265 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL D 285 " --> pdb=" O VAL D 302 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 240 through 244 removed outlier: 3.599A pdb=" N THR D 260 " --> pdb=" O GLN D 244 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TYR D 297 " --> pdb=" O GLY D 265 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL D 290 " --> pdb=" O SER D 298 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 273 through 276 removed outlier: 5.183A pdb=" N HIS D 322 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLY D 326 " --> pdb=" O HIS D 322 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 345 through 346 Processing sheet with id=AC5, first strand: chain 'D' and resid 345 through 346 Processing sheet with id=AC6, first strand: chain 'D' and resid 383 through 384 removed outlier: 4.045A pdb=" N GLU D 383 " --> pdb=" O HIS D 380 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AC8, first strand: chain 'E' and resid 46 through 51 removed outlier: 6.715A pdb=" N TRP E 37 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER E 51 " --> pdb=" O LYS E 35 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYS E 35 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR E 36 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY E 93 " --> pdb=" O TYR E 36 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 46 through 51 removed outlier: 6.715A pdb=" N TRP E 37 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER E 51 " --> pdb=" O LYS E 35 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYS E 35 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER E 89 " --> pdb=" O GLN E 40 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 120 through 124 removed outlier: 4.682A pdb=" N HIS E 120 " --> pdb=" O ASN E 214 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP E 216 " --> pdb=" O HIS E 120 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU E 199 " --> pdb=" O LYS E 150 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LYS E 145 " --> pdb=" O ASP E 160 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASP E 160 " --> pdb=" O LYS E 145 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU E 147 " --> pdb=" O VAL E 158 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 131 through 135 removed outlier: 3.764A pdb=" N TYR E 186 " --> pdb=" O PHE E 176 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 225 through 230 removed outlier: 6.386A pdb=" N GLU E 225 " --> pdb=" O GLN E 324 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N PHE E 326 " --> pdb=" O GLU E 225 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU E 227 " --> pdb=" O PHE E 326 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ASN E 328 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LYS E 229 " --> pdb=" O ASN E 328 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N HIS E 303 " --> pdb=" O MET E 255 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LYS E 250 " --> pdb=" O ASN E 265 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ASN E 265 " --> pdb=" O LYS E 250 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU E 252 " --> pdb=" O ILE E 263 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 225 through 230 removed outlier: 6.386A pdb=" N GLU E 225 " --> pdb=" O GLN E 324 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N PHE E 326 " --> pdb=" O GLU E 225 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU E 227 " --> pdb=" O PHE E 326 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ASN E 328 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LYS E 229 " --> pdb=" O ASN E 328 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N HIS E 303 " --> pdb=" O MET E 255 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 235 through 239 removed outlier: 3.660A pdb=" N LEU E 292 " --> pdb=" O LEU E 279 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 339 through 343 removed outlier: 3.564A pdb=" N TRP E 421 " --> pdb=" O CYS E 366 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N CYS E 366 " --> pdb=" O TRP E 421 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 347 through 353 removed outlier: 3.532A pdb=" N ALA E 395 " --> pdb=" O ILE E 408 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 454 through 457 removed outlier: 6.276A pdb=" N ALA E 454 " --> pdb=" O ALA E 545 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLU E 547 " --> pdb=" O ALA E 454 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ALA E 456 " --> pdb=" O GLU E 547 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TRP E 525 " --> pdb=" O TRP E 482 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TRP E 479 " --> pdb=" O LEU E 490 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 454 through 457 removed outlier: 6.276A pdb=" N ALA E 454 " --> pdb=" O ALA E 545 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLU E 547 " --> pdb=" O ALA E 454 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ALA E 456 " --> pdb=" O GLU E 547 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR E 535 " --> pdb=" O GLN E 532 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 462 through 467 removed outlier: 3.627A pdb=" N LEU E 510 " --> pdb=" O GLU E 495 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 74 through 75 Processing sheet with id=AE3, first strand: chain 'J' and resid 111 through 118 420 hydrogen bonds defined for protein. 987 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.36 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 11850 1.02 - 1.22: 10 1.22 - 1.42: 4969 1.42 - 1.61: 7586 1.61 - 1.81: 104 Bond restraints: 24519 Sorted by residual: bond pdb=" ND2 ASN J 107 " pdb="HD21 ASN J 107 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" ND2 ASN J 89 " pdb="HD21 ASN J 89 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" ND2 ASN J 59 " pdb="HD21 ASN J 59 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.63e+01 bond pdb=" ND2 ASN J 59 " pdb="HD22 ASN J 59 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" ND2 ASN J 92 " pdb="HD21 ASN J 92 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.60e+01 ... (remaining 24514 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.74: 44300 9.74 - 19.49: 11 19.49 - 29.23: 1 29.23 - 38.97: 0 38.97 - 48.71: 2 Bond angle restraints: 44314 Sorted by residual: angle pdb="HD21 ASN E 129 " pdb=" ND2 ASN E 129 " pdb="HD22 ASN E 129 " ideal model delta sigma weight residual 120.00 71.29 48.71 3.00e+00 1.11e-01 2.64e+02 angle pdb=" CG ASN E 129 " pdb=" ND2 ASN E 129 " pdb="HD22 ASN E 129 " ideal model delta sigma weight residual 120.00 73.31 46.69 3.00e+00 1.11e-01 2.42e+02 angle pdb=" CG ASN E 129 " pdb=" ND2 ASN E 129 " pdb="HD21 ASN E 129 " ideal model delta sigma weight residual 120.00 144.59 -24.59 3.00e+00 1.11e-01 6.72e+01 angle pdb=" N ILE C 443 " pdb=" CA ILE C 443 " pdb=" C ILE C 443 " ideal model delta sigma weight residual 107.24 118.87 -11.63 1.68e+00 3.54e-01 4.80e+01 angle pdb=" C SER A 255 " pdb=" CA SER A 255 " pdb=" CB SER A 255 " ideal model delta sigma weight residual 112.07 102.25 9.82 1.54e+00 4.22e-01 4.07e+01 ... (remaining 44309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.88: 11424 23.88 - 47.76: 419 47.76 - 71.63: 95 71.63 - 95.51: 21 95.51 - 119.39: 9 Dihedral angle restraints: 11968 sinusoidal: 6755 harmonic: 5213 Sorted by residual: dihedral pdb=" CB CYS B 261 " pdb=" SG CYS B 261 " pdb=" SG CYS B 318 " pdb=" CB CYS B 318 " ideal model delta sinusoidal sigma weight residual 93.00 158.70 -65.70 1 1.00e+01 1.00e-02 5.65e+01 dihedral pdb=" CB CYS A 237 " pdb=" SG CYS A 237 " pdb=" SG CYS A 296 " pdb=" CB CYS A 296 " ideal model delta sinusoidal sigma weight residual -86.00 -132.75 46.75 1 1.00e+01 1.00e-02 3.02e+01 dihedral pdb=" C SER A 255 " pdb=" N SER A 255 " pdb=" CA SER A 255 " pdb=" CB SER A 255 " ideal model delta harmonic sigma weight residual -122.60 -110.48 -12.12 0 2.50e+00 1.60e-01 2.35e+01 ... (remaining 11965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1842 0.099 - 0.198: 159 0.198 - 0.297: 16 0.297 - 0.396: 2 0.396 - 0.495: 1 Chirality restraints: 2020 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.17e+01 chirality pdb=" CA THR E 119 " pdb=" N THR E 119 " pdb=" C THR E 119 " pdb=" CB THR E 119 " both_signs ideal model delta sigma weight residual False 2.53 2.03 0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" CA SER A 255 " pdb=" N SER A 255 " pdb=" C SER A 255 " pdb=" CB SER A 255 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 2017 not shown) Planarity restraints: 3693 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN E 111 " 0.239 2.00e-02 2.50e+03 3.18e-01 1.52e+03 pdb=" CD GLN E 111 " -0.018 2.00e-02 2.50e+03 pdb=" OE1 GLN E 111 " -0.231 2.00e-02 2.50e+03 pdb=" NE2 GLN E 111 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN E 111 " -0.494 2.00e-02 2.50e+03 pdb="HE22 GLN E 111 " 0.504 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN J 81 " 0.230 2.00e-02 2.50e+03 2.89e-01 1.25e+03 pdb=" CD GLN J 81 " -0.017 2.00e-02 2.50e+03 pdb=" OE1 GLN J 81 " -0.221 2.00e-02 2.50e+03 pdb=" NE2 GLN J 81 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN J 81 " -0.442 2.00e-02 2.50e+03 pdb="HE22 GLN J 81 " 0.451 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 268 " -0.234 2.00e-02 2.50e+03 2.41e-01 8.70e+02 pdb=" CG ASN D 268 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN D 268 " 0.224 2.00e-02 2.50e+03 pdb=" ND2 ASN D 268 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN D 268 " -0.353 2.00e-02 2.50e+03 pdb="HD22 ASN D 268 " 0.344 2.00e-02 2.50e+03 ... (remaining 3690 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.06: 278 2.06 - 2.69: 37526 2.69 - 3.33: 66756 3.33 - 3.96: 86210 3.96 - 4.60: 133434 Nonbonded interactions: 324204 Sorted by model distance: nonbonded pdb=" HB2 PRO A 435 " pdb=" O CYS J 134 " model vdw 1.419 2.620 nonbonded pdb="HH22 ARG C 245 " pdb=" OE2 GLU C 432 " model vdw 1.615 2.450 nonbonded pdb=" OD1 ASN A 268 " pdb=" HE2 HIS A 322 " model vdw 1.627 2.450 nonbonded pdb=" OD1 ASN E 166 " pdb=" H SER E 168 " model vdw 1.664 2.450 nonbonded pdb=" HH TYR E 468 " pdb=" O PHE E 472 " model vdw 1.679 2.450 ... (remaining 324199 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 237 through 305 or (resid 306 and (name N or name CA or na \ me C or name O or name CB or name SG or name H or name HA or name HB2 or name HB \ 3)) or resid 307 through 451 or (resid 452 and (name N or name CA or name C or n \ ame O or name CB or name CG or name OD1 or name ND2 or name H or name HA or name \ HB2 or name HB3 or name HD21)) or resid 453 through 460)) selection = (chain 'B' and (resid 237 through 260 or (resid 261 and (name N or name CA or na \ me C or name O or name CB or name SG or name H or name HA or name HB2 or name HB \ 3)) or resid 262 through 305 or (resid 306 and (name N or name CA or name C or n \ ame O or name CB or name SG or name H or name HA or name HB2 or name HB3)) or re \ sid 307 through 317 or (resid 318 and (name N or name CA or name C or name O or \ name CB or name SG or name H or name HA or name HB2 or name HB3)) or resid 319 t \ hrough 436 or (resid 437 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name ND2 or name H or name HA or name HB2 or name HB3 o \ r name HD21)) or resid 438 through 451 or (resid 452 and (name N or name CA or n \ ame C or name O or name CB or name CG or name OD1 or name ND2 or name H or name \ HA or name HB2 or name HB3 or name HD21)) or resid 453 through 460)) selection = (chain 'C' and resid 237 through 460) selection = (chain 'D' and (resid 237 through 305 or (resid 306 and (name N or name CA or na \ me C or name O or name CB or name SG or name H or name HA or name HB2 or name HB \ 3)) or resid 307 through 436 or (resid 437 and (name N or name CA or name C or n \ ame O or name CB or name CG or name OD1 or name ND2 or name H or name HA or name \ HB2 or name HB3 or name HD21)) or resid 438 through 460)) } ncs_group { reference = chain 'H' 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: 5.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.130 Extract box with map and model: 0.500 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.570 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5986 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 : 0.010 0.586 12707 Z= 0.497 Angle : 0.829 28.146 17357 Z= 0.455 Chirality : 0.053 0.495 2020 Planarity : 0.003 0.038 2216 Dihedral : 12.465 119.390 4906 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.80 % Favored : 88.14 % Rotamer: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % 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: -3.98 (0.19), residues: 1568 helix: -3.64 (0.30), residues: 106 sheet: -2.78 (0.17), residues: 625 loop : -2.33 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 172 TYR 0.010 0.000 TYR J 104 PHE 0.004 0.000 PHE A 369 TRP 0.006 0.000 TRP E 479 HIS 0.001 0.000 HIS C 380 Details of bonding type rmsd covalent geometry : bond 0.00330 (12661) covalent geometry : angle 0.71152 (17251) SS BOND : bond 0.18826 ( 29) SS BOND : angle 7.25662 ( 58) hydrogen bonds : bond 0.22141 ( 360) hydrogen bonds : angle 9.34725 ( 987) Misc. bond : bond 0.00049 ( 1) link_ALPHA1-3 : bond 0.00370 ( 1) link_ALPHA1-3 : angle 1.62977 ( 3) link_ALPHA1-6 : bond 0.00451 ( 1) link_ALPHA1-6 : angle 1.60374 ( 3) link_BETA1-4 : bond 0.00659 ( 6) link_BETA1-4 : angle 1.87761 ( 18) link_NAG-ASN : bond 0.00357 ( 8) link_NAG-ASN : angle 1.70625 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 0.565 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: 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 260 THR cc_start: 0.8121 (m) cc_final: 0.7868 (m) REVERT: A 338 ASN cc_start: 0.5476 (p0) cc_final: 0.5251 (p0) REVERT: A 465 ILE cc_start: 0.8461 (mm) cc_final: 0.8192 (mt) REVERT: E 438 VAL cc_start: 0.6225 (t) cc_final: 0.5992 (t) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.2504 time to fit residues: 136.9247 Evaluate side-chains 209 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.0970 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN A 421 GLN C 268 ASN C 291 GLN ** C 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 HIS J 44 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.212312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.175711 restraints weight = 45969.845| |-----------------------------------------------------------------------------| r_work (start): 0.4490 rms_B_bonded: 3.21 r_work: 0.4295 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.4156 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 12707 Z= 0.220 Angle : 0.717 13.111 17357 Z= 0.362 Chirality : 0.049 0.249 2020 Planarity : 0.005 0.053 2216 Dihedral : 8.605 117.255 2013 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.57 % Favored : 93.37 % Rotamer: Outliers : 2.23 % Allowed : 10.05 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.34 (0.20), residues: 1568 helix: -2.62 (0.40), residues: 107 sheet: -2.29 (0.18), residues: 638 loop : -2.02 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 429 TYR 0.016 0.002 TYR E 251 PHE 0.029 0.002 PHE E 75 TRP 0.009 0.001 TRP B 310 HIS 0.007 0.001 HIS E 309 Details of bonding type rmsd covalent geometry : bond 0.00503 (12661) covalent geometry : angle 0.69830 (17251) SS BOND : bond 0.01440 ( 29) SS BOND : angle 1.43505 ( 58) hydrogen bonds : bond 0.03676 ( 360) hydrogen bonds : angle 6.63513 ( 987) Misc. bond : bond 0.00065 ( 1) link_ALPHA1-3 : bond 0.00196 ( 1) link_ALPHA1-3 : angle 1.93048 ( 3) link_ALPHA1-6 : bond 0.01420 ( 1) link_ALPHA1-6 : angle 1.37206 ( 3) link_BETA1-4 : bond 0.00566 ( 6) link_BETA1-4 : angle 2.63795 ( 18) link_NAG-ASN : bond 0.00705 ( 8) link_NAG-ASN : angle 3.18153 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 217 time to evaluate : 0.645 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: A 286 GLN cc_start: 0.6174 (mp-120) cc_final: 0.5811 (mp10) REVERT: A 465 ILE cc_start: 0.8588 (mm) cc_final: 0.8314 (mt) REVERT: C 456 SER cc_start: 0.8469 (m) cc_final: 0.7990 (p) REVERT: D 274 PHE cc_start: 0.5227 (m-80) cc_final: 0.4886 (m-80) REVERT: D 459 MET cc_start: 0.7534 (tpp) cc_final: 0.7307 (tpt) REVERT: J 9 ASP cc_start: 0.6719 (OUTLIER) cc_final: 0.6060 (m-30) outliers start: 31 outliers final: 18 residues processed: 237 average time/residue: 0.2404 time to fit residues: 82.1305 Evaluate side-chains 195 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 341 LYS Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 19 SER Chi-restraints excluded: chain J residue 22 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 141 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 chunk 107 optimal weight: 20.0000 chunk 15 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 380 HIS E 53 ASN ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.198476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.160844 restraints weight = 43312.501| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 2.65 r_work: 0.3926 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3795 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 12707 Z= 0.160 Angle : 0.586 13.165 17357 Z= 0.288 Chirality : 0.045 0.219 2020 Planarity : 0.004 0.047 2216 Dihedral : 7.393 110.642 2013 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.78 % Favored : 92.16 % Rotamer: Outliers : 1.79 % Allowed : 11.34 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.06 (0.21), residues: 1568 helix: -2.37 (0.41), residues: 113 sheet: -2.17 (0.18), residues: 665 loop : -1.73 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 16 TYR 0.012 0.001 TYR E 251 PHE 0.019 0.002 PHE E 75 TRP 0.008 0.001 TRP E 479 HIS 0.004 0.001 HIS J 63 Details of bonding type rmsd covalent geometry : bond 0.00379 (12661) covalent geometry : angle 0.56607 (17251) SS BOND : bond 0.00685 ( 29) SS BOND : angle 1.35654 ( 58) hydrogen bonds : bond 0.03623 ( 360) hydrogen bonds : angle 6.16459 ( 987) Misc. bond : bond 0.00017 ( 1) link_ALPHA1-3 : bond 0.00184 ( 1) link_ALPHA1-3 : angle 1.71522 ( 3) link_ALPHA1-6 : bond 0.01132 ( 1) link_ALPHA1-6 : angle 1.85052 ( 3) link_BETA1-4 : bond 0.00464 ( 6) link_BETA1-4 : angle 1.87245 ( 18) link_NAG-ASN : bond 0.00460 ( 8) link_NAG-ASN : angle 3.18198 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.595 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 286 GLN cc_start: 0.6269 (mp-120) cc_final: 0.5904 (mp10) REVERT: A 465 ILE cc_start: 0.8627 (mm) cc_final: 0.8352 (mt) REVERT: C 250 ASP cc_start: 0.7614 (p0) cc_final: 0.7296 (m-30) REVERT: C 456 SER cc_start: 0.8440 (m) cc_final: 0.7996 (p) REVERT: E 243 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.7032 (mmp80) REVERT: J 9 ASP cc_start: 0.6739 (OUTLIER) cc_final: 0.6239 (m-30) REVERT: J 124 MET cc_start: 0.7632 (mmm) cc_final: 0.7347 (mmt) outliers start: 25 outliers final: 18 residues processed: 196 average time/residue: 0.2473 time to fit residues: 69.2877 Evaluate side-chains 189 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain D residue 275 THR Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain E residue 243 ARG Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 341 LYS Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 22 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 43 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 124 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 140 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN ** B 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN ** E 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.192958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.156166 restraints weight = 43618.452| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 2.49 r_work: 0.3813 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12707 Z= 0.184 Angle : 0.626 14.343 17357 Z= 0.312 Chirality : 0.046 0.224 2020 Planarity : 0.005 0.059 2216 Dihedral : 6.861 101.733 2013 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.95 % Favored : 92.92 % Rotamer: Outliers : 2.30 % Allowed : 12.85 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.21), residues: 1568 helix: -1.76 (0.47), residues: 113 sheet: -2.00 (0.19), residues: 661 loop : -1.68 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 431 TYR 0.028 0.001 TYR D 297 PHE 0.024 0.002 PHE D 369 TRP 0.011 0.001 TRP E 479 HIS 0.013 0.001 HIS E 309 Details of bonding type rmsd covalent geometry : bond 0.00430 (12661) covalent geometry : angle 0.60536 (17251) SS BOND : bond 0.00509 ( 29) SS BOND : angle 1.46406 ( 58) hydrogen bonds : bond 0.02874 ( 360) hydrogen bonds : angle 5.84223 ( 987) Misc. bond : bond 0.00030 ( 1) link_ALPHA1-3 : bond 0.00140 ( 1) link_ALPHA1-3 : angle 1.74835 ( 3) link_ALPHA1-6 : bond 0.01028 ( 1) link_ALPHA1-6 : angle 2.35026 ( 3) link_BETA1-4 : bond 0.00408 ( 6) link_BETA1-4 : angle 1.75386 ( 18) link_NAG-ASN : bond 0.00505 ( 8) link_NAG-ASN : angle 3.41356 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 172 time to evaluate : 0.674 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 286 GLN cc_start: 0.6447 (mp-120) cc_final: 0.5936 (mp10) REVERT: C 250 ASP cc_start: 0.7995 (p0) cc_final: 0.7700 (m-30) REVERT: C 309 ARG cc_start: 0.7794 (tpt170) cc_final: 0.7502 (ttp80) REVERT: C 456 SER cc_start: 0.8756 (m) cc_final: 0.8322 (p) REVERT: D 409 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8132 (m) REVERT: D 437 ASN cc_start: 0.6751 (m-40) cc_final: 0.6489 (p0) outliers start: 32 outliers final: 22 residues processed: 195 average time/residue: 0.2543 time to fit residues: 69.9504 Evaluate side-chains 167 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 490 LEU Chi-restraints excluded: chain E residue 528 CYS Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 84 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 134 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 53 ASN E 309 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.190702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.152769 restraints weight = 43398.187| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.62 r_work: 0.3795 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.6065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 12707 Z= 0.173 Angle : 0.599 14.319 17357 Z= 0.295 Chirality : 0.045 0.220 2020 Planarity : 0.004 0.050 2216 Dihedral : 6.549 95.051 2013 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.37 % Allowed : 14.00 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.21), residues: 1568 helix: -1.68 (0.46), residues: 113 sheet: -1.86 (0.19), residues: 658 loop : -1.58 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 16 TYR 0.015 0.001 TYR J 118 PHE 0.017 0.002 PHE D 369 TRP 0.020 0.001 TRP E 482 HIS 0.008 0.001 HIS E 309 Details of bonding type rmsd covalent geometry : bond 0.00413 (12661) covalent geometry : angle 0.57842 (17251) SS BOND : bond 0.00492 ( 29) SS BOND : angle 1.32385 ( 58) hydrogen bonds : bond 0.02900 ( 360) hydrogen bonds : angle 5.72722 ( 987) Misc. bond : bond 0.00019 ( 1) link_ALPHA1-3 : bond 0.00238 ( 1) link_ALPHA1-3 : angle 1.69383 ( 3) link_ALPHA1-6 : bond 0.01129 ( 1) link_ALPHA1-6 : angle 2.69874 ( 3) link_BETA1-4 : bond 0.00430 ( 6) link_BETA1-4 : angle 1.53253 ( 18) link_NAG-ASN : bond 0.00431 ( 8) link_NAG-ASN : angle 3.43595 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.654 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: B 384 GLU cc_start: 0.6565 (tp30) cc_final: 0.6334 (pp20) REVERT: C 250 ASP cc_start: 0.7993 (p0) cc_final: 0.7731 (m-30) REVERT: C 456 SER cc_start: 0.8823 (m) cc_final: 0.8420 (p) REVERT: D 409 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8148 (m) REVERT: D 437 ASN cc_start: 0.6736 (m-40) cc_final: 0.6473 (p0) outliers start: 33 outliers final: 23 residues processed: 180 average time/residue: 0.2342 time to fit residues: 61.2469 Evaluate side-chains 169 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 528 CYS Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 125 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 120 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 100 optimal weight: 0.1980 chunk 146 optimal weight: 0.0770 chunk 133 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 53 ASN ** E 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.190977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.151772 restraints weight = 43243.763| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.76 r_work: 0.3794 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3658 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.6343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12707 Z= 0.130 Angle : 0.569 14.786 17357 Z= 0.277 Chirality : 0.044 0.221 2020 Planarity : 0.004 0.055 2216 Dihedral : 6.289 90.822 2013 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.08 % Allowed : 14.72 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.21), residues: 1568 helix: -1.41 (0.47), residues: 113 sheet: -1.68 (0.19), residues: 645 loop : -1.56 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 16 TYR 0.014 0.001 TYR E 251 PHE 0.017 0.001 PHE E 75 TRP 0.011 0.001 TRP E 482 HIS 0.003 0.001 HIS B 431 Details of bonding type rmsd covalent geometry : bond 0.00311 (12661) covalent geometry : angle 0.54834 (17251) SS BOND : bond 0.00357 ( 29) SS BOND : angle 1.10482 ( 58) hydrogen bonds : bond 0.02579 ( 360) hydrogen bonds : angle 5.47472 ( 987) Misc. bond : bond 0.00008 ( 1) link_ALPHA1-3 : bond 0.00262 ( 1) link_ALPHA1-3 : angle 1.62752 ( 3) link_ALPHA1-6 : bond 0.01133 ( 1) link_ALPHA1-6 : angle 2.86000 ( 3) link_BETA1-4 : bond 0.00417 ( 6) link_BETA1-4 : angle 1.54433 ( 18) link_NAG-ASN : bond 0.00376 ( 8) link_NAG-ASN : angle 3.47716 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.692 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: B 274 PHE cc_start: 0.5056 (m-80) cc_final: 0.4511 (m-80) REVERT: B 384 GLU cc_start: 0.6664 (tp30) cc_final: 0.6390 (pp20) REVERT: B 428 MET cc_start: 0.8030 (ttm) cc_final: 0.7801 (ttm) REVERT: C 250 ASP cc_start: 0.8009 (p0) cc_final: 0.7771 (m-30) REVERT: C 456 SER cc_start: 0.8861 (m) cc_final: 0.8433 (p) REVERT: D 409 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8224 (m) REVERT: D 437 ASN cc_start: 0.6716 (m-40) cc_final: 0.6379 (p0) outliers start: 29 outliers final: 21 residues processed: 172 average time/residue: 0.2292 time to fit residues: 58.0608 Evaluate side-chains 163 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 528 CYS Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 125 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 118 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 102 optimal weight: 7.9990 chunk 146 optimal weight: 0.3980 chunk 150 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 103 optimal weight: 0.0470 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN E 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.191806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.151907 restraints weight = 43133.141| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.83 r_work: 0.3811 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.6445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12707 Z= 0.108 Angle : 0.556 14.870 17357 Z= 0.268 Chirality : 0.043 0.215 2020 Planarity : 0.004 0.051 2216 Dihedral : 6.027 85.213 2013 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.72 % Allowed : 15.29 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.21), residues: 1568 helix: -1.47 (0.47), residues: 112 sheet: -1.58 (0.19), residues: 645 loop : -1.47 (0.23), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 16 TYR 0.007 0.001 TYR C 297 PHE 0.016 0.001 PHE E 75 TRP 0.010 0.001 TRP E 482 HIS 0.003 0.001 HIS E 309 Details of bonding type rmsd covalent geometry : bond 0.00262 (12661) covalent geometry : angle 0.53437 (17251) SS BOND : bond 0.00301 ( 29) SS BOND : angle 1.18460 ( 58) hydrogen bonds : bond 0.02461 ( 360) hydrogen bonds : angle 5.32783 ( 987) Misc. bond : bond 0.00001 ( 1) link_ALPHA1-3 : bond 0.00387 ( 1) link_ALPHA1-3 : angle 1.65075 ( 3) link_ALPHA1-6 : bond 0.01262 ( 1) link_ALPHA1-6 : angle 3.02992 ( 3) link_BETA1-4 : bond 0.00406 ( 6) link_BETA1-4 : angle 1.47542 ( 18) link_NAG-ASN : bond 0.00301 ( 8) link_NAG-ASN : angle 3.46218 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 0.522 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 444 ASP cc_start: 0.6381 (t70) cc_final: 0.5747 (p0) REVERT: B 384 GLU cc_start: 0.6623 (tp30) cc_final: 0.6385 (pp20) REVERT: B 428 MET cc_start: 0.8019 (ttm) cc_final: 0.7819 (ttm) REVERT: C 456 SER cc_start: 0.8870 (m) cc_final: 0.8477 (p) REVERT: D 437 ASN cc_start: 0.6704 (m-40) cc_final: 0.6384 (p0) outliers start: 24 outliers final: 20 residues processed: 163 average time/residue: 0.2219 time to fit residues: 53.7727 Evaluate side-chains 156 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain E residue 528 CYS Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 18 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 40 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.187454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.149093 restraints weight = 43421.098| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.87 r_work: 0.3735 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.6844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 12707 Z= 0.210 Angle : 0.635 14.861 17357 Z= 0.313 Chirality : 0.045 0.217 2020 Planarity : 0.005 0.054 2216 Dihedral : 6.102 75.802 2013 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 2.15 % Allowed : 15.29 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.21), residues: 1568 helix: -1.49 (0.45), residues: 113 sheet: -1.57 (0.20), residues: 636 loop : -1.66 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 16 TYR 0.017 0.002 TYR E 468 PHE 0.021 0.002 PHE D 369 TRP 0.013 0.001 TRP E 482 HIS 0.007 0.001 HIS E 309 Details of bonding type rmsd covalent geometry : bond 0.00496 (12661) covalent geometry : angle 0.60859 (17251) SS BOND : bond 0.00600 ( 29) SS BOND : angle 1.96858 ( 58) hydrogen bonds : bond 0.02779 ( 360) hydrogen bonds : angle 5.52602 ( 987) Misc. bond : bond 0.00046 ( 1) link_ALPHA1-3 : bond 0.00300 ( 1) link_ALPHA1-3 : angle 1.73395 ( 3) link_ALPHA1-6 : bond 0.01338 ( 1) link_ALPHA1-6 : angle 3.13925 ( 3) link_BETA1-4 : bond 0.00435 ( 6) link_BETA1-4 : angle 1.47964 ( 18) link_NAG-ASN : bond 0.00558 ( 8) link_NAG-ASN : angle 3.53633 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.612 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: B 274 PHE cc_start: 0.4983 (m-80) cc_final: 0.4420 (m-80) REVERT: B 384 GLU cc_start: 0.6861 (tp30) cc_final: 0.6548 (pp20) REVERT: C 456 SER cc_start: 0.8947 (m) cc_final: 0.8600 (p) REVERT: D 409 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8268 (m) REVERT: D 437 ASN cc_start: 0.6686 (m-40) cc_final: 0.6412 (p0) REVERT: J 124 MET cc_start: 0.7922 (mmm) cc_final: 0.7467 (mmt) outliers start: 30 outliers final: 23 residues processed: 174 average time/residue: 0.2097 time to fit residues: 54.6861 Evaluate side-chains 167 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 328 ASN Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 528 CYS Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 18 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 91 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 136 optimal weight: 0.0050 chunk 110 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 105 optimal weight: 1.9990 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.189980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.152148 restraints weight = 43202.055| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 2.76 r_work: 0.3800 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3661 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.6974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 12707 Z= 0.124 Angle : 0.585 15.005 17357 Z= 0.283 Chirality : 0.044 0.209 2020 Planarity : 0.004 0.050 2216 Dihedral : 5.574 55.743 2013 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.87 % Allowed : 15.87 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.21), residues: 1568 helix: -1.09 (0.48), residues: 112 sheet: -1.49 (0.20), residues: 635 loop : -1.45 (0.23), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 16 TYR 0.008 0.001 TYR J 104 PHE 0.015 0.001 PHE E 75 TRP 0.012 0.001 TRP E 482 HIS 0.004 0.001 HIS B 431 Details of bonding type rmsd covalent geometry : bond 0.00301 (12661) covalent geometry : angle 0.56015 (17251) SS BOND : bond 0.00303 ( 29) SS BOND : angle 1.69298 ( 58) hydrogen bonds : bond 0.02485 ( 360) hydrogen bonds : angle 5.26296 ( 987) Misc. bond : bond 0.00003 ( 1) link_ALPHA1-3 : bond 0.00232 ( 1) link_ALPHA1-3 : angle 1.67800 ( 3) link_ALPHA1-6 : bond 0.01549 ( 1) link_ALPHA1-6 : angle 2.87274 ( 3) link_BETA1-4 : bond 0.00376 ( 6) link_BETA1-4 : angle 1.37938 ( 18) link_NAG-ASN : bond 0.00325 ( 8) link_NAG-ASN : angle 3.50034 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.645 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: B 274 PHE cc_start: 0.4957 (m-80) cc_final: 0.4404 (m-80) REVERT: C 456 SER cc_start: 0.8943 (m) cc_final: 0.8590 (p) REVERT: D 437 ASN cc_start: 0.6638 (m-40) cc_final: 0.6378 (p0) REVERT: J 124 MET cc_start: 0.7806 (mmm) cc_final: 0.7409 (mmt) outliers start: 26 outliers final: 20 residues processed: 162 average time/residue: 0.2324 time to fit residues: 55.3798 Evaluate side-chains 155 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 390 TYR Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 528 CYS Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 18 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 111 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 148 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 53 ASN J 44 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.188436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.150352 restraints weight = 43348.884| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.83 r_work: 0.3757 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.7189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12707 Z= 0.164 Angle : 0.613 15.072 17357 Z= 0.298 Chirality : 0.044 0.210 2020 Planarity : 0.004 0.053 2216 Dihedral : 5.440 54.083 2013 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 1.65 % Allowed : 16.30 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.21), residues: 1568 helix: -1.04 (0.48), residues: 113 sheet: -1.45 (0.20), residues: 626 loop : -1.44 (0.23), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 16 TYR 0.026 0.002 TYR J 135 PHE 0.015 0.002 PHE E 75 TRP 0.012 0.001 TRP E 482 HIS 0.005 0.001 HIS B 431 Details of bonding type rmsd covalent geometry : bond 0.00395 (12661) covalent geometry : angle 0.58936 (17251) SS BOND : bond 0.00384 ( 29) SS BOND : angle 1.71611 ( 58) hydrogen bonds : bond 0.02549 ( 360) hydrogen bonds : angle 5.28697 ( 987) Misc. bond : bond 0.00029 ( 1) link_ALPHA1-3 : bond 0.00352 ( 1) link_ALPHA1-3 : angle 1.90779 ( 3) link_ALPHA1-6 : bond 0.01817 ( 1) link_ALPHA1-6 : angle 2.35555 ( 3) link_BETA1-4 : bond 0.00371 ( 6) link_BETA1-4 : angle 1.33925 ( 18) link_NAG-ASN : bond 0.00440 ( 8) link_NAG-ASN : angle 3.53022 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.697 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: B 274 PHE cc_start: 0.5033 (m-80) cc_final: 0.4485 (m-80) REVERT: C 456 SER cc_start: 0.8975 (m) cc_final: 0.8618 (p) REVERT: D 437 ASN cc_start: 0.6648 (m-40) cc_final: 0.6389 (p0) REVERT: J 124 MET cc_start: 0.7906 (mmm) cc_final: 0.7478 (mmt) outliers start: 23 outliers final: 20 residues processed: 154 average time/residue: 0.2165 time to fit residues: 50.2877 Evaluate side-chains 154 residues out of total 1393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 311 ASN Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 418 THR Chi-restraints excluded: chain D residue 297 TYR Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 361 SER Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 456 SER Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 424 THR Chi-restraints excluded: chain E residue 528 CYS Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 18 THR Chi-restraints excluded: chain J residue 44 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 147 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 53 ASN ** J 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.188599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.150555 restraints weight = 43319.676| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.92 r_work: 0.3760 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.7200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 12707 Z= 0.165 Angle : 0.827 59.200 17357 Z= 0.472 Chirality : 0.044 0.209 2020 Planarity : 0.004 0.053 2216 Dihedral : 5.436 54.120 2013 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 1.72 % Allowed : 16.08 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.21), residues: 1568 helix: -1.03 (0.48), residues: 113 sheet: -1.44 (0.20), residues: 626 loop : -1.43 (0.23), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 243 TYR 0.015 0.001 TYR J 135 PHE 0.015 0.001 PHE E 75 TRP 0.011 0.001 TRP E 482 HIS 0.004 0.001 HIS B 431 Details of bonding type rmsd covalent geometry : bond 0.00383 (12661) covalent geometry : angle 0.81123 (17251) SS BOND : bond 0.00340 ( 29) SS BOND : angle 1.61294 ( 58) hydrogen bonds : bond 0.02531 ( 360) hydrogen bonds : angle 5.28300 ( 987) Misc. bond : bond 0.00021 ( 1) link_ALPHA1-3 : bond 0.00841 ( 1) link_ALPHA1-3 : angle 2.42703 ( 3) link_ALPHA1-6 : bond 0.01577 ( 1) link_ALPHA1-6 : angle 2.33613 ( 3) link_BETA1-4 : bond 0.00386 ( 6) link_BETA1-4 : angle 1.38190 ( 18) link_NAG-ASN : bond 0.00422 ( 8) link_NAG-ASN : angle 3.53317 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7019.55 seconds wall clock time: 119 minutes 24.12 seconds (7164.12 seconds total)