Starting phenix.real_space_refine on Wed Aug 5 13:42:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o9l_70254/08_2026/9o9l_70254.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o9l_70254/08_2026/9o9l_70254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o9l_70254/08_2026/9o9l_70254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o9l_70254/08_2026/9o9l_70254.map" model { file = "/net/cci-nas-00/data/ceres_data/9o9l_70254/08_2026/9o9l_70254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o9l_70254/08_2026/9o9l_70254.cif" } resolution = 3.43 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 35 5.16 5 C 6120 2.51 5 N 1701 2.21 5 O 1902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9760 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1135 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Chain: "C" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1132 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 137} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3766 Classifications: {'peptide': 479} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 474} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3682 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 4, 'TRANS': 461} Chain breaks: 2 Chain: "E" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna2p_pur': 2} Link IDs: {'rna2p': 1} Time building chain proxies: 2.16, per 1000 atoms: 0.22 Number of scatterers: 9760 At special positions: 0 Unit cell: (76.725, 93.225, 122.925, 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 35 16.00 P 2 15.00 O 1902 8.00 N 1701 7.00 C 6120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 350.7 milliseconds 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2320 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 10 sheets defined 51.5% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'B' and resid 183 through 188 Processing helix chain 'B' and resid 192 through 213 Processing helix chain 'B' and resid 232 through 240 Processing helix chain 'B' and resid 243 through 256 removed outlier: 4.309A pdb=" N GLU B 247 " --> pdb=" O PHE B 243 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG B 256 " --> pdb=" O GLU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 290 removed outlier: 4.114A pdb=" N ARG B 290 " --> pdb=" O ILE B 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 190 removed outlier: 4.217A pdb=" N SER C 190 " --> pdb=" O ASP C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 214 removed outlier: 3.592A pdb=" N ARG C 214 " --> pdb=" O PHE C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 241 removed outlier: 3.715A pdb=" N LEU C 235 " --> pdb=" O ASP C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 255 Processing helix chain 'C' and resid 272 through 291 Processing helix chain 'D' and resid 183 through 188 Processing helix chain 'D' and resid 192 through 215 removed outlier: 4.069A pdb=" N SER D 213 " --> pdb=" O GLU D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 241 removed outlier: 3.676A pdb=" N LEU D 235 " --> pdb=" O ASP D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 256 removed outlier: 4.538A pdb=" N GLU D 247 " --> pdb=" O PHE D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 290 removed outlier: 3.539A pdb=" N ILE D 276 " --> pdb=" O ASN D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 337 Processing helix chain 'D' and resid 350 through 366 Processing helix chain 'D' and resid 382 through 396 Processing helix chain 'D' and resid 403 through 408 Processing helix chain 'D' and resid 429 through 436 removed outlier: 3.635A pdb=" N PHE D 436 " --> pdb=" O LEU D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 478 removed outlier: 3.603A pdb=" N LEU D 470 " --> pdb=" O SER D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 501 Processing helix chain 'D' and resid 509 through 522 Processing helix chain 'D' and resid 524 through 533 removed outlier: 3.523A pdb=" N ILE D 528 " --> pdb=" O ASP D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 549 removed outlier: 3.722A pdb=" N GLY D 549 " --> pdb=" O LEU D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 581 removed outlier: 3.848A pdb=" N ASP D 577 " --> pdb=" O SER D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 619 removed outlier: 4.151A pdb=" N GLU D 617 " --> pdb=" O ARG D 613 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N MET D 618 " --> pdb=" O ILE D 614 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY D 619 " --> pdb=" O MET D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 648 removed outlier: 3.778A pdb=" N LYS D 648 " --> pdb=" O LEU D 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 212 Processing helix chain 'A' and resid 232 through 241 removed outlier: 3.700A pdb=" N ASP A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 256 removed outlier: 4.181A pdb=" N GLU A 247 " --> pdb=" O PHE A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 291 Processing helix chain 'A' and resid 321 through 337 removed outlier: 3.564A pdb=" N ASP A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 368 removed outlier: 3.532A pdb=" N ASN A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE A 367 " --> pdb=" O PHE A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 396 Processing helix chain 'A' and resid 403 through 410 Processing helix chain 'A' and resid 423 through 427 Processing helix chain 'A' and resid 429 through 436 removed outlier: 3.680A pdb=" N TYR A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE A 436 " --> pdb=" O LEU A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 479 Processing helix chain 'A' and resid 485 through 501 Processing helix chain 'A' and resid 508 through 522 Processing helix chain 'A' and resid 524 through 532 Processing helix chain 'A' and resid 535 through 549 Processing helix chain 'A' and resid 568 through 581 Processing helix chain 'A' and resid 610 through 616 removed outlier: 3.592A pdb=" N ILE A 614 " --> pdb=" O ASN A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 652 Processing sheet with id=AA1, first strand: chain 'B' and resid 217 through 222 removed outlier: 4.153A pdb=" N PHE B 217 " --> pdb=" O PHE B 229 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ARG B 225 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR B 261 " --> pdb=" O ASP B 182 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA B 295 " --> pdb=" O PHE B 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 217 through 220 removed outlier: 4.082A pdb=" N PHE C 217 " --> pdb=" O PHE C 229 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR C 261 " --> pdb=" O ASP C 182 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR C 268 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA C 295 " --> pdb=" O PHE C 309 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE C 309 " --> pdb=" O ALA C 295 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 217 through 222 removed outlier: 6.702A pdb=" N ARG D 225 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR D 261 " --> pdb=" O ASP D 182 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN D 294 " --> pdb=" O LEU D 262 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG D 298 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR D 268 " --> pdb=" O ARG D 298 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 400 through 402 removed outlier: 7.346A pdb=" N LEU D 401 " --> pdb=" O ALA D 372 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ALA D 374 " --> pdb=" O LEU D 401 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL D 341 " --> pdb=" O TYR D 373 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL D 375 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL D 343 " --> pdb=" O VAL D 375 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER D 340 " --> pdb=" O LEU D 415 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL D 417 " --> pdb=" O SER D 340 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N PHE D 342 " --> pdb=" O VAL D 417 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N VAL D 419 " --> pdb=" O PHE D 342 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL D 344 " --> pdb=" O VAL D 419 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N SER D 414 " --> pdb=" O GLU D 438 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N ILE D 440 " --> pdb=" O SER D 414 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU D 416 " --> pdb=" O ILE D 440 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ILE D 442 " --> pdb=" O LEU D 416 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N MET D 418 " --> pdb=" O ILE D 442 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL D 439 " --> pdb=" O LEU D 457 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N PHE D 459 " --> pdb=" O VAL D 439 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL D 441 " --> pdb=" O PHE D 459 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 550 through 553 removed outlier: 5.783A pdb=" N ARG D 551 " --> pdb=" O VAL D 558 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL D 558 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL D 557 " --> pdb=" O PHE D 589 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ILE D 591 " --> pdb=" O VAL D 557 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ALA D 559 " --> pdb=" O ILE D 591 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ARG D 593 " --> pdb=" O ALA D 559 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 218 through 222 removed outlier: 6.680A pdb=" N ARG A 225 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR A 261 " --> pdb=" O ASP A 182 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TYR A 268 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 340 through 344 removed outlier: 8.288A pdb=" N ILE A 440 " --> pdb=" O SER A 414 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU A 416 " --> pdb=" O ILE A 440 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE A 442 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N MET A 418 " --> pdb=" O ILE A 442 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N PHE A 459 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL A 441 " --> pdb=" O PHE A 459 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 375 through 376 removed outlier: 3.820A pdb=" N TYR A 376 " --> pdb=" O LEU A 401 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 556 through 559 removed outlier: 5.447A pdb=" N VAL A 557 " --> pdb=" O PHE A 589 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A 588 " --> pdb=" O ARG A 604 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG A 604 " --> pdb=" O THR A 588 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 598 through 601 535 hydrogen bonds defined for protein. 1569 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: 1.23 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3336 1.34 - 1.46: 1429 1.46 - 1.57: 5066 1.57 - 1.69: 3 1.69 - 1.81: 66 Bond restraints: 9900 Sorted by residual: bond pdb=" CG1 ILE B 199 " pdb=" CD1 ILE B 199 " ideal model delta sigma weight residual 1.513 1.448 0.065 3.90e-02 6.57e+02 2.75e+00 bond pdb=" P A E 2 " pdb=" OP1 A E 2 " ideal model delta sigma weight residual 1.485 1.514 -0.029 2.00e-02 2.50e+03 2.04e+00 bond pdb=" CB THR A 472 " pdb=" CG2 THR A 472 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.65e+00 bond pdb=" CG1 ILE C 176 " pdb=" CD1 ILE C 176 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.60e+00 bond pdb=" C6 A E 1 " pdb=" N6 A E 1 " ideal model delta sigma weight residual 1.335 1.325 0.010 8.00e-03 1.56e+04 1.55e+00 ... (remaining 9895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 13044 1.66 - 3.32: 253 3.32 - 4.98: 40 4.98 - 6.65: 16 6.65 - 8.31: 7 Bond angle restraints: 13360 Sorted by residual: angle pdb=" C3' A E 1 " pdb=" C2' A E 1 " pdb=" C1' A E 1 " ideal model delta sigma weight residual 101.50 97.60 3.90 8.00e-01 1.56e+00 2.37e+01 angle pdb=" CA GLU A 215 " pdb=" CB GLU A 215 " pdb=" CG GLU A 215 " ideal model delta sigma weight residual 114.10 121.77 -7.67 2.00e+00 2.50e-01 1.47e+01 angle pdb=" CA GLU A 431 " pdb=" CB GLU A 431 " pdb=" CG GLU A 431 " ideal model delta sigma weight residual 114.10 121.23 -7.13 2.00e+00 2.50e-01 1.27e+01 angle pdb=" C4' A E 1 " pdb=" C3' A E 1 " pdb=" C2' A E 1 " ideal model delta sigma weight residual 102.60 99.21 3.39 1.00e+00 1.00e+00 1.15e+01 angle pdb=" CA GLN A 409 " pdb=" CB GLN A 409 " pdb=" CG GLN A 409 " ideal model delta sigma weight residual 114.10 120.38 -6.28 2.00e+00 2.50e-01 9.85e+00 ... (remaining 13355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 4967 17.57 - 35.14: 722 35.14 - 52.71: 241 52.71 - 70.28: 49 70.28 - 87.85: 21 Dihedral angle restraints: 6000 sinusoidal: 2423 harmonic: 3577 Sorted by residual: dihedral pdb=" CG ARG D 447 " pdb=" CD ARG D 447 " pdb=" NE ARG D 447 " pdb=" CZ ARG D 447 " ideal model delta sinusoidal sigma weight residual -90.00 -39.32 -50.68 2 1.50e+01 4.44e-03 1.28e+01 dihedral pdb=" CA ILE C 188 " pdb=" C ILE C 188 " pdb=" N GLU C 189 " pdb=" CA GLU C 189 " ideal model delta harmonic sigma weight residual 180.00 -162.76 -17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA ASN D 200 " pdb=" CB ASN D 200 " pdb=" CG ASN D 200 " pdb=" OD1 ASN D 200 " ideal model delta sinusoidal sigma weight residual -90.00 -164.52 74.52 2 2.00e+01 2.50e-03 1.11e+01 ... (remaining 5997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1462 0.096 - 0.191: 67 0.191 - 0.286: 0 0.286 - 0.382: 0 0.382 - 0.477: 2 Chirality restraints: 1531 Sorted by residual: chirality pdb=" P A E 2 " pdb=" OP1 A E 2 " pdb=" OP2 A E 2 " pdb=" O5' A E 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.89 -0.48 2.00e-01 2.50e+01 5.70e+00 chirality pdb=" P A E 1 " pdb=" OP1 A E 1 " pdb=" OP2 A E 1 " pdb=" O5' A E 1 " both_signs ideal model delta sigma weight residual True 2.41 2.81 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CA GLU A 215 " pdb=" N GLU A 215 " pdb=" C GLU A 215 " pdb=" CB GLU A 215 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.80e-01 ... (remaining 1528 not shown) Planarity restraints: 1741 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 214 " -0.251 9.50e-02 1.11e+02 1.13e-01 9.94e+00 pdb=" NE ARG A 214 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG A 214 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG A 214 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 214 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A E 2 " 0.025 2.00e-02 2.50e+03 1.35e-02 4.98e+00 pdb=" N9 A E 2 " -0.031 2.00e-02 2.50e+03 pdb=" C8 A E 2 " 0.011 2.00e-02 2.50e+03 pdb=" N7 A E 2 " -0.004 2.00e-02 2.50e+03 pdb=" C5 A E 2 " -0.006 2.00e-02 2.50e+03 pdb=" C6 A E 2 " 0.000 2.00e-02 2.50e+03 pdb=" N6 A E 2 " 0.011 2.00e-02 2.50e+03 pdb=" N1 A E 2 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A E 2 " 0.005 2.00e-02 2.50e+03 pdb=" N3 A E 2 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A E 2 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 616 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.96e+00 pdb=" C GLU D 616 " -0.039 2.00e-02 2.50e+03 pdb=" O GLU D 616 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU D 617 " 0.013 2.00e-02 2.50e+03 ... (remaining 1738 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 4721 2.96 - 3.45: 10735 3.45 - 3.93: 16157 3.93 - 4.42: 18903 4.42 - 4.90: 29693 Nonbonded interactions: 80209 Sorted by model distance: nonbonded pdb=" O THR D 508 " pdb=" OG1 THR D 508 " model vdw 2.478 3.040 nonbonded pdb=" OP2 A E 1 " pdb=" O2' A E 2 " model vdw 2.488 3.040 nonbonded pdb=" O ARG A 430 " pdb=" OD1 ASN A 434 " model vdw 2.519 3.040 nonbonded pdb=" O THR D 508 " pdb=" N ARG D 510 " model vdw 2.524 3.120 nonbonded pdb=" O GLN A 409 " pdb=" OE1 GLN A 409 " model vdw 2.536 3.040 ... (remaining 80204 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 172 through 650) selection = (chain 'D' and (resid 172 through 311 or resid 320 through 617 or resid 625 thro \ ugh 650)) } ncs_group { reference = (chain 'B' and (resid 172 through 187 or (resid 188 and (name N or name CA or na \ me C or name O or name CB )) or resid 189 through 311)) selection = chain 'C' } 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: 5.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.400 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 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 : 0.003 0.065 9900 Z= 0.156 Angle : 0.613 8.307 13360 Z= 0.341 Chirality : 0.046 0.477 1531 Planarity : 0.005 0.113 1741 Dihedral : 18.933 87.848 3680 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.78 % Favored : 94.89 % Rotamer: Outliers : 3.77 % Allowed : 36.53 % Favored : 59.70 % 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: -0.63 (0.24), residues: 1213 helix: 0.58 (0.20), residues: 614 sheet: -0.92 (0.34), residues: 248 loop : -1.64 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG A 214 TYR 0.009 0.001 TYR A 539 PHE 0.032 0.002 PHE D 217 HIS 0.003 0.001 HIS D 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 ( 9900) covalent geometry : angle 0.61255 / 0.34 (13360) hydrogen bonds : bond 0.15551 / 10.25 ( 535) hydrogen bonds : angle 6.54954 / 4.44 ( 1569) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 336 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 184 TYR cc_start: 0.7818 (t80) cc_final: 0.7549 (t80) REVERT: B 223 MET cc_start: 0.6975 (tpp) cc_final: 0.6660 (tpp) REVERT: B 250 ARG cc_start: 0.8550 (ttp-110) cc_final: 0.7636 (tpm170) REVERT: B 252 GLU cc_start: 0.8344 (tt0) cc_final: 0.8139 (tt0) REVERT: C 173 GLN cc_start: 0.8535 (mp10) cc_final: 0.8114 (mp10) REVERT: C 205 ASN cc_start: 0.8384 (m-40) cc_final: 0.7766 (m-40) REVERT: C 223 MET cc_start: 0.7025 (mmm) cc_final: 0.5524 (ptp) REVERT: C 235 LEU cc_start: 0.6876 (mt) cc_final: 0.6651 (tp) REVERT: C 251 LYS cc_start: 0.8825 (ttpp) cc_final: 0.8216 (mtpp) REVERT: C 286 ILE cc_start: 0.6988 (tt) cc_final: 0.6688 (pt) REVERT: D 327 MET cc_start: 0.7408 (tpp) cc_final: 0.7077 (mpp) REVERT: D 352 ASP cc_start: 0.6854 (t0) cc_final: 0.6139 (t0) REVERT: D 497 MET cc_start: 0.8321 (mtp) cc_final: 0.7936 (mtt) REVERT: D 524 ASP cc_start: 0.7629 (t0) cc_final: 0.7044 (m-30) REVERT: D 567 TYR cc_start: 0.7754 (m-80) cc_final: 0.7491 (m-80) REVERT: D 630 GLN cc_start: 0.8589 (mt0) cc_final: 0.8292 (mt0) REVERT: A 198 GLN cc_start: 0.7786 (tp-100) cc_final: 0.7575 (tp-100) REVERT: A 241 ASP cc_start: 0.7403 (p0) cc_final: 0.6848 (p0) REVERT: A 242 LYS cc_start: 0.8791 (mmmm) cc_final: 0.8452 (ttpt) REVERT: A 264 MET cc_start: 0.8844 (mtm) cc_final: 0.8562 (mtt) REVERT: A 296 VAL cc_start: 0.8542 (OUTLIER) cc_final: 0.8318 (m) REVERT: A 360 MET cc_start: 0.7504 (tpt) cc_final: 0.7215 (mmm) REVERT: A 398 THR cc_start: 0.7529 (t) cc_final: 0.7263 (t) REVERT: A 416 LEU cc_start: 0.5989 (tp) cc_final: 0.5774 (tp) REVERT: A 426 LEU cc_start: 0.8252 (mm) cc_final: 0.7924 (mm) REVERT: A 460 ILE cc_start: 0.5264 (OUTLIER) cc_final: 0.4443 (tt) REVERT: A 499 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.7066 (t0) REVERT: A 501 LYS cc_start: 0.8776 (mtmt) cc_final: 0.8464 (ttmm) REVERT: A 582 MET cc_start: 0.7934 (ttm) cc_final: 0.7467 (mtp) outliers start: 40 outliers final: 14 residues processed: 359 average time/residue: 0.0815 time to fit residues: 40.5696 Evaluate side-chains 227 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 210 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 243 PHE Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 483 HIS Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 499 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 chunk 117 optimal weight: 10.0000 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 200 ASN D 173 GLN D 198 GLN D 200 ASN D 275 GLN ** D 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 GLN D 581 ASN A 257 HIS A 476 GLN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.168502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.132390 restraints weight = 13047.039| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.96 r_work: 0.3608 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9900 Z= 0.169 Angle : 0.638 9.825 13360 Z= 0.349 Chirality : 0.045 0.210 1531 Planarity : 0.004 0.035 1741 Dihedral : 6.773 82.701 1378 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.04 % Favored : 95.71 % Rotamer: Outliers : 6.21 % Allowed : 30.79 % Favored : 62.99 % 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: -0.31 (0.24), residues: 1213 helix: 0.82 (0.20), residues: 626 sheet: -0.61 (0.34), residues: 246 loop : -1.68 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 219 TYR 0.015 0.002 TYR C 232 PHE 0.038 0.002 PHE D 624 HIS 0.027 0.002 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 ( 9900) covalent geometry : angle 0.63833 / 0.35 (13360) hydrogen bonds : bond 0.04508 / 2.98 ( 535) hydrogen bonds : angle 5.11761 / 3.50 ( 1569) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 229 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 223 MET cc_start: 0.7009 (tpp) cc_final: 0.6585 (tpp) REVERT: B 244 GLU cc_start: 0.7955 (pm20) cc_final: 0.7727 (pm20) REVERT: B 250 ARG cc_start: 0.8414 (ttp-110) cc_final: 0.7678 (tpm170) REVERT: B 254 GLN cc_start: 0.7902 (pt0) cc_final: 0.7637 (pt0) REVERT: B 290 ARG cc_start: 0.5453 (OUTLIER) cc_final: 0.3581 (mtp180) REVERT: C 173 GLN cc_start: 0.8565 (mp10) cc_final: 0.7903 (mp10) REVERT: C 236 ASP cc_start: 0.8153 (t70) cc_final: 0.7878 (t0) REVERT: C 286 ILE cc_start: 0.6634 (tt) cc_final: 0.6224 (pt) REVERT: D 244 GLU cc_start: 0.7244 (pm20) cc_final: 0.7016 (pm20) REVERT: D 323 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.6910 (mtm-85) REVERT: D 327 MET cc_start: 0.7513 (tpp) cc_final: 0.7109 (mpp) REVERT: D 352 ASP cc_start: 0.6890 (t0) cc_final: 0.6517 (t0) REVERT: D 497 MET cc_start: 0.8233 (mtp) cc_final: 0.7851 (mtt) REVERT: D 524 ASP cc_start: 0.7817 (t0) cc_final: 0.7362 (m-30) REVERT: D 529 GLN cc_start: 0.8757 (mt0) cc_final: 0.8473 (mt0) REVERT: D 585 ILE cc_start: 0.6927 (OUTLIER) cc_final: 0.6675 (tt) REVERT: A 198 GLN cc_start: 0.7879 (tp-100) cc_final: 0.7595 (tp-100) REVERT: A 214 ARG cc_start: 0.6303 (OUTLIER) cc_final: 0.4961 (mtm180) REVERT: A 242 LYS cc_start: 0.8874 (mmmm) cc_final: 0.8266 (ttpt) REVERT: A 243 PHE cc_start: 0.9122 (OUTLIER) cc_final: 0.7778 (t80) REVERT: A 264 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8584 (mtt) REVERT: A 360 MET cc_start: 0.7615 (tpt) cc_final: 0.7353 (mmm) REVERT: A 499 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.6796 (t0) REVERT: A 582 MET cc_start: 0.7657 (ttm) cc_final: 0.7231 (mtp) outliers start: 66 outliers final: 24 residues processed: 276 average time/residue: 0.0662 time to fit residues: 26.7769 Evaluate side-chains 237 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 206 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 299 GLU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 323 ARG Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 425 GLN Chi-restraints excluded: chain D residue 466 SER Chi-restraints excluded: chain D residue 478 GLN Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 523 SER Chi-restraints excluded: chain D residue 581 ASN Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 623 HIS Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 445 HIS Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 571 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 0.5980 chunk 100 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 95 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 76 optimal weight: 0.0770 chunk 46 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.2542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 198 GLN D 173 GLN ** D 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 GLN ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.165153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.128485 restraints weight = 13329.001| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.99 r_work: 0.3555 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9900 Z= 0.201 Angle : 0.639 8.646 13360 Z= 0.344 Chirality : 0.045 0.178 1531 Planarity : 0.003 0.038 1741 Dihedral : 6.146 79.882 1357 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.87 % Favored : 95.88 % Rotamer: Outliers : 5.74 % Allowed : 30.60 % Favored : 63.65 % 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: -0.32 (0.24), residues: 1213 helix: 0.87 (0.20), residues: 625 sheet: -0.75 (0.33), residues: 260 loop : -1.70 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 219 TYR 0.024 0.002 TYR A 433 PHE 0.029 0.003 PHE B 206 HIS 0.008 0.001 HIS D 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 ( 9900) covalent geometry : angle 0.63906 / 0.34 (13360) hydrogen bonds : bond 0.04190 / 2.77 ( 535) hydrogen bonds : angle 4.90675 / 3.36 ( 1569) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 211 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 184 TYR cc_start: 0.7784 (t80) cc_final: 0.7445 (t80) REVERT: B 195 ASP cc_start: 0.8146 (m-30) cc_final: 0.7816 (m-30) REVERT: B 215 GLU cc_start: 0.7281 (pm20) cc_final: 0.6971 (pm20) REVERT: B 223 MET cc_start: 0.7084 (tpp) cc_final: 0.6741 (tpp) REVERT: B 244 GLU cc_start: 0.8059 (pm20) cc_final: 0.7788 (pm20) REVERT: B 250 ARG cc_start: 0.8468 (ttp-110) cc_final: 0.7692 (tpm170) REVERT: B 290 ARG cc_start: 0.5532 (OUTLIER) cc_final: 0.3602 (mtp180) REVERT: C 173 GLN cc_start: 0.8635 (mp10) cc_final: 0.8134 (mp10) REVERT: C 236 ASP cc_start: 0.8135 (t70) cc_final: 0.7845 (t0) REVERT: C 252 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7234 (mt-10) REVERT: C 268 TYR cc_start: 0.8184 (p90) cc_final: 0.7960 (p90) REVERT: D 244 GLU cc_start: 0.7201 (pm20) cc_final: 0.6474 (pm20) REVERT: D 327 MET cc_start: 0.7571 (tpp) cc_final: 0.7239 (mpp) REVERT: D 352 ASP cc_start: 0.7268 (t0) cc_final: 0.6780 (t0) REVERT: D 497 MET cc_start: 0.8253 (mtp) cc_final: 0.7882 (mtt) REVERT: D 524 ASP cc_start: 0.7859 (t0) cc_final: 0.7337 (m-30) REVERT: D 529 GLN cc_start: 0.8797 (mt0) cc_final: 0.8516 (mt0) REVERT: D 600 CYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6924 (m) REVERT: A 198 GLN cc_start: 0.7924 (tp-100) cc_final: 0.7534 (tp-100) REVERT: A 214 ARG cc_start: 0.6248 (OUTLIER) cc_final: 0.4912 (mtm180) REVERT: A 242 LYS cc_start: 0.8898 (mmmm) cc_final: 0.8375 (ttpt) REVERT: A 243 PHE cc_start: 0.9171 (OUTLIER) cc_final: 0.7880 (t80) REVERT: A 264 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8571 (mtt) REVERT: A 360 MET cc_start: 0.7543 (tpt) cc_final: 0.7285 (mmm) REVERT: A 418 MET cc_start: 0.5057 (mpp) cc_final: 0.4773 (mpp) REVERT: A 419 VAL cc_start: 0.5892 (OUTLIER) cc_final: 0.5153 (m) REVERT: A 421 HIS cc_start: 0.6965 (p-80) cc_final: 0.6699 (p90) REVERT: A 460 ILE cc_start: 0.5053 (OUTLIER) cc_final: 0.4156 (tt) REVERT: A 499 ASP cc_start: 0.7483 (t0) cc_final: 0.6991 (t0) REVERT: A 582 MET cc_start: 0.7772 (ttm) cc_final: 0.7366 (mtp) outliers start: 61 outliers final: 39 residues processed: 258 average time/residue: 0.0673 time to fit residues: 25.8001 Evaluate side-chains 244 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 198 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 299 GLU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 323 ARG Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 425 GLN Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 466 SER Chi-restraints excluded: chain D residue 483 HIS Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 523 SER Chi-restraints excluded: chain D residue 566 SER Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 600 CYS Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 623 HIS Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 445 HIS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 571 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 25 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 110 optimal weight: 0.3980 chunk 67 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 198 GLN B 254 GLN ** D 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 GLN ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 GLN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.171205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.137184 restraints weight = 12972.156| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.62 r_work: 0.3649 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9900 Z= 0.150 Angle : 0.581 7.111 13360 Z= 0.317 Chirality : 0.043 0.166 1531 Planarity : 0.003 0.042 1741 Dihedral : 5.922 80.490 1355 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.38 % Favored : 96.29 % Rotamer: Outliers : 6.21 % Allowed : 30.70 % Favored : 63.09 % 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: -0.15 (0.24), residues: 1213 helix: 1.02 (0.20), residues: 627 sheet: -0.67 (0.33), residues: 264 loop : -1.67 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 219 TYR 0.014 0.002 TYR C 232 PHE 0.037 0.002 PHE B 206 HIS 0.006 0.001 HIS A 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 9900) covalent geometry : angle 0.58137 / 0.32 (13360) hydrogen bonds : bond 0.03797 / 2.52 ( 535) hydrogen bonds : angle 4.66151 / 3.21 ( 1569) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 210 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 199 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7819 (mp) REVERT: B 223 MET cc_start: 0.7252 (tpp) cc_final: 0.6561 (tpp) REVERT: B 244 GLU cc_start: 0.7688 (pm20) cc_final: 0.7420 (pm20) REVERT: B 246 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7408 (mp) REVERT: B 250 ARG cc_start: 0.8265 (ttp-110) cc_final: 0.7822 (tpp-160) REVERT: B 290 ARG cc_start: 0.6021 (OUTLIER) cc_final: 0.4075 (mtp180) REVERT: C 173 GLN cc_start: 0.8554 (mp10) cc_final: 0.8188 (mp10) REVERT: C 236 ASP cc_start: 0.8183 (t70) cc_final: 0.7947 (t0) REVERT: C 252 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7176 (mt-10) REVERT: C 268 TYR cc_start: 0.8104 (p90) cc_final: 0.7311 (p90) REVERT: D 207 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7916 (mt) REVERT: D 352 ASP cc_start: 0.7168 (t0) cc_final: 0.6760 (t0) REVERT: D 426 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8502 (mp) REVERT: D 497 MET cc_start: 0.8388 (mtp) cc_final: 0.8106 (mtt) REVERT: D 524 ASP cc_start: 0.7667 (t0) cc_final: 0.7334 (m-30) REVERT: D 600 CYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7296 (m) REVERT: D 609 ILE cc_start: 0.7457 (OUTLIER) cc_final: 0.7167 (tt) REVERT: A 198 GLN cc_start: 0.7648 (tp-100) cc_final: 0.7355 (tp-100) REVERT: A 242 LYS cc_start: 0.8709 (mmmm) cc_final: 0.8346 (ttpt) REVERT: A 243 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.8029 (t80) REVERT: A 360 MET cc_start: 0.7529 (tpt) cc_final: 0.7317 (mmm) REVERT: A 394 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7779 (tm-30) REVERT: A 418 MET cc_start: 0.5344 (mpp) cc_final: 0.5018 (mpp) REVERT: A 460 ILE cc_start: 0.5294 (OUTLIER) cc_final: 0.4463 (tt) REVERT: A 499 ASP cc_start: 0.7403 (t0) cc_final: 0.6959 (t0) REVERT: A 582 MET cc_start: 0.7984 (ttm) cc_final: 0.7629 (mtp) outliers start: 66 outliers final: 34 residues processed: 260 average time/residue: 0.0695 time to fit residues: 27.1891 Evaluate side-chains 240 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 197 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 247 GLU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 299 GLU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 323 ARG Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 425 GLN Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 466 SER Chi-restraints excluded: chain D residue 483 HIS Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 566 SER Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 600 CYS Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 623 HIS Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 445 HIS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 571 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 198 GLN B 254 GLN C 272 ASN ** D 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 GLN ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 ASN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.167417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.132409 restraints weight = 13230.896| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.73 r_work: 0.3582 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9900 Z= 0.216 Angle : 0.627 7.553 13360 Z= 0.340 Chirality : 0.045 0.164 1531 Planarity : 0.003 0.039 1741 Dihedral : 6.068 80.302 1355 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.20 % Favored : 95.47 % Rotamer: Outliers : 6.97 % Allowed : 30.32 % Favored : 62.71 % 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: -0.32 (0.24), residues: 1213 helix: 0.86 (0.20), residues: 626 sheet: -0.75 (0.33), residues: 261 loop : -1.69 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 214 TYR 0.018 0.002 TYR C 268 PHE 0.031 0.003 PHE A 342 HIS 0.008 0.001 HIS D 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 ( 9900) covalent geometry : angle 0.62678 / 0.34 (13360) hydrogen bonds : bond 0.03983 / 2.64 ( 535) hydrogen bonds : angle 4.69478 / 3.23 ( 1569) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 194 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 199 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7911 (mp) REVERT: B 223 MET cc_start: 0.7205 (tpp) cc_final: 0.6550 (tpp) REVERT: B 246 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7450 (mp) REVERT: B 250 ARG cc_start: 0.8237 (ttp-110) cc_final: 0.7836 (tpm170) REVERT: B 290 ARG cc_start: 0.6185 (OUTLIER) cc_final: 0.4334 (mtp180) REVERT: C 173 GLN cc_start: 0.8609 (mp10) cc_final: 0.8223 (mp10) REVERT: C 236 ASP cc_start: 0.8235 (t70) cc_final: 0.7978 (t0) REVERT: C 252 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7107 (mt-10) REVERT: D 352 ASP cc_start: 0.7571 (t0) cc_final: 0.7047 (t0) REVERT: D 426 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8582 (mp) REVERT: D 497 MET cc_start: 0.8422 (mtp) cc_final: 0.8125 (mtt) REVERT: D 524 ASP cc_start: 0.7885 (t0) cc_final: 0.7373 (m-30) REVERT: D 600 CYS cc_start: 0.7583 (OUTLIER) cc_final: 0.7284 (m) REVERT: D 609 ILE cc_start: 0.7534 (OUTLIER) cc_final: 0.7211 (tt) REVERT: A 198 GLN cc_start: 0.7766 (tp-100) cc_final: 0.7423 (tp-100) REVERT: A 242 LYS cc_start: 0.8821 (mmmm) cc_final: 0.8469 (ttpt) REVERT: A 243 PHE cc_start: 0.9144 (OUTLIER) cc_final: 0.7979 (t80) REVERT: A 418 MET cc_start: 0.5392 (mpp) cc_final: 0.5036 (mpp) REVERT: A 460 ILE cc_start: 0.5374 (OUTLIER) cc_final: 0.4552 (tt) REVERT: A 499 ASP cc_start: 0.7445 (t0) cc_final: 0.7031 (t0) REVERT: A 582 MET cc_start: 0.8022 (ttm) cc_final: 0.7670 (mtp) outliers start: 74 outliers final: 47 residues processed: 252 average time/residue: 0.0749 time to fit residues: 27.8632 Evaluate side-chains 244 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 189 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 247 GLU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 299 GLU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 323 ARG Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 425 GLN Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 466 SER Chi-restraints excluded: chain D residue 483 HIS Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 566 SER Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 600 CYS Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 618 MET Chi-restraints excluded: chain D residue 623 HIS Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 425 GLN Chi-restraints excluded: chain A residue 436 PHE Chi-restraints excluded: chain A residue 445 HIS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 571 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 96 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 18 optimal weight: 0.1980 chunk 115 optimal weight: 8.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 198 GLN B 254 GLN D 478 GLN ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 GLN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.166939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.131978 restraints weight = 13235.980| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.73 r_work: 0.3586 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9900 Z= 0.204 Angle : 0.625 8.104 13360 Z= 0.339 Chirality : 0.045 0.299 1531 Planarity : 0.003 0.032 1741 Dihedral : 6.098 80.486 1355 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.45 % Favored : 95.22 % Rotamer: Outliers : 6.50 % Allowed : 31.36 % Favored : 62.15 % 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: -0.39 (0.24), residues: 1213 helix: 0.84 (0.20), residues: 626 sheet: -0.83 (0.33), residues: 263 loop : -1.76 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 219 TYR 0.016 0.002 TYR A 433 PHE 0.028 0.003 PHE B 206 HIS 0.007 0.001 HIS D 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.20 ( 9900) covalent geometry : angle 0.62453 / 0.34 (13360) hydrogen bonds : bond 0.03922 / 2.62 ( 535) hydrogen bonds : angle 4.63133 / 3.19 ( 1569) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 187 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 195 ASP cc_start: 0.8276 (m-30) cc_final: 0.8037 (m-30) REVERT: B 199 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7887 (mp) REVERT: B 223 MET cc_start: 0.7197 (tpp) cc_final: 0.6502 (tpp) REVERT: B 246 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7410 (mp) REVERT: B 250 ARG cc_start: 0.8224 (ttp-110) cc_final: 0.7844 (tpm170) REVERT: B 290 ARG cc_start: 0.6194 (OUTLIER) cc_final: 0.4324 (mtp180) REVERT: C 173 GLN cc_start: 0.8620 (mp10) cc_final: 0.8225 (mp10) REVERT: C 223 MET cc_start: 0.7350 (mmm) cc_final: 0.7036 (mmp) REVERT: C 236 ASP cc_start: 0.8251 (t70) cc_final: 0.8040 (t0) REVERT: C 268 TYR cc_start: 0.8028 (p90) cc_final: 0.7447 (p90) REVERT: C 299 GLU cc_start: 0.4502 (tp30) cc_final: 0.4154 (tp30) REVERT: D 394 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8010 (tm-30) REVERT: D 399 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8653 (mt0) REVERT: D 426 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8586 (mp) REVERT: D 497 MET cc_start: 0.8394 (mtp) cc_final: 0.8118 (mtt) REVERT: D 524 ASP cc_start: 0.7774 (t0) cc_final: 0.7293 (m-30) REVERT: D 600 CYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7356 (m) REVERT: D 609 ILE cc_start: 0.7512 (OUTLIER) cc_final: 0.7174 (tt) REVERT: A 198 GLN cc_start: 0.7716 (tp-100) cc_final: 0.7335 (tp-100) REVERT: A 242 LYS cc_start: 0.8842 (mmmm) cc_final: 0.8500 (ttpt) REVERT: A 243 PHE cc_start: 0.9151 (OUTLIER) cc_final: 0.8020 (t80) REVERT: A 360 MET cc_start: 0.7471 (tpt) cc_final: 0.7188 (mmm) REVERT: A 394 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7863 (tm-30) REVERT: A 470 LEU cc_start: 0.6774 (OUTLIER) cc_final: 0.6373 (tt) REVERT: A 582 MET cc_start: 0.8047 (ttm) cc_final: 0.7714 (mtp) outliers start: 69 outliers final: 47 residues processed: 241 average time/residue: 0.0661 time to fit residues: 23.6361 Evaluate side-chains 234 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 178 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 257 HIS Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 247 GLU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 299 GLU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 323 ARG Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 399 GLN Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 425 GLN Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 466 SER Chi-restraints excluded: chain D residue 483 HIS Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 566 SER Chi-restraints excluded: chain D residue 577 ASP Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 600 CYS Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 618 MET Chi-restraints excluded: chain D residue 623 HIS Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 436 PHE Chi-restraints excluded: chain A residue 445 HIS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 525 ASN Chi-restraints excluded: chain A residue 571 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 7 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 198 GLN B 254 GLN B 300 ASN ** D 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 GLN ** A 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.167063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.132441 restraints weight = 13166.091| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.71 r_work: 0.3598 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9900 Z= 0.177 Angle : 0.617 7.596 13360 Z= 0.334 Chirality : 0.044 0.165 1531 Planarity : 0.003 0.028 1741 Dihedral : 6.103 80.641 1355 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.29 % Favored : 95.38 % Rotamer: Outliers : 6.50 % Allowed : 31.45 % Favored : 62.05 % 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: -0.34 (0.24), residues: 1213 helix: 0.91 (0.21), residues: 625 sheet: -0.84 (0.33), residues: 263 loop : -1.77 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 446 TYR 0.012 0.002 TYR B 268 PHE 0.029 0.002 PHE B 206 HIS 0.006 0.001 HIS D 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 ( 9900) covalent geometry : angle 0.61746 / 0.33 (13360) hydrogen bonds : bond 0.03783 / 2.53 ( 535) hydrogen bonds : angle 4.54034 / 3.14 ( 1569) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 191 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 195 ASP cc_start: 0.8347 (m-30) cc_final: 0.8145 (m-30) REVERT: B 223 MET cc_start: 0.7234 (tpp) cc_final: 0.6518 (tpp) REVERT: B 246 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7417 (mp) REVERT: B 250 ARG cc_start: 0.8196 (ttp-110) cc_final: 0.7859 (tpm170) REVERT: B 290 ARG cc_start: 0.6220 (OUTLIER) cc_final: 0.4308 (mtp180) REVERT: C 173 GLN cc_start: 0.8627 (mp10) cc_final: 0.8225 (mp10) REVERT: C 176 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7484 (mp) REVERT: C 219 ARG cc_start: 0.8084 (tpp80) cc_final: 0.7634 (tpt90) REVERT: C 223 MET cc_start: 0.7388 (mmm) cc_final: 0.7055 (mmt) REVERT: C 236 ASP cc_start: 0.8210 (t70) cc_final: 0.8007 (t0) REVERT: D 323 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.7083 (ttp-170) REVERT: D 352 ASP cc_start: 0.7561 (t0) cc_final: 0.7099 (t0) REVERT: D 394 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8033 (tm-30) REVERT: D 399 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8670 (mt0) REVERT: D 426 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8589 (mp) REVERT: D 497 MET cc_start: 0.8366 (mtp) cc_final: 0.8099 (mtt) REVERT: D 524 ASP cc_start: 0.7817 (t0) cc_final: 0.7360 (m-30) REVERT: D 609 ILE cc_start: 0.7588 (OUTLIER) cc_final: 0.7273 (tt) REVERT: A 198 GLN cc_start: 0.7595 (tp-100) cc_final: 0.7218 (tp-100) REVERT: A 242 LYS cc_start: 0.8839 (mmmm) cc_final: 0.8492 (ttpt) REVERT: A 243 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.8054 (t80) REVERT: A 360 MET cc_start: 0.7482 (tpt) cc_final: 0.7197 (mmm) REVERT: A 394 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7862 (tm-30) REVERT: A 418 MET cc_start: 0.4912 (mpp) cc_final: 0.4588 (mmt) REVERT: A 470 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6374 (tt) REVERT: A 582 MET cc_start: 0.8034 (ttm) cc_final: 0.7702 (mtp) outliers start: 69 outliers final: 45 residues processed: 245 average time/residue: 0.0687 time to fit residues: 25.2695 Evaluate side-chains 237 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 183 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 257 HIS Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 247 GLU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 299 GLU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 323 ARG Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 399 GLN Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 425 GLN Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 466 SER Chi-restraints excluded: chain D residue 483 HIS Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 566 SER Chi-restraints excluded: chain D residue 577 ASP Chi-restraints excluded: chain D residue 585 ILE Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 618 MET Chi-restraints excluded: chain D residue 623 HIS Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 571 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 84 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 77 optimal weight: 0.3980 chunk 3 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 198 GLN D 272 ASN D 275 GLN ** D 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 GLN A 397 HIS ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.169314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.135449 restraints weight = 13065.572| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.60 r_work: 0.3633 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9900 Z= 0.141 Angle : 0.589 7.473 13360 Z= 0.319 Chirality : 0.043 0.171 1531 Planarity : 0.003 0.022 1741 Dihedral : 5.972 80.856 1355 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.96 % Favored : 95.80 % Rotamer: Outliers : 5.08 % Allowed : 33.24 % Favored : 61.68 % 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: -0.17 (0.25), residues: 1213 helix: 1.05 (0.21), residues: 625 sheet: -0.71 (0.33), residues: 262 loop : -1.75 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 446 TYR 0.031 0.002 TYR C 268 PHE 0.033 0.002 PHE B 206 HIS 0.004 0.001 HIS D 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 9900) covalent geometry : angle 0.58917 / 0.32 (13360) hydrogen bonds : bond 0.03584 / 2.40 ( 535) hydrogen bonds : angle 4.41691 / 3.07 ( 1569) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 201 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: B 223 MET cc_start: 0.7326 (tpp) cc_final: 0.6604 (tpp) REVERT: B 246 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7384 (mp) REVERT: B 290 ARG cc_start: 0.6211 (OUTLIER) cc_final: 0.4282 (mtp180) REVERT: C 173 GLN cc_start: 0.8590 (mp10) cc_final: 0.8204 (mp10) REVERT: C 176 ILE cc_start: 0.7838 (OUTLIER) cc_final: 0.7522 (mp) REVERT: C 219 ARG cc_start: 0.8023 (tpp80) cc_final: 0.7631 (tpt90) REVERT: C 223 MET cc_start: 0.7338 (mmm) cc_final: 0.7046 (mmp) REVERT: D 272 ASN cc_start: 0.8095 (OUTLIER) cc_final: 0.7787 (m-40) REVERT: D 323 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.7065 (ttp-170) REVERT: D 352 ASP cc_start: 0.7273 (t0) cc_final: 0.6883 (t0) REVERT: D 394 GLU cc_start: 0.8595 (tm-30) cc_final: 0.7970 (tm-30) REVERT: D 426 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8533 (mp) REVERT: D 497 MET cc_start: 0.8379 (mtp) cc_final: 0.8170 (mtt) REVERT: D 524 ASP cc_start: 0.7709 (t0) cc_final: 0.7328 (m-30) REVERT: D 615 MET cc_start: 0.8512 (mmm) cc_final: 0.8265 (mmp) REVERT: A 198 GLN cc_start: 0.7490 (tp-100) cc_final: 0.7154 (tp-100) REVERT: A 242 LYS cc_start: 0.8790 (mmmm) cc_final: 0.8474 (ttpt) REVERT: A 243 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8072 (t80) REVERT: A 360 MET cc_start: 0.7459 (tpt) cc_final: 0.7183 (mmm) REVERT: A 394 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7829 (tm-30) REVERT: A 418 MET cc_start: 0.4831 (mpp) cc_final: 0.4501 (mmt) REVERT: A 470 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6419 (tt) REVERT: A 574 LYS cc_start: 0.6793 (ttpt) cc_final: 0.6379 (mptt) REVERT: A 582 MET cc_start: 0.8028 (ttm) cc_final: 0.7669 (mtp) outliers start: 54 outliers final: 38 residues processed: 241 average time/residue: 0.0711 time to fit residues: 25.1955 Evaluate side-chains 236 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 190 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 290 ARG Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 247 GLU Chi-restraints excluded: chain D residue 272 ASN Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 323 ARG Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 425 GLN Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 466 SER Chi-restraints excluded: chain D residue 483 HIS Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 566 SER Chi-restraints excluded: chain D residue 577 ASP Chi-restraints excluded: chain D residue 618 MET Chi-restraints excluded: chain D residue 623 HIS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 436 PHE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 571 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 105 optimal weight: 0.0980 chunk 54 optimal weight: 0.1980 chunk 88 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 118 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 198 GLN B 254 GLN D 303 HIS D 399 GLN ** D 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 GLN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.170207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.136157 restraints weight = 13079.684| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.62 r_work: 0.3641 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9900 Z= 0.138 Angle : 0.598 8.139 13360 Z= 0.324 Chirality : 0.043 0.175 1531 Planarity : 0.003 0.022 1741 Dihedral : 5.684 80.947 1353 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.96 % Favored : 95.80 % Rotamer: Outliers : 4.61 % Allowed : 33.62 % Favored : 61.77 % 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: -0.10 (0.25), residues: 1213 helix: 1.10 (0.21), residues: 625 sheet: -0.61 (0.34), residues: 260 loop : -1.77 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 446 TYR 0.026 0.002 TYR A 517 PHE 0.035 0.002 PHE B 206 HIS 0.012 0.001 HIS D 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 9900) covalent geometry : angle 0.59794 / 0.32 (13360) hydrogen bonds : bond 0.03510 / 2.36 ( 535) hydrogen bonds : angle 4.34958 / 3.04 ( 1569) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 195 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 223 MET cc_start: 0.7366 (tpp) cc_final: 0.6672 (tpp) REVERT: B 246 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7359 (mp) REVERT: C 173 GLN cc_start: 0.8568 (mp10) cc_final: 0.8197 (mp10) REVERT: C 176 ILE cc_start: 0.7790 (OUTLIER) cc_final: 0.7480 (mp) REVERT: C 219 ARG cc_start: 0.8065 (tpp80) cc_final: 0.7653 (tpt90) REVERT: C 223 MET cc_start: 0.7296 (mmm) cc_final: 0.7066 (mmp) REVERT: D 323 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.7168 (ttp-170) REVERT: D 352 ASP cc_start: 0.7274 (t0) cc_final: 0.6897 (t0) REVERT: D 394 GLU cc_start: 0.8570 (tm-30) cc_final: 0.7952 (tm-30) REVERT: D 426 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8489 (mp) REVERT: D 497 MET cc_start: 0.8355 (mtp) cc_final: 0.8108 (mtt) REVERT: D 524 ASP cc_start: 0.7681 (t0) cc_final: 0.7320 (m-30) REVERT: D 615 MET cc_start: 0.8503 (mmm) cc_final: 0.8271 (mmp) REVERT: A 198 GLN cc_start: 0.7475 (tp-100) cc_final: 0.7134 (tp-100) REVERT: A 242 LYS cc_start: 0.8770 (mmmm) cc_final: 0.8459 (ttpt) REVERT: A 243 PHE cc_start: 0.9134 (OUTLIER) cc_final: 0.8108 (t80) REVERT: A 360 MET cc_start: 0.7425 (tpt) cc_final: 0.7144 (mmm) REVERT: A 394 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7797 (tm-30) REVERT: A 418 MET cc_start: 0.4806 (mpp) cc_final: 0.4518 (mmt) REVERT: A 470 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.6430 (tt) REVERT: A 574 LYS cc_start: 0.6816 (ttpt) cc_final: 0.6406 (mptt) REVERT: A 579 MET cc_start: 0.6152 (mmt) cc_final: 0.5917 (mmm) REVERT: A 582 MET cc_start: 0.7974 (ttm) cc_final: 0.7592 (mtp) outliers start: 49 outliers final: 39 residues processed: 232 average time/residue: 0.0709 time to fit residues: 24.5180 Evaluate side-chains 233 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 188 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 247 GLU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 303 HIS Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 323 ARG Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 425 GLN Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 466 SER Chi-restraints excluded: chain D residue 483 HIS Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 566 SER Chi-restraints excluded: chain D residue 577 ASP Chi-restraints excluded: chain D residue 618 MET Chi-restraints excluded: chain D residue 623 HIS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 436 PHE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 571 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 99 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 76 optimal weight: 0.0470 chunk 79 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 111 optimal weight: 0.6980 chunk 83 optimal weight: 0.0670 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 198 GLN ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN D 240 GLN D 275 GLN D 303 HIS ** D 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 GLN A 397 HIS ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.170612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.136515 restraints weight = 13013.914| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.61 r_work: 0.3650 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9900 Z= 0.137 Angle : 0.612 8.362 13360 Z= 0.330 Chirality : 0.043 0.184 1531 Planarity : 0.003 0.022 1741 Dihedral : 5.648 80.945 1353 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.96 % Favored : 95.80 % Rotamer: Outliers : 4.61 % Allowed : 33.99 % Favored : 61.39 % 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: -0.07 (0.25), residues: 1213 helix: 1.14 (0.21), residues: 621 sheet: -0.55 (0.34), residues: 256 loop : -1.79 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 446 TYR 0.027 0.002 TYR A 373 PHE 0.036 0.002 PHE B 206 HIS 0.007 0.001 HIS D 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 9900) covalent geometry : angle 0.61229 / 0.33 (13360) hydrogen bonds : bond 0.03474 / 2.33 ( 535) hydrogen bonds : angle 4.32664 / 3.03 ( 1569) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 194 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 223 MET cc_start: 0.7369 (tpp) cc_final: 0.6674 (tpp) REVERT: B 246 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7356 (mp) REVERT: C 173 GLN cc_start: 0.8581 (mp10) cc_final: 0.8179 (mp10) REVERT: C 176 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7447 (mp) REVERT: C 219 ARG cc_start: 0.8097 (tpp80) cc_final: 0.7664 (tpt90) REVERT: C 223 MET cc_start: 0.7298 (mmm) cc_final: 0.7038 (mmp) REVERT: C 235 LEU cc_start: 0.7402 (tp) cc_final: 0.7171 (tp) REVERT: C 272 ASN cc_start: 0.7237 (m110) cc_final: 0.7025 (m110) REVERT: D 352 ASP cc_start: 0.7179 (t0) cc_final: 0.6796 (t0) REVERT: D 394 GLU cc_start: 0.8571 (tm-30) cc_final: 0.7937 (tm-30) REVERT: D 426 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8449 (mp) REVERT: D 497 MET cc_start: 0.8334 (mtp) cc_final: 0.8079 (mtt) REVERT: D 524 ASP cc_start: 0.7712 (t0) cc_final: 0.7310 (m-30) REVERT: D 615 MET cc_start: 0.8523 (mmm) cc_final: 0.8301 (mmp) REVERT: A 198 GLN cc_start: 0.7488 (tp-100) cc_final: 0.7136 (tp-100) REVERT: A 242 LYS cc_start: 0.8780 (mmmm) cc_final: 0.8462 (ttpt) REVERT: A 243 PHE cc_start: 0.9127 (OUTLIER) cc_final: 0.8027 (t80) REVERT: A 360 MET cc_start: 0.7415 (tpt) cc_final: 0.7142 (mmm) REVERT: A 394 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7785 (tm-30) REVERT: A 418 MET cc_start: 0.4801 (mpp) cc_final: 0.4519 (mmt) REVERT: A 470 LEU cc_start: 0.6803 (OUTLIER) cc_final: 0.6415 (tt) REVERT: A 499 ASP cc_start: 0.7437 (t0) cc_final: 0.6623 (t0) REVERT: A 574 LYS cc_start: 0.6837 (ttpt) cc_final: 0.6409 (mptt) REVERT: A 579 MET cc_start: 0.6232 (mmt) cc_final: 0.6025 (mmm) REVERT: A 582 MET cc_start: 0.7948 (ttm) cc_final: 0.7567 (mtp) outliers start: 49 outliers final: 39 residues processed: 233 average time/residue: 0.0715 time to fit residues: 24.8054 Evaluate side-chains 231 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 187 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 254 GLN Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain D residue 247 GLU Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 299 GLU Chi-restraints excluded: chain D residue 303 HIS Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 425 GLN Chi-restraints excluded: chain D residue 426 LEU Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 466 SER Chi-restraints excluded: chain D residue 483 HIS Chi-restraints excluded: chain D residue 504 SER Chi-restraints excluded: chain D residue 566 SER Chi-restraints excluded: chain D residue 577 ASP Chi-restraints excluded: chain D residue 623 HIS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 243 PHE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 436 PHE Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 571 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 198 GLN ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 GLN B 273 HIS D 303 HIS ** D 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 GLN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.169798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.135265 restraints weight = 13094.768| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.70 r_work: 0.3626 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9900 Z= 0.157 Angle : 0.616 8.750 13360 Z= 0.335 Chirality : 0.044 0.191 1531 Planarity : 0.003 0.038 1741 Dihedral : 5.673 80.743 1353 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.87 % Favored : 95.88 % Rotamer: Outliers : 4.61 % Allowed : 33.52 % Favored : 61.86 % 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: -0.03 (0.25), residues: 1213 helix: 1.17 (0.21), residues: 621 sheet: -0.66 (0.33), residues: 263 loop : -1.67 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 540 TYR 0.025 0.002 TYR A 517 PHE 0.035 0.002 PHE B 206 HIS 0.010 0.001 HIS D 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 9900) covalent geometry : angle 0.61606 / 0.34 (13360) hydrogen bonds : bond 0.03511 / 2.36 ( 535) hydrogen bonds : angle 4.33360 / 3.03 ( 1569) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1940.55 seconds wall clock time: 34 minutes 0.74 seconds (2040.74 seconds total)