Starting phenix.real_space_refine on Wed Feb 14 15:59:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dnz_30791/02_2024/7dnz_30791.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dnz_30791/02_2024/7dnz_30791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dnz_30791/02_2024/7dnz_30791.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dnz_30791/02_2024/7dnz_30791.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dnz_30791/02_2024/7dnz_30791.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dnz_30791/02_2024/7dnz_30791.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.003 sd= 0.046 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 Fe 1 7.16 5 S 38 5.16 5 C 6256 2.51 5 N 1634 2.21 5 O 1742 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 397": "OD1" <-> "OD2" Residue "A TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A ARG 435": "NH1" <-> "NH2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 478": "OE1" <-> "OE2" Residue "A TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 714": "OE1" <-> "OE2" Residue "A TYR 716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 722": "OE1" <-> "OE2" Residue "A GLU 752": "OE1" <-> "OE2" Residue "A ASP 758": "OD1" <-> "OD2" Residue "A ASP 792": "OD1" <-> "OD2" Residue "B PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 397": "OD1" <-> "OD2" Residue "B TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 433": "OE1" <-> "OE2" Residue "B ARG 435": "NH1" <-> "NH2" Residue "B PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "B PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 478": "OE1" <-> "OE2" Residue "B TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 714": "OE1" <-> "OE2" Residue "B TYR 716": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 722": "OE1" <-> "OE2" Residue "B GLU 752": "OE1" <-> "OE2" Residue "B ASP 758": "OD1" <-> "OD2" Residue "B ASP 792": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9671 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4669 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 577} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 4669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4669 Classifications: {'peptide': 591} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 577} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 145 Unusual residues: {'GSH': 2, 'Y01': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 188 Unusual residues: {'GSH': 2, 'HEM': 1, 'Y01': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 5.88, per 1000 atoms: 0.61 Number of scatterers: 9671 At special positions: 0 Unit cell: (80.51, 98.77, 137.78, 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) Fe 1 26.01 S 38 16.00 O 1742 8.00 N 1634 7.00 C 6256 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.04 Conformation dependent library (CDL) restraints added in 1.7 seconds 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2176 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 8 sheets defined 70.7% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 239 through 254 removed outlier: 3.610A pdb=" N GLY A 243 " --> pdb=" O TRP A 239 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ARG A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TRP A 254 " --> pdb=" O SER A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 295 removed outlier: 4.006A pdb=" N VAL A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) Proline residue: A 283 - end of helix removed outlier: 3.656A pdb=" N GLU A 295 " --> pdb=" O ASN A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 316 removed outlier: 3.637A pdb=" N LEU A 302 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 355 removed outlier: 3.512A pdb=" N ARG A 330 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ARG A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN A 338 " --> pdb=" O TRP A 334 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN A 339 " --> pdb=" O ILE A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 364 removed outlier: 3.946A pdb=" N HIS A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 390 removed outlier: 3.806A pdb=" N VAL A 369 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU A 370 " --> pdb=" O THR A 366 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ARG A 371 " --> pdb=" O GLY A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 409 Processing helix chain 'A' and resid 410 through 459 removed outlier: 3.700A pdb=" N GLY A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LYS A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N PHE A 438 " --> pdb=" O TRP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 467 removed outlier: 3.513A pdb=" N ASN A 467 " --> pdb=" O VAL A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 522 removed outlier: 4.276A pdb=" N LYS A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 545 removed outlier: 4.327A pdb=" N VAL A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) Proline residue: A 543 - end of helix Processing helix chain 'A' and resid 546 through 570 removed outlier: 3.699A pdb=" N TYR A 550 " --> pdb=" O TRP A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 637 Processing helix chain 'A' and resid 658 through 665 Processing helix chain 'A' and resid 680 through 685 Processing helix chain 'A' and resid 692 through 704 Processing helix chain 'A' and resid 705 through 712 Processing helix chain 'A' and resid 728 through 744 Processing helix chain 'A' and resid 758 through 773 Processing helix chain 'A' and resid 784 through 790 Processing helix chain 'A' and resid 807 through 815 Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.672A pdb=" N ASP A 820 " --> pdb=" O GLY A 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 254 removed outlier: 3.610A pdb=" N GLY B 243 " --> pdb=" O TRP B 239 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ARG B 244 " --> pdb=" O ARG B 240 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS B 245 " --> pdb=" O ASP B 241 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TRP B 254 " --> pdb=" O SER B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 295 removed outlier: 4.006A pdb=" N VAL B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) Proline residue: B 283 - end of helix removed outlier: 3.656A pdb=" N GLU B 295 " --> pdb=" O ASN B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 316 removed outlier: 3.638A pdb=" N LEU B 302 " --> pdb=" O PRO B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 355 removed outlier: 4.887A pdb=" N ARG B 336 " --> pdb=" O PHE B 332 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN B 338 " --> pdb=" O TRP B 334 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN B 339 " --> pdb=" O ILE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 364 removed outlier: 3.946A pdb=" N HIS B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY B 363 " --> pdb=" O ARG B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 390 removed outlier: 3.805A pdb=" N VAL B 369 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU B 370 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ARG B 371 " --> pdb=" O GLY B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 409 Processing helix chain 'B' and resid 410 through 459 removed outlier: 3.700A pdb=" N GLY B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LYS B 437 " --> pdb=" O GLU B 433 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N PHE B 438 " --> pdb=" O TRP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 467 removed outlier: 3.513A pdb=" N ASN B 467 " --> pdb=" O VAL B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 522 removed outlier: 4.276A pdb=" N LYS B 489 " --> pdb=" O GLY B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 545 removed outlier: 4.327A pdb=" N VAL B 531 " --> pdb=" O VAL B 527 " (cutoff:3.500A) Proline residue: B 543 - end of helix Processing helix chain 'B' and resid 546 through 570 removed outlier: 3.699A pdb=" N TYR B 550 " --> pdb=" O TRP B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 637 Processing helix chain 'B' and resid 658 through 665 Processing helix chain 'B' and resid 680 through 685 Processing helix chain 'B' and resid 692 through 704 Processing helix chain 'B' and resid 705 through 712 Processing helix chain 'B' and resid 728 through 744 Processing helix chain 'B' and resid 758 through 773 Processing helix chain 'B' and resid 784 through 790 Processing helix chain 'B' and resid 807 through 815 Processing helix chain 'B' and resid 816 through 825 removed outlier: 3.671A pdb=" N ASP B 820 " --> pdb=" O GLY B 816 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 590 through 596 removed outlier: 3.524A pdb=" N GLU A 591 " --> pdb=" O ARG A 648 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG A 648 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 593 " --> pdb=" O CYS A 646 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS A 646 " --> pdb=" O GLU A 593 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL A 595 " --> pdb=" O SER A 644 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER A 644 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 618 through 621 removed outlier: 3.652A pdb=" N ILE A 779 " --> pdb=" O ILE A 748 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 781 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 678 through 679 Processing sheet with id=AA4, first strand: chain 'A' and resid 794 through 798 removed outlier: 3.839A pdb=" N GLY A 806 " --> pdb=" O ILE A 794 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 804 " --> pdb=" O VAL A 796 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LYS A 798 " --> pdb=" O ILE A 802 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE A 802 " --> pdb=" O LYS A 798 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 590 through 596 removed outlier: 3.525A pdb=" N GLU B 591 " --> pdb=" O ARG B 648 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG B 648 " --> pdb=" O GLU B 591 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU B 593 " --> pdb=" O CYS B 646 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS B 646 " --> pdb=" O GLU B 593 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL B 595 " --> pdb=" O SER B 644 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N SER B 644 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 618 through 621 removed outlier: 3.652A pdb=" N ILE B 779 " --> pdb=" O ILE B 748 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL B 781 " --> pdb=" O LEU B 750 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 678 through 679 Processing sheet with id=AA8, first strand: chain 'B' and resid 794 through 798 removed outlier: 3.839A pdb=" N GLY B 806 " --> pdb=" O ILE B 794 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU B 804 " --> pdb=" O VAL B 796 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LYS B 798 " --> pdb=" O ILE B 802 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE B 802 " --> pdb=" O LYS B 798 " (cutoff:3.500A) 625 hydrogen bonds defined for protein. 1857 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: 2.75 Time building geometry restraints manager: 4.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 3768 1.38 - 1.56: 6038 1.56 - 1.74: 4 1.74 - 1.92: 61 1.92 - 2.10: 3 Bond restraints: 9874 Sorted by residual: bond pdb=" C3C HEM B 901 " pdb=" CAC HEM B 901 " ideal model delta sigma weight residual 1.544 1.471 0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C3B HEM B 901 " pdb=" CAB HEM B 901 " ideal model delta sigma weight residual 1.544 1.475 0.069 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C1 GSH B 903 " pdb=" O12 GSH B 903 " ideal model delta sigma weight residual 1.307 1.244 0.063 1.90e-02 2.77e+03 1.09e+01 bond pdb=" C1 GSH A 902 " pdb=" O12 GSH A 902 " ideal model delta sigma weight residual 1.307 1.245 0.062 1.90e-02 2.77e+03 1.07e+01 bond pdb=" C1 GSH B 902 " pdb=" O11 GSH B 902 " ideal model delta sigma weight residual 1.213 1.246 -0.033 1.00e-02 1.00e+04 1.06e+01 ... (remaining 9869 not shown) Histogram of bond angle deviations from ideal: 85.92 - 104.22: 111 104.22 - 122.53: 12199 122.53 - 140.83: 1120 140.83 - 159.14: 0 159.14 - 177.44: 2 Bond angle restraints: 13432 Sorted by residual: angle pdb=" C PHE B 325 " pdb=" N VAL B 326 " pdb=" CA VAL B 326 " ideal model delta sigma weight residual 122.63 113.76 8.87 1.19e+00 7.06e-01 5.56e+01 angle pdb=" C THR A 320 " pdb=" CA THR A 320 " pdb=" CB THR A 320 " ideal model delta sigma weight residual 109.72 119.03 -9.31 1.66e+00 3.63e-01 3.15e+01 angle pdb=" N GLY A 318 " pdb=" CA GLY A 318 " pdb=" C GLY A 318 " ideal model delta sigma weight residual 112.73 106.03 6.70 1.20e+00 6.94e-01 3.12e+01 angle pdb=" N VAL A 280 " pdb=" CA VAL A 280 " pdb=" C VAL A 280 " ideal model delta sigma weight residual 112.96 108.41 4.55 1.00e+00 1.00e+00 2.07e+01 angle pdb=" N SER B 322 " pdb=" CA SER B 322 " pdb=" C SER B 322 " ideal model delta sigma weight residual 108.24 102.24 6.00 1.32e+00 5.74e-01 2.07e+01 ... (remaining 13427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5390 17.94 - 35.88: 578 35.88 - 53.82: 111 53.82 - 71.76: 30 71.76 - 89.69: 11 Dihedral angle restraints: 6120 sinusoidal: 2720 harmonic: 3400 Sorted by residual: dihedral pdb=" C2B HEM B 901 " pdb=" C3B HEM B 901 " pdb=" CAB HEM B 901 " pdb=" CBB HEM B 901 " ideal model delta sinusoidal sigma weight residual 0.00 71.87 -71.87 2 1.00e+01 1.00e-02 4.34e+01 dihedral pdb=" C2C HEM B 901 " pdb=" C3C HEM B 901 " pdb=" CAC HEM B 901 " pdb=" CBC HEM B 901 " ideal model delta sinusoidal sigma weight residual -0.00 -65.50 65.50 2 1.00e+01 1.00e-02 3.97e+01 dihedral pdb=" C THR A 320 " pdb=" N THR A 320 " pdb=" CA THR A 320 " pdb=" CB THR A 320 " ideal model delta harmonic sigma weight residual -122.00 -136.24 14.24 0 2.50e+00 1.60e-01 3.24e+01 ... (remaining 6117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1360 0.094 - 0.187: 178 0.187 - 0.281: 9 0.281 - 0.375: 0 0.375 - 0.468: 1 Chirality restraints: 1548 Sorted by residual: chirality pdb=" CA THR A 320 " pdb=" N THR A 320 " pdb=" C THR A 320 " pdb=" CB THR A 320 " both_signs ideal model delta sigma weight residual False 2.53 2.06 0.47 2.00e-01 2.50e+01 5.48e+00 chirality pdb=" CA PHE B 408 " pdb=" N PHE B 408 " pdb=" C PHE B 408 " pdb=" CB PHE B 408 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA THR B 320 " pdb=" N THR B 320 " pdb=" C THR B 320 " pdb=" CB THR B 320 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 1545 not shown) Planarity restraints: 1668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG1 GSH A 901 " 0.162 2.00e-02 2.50e+03 1.94e-01 4.71e+02 pdb=" CD1 GSH A 901 " -0.064 2.00e-02 2.50e+03 pdb=" OE1 GSH A 901 " -0.009 2.00e-02 2.50e+03 pdb=" CA2 GSH A 901 " 0.233 2.00e-02 2.50e+03 pdb=" N2 GSH A 901 " -0.322 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG1 GSH B 902 " 0.136 2.00e-02 2.50e+03 1.56e-01 3.05e+02 pdb=" CD1 GSH B 902 " -0.051 2.00e-02 2.50e+03 pdb=" OE1 GSH B 902 " -0.018 2.00e-02 2.50e+03 pdb=" CA2 GSH B 902 " 0.188 2.00e-02 2.50e+03 pdb=" N2 GSH B 902 " -0.255 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 GSH B 902 " -0.043 2.00e-02 2.50e+03 1.26e-01 1.97e+02 pdb=" CA2 GSH B 902 " 0.113 2.00e-02 2.50e+03 pdb=" CA3 GSH B 902 " 0.153 2.00e-02 2.50e+03 pdb=" N3 GSH B 902 " -0.201 2.00e-02 2.50e+03 pdb=" O2 GSH B 902 " -0.022 2.00e-02 2.50e+03 ... (remaining 1665 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2824 2.82 - 3.34: 9775 3.34 - 3.86: 15813 3.86 - 4.38: 16673 4.38 - 4.90: 28224 Nonbonded interactions: 73309 Sorted by model distance: nonbonded pdb=" ND1 HIS B 808 " pdb=" OH TYR B 818 " model vdw 2.295 2.520 nonbonded pdb=" ND1 HIS A 808 " pdb=" OH TYR A 818 " model vdw 2.295 2.520 nonbonded pdb=" NH1 ARG B 638 " pdb=" O ILE B 654 " model vdw 2.303 2.520 nonbonded pdb=" NH1 ARG A 638 " pdb=" O ILE A 654 " model vdw 2.303 2.520 nonbonded pdb=" OH TYR A 424 " pdb=" OE1 GLN A 501 " model vdw 2.312 2.440 ... (remaining 73304 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 236 through 826 or resid 902 or resid 904 through 905)) selection = (chain 'B' and (resid 236 through 826 or resid 902 or resid 904 through 905)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.950 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: 5.150 Check model and map are aligned: 0.160 Set scattering table: 0.140 Process input model: 29.370 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 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 : 0.009 0.219 9874 Z= 0.611 Angle : 1.121 9.926 13432 Z= 0.636 Chirality : 0.061 0.468 1548 Planarity : 0.010 0.194 1668 Dihedral : 15.293 89.694 3944 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.60 % Allowed : 1.10 % Favored : 98.29 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.23), residues: 1178 helix: 0.53 (0.18), residues: 780 sheet: -2.29 (0.65), residues: 50 loop : -2.39 (0.28), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 304 HIS 0.007 0.002 HIS A 352 PHE 0.050 0.004 PHE B 460 TYR 0.032 0.003 TYR B 466 ARG 0.006 0.001 ARG B 663 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 145 time to evaluate : 1.140 Fit side-chains revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8517 (tm-30) REVERT: A 408 PHE cc_start: 0.7597 (m-80) cc_final: 0.7083 (m-10) REVERT: A 452 ARG cc_start: 0.8129 (ttm170) cc_final: 0.7864 (tpp80) REVERT: A 614 MET cc_start: 0.8929 (mpp) cc_final: 0.8299 (mpp) REVERT: A 748 ILE cc_start: 0.8701 (mt) cc_final: 0.8475 (mt) REVERT: B 275 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8453 (tm-30) REVERT: B 408 PHE cc_start: 0.7738 (m-80) cc_final: 0.7112 (m-10) REVERT: B 452 ARG cc_start: 0.8203 (ttm170) cc_final: 0.7951 (tpp80) REVERT: B 614 MET cc_start: 0.8889 (mpp) cc_final: 0.8231 (mpp) REVERT: B 748 ILE cc_start: 0.8667 (mt) cc_final: 0.8430 (mt) outliers start: 6 outliers final: 3 residues processed: 147 average time/residue: 0.1996 time to fit residues: 44.3497 Evaluate side-chains 95 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 455 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 47 optimal weight: 0.0470 chunk 92 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 56 optimal weight: 30.0000 chunk 68 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 GLN ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 HIS ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 ASN ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 GLN ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 HIS ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 ASN ** B 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9874 Z= 0.180 Angle : 0.594 12.871 13432 Z= 0.292 Chirality : 0.038 0.138 1548 Planarity : 0.003 0.040 1668 Dihedral : 10.033 87.561 1819 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.01 % Allowed : 10.44 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.25), residues: 1178 helix: 1.54 (0.19), residues: 800 sheet: -0.07 (0.73), residues: 30 loop : -2.41 (0.29), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 334 HIS 0.002 0.001 HIS B 352 PHE 0.016 0.001 PHE A 519 TYR 0.013 0.001 TYR B 465 ARG 0.001 0.000 ARG B 814 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8384 (tm-30) REVERT: A 614 MET cc_start: 0.8965 (mpp) cc_final: 0.8315 (mpp) REVERT: A 666 ILE cc_start: 0.8850 (tp) cc_final: 0.8636 (tp) REVERT: A 671 GLN cc_start: 0.7012 (tp-100) cc_final: 0.6697 (tp-100) REVERT: A 748 ILE cc_start: 0.8338 (mt) cc_final: 0.8120 (mt) REVERT: B 275 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8378 (tm-30) REVERT: B 407 MET cc_start: 0.8175 (tmm) cc_final: 0.7911 (tmm) REVERT: B 614 MET cc_start: 0.8976 (mpp) cc_final: 0.8364 (mpp) REVERT: B 748 ILE cc_start: 0.8402 (mt) cc_final: 0.8186 (mt) outliers start: 20 outliers final: 16 residues processed: 139 average time/residue: 0.1625 time to fit residues: 34.7906 Evaluate side-chains 116 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 697 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 30.0000 chunk 33 optimal weight: 0.0010 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 106 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9874 Z= 0.193 Angle : 0.563 12.057 13432 Z= 0.276 Chirality : 0.037 0.147 1548 Planarity : 0.003 0.035 1668 Dihedral : 9.251 78.025 1818 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.61 % Allowed : 15.46 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.25), residues: 1178 helix: 1.96 (0.19), residues: 806 sheet: 0.27 (0.68), residues: 34 loop : -2.23 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 334 HIS 0.003 0.001 HIS B 352 PHE 0.014 0.001 PHE B 408 TYR 0.011 0.001 TYR B 465 ARG 0.002 0.000 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 115 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8422 (tm-30) REVERT: A 338 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8136 (tm-30) REVERT: A 614 MET cc_start: 0.8871 (mpp) cc_final: 0.8269 (mpp) REVERT: A 705 ILE cc_start: 0.6681 (OUTLIER) cc_final: 0.6416 (mp) REVERT: A 748 ILE cc_start: 0.8342 (mt) cc_final: 0.8123 (mt) REVERT: A 750 LEU cc_start: 0.8680 (tt) cc_final: 0.8409 (tt) REVERT: B 275 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8390 (tm-30) REVERT: B 338 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8200 (tm-30) REVERT: B 614 MET cc_start: 0.8914 (mpp) cc_final: 0.8346 (mpp) REVERT: B 705 ILE cc_start: 0.7170 (OUTLIER) cc_final: 0.6888 (mp) REVERT: B 748 ILE cc_start: 0.8337 (mt) cc_final: 0.8122 (mt) outliers start: 26 outliers final: 18 residues processed: 132 average time/residue: 0.1789 time to fit residues: 37.5934 Evaluate side-chains 117 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 107 optimal weight: 0.0030 chunk 114 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 overall best weight: 1.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 HIS ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 ASN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 HIS ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 ASN B 671 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9874 Z= 0.259 Angle : 0.615 10.908 13432 Z= 0.296 Chirality : 0.038 0.148 1548 Planarity : 0.003 0.032 1668 Dihedral : 8.754 73.162 1818 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.51 % Allowed : 16.87 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.25), residues: 1178 helix: 2.04 (0.19), residues: 808 sheet: 0.41 (0.69), residues: 34 loop : -2.15 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 334 HIS 0.004 0.001 HIS B 352 PHE 0.010 0.001 PHE A 533 TYR 0.010 0.001 TYR A 466 ARG 0.003 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 98 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8798 (tm-30) cc_final: 0.8395 (tm-30) REVERT: A 614 MET cc_start: 0.8897 (mpp) cc_final: 0.8295 (mpp) REVERT: A 637 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.8325 (t80) REVERT: A 671 GLN cc_start: 0.7055 (tp40) cc_final: 0.6834 (tp-100) REVERT: A 705 ILE cc_start: 0.6753 (OUTLIER) cc_final: 0.6449 (mp) REVERT: A 748 ILE cc_start: 0.8382 (mt) cc_final: 0.8151 (mt) REVERT: A 750 LEU cc_start: 0.8781 (tt) cc_final: 0.8440 (tt) REVERT: B 275 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8369 (tm-30) REVERT: B 315 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8597 (mp) REVERT: B 614 MET cc_start: 0.8899 (mpp) cc_final: 0.8299 (mpp) REVERT: B 637 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8418 (t80) REVERT: B 705 ILE cc_start: 0.7128 (OUTLIER) cc_final: 0.6860 (mp) REVERT: B 748 ILE cc_start: 0.8351 (mt) cc_final: 0.8140 (mt) REVERT: B 750 LEU cc_start: 0.8746 (tt) cc_final: 0.8402 (tt) outliers start: 35 outliers final: 24 residues processed: 125 average time/residue: 0.1468 time to fit residues: 29.4508 Evaluate side-chains 119 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 90 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 637 PHE Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 HIS ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 GLN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 HIS ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9874 Z= 0.351 Angle : 0.678 13.632 13432 Z= 0.325 Chirality : 0.040 0.161 1548 Planarity : 0.003 0.032 1668 Dihedral : 8.635 72.649 1818 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.62 % Allowed : 18.67 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.25), residues: 1178 helix: 2.00 (0.19), residues: 808 sheet: 0.35 (0.66), residues: 34 loop : -2.14 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 334 HIS 0.012 0.001 HIS B 354 PHE 0.014 0.001 PHE A 408 TYR 0.015 0.001 TYR A 465 ARG 0.002 0.000 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 90 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8370 (tm-30) REVERT: A 315 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8796 (tp) REVERT: A 614 MET cc_start: 0.8935 (mpp) cc_final: 0.8331 (mpp) REVERT: A 637 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8510 (t80) REVERT: A 705 ILE cc_start: 0.6801 (OUTLIER) cc_final: 0.6475 (mp) REVERT: A 748 ILE cc_start: 0.8396 (mt) cc_final: 0.8145 (mt) REVERT: A 750 LEU cc_start: 0.8756 (tt) cc_final: 0.8397 (tt) REVERT: B 275 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8390 (tm-30) REVERT: B 354 HIS cc_start: 0.8283 (OUTLIER) cc_final: 0.7899 (t70) REVERT: B 614 MET cc_start: 0.8935 (mpp) cc_final: 0.8341 (mpp) REVERT: B 637 PHE cc_start: 0.9008 (OUTLIER) cc_final: 0.8456 (t80) REVERT: B 705 ILE cc_start: 0.7062 (OUTLIER) cc_final: 0.6778 (mp) REVERT: B 748 ILE cc_start: 0.8367 (mt) cc_final: 0.8126 (mt) REVERT: B 750 LEU cc_start: 0.8781 (tt) cc_final: 0.8368 (tt) outliers start: 46 outliers final: 32 residues processed: 128 average time/residue: 0.1700 time to fit residues: 35.4195 Evaluate side-chains 124 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 86 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 354 HIS Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 354 HIS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 637 PHE Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 114 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 30.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 HIS ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 HIS ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9874 Z= 0.163 Angle : 0.590 11.598 13432 Z= 0.273 Chirality : 0.037 0.141 1548 Planarity : 0.003 0.027 1668 Dihedral : 8.219 77.068 1818 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.41 % Allowed : 21.08 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.26), residues: 1178 helix: 2.23 (0.19), residues: 812 sheet: 0.55 (0.70), residues: 34 loop : -2.16 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 334 HIS 0.015 0.001 HIS B 354 PHE 0.012 0.001 PHE B 408 TYR 0.020 0.001 TYR A 465 ARG 0.001 0.000 ARG A 776 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 105 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8383 (tm-30) REVERT: A 614 MET cc_start: 0.8874 (mpp) cc_final: 0.8285 (mpp) REVERT: A 637 PHE cc_start: 0.8962 (OUTLIER) cc_final: 0.8318 (t80) REVERT: A 671 GLN cc_start: 0.7141 (tp-100) cc_final: 0.6923 (tp-100) REVERT: A 705 ILE cc_start: 0.6845 (OUTLIER) cc_final: 0.6564 (mp) REVERT: A 748 ILE cc_start: 0.8308 (mt) cc_final: 0.8088 (mt) REVERT: A 750 LEU cc_start: 0.8735 (tt) cc_final: 0.8371 (tt) REVERT: B 275 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8339 (tm-30) REVERT: B 614 MET cc_start: 0.8876 (mpp) cc_final: 0.8276 (mpp) REVERT: B 637 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8292 (t80) REVERT: B 671 GLN cc_start: 0.6987 (tp-100) cc_final: 0.6605 (tp-100) REVERT: B 705 ILE cc_start: 0.7110 (OUTLIER) cc_final: 0.6866 (mp) REVERT: B 748 ILE cc_start: 0.8292 (mt) cc_final: 0.8089 (mt) REVERT: B 750 LEU cc_start: 0.8706 (tt) cc_final: 0.8329 (tt) outliers start: 34 outliers final: 22 residues processed: 129 average time/residue: 0.1743 time to fit residues: 36.5022 Evaluate side-chains 124 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 98 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 637 PHE Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 69 optimal weight: 0.4980 chunk 52 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9874 Z= 0.195 Angle : 0.601 12.185 13432 Z= 0.278 Chirality : 0.037 0.144 1548 Planarity : 0.003 0.026 1668 Dihedral : 8.155 81.941 1818 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.91 % Allowed : 22.89 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.25), residues: 1178 helix: 2.27 (0.19), residues: 812 sheet: 0.65 (0.72), residues: 34 loop : -2.11 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 334 HIS 0.005 0.001 HIS A 352 PHE 0.011 0.001 PHE A 408 TYR 0.022 0.001 TYR A 465 ARG 0.001 0.000 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 105 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8410 (tm-30) REVERT: A 614 MET cc_start: 0.8884 (mpp) cc_final: 0.8280 (mpp) REVERT: A 637 PHE cc_start: 0.8967 (OUTLIER) cc_final: 0.8323 (t80) REVERT: A 705 ILE cc_start: 0.6876 (OUTLIER) cc_final: 0.6586 (mp) REVERT: A 748 ILE cc_start: 0.8276 (mt) cc_final: 0.8068 (mt) REVERT: A 750 LEU cc_start: 0.8753 (tt) cc_final: 0.8385 (tt) REVERT: B 275 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8349 (tm-30) REVERT: B 465 TYR cc_start: 0.8967 (m-80) cc_final: 0.8690 (m-80) REVERT: B 614 MET cc_start: 0.8867 (mpp) cc_final: 0.8259 (mpp) REVERT: B 637 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8307 (t80) REVERT: B 705 ILE cc_start: 0.7125 (OUTLIER) cc_final: 0.6870 (mp) REVERT: B 748 ILE cc_start: 0.8276 (mt) cc_final: 0.8057 (mt) REVERT: B 750 LEU cc_start: 0.8677 (tt) cc_final: 0.8306 (tt) outliers start: 29 outliers final: 24 residues processed: 125 average time/residue: 0.1547 time to fit residues: 31.3316 Evaluate side-chains 128 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 100 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 637 PHE Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9874 Z= 0.164 Angle : 0.592 10.832 13432 Z= 0.271 Chirality : 0.037 0.140 1548 Planarity : 0.002 0.026 1668 Dihedral : 8.071 88.618 1818 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.01 % Allowed : 22.79 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.26), residues: 1178 helix: 2.37 (0.19), residues: 812 sheet: 0.77 (0.74), residues: 34 loop : -2.04 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 334 HIS 0.004 0.001 HIS A 352 PHE 0.007 0.001 PHE A 533 TYR 0.020 0.001 TYR A 465 ARG 0.001 0.000 ARG A 723 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 115 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8337 (tm-30) REVERT: A 637 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.8256 (t80) REVERT: A 705 ILE cc_start: 0.6910 (OUTLIER) cc_final: 0.6633 (mp) REVERT: A 750 LEU cc_start: 0.8761 (tt) cc_final: 0.8391 (tt) REVERT: B 275 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8335 (tm-30) REVERT: B 465 TYR cc_start: 0.8909 (m-80) cc_final: 0.8634 (m-80) REVERT: B 637 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.8240 (t80) REVERT: B 686 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.8224 (t80) REVERT: B 705 ILE cc_start: 0.7061 (OUTLIER) cc_final: 0.6831 (mp) REVERT: B 750 LEU cc_start: 0.8690 (tt) cc_final: 0.8297 (tt) outliers start: 30 outliers final: 21 residues processed: 131 average time/residue: 0.1507 time to fit residues: 31.5040 Evaluate side-chains 137 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 111 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 637 PHE Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 686 TYR Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 4.9990 chunk 99 optimal weight: 0.0370 chunk 105 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 100 optimal weight: 0.0980 chunk 69 optimal weight: 0.9980 chunk 112 optimal weight: 8.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9874 Z= 0.149 Angle : 0.593 8.986 13432 Z= 0.271 Chirality : 0.037 0.160 1548 Planarity : 0.002 0.023 1668 Dihedral : 8.035 84.648 1818 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.01 % Allowed : 23.19 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.26), residues: 1178 helix: 2.52 (0.19), residues: 808 sheet: 0.91 (0.80), residues: 34 loop : -2.00 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 334 HIS 0.003 0.001 HIS B 352 PHE 0.013 0.001 PHE B 408 TYR 0.017 0.001 TYR A 465 ARG 0.001 0.000 ARG A 634 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 124 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8400 (tm-30) REVERT: A 637 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8152 (t80) REVERT: A 750 LEU cc_start: 0.8741 (tt) cc_final: 0.8362 (tt) REVERT: B 275 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8387 (tm-30) REVERT: B 465 TYR cc_start: 0.8849 (m-80) cc_final: 0.8576 (m-80) REVERT: B 637 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.8203 (t80) REVERT: B 686 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.8130 (t80) REVERT: B 705 ILE cc_start: 0.7069 (OUTLIER) cc_final: 0.6838 (mp) REVERT: B 750 LEU cc_start: 0.8660 (tt) cc_final: 0.8263 (tt) outliers start: 30 outliers final: 21 residues processed: 142 average time/residue: 0.1522 time to fit residues: 34.4244 Evaluate side-chains 140 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 115 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 637 PHE Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 686 TYR Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 99 optimal weight: 0.0770 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9874 Z= 0.168 Angle : 0.636 9.385 13432 Z= 0.290 Chirality : 0.037 0.189 1548 Planarity : 0.003 0.024 1668 Dihedral : 7.959 82.979 1818 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.11 % Allowed : 24.00 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.26), residues: 1178 helix: 2.48 (0.19), residues: 812 sheet: 0.91 (0.80), residues: 34 loop : -1.92 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 334 HIS 0.008 0.001 HIS A 706 PHE 0.011 0.001 PHE A 519 TYR 0.021 0.001 TYR A 465 ARG 0.002 0.000 ARG B 330 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 115 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8393 (tm-30) REVERT: A 637 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.8217 (t80) REVERT: A 686 TYR cc_start: 0.8611 (OUTLIER) cc_final: 0.8232 (t80) REVERT: A 750 LEU cc_start: 0.8749 (tt) cc_final: 0.8361 (tt) REVERT: B 275 GLU cc_start: 0.8756 (tm-30) cc_final: 0.8382 (tm-30) REVERT: B 637 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.8241 (t80) REVERT: B 686 TYR cc_start: 0.8502 (OUTLIER) cc_final: 0.8171 (t80) REVERT: B 705 ILE cc_start: 0.7075 (OUTLIER) cc_final: 0.6832 (mp) REVERT: B 750 LEU cc_start: 0.8726 (tt) cc_final: 0.8329 (tt) outliers start: 31 outliers final: 23 residues processed: 133 average time/residue: 0.1494 time to fit residues: 31.6710 Evaluate side-chains 140 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 112 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 455 ASP Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 637 PHE Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 686 TYR Chi-restraints excluded: chain A residue 697 GLU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 505 ILE Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 554 ILE Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 637 PHE Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 669 VAL Chi-restraints excluded: chain B residue 686 TYR Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 705 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.149276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.105122 restraints weight = 16264.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.108298 restraints weight = 7196.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.110471 restraints weight = 4296.841| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3711 r_free = 0.3711 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3707 r_free = 0.3707 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9874 Z= 0.196 Angle : 0.660 10.594 13432 Z= 0.303 Chirality : 0.038 0.242 1548 Planarity : 0.003 0.028 1668 Dihedral : 7.807 81.356 1818 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.11 % Allowed : 24.20 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.26), residues: 1178 helix: 2.55 (0.19), residues: 800 sheet: 0.86 (0.80), residues: 34 loop : -1.97 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 334 HIS 0.010 0.001 HIS A 706 PHE 0.022 0.001 PHE B 408 TYR 0.026 0.001 TYR A 465 ARG 0.002 0.000 ARG B 330 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1858.34 seconds wall clock time: 35 minutes 3.32 seconds (2103.32 seconds total)