Starting phenix.real_space_refine on Sun Sep 13 02:27:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ca3_30323/09_2026/7ca3_30323.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ca3_30323/09_2026/7ca3_30323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ca3_30323/09_2026/7ca3_30323.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ca3_30323/09_2026/7ca3_30323.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ca3_30323/09_2026/7ca3_30323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ca3_30323/09_2026/7ca3_30323.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ca3_30323/09_2026/7ca3_30323.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ca3_30323/09_2026/7ca3_30323.cif" } resolution = 4.5 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians S 58 5.16 5 C 6861 2.51 5 N 1744 2.21 5 O 1889 1.98 5 F 3 1.80 5 H 9307 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19862 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 9628 Classifications: {'peptide': 669} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 27, 'TRANS': 641} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ARG:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 5, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 4, 'HIS:plan': 1, 'TRP:plan': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 113 Chain: "B" Number of atoms: 10127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 10127 Classifications: {'peptide': 681} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 651} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2, 'HIS:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'CLR': 1, 'FN0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.43, per 1000 atoms: 0.17 Number of scatterers: 19862 At special positions: 0 Unit cell: (156.87, 149.4, 101.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 F 3 9.00 O 1889 8.00 N 1744 7.00 C 6861 6.00 H 9307 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 246 " distance=2.04 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 410 " distance=2.03 Simple disulfide: pdb=" SG CYS A 663 " - pdb=" SG CYS A 761 " distance=1.52 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=3.00 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 266 " distance=2.97 Simple disulfide: pdb=" SG CYS B 265 " - pdb=" SG CYS B 302 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 540.4 milliseconds 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2526 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 12 sheets defined 53.6% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 187 through 200 removed outlier: 3.790A pdb=" N VAL A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 235 removed outlier: 3.671A pdb=" N ASN A 235 " --> pdb=" O GLU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 258 removed outlier: 3.856A pdb=" N GLU A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 289 through 291 No H-bonds generated for 'chain 'A' and resid 289 through 291' Processing helix chain 'A' and resid 292 through 304 removed outlier: 3.930A pdb=" N THR A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 332 removed outlier: 3.972A pdb=" N SER A 321 " --> pdb=" O GLU A 317 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 356 removed outlier: 4.568A pdb=" N VAL A 351 " --> pdb=" O PRO A 347 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG A 356 " --> pdb=" O LYS A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 380 removed outlier: 4.741A pdb=" N LYS A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS A 380 " --> pdb=" O CYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 419 Processing helix chain 'A' and resid 442 through 453 Processing helix chain 'A' and resid 467 through 485 removed outlier: 4.028A pdb=" N TYR A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N TRP A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 516 Processing helix chain 'A' and resid 588 through 616 removed outlier: 3.780A pdb=" N PHE A 592 " --> pdb=" O SER A 588 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N SER A 594 " --> pdb=" O LYS A 590 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 643 removed outlier: 4.242A pdb=" N ASN A 630 " --> pdb=" O GLN A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 648 removed outlier: 4.119A pdb=" N LEU A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 664 Processing helix chain 'A' and resid 664 through 691 removed outlier: 3.548A pdb=" N TRP A 668 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY A 671 " --> pdb=" O LEU A 667 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 672 " --> pdb=" O TRP A 668 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LEU A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY A 677 " --> pdb=" O GLY A 673 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE A 682 " --> pdb=" O TYR A 678 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS A 684 " --> pdb=" O SER A 680 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TRP A 687 " --> pdb=" O THR A 683 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL A 688 " --> pdb=" O LYS A 684 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N HIS A 689 " --> pdb=" O ILE A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 730 removed outlier: 4.045A pdb=" N TRP A 728 " --> pdb=" O THR A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 791 removed outlier: 3.711A pdb=" N PHE A 773 " --> pdb=" O TRP A 769 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU A 780 " --> pdb=" O TYR A 776 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU A 781 " --> pdb=" O LYS A 777 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A 786 " --> pdb=" O LEU A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 826 removed outlier: 3.649A pdb=" N MET A 807 " --> pdb=" O ARG A 803 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 815 " --> pdb=" O ASN A 811 " (cutoff:3.500A) Proline residue: A 821 - end of helix Processing helix chain 'A' and resid 827 through 828 No H-bonds generated for 'chain 'A' and resid 827 through 828' Processing helix chain 'A' and resid 829 through 831 No H-bonds generated for 'chain 'A' and resid 829 through 831' Processing helix chain 'A' and resid 832 through 846 removed outlier: 3.931A pdb=" N PHE A 836 " --> pdb=" O ALA A 832 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER A 838 " --> pdb=" O PHE A 834 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU A 839 " --> pdb=" O ALA A 835 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE A 841 " --> pdb=" O ALA A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 860 removed outlier: 3.656A pdb=" N PHE A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 854 " --> pdb=" O VAL A 850 " (cutoff:3.500A) Proline residue: A 855 - end of helix Processing helix chain 'B' and resid 70 through 77 removed outlier: 3.722A pdb=" N VAL B 77 " --> pdb=" O ILE B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.688A pdb=" N VAL B 81 " --> pdb=" O VAL B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 123 removed outlier: 3.599A pdb=" N GLY B 113 " --> pdb=" O ASP B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 143 removed outlier: 3.790A pdb=" N THR B 139 " --> pdb=" O CYS B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 160 through 165 removed outlier: 3.769A pdb=" N LEU B 163 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP B 165 " --> pdb=" O VAL B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 181 Processing helix chain 'B' and resid 182 through 194 Processing helix chain 'B' and resid 205 through 219 removed outlier: 4.596A pdb=" N VAL B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLY B 217 " --> pdb=" O ASN B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 245 Processing helix chain 'B' and resid 256 through 258 No H-bonds generated for 'chain 'B' and resid 256 through 258' Processing helix chain 'B' and resid 259 through 269 removed outlier: 3.749A pdb=" N GLU B 269 " --> pdb=" O CYS B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 312 removed outlier: 3.785A pdb=" N LEU B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 346 Processing helix chain 'B' and resid 355 through 374 Processing helix chain 'B' and resid 377 through 385 removed outlier: 4.363A pdb=" N GLN B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 404 removed outlier: 3.512A pdb=" N GLY B 396 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 507 removed outlier: 4.517A pdb=" N ASN B 506 " --> pdb=" O PHE B 502 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG B 507 " --> pdb=" O ASN B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 515 Processing helix chain 'B' and resid 516 through 533 removed outlier: 4.130A pdb=" N ASN B 520 " --> pdb=" O SER B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 538 Processing helix chain 'B' and resid 548 through 583 removed outlier: 3.606A pdb=" N VAL B 555 " --> pdb=" O THR B 551 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU B 560 " --> pdb=" O ARG B 556 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N MET B 571 " --> pdb=" O ALA B 567 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N PHE B 572 " --> pdb=" O PHE B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 616 removed outlier: 3.879A pdb=" N LEU B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 679 removed outlier: 4.036A pdb=" N LEU B 674 " --> pdb=" O PHE B 670 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 675 " --> pdb=" O GLY B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 681 No H-bonds generated for 'chain 'B' and resid 680 through 681' Processing helix chain 'B' and resid 682 through 686 removed outlier: 4.081A pdb=" N ALA B 685 " --> pdb=" O SER B 682 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU B 686 " --> pdb=" O ILE B 683 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 682 through 686' Processing helix chain 'B' and resid 688 through 712 removed outlier: 3.719A pdb=" N MET B 694 " --> pdb=" O LYS B 690 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER B 695 " --> pdb=" O TYR B 691 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE B 711 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 716 through 741 removed outlier: 3.724A pdb=" N GLN B 720 " --> pdb=" O GLN B 716 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N CYS B 722 " --> pdb=" O ASN B 718 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL B 724 " --> pdb=" O GLN B 720 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA B 725 " --> pdb=" O PHE B 721 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE B 728 " --> pdb=" O VAL B 724 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LEU B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 746 Processing sheet with id=AA1, first strand: chain 'A' and resid 216 through 217 removed outlier: 3.567A pdb=" N PHE A 176 " --> pdb=" O HIS A 216 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY A 173 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET A 243 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LEU A 242 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL A 264 " --> pdb=" O PHE A 284 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 363 removed outlier: 6.635A pdb=" N ILE A 362 " --> pdb=" O PHE A 391 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 423 through 427 Processing sheet with id=AA4, first strand: chain 'A' and resid 551 through 554 Processing sheet with id=AA5, first strand: chain 'A' and resid 738 through 740 Processing sheet with id=AA6, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA7, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.639A pdb=" N MET B 62 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N MET B 59 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL B 130 " --> pdb=" O VAL B 152 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 250 through 252 removed outlier: 7.208A pdb=" N ILE B 426 " --> pdb=" O GLU B 441 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLU B 441 " --> pdb=" O ILE B 426 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N PHE B 428 " --> pdb=" O VAL B 439 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 408 through 410 removed outlier: 3.759A pdb=" N PHE B 408 " --> pdb=" O VAL B 415 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 417 through 418 Processing sheet with id=AB2, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AB3, first strand: chain 'B' and resid 626 through 627 474 hydrogen bonds defined for protein. 1374 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: 3.87 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 9294 1.02 - 1.23: 40 1.23 - 1.43: 4586 1.43 - 1.63: 6101 1.63 - 1.83: 92 Bond restraints: 20113 Sorted by residual: bond pdb=" C THR B 654 " pdb=" N ILE B 655 " ideal model delta sigma weight residual 1.331 1.478 -0.147 1.01e-02 9.80e+03 2.13e+02 bond pdb=" N LEU A 852 " pdb=" H LEU A 852 " ideal model delta sigma weight residual 0.860 1.072 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C SER B 137 " pdb=" N VAL B 138 " ideal model delta sigma weight residual 1.334 1.462 -0.128 1.26e-02 6.30e+03 1.03e+02 bond pdb=" ND2 ASN B 443 " pdb="HD22 ASN B 443 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" ND2 ASN B 443 " pdb="HD21 ASN B 443 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.59e+01 ... (remaining 20108 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.15: 35735 11.15 - 22.31: 13 22.31 - 33.46: 25 33.46 - 44.61: 19 44.61 - 55.77: 4 Bond angle restraints: 35796 Sorted by residual: angle pdb=" C VAL B 719 " pdb=" N GLN B 720 " pdb=" H GLN B 720 " ideal model delta sigma weight residual 124.96 69.19 55.77 3.00e+00 1.11e-01 3.46e+02 angle pdb=" CA GLN B 720 " pdb=" N GLN B 720 " pdb=" H GLN B 720 " ideal model delta sigma weight residual 114.66 60.14 54.52 3.00e+00 1.11e-01 3.30e+02 angle pdb=" CA GLN B 386 " pdb=" N GLN B 386 " pdb=" H GLN B 386 " ideal model delta sigma weight residual 114.63 62.89 51.74 3.00e+00 1.11e-01 2.97e+02 angle pdb=" C ILE B 385 " pdb=" N GLN B 386 " pdb=" H GLN B 386 " ideal model delta sigma weight residual 124.93 74.46 50.47 3.00e+00 1.11e-01 2.83e+02 angle pdb=" N ASP B 608 " pdb=" CA ASP B 608 " pdb=" HA ASP B 608 " ideal model delta sigma weight residual 110.00 68.17 41.83 3.00e+00 1.11e-01 1.94e+02 ... (remaining 35791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 8078 17.82 - 35.64: 1165 35.64 - 53.45: 315 53.45 - 71.27: 73 71.27 - 89.09: 15 Dihedral angle restraints: 9646 sinusoidal: 5003 harmonic: 4643 Sorted by residual: dihedral pdb=" CB CYS B 237 " pdb=" SG CYS B 237 " pdb=" SG CYS B 266 " pdb=" CB CYS B 266 " ideal model delta sinusoidal sigma weight residual -86.00 -4.77 -81.23 1 1.00e+01 1.00e-02 8.14e+01 dihedral pdb=" C TYR A 234 " pdb=" N TYR A 234 " pdb=" CA TYR A 234 " pdb=" CB TYR A 234 " ideal model delta harmonic sigma weight residual -122.60 -143.85 21.25 0 2.50e+00 1.60e-01 7.22e+01 dihedral pdb=" C VAL A 851 " pdb=" N VAL A 851 " pdb=" CA VAL A 851 " pdb=" CB VAL A 851 " ideal model delta harmonic sigma weight residual -122.00 -140.89 18.89 0 2.50e+00 1.60e-01 5.71e+01 ... (remaining 9643 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.373: 1675 0.373 - 0.746: 3 0.746 - 1.119: 1 1.119 - 1.492: 0 1.492 - 1.865: 3 Chirality restraints: 1682 Sorted by residual: chirality pdb=" CB ILE B 398 " pdb=" CA ILE B 398 " pdb=" CG1 ILE B 398 " pdb=" CG2 ILE B 398 " both_signs ideal model delta sigma weight residual False 2.64 0.78 1.86 2.00e-01 2.50e+01 8.69e+01 chirality pdb=" CG LEU B 609 " pdb=" CB LEU B 609 " pdb=" CD1 LEU B 609 " pdb=" CD2 LEU B 609 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.31e+01 chirality pdb=" CG LEU B 597 " pdb=" CB LEU B 597 " pdb=" CD1 LEU B 597 " pdb=" CD2 LEU B 597 " both_signs ideal model delta sigma weight residual False -2.59 -1.00 -1.59 2.00e-01 2.50e+01 6.29e+01 ... (remaining 1679 not shown) Planarity restraints: 2949 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 851 " -0.123 2.00e-02 2.50e+03 2.07e-01 4.28e+02 pdb=" N LEU A 852 " 0.358 2.00e-02 2.50e+03 pdb=" CA LEU A 852 " -0.114 2.00e-02 2.50e+03 pdb=" H LEU A 852 " -0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 654 " 0.054 2.00e-02 2.50e+03 1.28e-01 1.64e+02 pdb=" N ILE B 655 " -0.218 2.00e-02 2.50e+03 pdb=" CA ILE B 655 " 0.052 2.00e-02 2.50e+03 pdb=" H ILE B 655 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 852 " -0.043 2.00e-02 2.50e+03 8.10e-02 6.56e+01 pdb=" N PHE A 853 " 0.139 2.00e-02 2.50e+03 pdb=" CA PHE A 853 " -0.036 2.00e-02 2.50e+03 pdb=" H PHE A 853 " -0.061 2.00e-02 2.50e+03 ... (remaining 2946 not shown) Histogram of nonbonded interaction distances: 1.09 - 1.79: 101 1.79 - 2.49: 15853 2.49 - 3.20: 58592 3.20 - 3.90: 70067 3.90 - 4.60: 108884 Nonbonded interactions: 253497 Sorted by model distance: nonbonded pdb=" H THR B 238 " pdb=" H SER B 239 " model vdw 1.089 2.100 nonbonded pdb=" O PRO A 237 " pdb=" HZ1 LYS A 239 " model vdw 1.281 2.450 nonbonded pdb=" O PRO A 237 " pdb=" HZ3 LYS A 239 " model vdw 1.347 2.450 nonbonded pdb=" O PRO A 237 " pdb=" NZ LYS A 239 " model vdw 1.348 2.950 nonbonded pdb=" HD2 TYR A 171 " pdb=" HG2 PRO A 237 " model vdw 1.399 2.270 ... (remaining 253492 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 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: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.160 Extract box with map and model: 0.420 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.190 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 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 : 0.022 0.965 10812 Z= 1.030 Angle : 1.441 57.072 14716 Z= 0.809 Chirality : 0.110 1.865 1682 Planarity : 0.008 0.067 1824 Dihedral : 15.834 89.087 3852 Min Nonbonded Distance : 1.348 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.60 % Allowed : 15.19 % Favored : 84.21 % Rotamer: Outliers : 1.01 % Allowed : 10.84 % Favored : 88.15 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 1.79 % 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: -4.98 (0.19), residues: 1336 helix: -2.84 (0.15), residues: 612 sheet: -3.63 (0.32), residues: 159 loop : -3.64 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 666 TYR 0.044 0.004 TYR B 314 PHE 0.045 0.004 PHE A 366 TRP 0.028 0.003 TRP B 558 HIS 0.012 0.003 HIS A 735 Details of bonding type rmsd/Z covalent geometry : bond 0.01709 / 0.76 (10806) covalent geometry : angle 1.28506 / 0.75 (14704) SS BOND : bond 0.58862 / 37.06 ( 6) SS BOND : angle 22.87915 / 21.02 ( 12) hydrogen bonds : bond 0.17517 / 11.75 ( 474) hydrogen bonds : angle 7.49341 / 5.18 ( 1374) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 588 is missing expected H atoms. Skipping. Residue TYR 652 is missing expected H atoms. Skipping. Residue ILE 654 is missing expected H atoms. Skipping. Residue MET 766 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue VAL 618 is missing expected H atoms. Skipping. Residue ALA 675 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 197 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 GLU cc_start: 0.8639 (pt0) cc_final: 0.8345 (tm-30) REVERT: A 441 MET cc_start: 0.8393 (mmm) cc_final: 0.7573 (mmm) REVERT: A 446 PHE cc_start: 0.9441 (t80) cc_final: 0.9218 (t80) REVERT: A 465 GLN cc_start: 0.8886 (mm110) cc_final: 0.8675 (tp-100) REVERT: A 834 PHE cc_start: 0.7166 (t80) cc_final: 0.6927 (t80) REVERT: B 82 GLU cc_start: 0.9491 (mp0) cc_final: 0.9245 (mp0) REVERT: B 144 GLU cc_start: 0.8547 (pt0) cc_final: 0.8291 (pt0) REVERT: B 485 LEU cc_start: 0.6128 (OUTLIER) cc_final: 0.5871 (pp) REVERT: B 524 ILE cc_start: 0.6587 (pt) cc_final: 0.6184 (pt) outliers start: 11 outliers final: 6 residues processed: 204 average time/residue: 0.1804 time to fit residues: 53.7030 Evaluate side-chains 154 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 147 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 30.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 189 GLN ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 GLN ** A 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 HIS A 664 GLN B 87 GLN B 110 ASN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN B 337 GLN B 383 GLN B 459 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.100768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.081342 restraints weight = 95117.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.084307 restraints weight = 48724.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.086248 restraints weight = 30325.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.087623 restraints weight = 21559.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.088435 restraints weight = 16715.192| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10812 Z= 0.179 Angle : 0.786 14.686 14716 Z= 0.418 Chirality : 0.087 1.705 1682 Planarity : 0.006 0.055 1824 Dihedral : 7.630 51.517 1515 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.40 % Favored : 89.52 % Rotamer: Outliers : 0.18 % Allowed : 4.04 % Favored : 95.78 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -4.06 (0.20), residues: 1336 helix: -1.97 (0.17), residues: 649 sheet: -2.66 (0.37), residues: 155 loop : -3.54 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 511 TYR 0.015 0.002 TYR B 531 PHE 0.019 0.002 PHE A 391 TRP 0.021 0.001 TRP B 558 HIS 0.005 0.001 HIS A 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.18 (10806) covalent geometry : angle 0.78368 / 0.42 (14704) SS BOND : bond 0.02223 / 1.31 ( 6) SS BOND : angle 2.09933 / 1.25 ( 12) hydrogen bonds : bond 0.05923 / 4.08 ( 474) hydrogen bonds : angle 6.08341 / 4.17 ( 1374) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 588 is missing expected H atoms. Skipping. Residue TYR 652 is missing expected H atoms. Skipping. Residue ILE 654 is missing expected H atoms. Skipping. Residue MET 766 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue VAL 618 is missing expected H atoms. Skipping. Residue ALA 675 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 192 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 GLU cc_start: 0.8036 (pt0) cc_final: 0.7751 (tm-30) REVERT: A 609 CYS cc_start: 0.8662 (m) cc_final: 0.7991 (p) REVERT: A 610 LEU cc_start: 0.9479 (tp) cc_final: 0.9202 (tp) REVERT: A 637 CYS cc_start: 0.9142 (t) cc_final: 0.8879 (t) REVERT: A 834 PHE cc_start: 0.8235 (t80) cc_final: 0.7939 (t80) REVERT: B 213 ASN cc_start: 0.9068 (m-40) cc_final: 0.8597 (m-40) REVERT: B 514 MET cc_start: 0.7651 (mtp) cc_final: 0.7353 (mtp) REVERT: B 609 LEU cc_start: 0.8855 (pp) cc_final: 0.8623 (pp) outliers start: 2 outliers final: 1 residues processed: 194 average time/residue: 0.1812 time to fit residues: 53.4777 Evaluate side-chains 145 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 7 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 11 optimal weight: 0.0170 chunk 23 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 357 GLN B 87 GLN ** B 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.099911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.080433 restraints weight = 96109.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.083299 restraints weight = 50392.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.085205 restraints weight = 31781.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.086439 restraints weight = 22805.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.087319 restraints weight = 17987.619| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10812 Z= 0.163 Angle : 0.710 15.039 14716 Z= 0.379 Chirality : 0.086 1.699 1682 Planarity : 0.005 0.053 1824 Dihedral : 6.922 54.317 1515 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.45 % Favored : 88.47 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.49 (0.21), residues: 1336 helix: -1.43 (0.19), residues: 646 sheet: -2.39 (0.37), residues: 172 loop : -3.36 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 285 TYR 0.014 0.001 TYR B 277 PHE 0.015 0.001 PHE B 319 TRP 0.019 0.001 TRP B 558 HIS 0.004 0.001 HIS A 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (10806) covalent geometry : angle 0.70723 / 0.38 (14704) SS BOND : bond 0.00412 / 0.29 ( 6) SS BOND : angle 2.10971 / 1.05 ( 12) hydrogen bonds : bond 0.05208 / 3.60 ( 474) hydrogen bonds : angle 5.66178 / 3.88 ( 1374) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 588 is missing expected H atoms. Skipping. Residue TYR 652 is missing expected H atoms. Skipping. Residue ILE 654 is missing expected H atoms. Skipping. Residue MET 766 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue VAL 618 is missing expected H atoms. Skipping. Residue ALA 675 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 GLU cc_start: 0.8073 (pt0) cc_final: 0.7751 (tm-30) REVERT: A 609 CYS cc_start: 0.8832 (m) cc_final: 0.8326 (p) REVERT: A 610 LEU cc_start: 0.9501 (tp) cc_final: 0.9186 (tp) REVERT: A 637 CYS cc_start: 0.9134 (t) cc_final: 0.8401 (p) REVERT: A 839 LEU cc_start: 0.9467 (mp) cc_final: 0.9161 (tt) REVERT: B 213 ASN cc_start: 0.9035 (m-40) cc_final: 0.8575 (m-40) REVERT: B 514 MET cc_start: 0.7706 (mtp) cc_final: 0.7336 (mtp) REVERT: B 609 LEU cc_start: 0.8856 (pp) cc_final: 0.8643 (pp) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1759 time to fit residues: 48.3284 Evaluate side-chains 146 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 48 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 116 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 99 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN B 257 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.106018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.086171 restraints weight = 95308.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.089163 restraints weight = 49146.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.091170 restraints weight = 30579.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.092543 restraints weight = 21664.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.093504 restraints weight = 16824.821| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 10812 Z= 0.121 Angle : 0.661 14.938 14716 Z= 0.350 Chirality : 0.085 1.666 1682 Planarity : 0.004 0.051 1824 Dihedral : 6.467 54.976 1515 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.13 % Favored : 90.79 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.22), residues: 1336 helix: -1.03 (0.19), residues: 636 sheet: -2.17 (0.38), residues: 177 loop : -3.04 (0.27), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 285 TYR 0.015 0.001 TYR B 663 PHE 0.017 0.001 PHE A 446 TRP 0.023 0.001 TRP B 676 HIS 0.003 0.001 HIS B 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (10806) covalent geometry : angle 0.65931 / 0.35 (14704) SS BOND : bond 0.00365 / 0.22 ( 6) SS BOND : angle 1.89700 / 0.90 ( 12) hydrogen bonds : bond 0.04519 / 3.13 ( 474) hydrogen bonds : angle 5.32668 / 3.65 ( 1374) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 588 is missing expected H atoms. Skipping. Residue TYR 652 is missing expected H atoms. Skipping. Residue ILE 654 is missing expected H atoms. Skipping. Residue MET 766 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue VAL 618 is missing expected H atoms. Skipping. Residue ALA 675 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 MET cc_start: 0.8601 (ttt) cc_final: 0.8250 (tmm) REVERT: A 265 LEU cc_start: 0.9179 (tp) cc_final: 0.8824 (tp) REVERT: A 417 GLU cc_start: 0.8114 (pt0) cc_final: 0.7796 (tm-30) REVERT: A 609 CYS cc_start: 0.8949 (m) cc_final: 0.8300 (p) REVERT: A 610 LEU cc_start: 0.9541 (tp) cc_final: 0.9195 (tp) REVERT: A 637 CYS cc_start: 0.9030 (t) cc_final: 0.8784 (t) REVERT: A 824 MET cc_start: 0.8932 (tmm) cc_final: 0.8723 (tmm) REVERT: A 839 LEU cc_start: 0.9463 (mp) cc_final: 0.9195 (tt) REVERT: B 213 ASN cc_start: 0.8996 (m-40) cc_final: 0.8468 (m-40) REVERT: B 235 ASP cc_start: 0.8832 (t70) cc_final: 0.8610 (t0) REVERT: B 514 MET cc_start: 0.7614 (mtp) cc_final: 0.7248 (mtp) REVERT: B 524 ILE cc_start: 0.9696 (pt) cc_final: 0.9476 (pt) REVERT: B 609 LEU cc_start: 0.8858 (pp) cc_final: 0.8645 (pp) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1846 time to fit residues: 50.4792 Evaluate side-chains 137 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 21 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 543 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 = 0.3552 r_free = 0.3552 target = 0.099199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.079481 restraints weight = 95279.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.082362 restraints weight = 49514.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.084284 restraints weight = 31292.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.085599 restraints weight = 22404.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.086516 restraints weight = 17595.298| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10812 Z= 0.153 Angle : 0.655 15.161 14716 Z= 0.347 Chirality : 0.085 1.692 1682 Planarity : 0.004 0.049 1824 Dihedral : 6.255 55.283 1515 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.33 % Favored : 89.60 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.23), residues: 1336 helix: -0.75 (0.20), residues: 640 sheet: -2.15 (0.37), residues: 196 loop : -2.94 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 422 TYR 0.017 0.001 TYR B 691 PHE 0.011 0.001 PHE B 319 TRP 0.026 0.001 TRP B 676 HIS 0.008 0.001 HIS B 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (10806) covalent geometry : angle 0.65326 / 0.35 (14704) SS BOND : bond 0.00241 / 0.13 ( 6) SS BOND : angle 1.58403 / 0.77 ( 12) hydrogen bonds : bond 0.04410 / 3.06 ( 474) hydrogen bonds : angle 5.21438 / 3.59 ( 1374) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 588 is missing expected H atoms. Skipping. Residue TYR 652 is missing expected H atoms. Skipping. Residue ILE 654 is missing expected H atoms. Skipping. Residue MET 766 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue VAL 618 is missing expected H atoms. Skipping. Residue ALA 675 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LEU cc_start: 0.9201 (tp) cc_final: 0.8877 (tp) REVERT: A 417 GLU cc_start: 0.8115 (pt0) cc_final: 0.7727 (tm-30) REVERT: A 609 CYS cc_start: 0.8967 (m) cc_final: 0.8269 (p) REVERT: A 610 LEU cc_start: 0.9537 (tp) cc_final: 0.9198 (tp) REVERT: A 637 CYS cc_start: 0.8950 (t) cc_final: 0.8719 (t) REVERT: A 839 LEU cc_start: 0.9478 (mp) cc_final: 0.9245 (tt) REVERT: B 75 ARG cc_start: 0.7656 (mtt180) cc_final: 0.7377 (mtp85) REVERT: B 213 ASN cc_start: 0.9023 (m-40) cc_final: 0.8635 (m-40) REVERT: B 235 ASP cc_start: 0.8865 (t70) cc_final: 0.8630 (t0) REVERT: B 514 MET cc_start: 0.7692 (mtp) cc_final: 0.7163 (mtp) REVERT: B 524 ILE cc_start: 0.9692 (pt) cc_final: 0.9472 (pt) REVERT: B 609 LEU cc_start: 0.8852 (pp) cc_final: 0.8640 (pp) REVERT: B 694 MET cc_start: 0.9195 (ttt) cc_final: 0.8043 (ttm) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1825 time to fit residues: 48.5680 Evaluate side-chains 137 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 42 optimal weight: 0.0870 chunk 104 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 89 optimal weight: 0.5980 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 GLN A 811 ASN B 579 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.100177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.079814 restraints weight = 95177.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.082857 restraints weight = 48782.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.084901 restraints weight = 30582.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.086304 restraints weight = 21835.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.087302 restraints weight = 17008.675| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10812 Z= 0.120 Angle : 0.634 15.007 14716 Z= 0.335 Chirality : 0.085 1.671 1682 Planarity : 0.004 0.087 1824 Dihedral : 6.086 54.787 1515 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.28 % Favored : 90.64 % Rotamer: Outliers : 0.09 % Allowed : 1.29 % Favored : 98.62 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.23), residues: 1336 helix: -0.54 (0.20), residues: 634 sheet: -1.81 (0.38), residues: 186 loop : -2.84 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 422 TYR 0.027 0.001 TYR B 697 PHE 0.019 0.001 PHE A 284 TRP 0.024 0.001 TRP B 676 HIS 0.008 0.001 HIS B 579 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (10806) covalent geometry : angle 0.63138 / 0.33 (14704) SS BOND : bond 0.00284 / 0.19 ( 6) SS BOND : angle 2.26625 / 1.04 ( 12) hydrogen bonds : bond 0.04229 / 2.91 ( 474) hydrogen bonds : angle 5.05226 / 3.48 ( 1374) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 588 is missing expected H atoms. Skipping. Residue TYR 652 is missing expected H atoms. Skipping. Residue ILE 654 is missing expected H atoms. Skipping. Residue MET 766 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue VAL 618 is missing expected H atoms. Skipping. Residue ALA 675 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LEU cc_start: 0.9169 (tp) cc_final: 0.8856 (tp) REVERT: A 417 GLU cc_start: 0.8095 (pt0) cc_final: 0.7721 (tm-30) REVERT: A 609 CYS cc_start: 0.8952 (m) cc_final: 0.8221 (p) REVERT: A 610 LEU cc_start: 0.9547 (tp) cc_final: 0.9193 (tp) REVERT: A 637 CYS cc_start: 0.8932 (t) cc_final: 0.8670 (t) REVERT: A 834 PHE cc_start: 0.8282 (t80) cc_final: 0.8076 (t80) REVERT: A 839 LEU cc_start: 0.9468 (mp) cc_final: 0.9220 (tt) REVERT: B 75 ARG cc_start: 0.7672 (mtt180) cc_final: 0.7422 (mtp85) REVERT: B 213 ASN cc_start: 0.9008 (m-40) cc_final: 0.8613 (m-40) REVERT: B 235 ASP cc_start: 0.8905 (t70) cc_final: 0.8672 (t0) REVERT: B 514 MET cc_start: 0.7526 (mtp) cc_final: 0.7246 (mtp) REVERT: B 524 ILE cc_start: 0.9679 (pt) cc_final: 0.9466 (pt) REVERT: B 568 PHE cc_start: 0.7707 (t80) cc_final: 0.7310 (t80) REVERT: B 571 MET cc_start: 0.9234 (pmm) cc_final: 0.8807 (pmm) REVERT: B 694 MET cc_start: 0.9253 (ttt) cc_final: 0.8603 (ttm) outliers start: 1 outliers final: 1 residues processed: 179 average time/residue: 0.1583 time to fit residues: 43.3541 Evaluate side-chains 144 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 127 optimal weight: 0.0870 chunk 68 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 118 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.3160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 200 ASN ** 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 = 0.3580 r_free = 0.3580 target = 0.104484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.084537 restraints weight = 96185.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.087471 restraints weight = 49742.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.089460 restraints weight = 31132.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.090813 restraints weight = 22209.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.091818 restraints weight = 17314.178| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10812 Z= 0.118 Angle : 0.627 15.048 14716 Z= 0.332 Chirality : 0.084 1.699 1682 Planarity : 0.004 0.046 1824 Dihedral : 5.899 55.918 1515 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.21 % Favored : 90.72 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.23), residues: 1336 helix: -0.31 (0.21), residues: 632 sheet: -1.80 (0.38), residues: 186 loop : -2.71 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 422 TYR 0.020 0.001 TYR B 697 PHE 0.015 0.001 PHE A 283 TRP 0.035 0.001 TRP B 279 HIS 0.003 0.001 HIS B 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (10806) covalent geometry : angle 0.62414 / 0.33 (14704) SS BOND : bond 0.00249 / 0.18 ( 6) SS BOND : angle 2.13092 / 1.04 ( 12) hydrogen bonds : bond 0.04116 / 2.85 ( 474) hydrogen bonds : angle 4.92671 / 3.38 ( 1374) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 588 is missing expected H atoms. Skipping. Residue TYR 652 is missing expected H atoms. Skipping. Residue ILE 654 is missing expected H atoms. Skipping. Residue MET 766 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue VAL 618 is missing expected H atoms. Skipping. Residue ALA 675 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LEU cc_start: 0.9156 (tp) cc_final: 0.8809 (tp) REVERT: A 417 GLU cc_start: 0.8053 (pt0) cc_final: 0.7677 (tm-30) REVERT: A 609 CYS cc_start: 0.8979 (m) cc_final: 0.8343 (p) REVERT: A 610 LEU cc_start: 0.9546 (tp) cc_final: 0.9179 (tp) REVERT: A 637 CYS cc_start: 0.8942 (t) cc_final: 0.8632 (t) REVERT: A 839 LEU cc_start: 0.9474 (mp) cc_final: 0.9233 (tt) REVERT: B 75 ARG cc_start: 0.7591 (mtt180) cc_final: 0.7369 (mtp85) REVERT: B 108 CYS cc_start: 0.6097 (t) cc_final: 0.5717 (t) REVERT: B 213 ASN cc_start: 0.8973 (m-40) cc_final: 0.8651 (m-40) REVERT: B 235 ASP cc_start: 0.8909 (t70) cc_final: 0.8669 (t0) REVERT: B 514 MET cc_start: 0.7442 (mtp) cc_final: 0.7204 (mtp) REVERT: B 524 ILE cc_start: 0.9685 (pt) cc_final: 0.9464 (pt) REVERT: B 694 MET cc_start: 0.9304 (ttt) cc_final: 0.8636 (ttm) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1725 time to fit residues: 46.5583 Evaluate side-chains 145 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 77 optimal weight: 0.0970 chunk 116 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 200 ASN ** 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 = 0.3578 r_free = 0.3578 target = 0.104292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.084363 restraints weight = 95580.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.087330 restraints weight = 49044.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.089322 restraints weight = 30551.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.090685 restraints weight = 21801.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.091615 restraints weight = 16969.368| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10812 Z= 0.113 Angle : 0.619 15.031 14716 Z= 0.325 Chirality : 0.083 1.673 1682 Planarity : 0.004 0.063 1824 Dihedral : 5.780 56.917 1515 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.06 % Favored : 90.87 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.23), residues: 1336 helix: -0.12 (0.21), residues: 633 sheet: -1.74 (0.38), residues: 186 loop : -2.67 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 422 TYR 0.015 0.001 TYR B 697 PHE 0.015 0.001 PHE A 834 TRP 0.020 0.001 TRP B 279 HIS 0.002 0.001 HIS B 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (10806) covalent geometry : angle 0.61702 / 0.32 (14704) SS BOND : bond 0.00367 / 0.23 ( 6) SS BOND : angle 1.82827 / 0.95 ( 12) hydrogen bonds : bond 0.04001 / 2.77 ( 474) hydrogen bonds : angle 4.83328 / 3.32 ( 1374) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 588 is missing expected H atoms. Skipping. Residue TYR 652 is missing expected H atoms. Skipping. Residue ILE 654 is missing expected H atoms. Skipping. Residue MET 766 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue VAL 618 is missing expected H atoms. Skipping. Residue ALA 675 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LEU cc_start: 0.9211 (tp) cc_final: 0.8876 (tp) REVERT: A 417 GLU cc_start: 0.8089 (pt0) cc_final: 0.7712 (tm-30) REVERT: A 609 CYS cc_start: 0.8921 (m) cc_final: 0.8318 (p) REVERT: A 610 LEU cc_start: 0.9558 (tp) cc_final: 0.9175 (tp) REVERT: A 637 CYS cc_start: 0.8903 (t) cc_final: 0.8622 (t) REVERT: A 839 LEU cc_start: 0.9479 (mp) cc_final: 0.9221 (tt) REVERT: B 213 ASN cc_start: 0.8993 (m-40) cc_final: 0.8705 (m-40) REVERT: B 235 ASP cc_start: 0.8940 (t70) cc_final: 0.8687 (t0) REVERT: B 514 MET cc_start: 0.7457 (mtp) cc_final: 0.7214 (mtp) REVERT: B 524 ILE cc_start: 0.9685 (pt) cc_final: 0.9450 (pt) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1709 time to fit residues: 45.1960 Evaluate side-chains 139 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 36 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 67 optimal weight: 0.0170 chunk 133 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 200 ASN ** 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 = 0.3569 r_free = 0.3569 target = 0.101740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.081969 restraints weight = 93905.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.084910 restraints weight = 47952.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.086851 restraints weight = 29952.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.088231 restraints weight = 21354.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.089149 restraints weight = 16604.860| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10812 Z= 0.107 Angle : 0.612 15.001 14716 Z= 0.321 Chirality : 0.083 1.670 1682 Planarity : 0.004 0.045 1824 Dihedral : 5.626 57.878 1515 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.68 % Favored : 91.24 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.24), residues: 1336 helix: 0.13 (0.21), residues: 631 sheet: -1.66 (0.39), residues: 186 loop : -2.61 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 75 TYR 0.013 0.001 TYR A 234 PHE 0.015 0.001 PHE A 834 TRP 0.017 0.001 TRP B 279 HIS 0.002 0.001 HIS A 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (10806) covalent geometry : angle 0.61007 / 0.32 (14704) SS BOND : bond 0.00327 / 0.22 ( 6) SS BOND : angle 1.62040 / 0.83 ( 12) hydrogen bonds : bond 0.03817 / 2.63 ( 474) hydrogen bonds : angle 4.71961 / 3.24 ( 1374) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 588 is missing expected H atoms. Skipping. Residue TYR 652 is missing expected H atoms. Skipping. Residue ILE 654 is missing expected H atoms. Skipping. Residue MET 766 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue VAL 618 is missing expected H atoms. Skipping. Residue ALA 675 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LEU cc_start: 0.9181 (tp) cc_final: 0.8788 (tp) REVERT: A 417 GLU cc_start: 0.8054 (pt0) cc_final: 0.7694 (tm-30) REVERT: A 441 MET cc_start: 0.8605 (tpt) cc_final: 0.8388 (tpt) REVERT: A 609 CYS cc_start: 0.8832 (m) cc_final: 0.8320 (p) REVERT: A 610 LEU cc_start: 0.9573 (tp) cc_final: 0.9192 (tp) REVERT: A 637 CYS cc_start: 0.8824 (t) cc_final: 0.8529 (t) REVERT: A 839 LEU cc_start: 0.9479 (mp) cc_final: 0.9216 (tt) REVERT: B 213 ASN cc_start: 0.8963 (m-40) cc_final: 0.8696 (m-40) REVERT: B 235 ASP cc_start: 0.8939 (t70) cc_final: 0.8670 (t0) REVERT: B 514 MET cc_start: 0.7413 (mtp) cc_final: 0.7200 (mtp) REVERT: B 524 ILE cc_start: 0.9687 (pt) cc_final: 0.9455 (pt) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1673 time to fit residues: 45.1575 Evaluate side-chains 141 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 44 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 200 ASN ** 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 = 0.3539 r_free = 0.3539 target = 0.100592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.080787 restraints weight = 95319.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.083664 restraints weight = 48701.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.085641 restraints weight = 30569.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.086972 restraints weight = 21767.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.087922 restraints weight = 17046.687| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10812 Z= 0.161 Angle : 0.635 15.250 14716 Z= 0.337 Chirality : 0.083 1.672 1682 Planarity : 0.004 0.044 1824 Dihedral : 5.683 58.739 1515 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.66 % Favored : 90.27 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.23), residues: 1336 helix: 0.08 (0.21), residues: 648 sheet: -1.68 (0.38), residues: 186 loop : -2.79 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 422 TYR 0.034 0.002 TYR B 697 PHE 0.015 0.001 PHE A 834 TRP 0.013 0.001 TRP B 279 HIS 0.003 0.001 HIS A 735 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (10806) covalent geometry : angle 0.63363 / 0.34 (14704) SS BOND : bond 0.00312 / 0.22 ( 6) SS BOND : angle 1.68627 / 0.84 ( 12) hydrogen bonds : bond 0.03961 / 2.74 ( 474) hydrogen bonds : angle 4.84286 / 3.33 ( 1374) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2672 Ramachandran restraints generated. 1336 Oldfield, 0 Emsley, 1336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 588 is missing expected H atoms. Skipping. Residue TYR 652 is missing expected H atoms. Skipping. Residue ILE 654 is missing expected H atoms. Skipping. Residue MET 766 is missing expected H atoms. Skipping. Residue THR 468 is missing expected H atoms. Skipping. Residue ILE 469 is missing expected H atoms. Skipping. Residue SER 478 is missing expected H atoms. Skipping. Residue LEU 479 is missing expected H atoms. Skipping. Residue SER 516 is missing expected H atoms. Skipping. Residue LYS 583 is missing expected H atoms. Skipping. Residue VAL 618 is missing expected H atoms. Skipping. Residue ALA 675 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LEU cc_start: 0.9278 (tp) cc_final: 0.8966 (tp) REVERT: A 417 GLU cc_start: 0.8204 (pt0) cc_final: 0.7809 (tm-30) REVERT: A 609 CYS cc_start: 0.8885 (m) cc_final: 0.8325 (p) REVERT: A 610 LEU cc_start: 0.9591 (tp) cc_final: 0.9202 (tp) REVERT: A 637 CYS cc_start: 0.8957 (t) cc_final: 0.8651 (t) REVERT: A 839 LEU cc_start: 0.9492 (mp) cc_final: 0.9228 (tt) REVERT: B 235 ASP cc_start: 0.8997 (t70) cc_final: 0.8705 (t0) REVERT: B 514 MET cc_start: 0.7462 (mtp) cc_final: 0.7227 (mtp) REVERT: B 524 ILE cc_start: 0.9690 (pt) cc_final: 0.9469 (pt) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1755 time to fit residues: 44.4985 Evaluate side-chains 135 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 114 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 chunk 37 optimal weight: 8.9990 chunk 108 optimal weight: 0.4980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 200 ASN ** 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 = 0.3545 r_free = 0.3545 target = 0.100871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.080995 restraints weight = 94226.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.083886 restraints weight = 48265.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.085840 restraints weight = 30304.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.087218 restraints weight = 21654.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.088155 restraints weight = 16847.661| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10812 Z= 0.119 Angle : 0.616 15.080 14716 Z= 0.326 Chirality : 0.083 1.668 1682 Planarity : 0.004 0.045 1824 Dihedral : 5.606 57.307 1515 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.13 % Favored : 90.79 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.23), residues: 1336 helix: 0.20 (0.21), residues: 645 sheet: -1.63 (0.38), residues: 186 loop : -2.80 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 422 TYR 0.037 0.001 TYR B 697 PHE 0.011 0.001 PHE A 786 TRP 0.032 0.001 TRP B 656 HIS 0.002 0.001 HIS A 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (10806) covalent geometry : angle 0.61469 / 0.33 (14704) SS BOND : bond 0.00301 / 0.21 ( 6) SS BOND : angle 1.59758 / 0.80 ( 12) hydrogen bonds : bond 0.03852 / 2.64 ( 474) hydrogen bonds : angle 4.72046 / 3.25 ( 1374) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3041.96 seconds wall clock time: 52 minutes 46.43 seconds (3166.43 seconds total)