Starting phenix.real_space_refine on Thu Aug 6 10:35:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8olx_16964/08_2026/8olx_16964.cif Found real_map, /net/cci-nas-00/data/ceres_data/8olx_16964/08_2026/8olx_16964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8olx_16964/08_2026/8olx_16964.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8olx_16964/08_2026/8olx_16964.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8olx_16964/08_2026/8olx_16964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8olx_16964/08_2026/8olx_16964.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8olx_16964/08_2026/8olx_16964.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8olx_16964/08_2026/8olx_16964.cif" } resolution = 3.1 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= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 47 5.49 5 Mg 1 5.21 5 S 65 5.16 5 C 9068 2.51 5 N 2488 2.21 5 O 2823 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14492 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 863, 6832 Classifications: {'peptide': 863} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 836} Chain breaks: 6 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 6709 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 836, 6706 Classifications: {'peptide': 836} Link IDs: {'PTRANS': 25, 'TRANS': 810} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 836, 6706 Classifications: {'peptide': 836} Link IDs: {'PTRANS': 25, 'TRANS': 810} Chain breaks: 5 bond proxies already assigned to first conformer: 6825 Chain: "C" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 408 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain breaks: 1 Chain: "D" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 515 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.13, per 1000 atoms: 0.28 Number of scatterers: 14492 At special positions: 0 Unit cell: (93.2484, 118.846, 169.127, 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 65 16.00 P 47 15.00 Mg 1 11.99 O 2823 8.00 N 2488 7.00 C 9068 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 726.3 milliseconds 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3230 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 10 sheets defined 54.6% alpha, 12.3% beta 18 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 16 through 26 removed outlier: 3.741A pdb=" N VAL A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 57 Processing helix chain 'A' and resid 60 through 64 removed outlier: 3.998A pdb=" N VAL A 63 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 94 Processing helix chain 'A' and resid 184 through 195 removed outlier: 3.511A pdb=" N GLU A 188 " --> pdb=" O PHE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 219 Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 236 through 243 Processing helix chain 'A' and resid 254 through 262 removed outlier: 3.761A pdb=" N LEU A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) Proline residue: A 259 - end of helix Processing helix chain 'A' and resid 263 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.584A pdb=" N PHE A 286 " --> pdb=" O ASP A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 299 removed outlier: 3.775A pdb=" N TYR A 299 " --> pdb=" O PHE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 310 Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 335 through 348 Processing helix chain 'A' and resid 352 through 369 removed outlier: 3.623A pdb=" N ILE A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 removed outlier: 3.929A pdb=" N ARG A 373 " --> pdb=" O ASP A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 386 through 396 Processing helix chain 'A' and resid 400 through 422 Proline residue: A 415 - end of helix removed outlier: 3.542A pdb=" N GLU A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 445 removed outlier: 3.601A pdb=" N VAL A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 436 " --> pdb=" O LEU A 432 " (cutoff:3.500A) Proline residue: A 439 - end of helix Processing helix chain 'A' and resid 447 through 457 Processing helix chain 'A' and resid 459 through 463 Processing helix chain 'A' and resid 475 through 504 Processing helix chain 'A' and resid 529 through 534 removed outlier: 4.558A pdb=" N ARG A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 587 removed outlier: 3.651A pdb=" N THR A 568 " --> pdb=" O THR A 564 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 614 Processing helix chain 'A' and resid 641 through 645 removed outlier: 3.516A pdb=" N VAL A 644 " --> pdb=" O CYS A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 692 Processing helix chain 'A' and resid 724 through 739 Processing helix chain 'A' and resid 755 through 773 Processing helix chain 'A' and resid 784 through 793 removed outlier: 3.954A pdb=" N ALA A 789 " --> pdb=" O GLU A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 834 removed outlier: 3.606A pdb=" N ALA A 831 " --> pdb=" O GLY A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 852 Processing helix chain 'A' and resid 880 through 893 Processing helix chain 'A' and resid 900 through 919 removed outlier: 4.110A pdb=" N GLU A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL A 915 " --> pdb=" O LEU A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 922 No H-bonds generated for 'chain 'A' and resid 920 through 922' Processing helix chain 'B' and resid 230 through 243 removed outlier: 3.922A pdb=" N GLN B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 271 removed outlier: 3.958A pdb=" N GLU B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 300 removed outlier: 3.544A pdb=" N HIS B 293 " --> pdb=" O ARG B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 319 removed outlier: 3.620A pdb=" N LYS B 316 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA B 317 " --> pdb=" O ALA B 313 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 318 " --> pdb=" O ALA B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 422 Processing helix chain 'B' and resid 433 through 446 Processing helix chain 'B' and resid 459 through 463 Processing helix chain 'B' and resid 464 through 476 Processing helix chain 'B' and resid 490 through 495 Processing helix chain 'B' and resid 496 through 512 removed outlier: 3.510A pdb=" N GLU B 512 " --> pdb=" O LYS B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 520 removed outlier: 3.621A pdb=" N MET B 518 " --> pdb=" O LEU B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 538 through 545 Processing helix chain 'B' and resid 559 through 565 Processing helix chain 'B' and resid 570 through 582 Processing helix chain 'B' and resid 586 through 603 Processing helix chain 'B' and resid 606 through 615 Processing helix chain 'B' and resid 620 through 630 Processing helix chain 'B' and resid 634 through 655 Processing helix chain 'B' and resid 655 through 663 Processing helix chain 'B' and resid 665 through 673 Processing helix chain 'B' and resid 674 through 679 Processing helix chain 'B' and resid 680 through 686 Processing helix chain 'B' and resid 690 through 697 Processing helix chain 'B' and resid 709 through 738 removed outlier: 4.412A pdb=" N LYS B 713 " --> pdb=" O PHE B 709 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS B 714 " --> pdb=" O PRO B 710 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG B 715 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 730 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLN B 731 " --> pdb=" O ARG B 727 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU B 732 " --> pdb=" O MET B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 815 Processing helix chain 'B' and resid 817 through 841 Processing helix chain 'B' and resid 864 through 871 removed outlier: 3.517A pdb=" N VAL B 869 " --> pdb=" O PRO B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 919 removed outlier: 4.302A pdb=" N SER B 903 " --> pdb=" O MET B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 966 removed outlier: 3.756A pdb=" N GLU B 955 " --> pdb=" O THR B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1000 Processing helix chain 'B' and resid 1011 through 1016 removed outlier: 4.073A pdb=" N CYS B1015 " --> pdb=" O TYR B1011 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU B1016 " --> pdb=" O PRO B1012 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1011 through 1016' Processing helix chain 'B' and resid 1017 through 1020 Processing helix chain 'B' and resid 1068 through 1076 Processing helix chain 'B' and resid 1079 through 1113 removed outlier: 3.511A pdb=" N LEU B1083 " --> pdb=" O PRO B1079 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 80 removed outlier: 4.335A pdb=" N HIS A 46 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ARG A 35 " --> pdb=" O HIS A 46 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL A 34 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N TYR A 103 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU A 36 " --> pdb=" O TYR A 103 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N ASN A 105 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N ASP A 38 " --> pdb=" O ASN A 105 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS A 104 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU A 119 " --> pdb=" O LYS A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 223 through 224 removed outlier: 5.746A pdb=" N VAL A 147 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL A 166 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ARG A 159 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 301 through 302 removed outlier: 6.898A pdb=" N LYS A 301 " --> pdb=" O ILE A 708 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ALA A 710 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N CYS A 707 " --> pdb=" O LEU A 744 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE A 746 " --> pdb=" O CYS A 707 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU A 709 " --> pdb=" O ILE A 746 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ASP A 748 " --> pdb=" O LEU A 709 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ARG A 711 " --> pdb=" O ASP A 748 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE A 745 " --> pdb=" O MET A 779 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ALA A 781 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE A 747 " --> pdb=" O ALA A 781 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N HIS A 665 " --> pdb=" O PHE A 780 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N PHE A 664 " --> pdb=" O ASN A 798 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU A 800 " --> pdb=" O PHE A 664 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ILE A 666 " --> pdb=" O LEU A 800 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL A 802 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR A 668 " --> pdb=" O VAL A 802 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N ALA A 804 " --> pdb=" O THR A 668 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLN A 816 " --> pdb=" O THR A 803 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N LEU A 805 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU A 814 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 511 through 514 removed outlier: 6.645A pdb=" N LYS A 550 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 653 through 655 removed outlier: 5.565A pdb=" N ASN A 653 " --> pdb=" O ALA A 636 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ALA A 636 " --> pdb=" O ASN A 653 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER A 637 " --> pdb=" O CYS A 697 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N CYS A 697 " --> pdb=" O SER A 637 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 283 through 286 removed outlier: 6.184A pdb=" N VAL B 247 " --> pdb=" O GLY B 305 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N VAL B 307 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N CYS B 249 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N GLN B 309 " --> pdb=" O CYS B 249 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N GLU B 251 " --> pdb=" O GLN B 309 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA B 332 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYS B 308 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU B 330 " --> pdb=" O LYS B 308 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 454 through 458 removed outlier: 6.786A pdb=" N TYR B 367 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU B 426 " --> pdb=" O TYR B 367 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU B 369 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LEU B 428 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE B 371 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL B 400 " --> pdb=" O LYS B 526 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 536 through 537 removed outlier: 3.624A pdb=" N ILE B 935 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLY B 934 " --> pdb=" O LEU B 971 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ILE B 973 " --> pdb=" O GLY B 934 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE B 936 " --> pdb=" O ILE B 973 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ASP B 975 " --> pdb=" O PHE B 936 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ARG B 938 " --> pdb=" O ASP B 975 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET B1030 " --> pdb=" O THR B 895 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 745 through 747 removed outlier: 7.765A pdb=" N VAL B 747 " --> pdb=" O GLU B 751 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLU B 751 " --> pdb=" O VAL B 747 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 754 " --> pdb=" O PHE B 780 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 880 through 885 removed outlier: 6.996A pdb=" N THR B 882 " --> pdb=" O LYS B 860 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LYS B 860 " --> pdb=" O THR B 882 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU B 884 " --> pdb=" O VAL B 858 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL B 858 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU B 926 " --> pdb=" O LYS B 860 " (cutoff:3.500A) 705 hydrogen bonds defined for protein. 1995 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 2.95 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3881 1.34 - 1.46: 4136 1.46 - 1.58: 6621 1.58 - 1.70: 87 1.70 - 1.82: 105 Bond restraints: 14830 Sorted by residual: bond pdb=" C1' DG D 42 " pdb=" N9 DG D 42 " ideal model delta sigma weight residual 1.468 1.376 0.092 1.40e-02 5.10e+03 4.35e+01 bond pdb=" C1' G C 26 " pdb=" N9 G C 26 " ideal model delta sigma weight residual 1.468 1.376 0.092 1.40e-02 5.10e+03 4.27e+01 bond pdb=" C1' G C 21 " pdb=" N9 G C 21 " ideal model delta sigma weight residual 1.468 1.377 0.091 1.40e-02 5.10e+03 4.24e+01 bond pdb=" C1' DG D 38 " pdb=" N9 DG D 38 " ideal model delta sigma weight residual 1.468 1.379 0.089 1.40e-02 5.10e+03 4.05e+01 bond pdb=" C1' DC D 46 " pdb=" N1 DC D 46 " ideal model delta sigma weight residual 1.468 1.553 -0.085 1.40e-02 5.10e+03 3.65e+01 ... (remaining 14825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.77: 20090 3.77 - 7.53: 97 7.53 - 11.30: 3 11.30 - 15.07: 0 15.07 - 18.83: 1 Bond angle restraints: 20191 Sorted by residual: angle pdb=" N PRO A 415 " pdb=" CD PRO A 415 " pdb=" CG PRO A 415 " ideal model delta sigma weight residual 103.20 84.37 18.83 1.50e+00 4.44e-01 1.58e+02 angle pdb=" CA PRO A 415 " pdb=" N PRO A 415 " pdb=" CD PRO A 415 " ideal model delta sigma weight residual 112.00 105.06 6.94 1.40e+00 5.10e-01 2.46e+01 angle pdb=" N PRO A 415 " pdb=" CA PRO A 415 " pdb=" CB PRO A 415 " ideal model delta sigma weight residual 103.25 98.17 5.08 1.05e+00 9.07e-01 2.34e+01 angle pdb=" CA ASP B 320 " pdb=" CB ASP B 320 " pdb=" CG ASP B 320 " ideal model delta sigma weight residual 112.60 116.86 -4.26 1.00e+00 1.00e+00 1.81e+01 angle pdb=" CA ASP B 705 " pdb=" CB ASP B 705 " pdb=" CG ASP B 705 " ideal model delta sigma weight residual 112.60 116.81 -4.21 1.00e+00 1.00e+00 1.77e+01 ... (remaining 20186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.41: 8159 29.41 - 58.81: 699 58.81 - 88.22: 54 88.22 - 117.62: 4 117.62 - 147.03: 1 Dihedral angle restraints: 8917 sinusoidal: 3947 harmonic: 4970 Sorted by residual: dihedral pdb=" C5' ADP A1001 " pdb=" O5' ADP A1001 " pdb=" PA ADP A1001 " pdb=" O2A ADP A1001 " ideal model delta sinusoidal sigma weight residual -60.00 87.03 -147.03 1 2.00e+01 2.50e-03 4.41e+01 dihedral pdb=" CD ARG B 979 " pdb=" NE ARG B 979 " pdb=" CZ ARG B 979 " pdb=" NH1 ARG B 979 " ideal model delta sinusoidal sigma weight residual 0.00 -50.78 50.78 1 1.00e+01 1.00e-02 3.53e+01 dihedral pdb=" O2A ADP A1001 " pdb=" O3A ADP A1001 " pdb=" PA ADP A1001 " pdb=" PB ADP A1001 " ideal model delta sinusoidal sigma weight residual -60.00 57.59 -117.59 1 2.00e+01 2.50e-03 3.51e+01 ... (remaining 8914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1554 0.075 - 0.150: 674 0.150 - 0.226: 76 0.226 - 0.301: 4 0.301 - 0.376: 2 Chirality restraints: 2310 Sorted by residual: chirality pdb=" CA PRO A 415 " pdb=" N PRO A 415 " pdb=" C PRO A 415 " pdb=" CB PRO A 415 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CA MET A 492 " pdb=" N MET A 492 " pdb=" C MET A 492 " pdb=" CB MET A 492 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA PRO A 591 " pdb=" N PRO A 591 " pdb=" C PRO A 591 " pdb=" CB PRO A 591 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 2307 not shown) Planarity restraints: 2416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 979 " 0.827 9.50e-02 1.11e+02 3.71e-01 8.36e+01 pdb=" NE ARG B 979 " -0.050 2.00e-02 2.50e+03 pdb=" CZ ARG B 979 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 979 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 979 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 414 " 0.018 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C LEU A 414 " -0.059 2.00e-02 2.50e+03 pdb=" O LEU A 414 " 0.021 2.00e-02 2.50e+03 pdb=" N PRO A 415 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 414 " 0.055 5.00e-02 4.00e+02 7.99e-02 1.02e+01 pdb=" N PRO A 415 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 415 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 415 " 0.043 5.00e-02 4.00e+02 ... (remaining 2413 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 135 2.57 - 3.16: 11879 3.16 - 3.74: 24133 3.74 - 4.32: 32496 4.32 - 4.90: 52517 Nonbonded interactions: 121160 Sorted by model distance: nonbonded pdb=" NZ LYS B 757 " pdb=" C7 DT C 20 " model vdw 1.992 3.540 nonbonded pdb=" OG SER A 676 " pdb="MG MG A1000 " model vdw 2.063 2.170 nonbonded pdb="MG MG A1000 " pdb=" O1B ADP A1001 " model vdw 2.088 2.170 nonbonded pdb=" NH2 ARG B 574 " pdb=" OE1 GLU B 622 " model vdw 2.125 3.120 nonbonded pdb=" OG1 THR B 230 " pdb=" OE1 GLU B 233 " model vdw 2.174 3.040 ... (remaining 121155 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=0.39 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.260 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:1.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 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 : 0.007 0.100 14830 Z= 0.464 Angle : 0.962 18.833 20191 Z= 0.632 Chirality : 0.075 0.376 2310 Planarity : 0.009 0.371 2416 Dihedral : 19.708 147.026 5687 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.00 % Allowed : 25.90 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.21), residues: 1674 helix: 0.88 (0.18), residues: 795 sheet: -0.83 (0.36), residues: 211 loop : -1.30 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 219 TYR 0.017 0.004 TYR B 236 PHE 0.025 0.003 PHE B 752 TRP 0.018 0.003 TRP B 807 HIS 0.007 0.002 HIS B 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00695 / 0.46 (14830) covalent geometry : angle 0.96214 / 0.63 (20191) hydrogen bonds : bond 0.15866 / 10.56 ( 751) hydrogen bonds : angle 6.10087 / 4.18 ( 2087) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 394 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 VAL cc_start: 0.7838 (OUTLIER) cc_final: 0.7482 (p) REVERT: A 67 MET cc_start: 0.7949 (ttt) cc_final: 0.7643 (ttt) REVERT: A 159 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6926 (mtm-85) REVERT: A 254 ASN cc_start: 0.6863 (t0) cc_final: 0.6582 (t0) REVERT: A 313 PHE cc_start: 0.7516 (m-10) cc_final: 0.7283 (m-10) REVERT: A 471 LYS cc_start: 0.8322 (ptpt) cc_final: 0.8097 (ttmt) REVERT: A 574 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.8020 (tt0) REVERT: A 658 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7398 (mt-10) REVERT: B 320 ASP cc_start: 0.8545 (p0) cc_final: 0.8283 (p0) REVERT: B 445 SER cc_start: 0.7952 (t) cc_final: 0.7324 (m) REVERT: B 452 ARG cc_start: 0.8177 (ttt-90) cc_final: 0.7821 (ttt-90) REVERT: B 812 GLU cc_start: 0.8022 (tp30) cc_final: 0.7653 (tp30) REVERT: B 985 ASP cc_start: 0.8280 (m-30) cc_final: 0.7925 (t0) outliers start: 30 outliers final: 16 residues processed: 411 average time/residue: 0.1321 time to fit residues: 77.8140 Evaluate side-chains 403 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 384 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 159 ARG Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain B residue 242 GLN Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 508 LYS Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 677 GLU Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 1060 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.1980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 ASN A 288 GLN A 298 GLN A 377 GLN A 395 GLN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 ASN A 560 ASN A 799 ASN A 824 GLN B 243 HIS B 309 GLN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 743 GLN ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 HIS B1020 ASN B1027 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.163018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.133375 restraints weight = 22575.807| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.46 r_work: 0.3532 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (5 function evaluations) r_final: 0.3535 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14830 Z= 0.171 Angle : 0.638 7.429 20191 Z= 0.342 Chirality : 0.044 0.175 2310 Planarity : 0.004 0.049 2416 Dihedral : 17.566 134.249 2344 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.93 % Allowed : 25.37 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.21), residues: 1674 helix: 0.89 (0.18), residues: 813 sheet: -0.74 (0.37), residues: 202 loop : -1.18 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 680 TYR 0.018 0.001 TYR A 678 PHE 0.023 0.002 PHE B 752 TRP 0.008 0.001 TRP A 764 HIS 0.007 0.001 HIS B 984 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (14830) covalent geometry : angle 0.63751 / 0.34 (20191) hydrogen bonds : bond 0.05027 / 3.28 ( 751) hydrogen bonds : angle 4.71159 / 3.23 ( 2087) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 386 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.7587 (ttt) cc_final: 0.7330 (ttt) REVERT: A 119 LEU cc_start: 0.8311 (tp) cc_final: 0.8003 (tp) REVERT: A 215 GLN cc_start: 0.7484 (tm-30) cc_final: 0.7108 (tm-30) REVERT: A 313 PHE cc_start: 0.7589 (m-10) cc_final: 0.7243 (m-10) REVERT: A 351 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7241 (mpp) REVERT: A 471 LYS cc_start: 0.7904 (ptpt) cc_final: 0.7667 (ttmt) REVERT: A 481 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7989 (mp) REVERT: A 482 ARG cc_start: 0.8031 (tpp80) cc_final: 0.7514 (tpp80) REVERT: A 514 ASP cc_start: 0.7684 (t0) cc_final: 0.7403 (t0) REVERT: A 530 GLU cc_start: 0.5928 (OUTLIER) cc_final: 0.5560 (mp0) REVERT: A 562 GLU cc_start: 0.7317 (mm-30) cc_final: 0.7106 (mm-30) REVERT: A 569 GLU cc_start: 0.7473 (tp30) cc_final: 0.7170 (tp30) REVERT: A 658 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7435 (mt-10) REVERT: A 691 ILE cc_start: 0.8384 (tt) cc_final: 0.7885 (pt) REVERT: A 706 ASP cc_start: 0.7896 (t0) cc_final: 0.7686 (t0) REVERT: A 799 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8525 (p0) REVERT: A 899 MET cc_start: 0.2103 (tmm) cc_final: 0.1889 (tmm) REVERT: B 264 GLU cc_start: 0.7231 (mp0) cc_final: 0.6868 (mp0) REVERT: B 445 SER cc_start: 0.7975 (t) cc_final: 0.7582 (m) REVERT: B 452 ARG cc_start: 0.7365 (ttt-90) cc_final: 0.7077 (ttt-90) REVERT: B 508 LYS cc_start: 0.8156 (ttmm) cc_final: 0.7955 (ttmm) REVERT: B 550 ASN cc_start: 0.8115 (OUTLIER) cc_final: 0.7734 (p0) REVERT: B 606 SER cc_start: 0.7928 (m) cc_final: 0.7583 (p) REVERT: B 802 ASP cc_start: 0.7399 (m-30) cc_final: 0.7183 (m-30) REVERT: B 860 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7949 (ttpt) REVERT: B 961 GLU cc_start: 0.7427 (mm-30) cc_final: 0.6992 (mm-30) REVERT: B 969 GLN cc_start: 0.8288 (mp10) cc_final: 0.8083 (mp10) REVERT: B 1063 ILE cc_start: 0.7708 (mm) cc_final: 0.7458 (mm) outliers start: 44 outliers final: 20 residues processed: 408 average time/residue: 0.1335 time to fit residues: 78.0703 Evaluate side-chains 400 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 374 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 550 ASN Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 908 GLN Chi-restraints excluded: chain B residue 1020 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 38 optimal weight: 0.6980 chunk 105 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 154 optimal weight: 0.8980 chunk 130 optimal weight: 0.0670 chunk 8 optimal weight: 0.6980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 799 ASN B 538 ASN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 HIS ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.163702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.132823 restraints weight = 29053.355| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.88 r_work: 0.3506 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14830 Z= 0.153 Angle : 0.595 6.815 20191 Z= 0.319 Chirality : 0.042 0.192 2310 Planarity : 0.004 0.052 2416 Dihedral : 17.315 127.922 2308 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.00 % Allowed : 25.83 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.21), residues: 1674 helix: 1.04 (0.18), residues: 813 sheet: -0.76 (0.37), residues: 204 loop : -1.14 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 382 TYR 0.015 0.001 TYR A 678 PHE 0.016 0.002 PHE A 760 TRP 0.007 0.001 TRP A 764 HIS 0.004 0.001 HIS B 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (14830) covalent geometry : angle 0.59454 / 0.32 (20191) hydrogen bonds : bond 0.04522 / 2.96 ( 751) hydrogen bonds : angle 4.52437 / 3.11 ( 2087) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 390 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.7658 (ttt) cc_final: 0.7410 (ttt) REVERT: A 172 LYS cc_start: 0.7669 (mmtt) cc_final: 0.7369 (mptt) REVERT: A 215 GLN cc_start: 0.7584 (tm-30) cc_final: 0.7119 (tm-30) REVERT: A 313 PHE cc_start: 0.7569 (m-10) cc_final: 0.7219 (m-10) REVERT: A 351 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7169 (mpp) REVERT: A 402 GLN cc_start: 0.7107 (tt0) cc_final: 0.6607 (tp40) REVERT: A 430 LYS cc_start: 0.5803 (mmmt) cc_final: 0.5255 (mmmt) REVERT: A 471 LYS cc_start: 0.7927 (ptpt) cc_final: 0.7691 (ttmt) REVERT: A 485 MET cc_start: 0.7997 (mmt) cc_final: 0.7767 (mmt) REVERT: A 514 ASP cc_start: 0.7795 (t0) cc_final: 0.7522 (t0) REVERT: A 530 GLU cc_start: 0.5956 (OUTLIER) cc_final: 0.5594 (mp0) REVERT: A 562 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7171 (mm-30) REVERT: A 567 LYS cc_start: 0.8312 (tppp) cc_final: 0.8068 (tppp) REVERT: A 569 GLU cc_start: 0.7586 (tp30) cc_final: 0.7166 (tp30) REVERT: A 658 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7497 (mt-10) REVERT: A 691 ILE cc_start: 0.8414 (tt) cc_final: 0.7890 (pt) REVERT: A 706 ASP cc_start: 0.7966 (t0) cc_final: 0.7716 (t0) REVERT: A 728 GLU cc_start: 0.6713 (tm-30) cc_final: 0.6501 (tm-30) REVERT: A 899 MET cc_start: 0.2320 (tmm) cc_final: 0.1924 (tmm) REVERT: B 264 GLU cc_start: 0.7274 (mp0) cc_final: 0.6961 (mp0) REVERT: B 445 SER cc_start: 0.7951 (t) cc_final: 0.7631 (m) REVERT: B 452 ARG cc_start: 0.7415 (ttt-90) cc_final: 0.7084 (ttt-90) REVERT: B 453 ILE cc_start: 0.8377 (mt) cc_final: 0.8074 (tt) REVERT: B 508 LYS cc_start: 0.8181 (ttmm) cc_final: 0.7880 (ttmm) REVERT: B 550 ASN cc_start: 0.8213 (OUTLIER) cc_final: 0.7828 (p0) REVERT: B 606 SER cc_start: 0.7818 (m) cc_final: 0.7460 (p) REVERT: B 802 ASP cc_start: 0.7441 (m-30) cc_final: 0.7232 (m-30) REVERT: B 860 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7942 (ttpt) REVERT: B 899 MET cc_start: 0.6144 (ppp) cc_final: 0.5733 (ppp) REVERT: B 926 GLU cc_start: 0.7212 (mp0) cc_final: 0.6761 (mp0) REVERT: B 961 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7014 (mm-30) REVERT: B 969 GLN cc_start: 0.8327 (mp10) cc_final: 0.8076 (mp10) REVERT: B 1063 ILE cc_start: 0.7698 (mm) cc_final: 0.7438 (mm) outliers start: 45 outliers final: 22 residues processed: 411 average time/residue: 0.1379 time to fit residues: 81.3167 Evaluate side-chains 402 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 376 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 550 ASN Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 1096 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 131 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 ASN A 799 ASN B 613 ASN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.163079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.133366 restraints weight = 23123.587| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.50 r_work: 0.3526 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14830 Z= 0.185 Angle : 0.595 7.143 20191 Z= 0.317 Chirality : 0.043 0.163 2310 Planarity : 0.004 0.055 2416 Dihedral : 17.296 121.057 2308 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.93 % Allowed : 25.30 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.21), residues: 1674 helix: 1.06 (0.18), residues: 813 sheet: -0.80 (0.36), residues: 204 loop : -1.09 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 257 TYR 0.016 0.002 TYR A 678 PHE 0.020 0.002 PHE A 760 TRP 0.009 0.001 TRP B 807 HIS 0.005 0.001 HIS B 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.19 (14830) covalent geometry : angle 0.59452 / 0.32 (20191) hydrogen bonds : bond 0.04348 / 2.85 ( 751) hydrogen bonds : angle 4.43191 / 3.05 ( 2087) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 391 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.7571 (ttt) cc_final: 0.7330 (ttt) REVERT: A 178 PHE cc_start: 0.7929 (p90) cc_final: 0.7359 (p90) REVERT: A 180 ASP cc_start: 0.7106 (t0) cc_final: 0.6884 (t0) REVERT: A 215 GLN cc_start: 0.7586 (tm-30) cc_final: 0.7108 (tm-30) REVERT: A 261 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7247 (tmm) REVERT: A 298 GLN cc_start: 0.8125 (mt0) cc_final: 0.7787 (mt0) REVERT: A 313 PHE cc_start: 0.7613 (m-10) cc_final: 0.7222 (m-10) REVERT: A 334 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7508 (mtpp) REVERT: A 371 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7806 (mm-30) REVERT: A 402 GLN cc_start: 0.7105 (tt0) cc_final: 0.6725 (tp40) REVERT: A 430 LYS cc_start: 0.5852 (mmmt) cc_final: 0.5097 (mmmt) REVERT: A 452 GLU cc_start: 0.7143 (pp20) cc_final: 0.6846 (pp20) REVERT: A 471 LYS cc_start: 0.7914 (ptpt) cc_final: 0.7703 (ttmt) REVERT: A 485 MET cc_start: 0.8007 (mmt) cc_final: 0.7683 (mmt) REVERT: A 530 GLU cc_start: 0.5932 (OUTLIER) cc_final: 0.5616 (mp0) REVERT: A 562 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7141 (mm-30) REVERT: A 567 LYS cc_start: 0.8267 (tppp) cc_final: 0.8023 (tppp) REVERT: A 569 GLU cc_start: 0.7591 (tp30) cc_final: 0.7145 (tp30) REVERT: A 658 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7534 (mt-10) REVERT: A 691 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.7909 (pt) REVERT: A 706 ASP cc_start: 0.7936 (t0) cc_final: 0.7657 (t0) REVERT: A 726 MET cc_start: 0.7867 (tpt) cc_final: 0.7621 (tpp) REVERT: A 728 GLU cc_start: 0.6701 (tm-30) cc_final: 0.6477 (tm-30) REVERT: A 850 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7565 (tm-30) REVERT: A 899 MET cc_start: 0.2461 (tmm) cc_final: 0.1895 (tmm) REVERT: B 257 ARG cc_start: 0.8313 (mmm-85) cc_final: 0.8081 (mtm-85) REVERT: B 445 SER cc_start: 0.8008 (t) cc_final: 0.7629 (m) REVERT: B 508 LYS cc_start: 0.8074 (ttmm) cc_final: 0.7789 (ttmm) REVERT: B 550 ASN cc_start: 0.8200 (OUTLIER) cc_final: 0.7822 (p0) REVERT: B 606 SER cc_start: 0.7875 (m) cc_final: 0.7338 (p) REVERT: B 899 MET cc_start: 0.6141 (ppp) cc_final: 0.5828 (ppp) REVERT: B 961 GLU cc_start: 0.7415 (mm-30) cc_final: 0.6978 (mm-30) REVERT: B 1063 ILE cc_start: 0.7746 (mm) cc_final: 0.7498 (mm) outliers start: 59 outliers final: 37 residues processed: 421 average time/residue: 0.1349 time to fit residues: 81.1866 Evaluate side-chains 420 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 378 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 798 ASN Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 550 ASN Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 753 MET Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 904 SER Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain B residue 1057 TYR Chi-restraints excluded: chain B residue 1096 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 103 optimal weight: 0.5980 chunk 128 optimal weight: 0.1980 chunk 26 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 729 HIS ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 984 HIS ** 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 = 0.4090 r_free = 0.4090 target = 0.163090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.133708 restraints weight = 22647.366| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.41 r_work: 0.3550 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14830 Z= 0.169 Angle : 0.599 9.925 20191 Z= 0.318 Chirality : 0.043 0.167 2310 Planarity : 0.004 0.056 2416 Dihedral : 17.264 121.956 2308 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.66 % Allowed : 25.97 % Favored : 70.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.21), residues: 1674 helix: 1.03 (0.18), residues: 814 sheet: -0.84 (0.36), residues: 208 loop : -1.09 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 382 TYR 0.049 0.002 TYR B 334 PHE 0.034 0.002 PHE A 232 TRP 0.008 0.001 TRP B 807 HIS 0.012 0.001 HIS B 984 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (14830) covalent geometry : angle 0.59853 / 0.32 (20191) hydrogen bonds : bond 0.04213 / 2.76 ( 751) hydrogen bonds : angle 4.41189 / 3.04 ( 2087) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 384 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 TYR cc_start: 0.7375 (m-80) cc_final: 0.6942 (m-80) REVERT: A 160 GLN cc_start: 0.7574 (tt0) cc_final: 0.7176 (tt0) REVERT: A 178 PHE cc_start: 0.7891 (p90) cc_final: 0.7357 (p90) REVERT: A 180 ASP cc_start: 0.7052 (t0) cc_final: 0.6814 (t0) REVERT: A 261 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7260 (tmm) REVERT: A 298 GLN cc_start: 0.8082 (mt0) cc_final: 0.7759 (mt0) REVERT: A 371 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7736 (mm-30) REVERT: A 402 GLN cc_start: 0.6966 (tt0) cc_final: 0.6626 (tp40) REVERT: A 430 LYS cc_start: 0.5940 (mmmt) cc_final: 0.5058 (mmmt) REVERT: A 485 MET cc_start: 0.7964 (mmt) cc_final: 0.7610 (mmt) REVERT: A 514 ASP cc_start: 0.7570 (t0) cc_final: 0.7358 (t0) REVERT: A 530 GLU cc_start: 0.5873 (OUTLIER) cc_final: 0.5501 (mp0) REVERT: A 562 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7120 (mm-30) REVERT: A 567 LYS cc_start: 0.8245 (tppp) cc_final: 0.7989 (tppp) REVERT: A 569 GLU cc_start: 0.7517 (tp30) cc_final: 0.7043 (tp30) REVERT: A 658 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7529 (mt-10) REVERT: A 691 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.7901 (pt) REVERT: A 706 ASP cc_start: 0.7913 (t0) cc_final: 0.7653 (t0) REVERT: A 726 MET cc_start: 0.7883 (tpt) cc_final: 0.7624 (tpp) REVERT: A 728 GLU cc_start: 0.6685 (tm-30) cc_final: 0.6477 (tm-30) REVERT: A 899 MET cc_start: 0.2500 (tmm) cc_final: 0.1931 (tmm) REVERT: B 264 GLU cc_start: 0.7161 (mp0) cc_final: 0.6936 (mp0) REVERT: B 445 SER cc_start: 0.8003 (t) cc_final: 0.7608 (m) REVERT: B 453 ILE cc_start: 0.8380 (mt) cc_final: 0.8074 (tt) REVERT: B 508 LYS cc_start: 0.8055 (ttmm) cc_final: 0.7790 (ttmm) REVERT: B 606 SER cc_start: 0.7848 (m) cc_final: 0.7312 (p) REVERT: B 812 GLU cc_start: 0.7647 (tp30) cc_final: 0.7351 (tp30) REVERT: B 899 MET cc_start: 0.6114 (ppp) cc_final: 0.5814 (ppp) REVERT: B 1063 ILE cc_start: 0.7742 (mm) cc_final: 0.7503 (mm) outliers start: 55 outliers final: 34 residues processed: 409 average time/residue: 0.1231 time to fit residues: 72.5601 Evaluate side-chains 419 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 382 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 798 ASN Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 894 MET Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 904 SER Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1057 TYR Chi-restraints excluded: chain B residue 1096 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 126 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 25 optimal weight: 0.0770 chunk 22 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 115 optimal weight: 0.3980 chunk 168 optimal weight: 20.0000 chunk 84 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 GLN A 288 GLN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 ASN A 799 ASN B 271 ASN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.162449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.130838 restraints weight = 35543.969| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 3.16 r_work: 0.3474 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 14830 Z= 0.189 Angle : 0.596 9.906 20191 Z= 0.317 Chirality : 0.043 0.176 2310 Planarity : 0.004 0.058 2416 Dihedral : 17.229 125.154 2308 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.20 % Favored : 94.74 % Rotamer: Outliers : 4.19 % Allowed : 26.10 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.21), residues: 1674 helix: 1.05 (0.18), residues: 814 sheet: -0.85 (0.35), residues: 218 loop : -1.06 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 382 TYR 0.033 0.002 TYR B 334 PHE 0.029 0.002 PHE A 232 TRP 0.009 0.001 TRP B 807 HIS 0.005 0.001 HIS B 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (14830) covalent geometry : angle 0.59562 / 0.32 (20191) hydrogen bonds : bond 0.04174 / 2.73 ( 751) hydrogen bonds : angle 4.38563 / 3.02 ( 2087) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 388 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7586 (mm-40) REVERT: A 160 GLN cc_start: 0.7614 (tt0) cc_final: 0.7216 (tt0) REVERT: A 178 PHE cc_start: 0.7917 (p90) cc_final: 0.7362 (p90) REVERT: A 180 ASP cc_start: 0.7143 (t0) cc_final: 0.6873 (t0) REVERT: A 254 ASN cc_start: 0.6677 (t0) cc_final: 0.6464 (t0) REVERT: A 261 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7331 (tmm) REVERT: A 298 GLN cc_start: 0.8179 (mt0) cc_final: 0.7852 (mt0) REVERT: A 371 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7868 (mm-30) REVERT: A 402 GLN cc_start: 0.7085 (tt0) cc_final: 0.6761 (tp40) REVERT: A 430 LYS cc_start: 0.6079 (mmmt) cc_final: 0.5076 (mmtt) REVERT: A 485 MET cc_start: 0.8071 (mmt) cc_final: 0.7724 (mmt) REVERT: A 515 SER cc_start: 0.8282 (m) cc_final: 0.7983 (m) REVERT: A 530 GLU cc_start: 0.5948 (OUTLIER) cc_final: 0.5575 (mp0) REVERT: A 555 LYS cc_start: 0.8983 (tmmt) cc_final: 0.8766 (tmmt) REVERT: A 562 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7208 (mm-30) REVERT: A 567 LYS cc_start: 0.8302 (tppp) cc_final: 0.8025 (tppp) REVERT: A 569 GLU cc_start: 0.7652 (tp30) cc_final: 0.7175 (tp30) REVERT: A 658 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7566 (mt-10) REVERT: A 691 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.7959 (pt) REVERT: A 706 ASP cc_start: 0.7946 (t0) cc_final: 0.7672 (t0) REVERT: A 726 MET cc_start: 0.7980 (tpt) cc_final: 0.7701 (tpp) REVERT: A 728 GLU cc_start: 0.6740 (tm-30) cc_final: 0.6529 (tm-30) REVERT: A 799 ASN cc_start: 0.8684 (OUTLIER) cc_final: 0.8474 (p0) REVERT: A 850 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7605 (tm-30) REVERT: A 899 MET cc_start: 0.2666 (OUTLIER) cc_final: 0.2103 (tmm) REVERT: B 257 ARG cc_start: 0.8286 (mmm-85) cc_final: 0.8042 (mtm180) REVERT: B 264 GLU cc_start: 0.7301 (mp0) cc_final: 0.7050 (mp0) REVERT: B 445 SER cc_start: 0.8033 (t) cc_final: 0.7370 (m) REVERT: B 452 ARG cc_start: 0.7631 (ttt-90) cc_final: 0.7299 (ttt-90) REVERT: B 508 LYS cc_start: 0.8133 (ttmm) cc_final: 0.7886 (ttmm) REVERT: B 550 ASN cc_start: 0.8241 (OUTLIER) cc_final: 0.7871 (p0) REVERT: B 606 SER cc_start: 0.7906 (m) cc_final: 0.7372 (p) REVERT: B 899 MET cc_start: 0.6213 (ppp) cc_final: 0.5910 (ppp) REVERT: B 961 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7068 (mm-30) REVERT: B 1063 ILE cc_start: 0.7800 (mm) cc_final: 0.7546 (mm) outliers start: 63 outliers final: 43 residues processed: 420 average time/residue: 0.1171 time to fit residues: 70.7329 Evaluate side-chains 432 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 383 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 799 ASN Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 894 MET Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 550 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 904 SER Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1057 TYR Chi-restraints excluded: chain B residue 1096 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 117 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 167 optimal weight: 9.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 ASN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.162746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.134187 restraints weight = 20384.559| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.22 r_work: 0.3565 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14830 Z= 0.178 Angle : 0.596 9.454 20191 Z= 0.316 Chirality : 0.042 0.171 2310 Planarity : 0.004 0.059 2416 Dihedral : 17.208 127.416 2308 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.96 % Favored : 94.98 % Rotamer: Outliers : 3.86 % Allowed : 26.56 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.21), residues: 1674 helix: 1.09 (0.18), residues: 814 sheet: -0.83 (0.36), residues: 209 loop : -1.07 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 382 TYR 0.044 0.002 TYR B 334 PHE 0.024 0.002 PHE A 232 TRP 0.008 0.001 TRP B 807 HIS 0.006 0.001 HIS B 984 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 (14830) covalent geometry : angle 0.59612 / 0.32 (20191) hydrogen bonds : bond 0.04123 / 2.69 ( 751) hydrogen bonds : angle 4.36852 / 3.01 ( 2087) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 385 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 TYR cc_start: 0.7564 (m-80) cc_final: 0.7127 (m-80) REVERT: A 97 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7681 (mm-40) REVERT: A 160 GLN cc_start: 0.7666 (tt0) cc_final: 0.7272 (tt0) REVERT: A 254 ASN cc_start: 0.6724 (t0) cc_final: 0.6505 (t0) REVERT: A 261 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7401 (tmm) REVERT: A 298 GLN cc_start: 0.8262 (mt0) cc_final: 0.7954 (mt0) REVERT: A 371 GLU cc_start: 0.8216 (mm-30) cc_final: 0.8002 (mm-30) REVERT: A 402 GLN cc_start: 0.7317 (tt0) cc_final: 0.7052 (tp40) REVERT: A 430 LYS cc_start: 0.6234 (mmmt) cc_final: 0.5268 (mmmt) REVERT: A 485 MET cc_start: 0.8144 (mmt) cc_final: 0.7804 (mmt) REVERT: A 530 GLU cc_start: 0.5925 (OUTLIER) cc_final: 0.5534 (mp0) REVERT: A 555 LYS cc_start: 0.8979 (tmmt) cc_final: 0.8772 (tmmt) REVERT: A 562 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7299 (mm-30) REVERT: A 565 LYS cc_start: 0.8719 (tmtt) cc_final: 0.8382 (tmtt) REVERT: A 567 LYS cc_start: 0.8367 (tppp) cc_final: 0.8101 (tppp) REVERT: A 569 GLU cc_start: 0.7749 (tp30) cc_final: 0.7261 (tp30) REVERT: A 658 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7696 (mt-10) REVERT: A 691 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.7990 (pt) REVERT: A 706 ASP cc_start: 0.8040 (t0) cc_final: 0.7745 (t0) REVERT: A 726 MET cc_start: 0.8085 (tpt) cc_final: 0.7784 (tpp) REVERT: A 899 MET cc_start: 0.2711 (OUTLIER) cc_final: 0.2141 (tmm) REVERT: B 257 ARG cc_start: 0.8354 (mmm-85) cc_final: 0.8112 (mtm180) REVERT: B 264 GLU cc_start: 0.7461 (mp0) cc_final: 0.7168 (mp0) REVERT: B 445 SER cc_start: 0.8007 (t) cc_final: 0.7341 (m) REVERT: B 452 ARG cc_start: 0.7735 (ttt-90) cc_final: 0.7404 (ttt-90) REVERT: B 508 LYS cc_start: 0.8240 (ttmm) cc_final: 0.7992 (ttmm) REVERT: B 550 ASN cc_start: 0.8257 (OUTLIER) cc_final: 0.7909 (p0) REVERT: B 606 SER cc_start: 0.7969 (m) cc_final: 0.7429 (p) REVERT: B 899 MET cc_start: 0.6355 (ppp) cc_final: 0.6062 (ppp) REVERT: B 1063 ILE cc_start: 0.7833 (mm) cc_final: 0.7581 (mm) outliers start: 58 outliers final: 44 residues processed: 416 average time/residue: 0.1230 time to fit residues: 73.4649 Evaluate side-chains 428 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 379 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 574 GLN Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 894 MET Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 550 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 904 SER Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1057 TYR Chi-restraints excluded: chain B residue 1096 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 16 optimal weight: 0.5980 chunk 163 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 ASN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.163346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.132723 restraints weight = 28925.927| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.86 r_work: 0.3503 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14830 Z= 0.182 Angle : 0.603 9.069 20191 Z= 0.319 Chirality : 0.043 0.176 2310 Planarity : 0.004 0.059 2416 Dihedral : 17.189 132.520 2308 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.84 % Favored : 95.10 % Rotamer: Outliers : 3.73 % Allowed : 26.23 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.21), residues: 1674 helix: 1.07 (0.18), residues: 815 sheet: -0.79 (0.36), residues: 212 loop : -1.08 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 382 TYR 0.045 0.002 TYR B 334 PHE 0.029 0.002 PHE A 232 TRP 0.008 0.001 TRP B 807 HIS 0.005 0.001 HIS B 984 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (14830) covalent geometry : angle 0.60260 / 0.32 (20191) hydrogen bonds : bond 0.04089 / 2.66 ( 751) hydrogen bonds : angle 4.35089 / 3.00 ( 2087) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 384 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 TYR cc_start: 0.7560 (m-80) cc_final: 0.7087 (m-80) REVERT: A 97 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7539 (mm-40) REVERT: A 160 GLN cc_start: 0.7560 (tt0) cc_final: 0.7169 (tt0) REVERT: A 254 ASN cc_start: 0.6700 (t0) cc_final: 0.6460 (t0) REVERT: A 261 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7272 (tmm) REVERT: A 298 GLN cc_start: 0.8178 (mt0) cc_final: 0.7880 (mt0) REVERT: A 371 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7839 (mm-30) REVERT: A 402 GLN cc_start: 0.7181 (tt0) cc_final: 0.6839 (tp40) REVERT: A 430 LYS cc_start: 0.6112 (mmmt) cc_final: 0.5234 (mmmt) REVERT: A 515 SER cc_start: 0.8309 (m) cc_final: 0.8049 (t) REVERT: A 530 GLU cc_start: 0.5913 (OUTLIER) cc_final: 0.5539 (mp0) REVERT: A 555 LYS cc_start: 0.9017 (tmmt) cc_final: 0.8784 (tmmt) REVERT: A 562 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7256 (mm-30) REVERT: A 569 GLU cc_start: 0.7609 (tp30) cc_final: 0.7097 (tp30) REVERT: A 658 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7504 (mt-10) REVERT: A 691 ILE cc_start: 0.8409 (tt) cc_final: 0.7891 (pt) REVERT: A 706 ASP cc_start: 0.7915 (t0) cc_final: 0.7659 (t0) REVERT: A 726 MET cc_start: 0.7984 (tpt) cc_final: 0.7705 (tpp) REVERT: A 850 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7555 (tm-30) REVERT: A 899 MET cc_start: 0.2758 (OUTLIER) cc_final: 0.2182 (tmm) REVERT: B 257 ARG cc_start: 0.8260 (mmm-85) cc_final: 0.7957 (mtm-85) REVERT: B 264 GLU cc_start: 0.7293 (mp0) cc_final: 0.6997 (mp0) REVERT: B 445 SER cc_start: 0.8012 (t) cc_final: 0.7351 (m) REVERT: B 452 ARG cc_start: 0.7630 (ttt-90) cc_final: 0.7156 (ttt-90) REVERT: B 508 LYS cc_start: 0.8105 (ttmm) cc_final: 0.7901 (ttmm) REVERT: B 550 ASN cc_start: 0.8231 (OUTLIER) cc_final: 0.7873 (p0) REVERT: B 606 SER cc_start: 0.7895 (m) cc_final: 0.7354 (p) REVERT: B 899 MET cc_start: 0.6214 (ppp) cc_final: 0.5951 (ppp) REVERT: B 1063 ILE cc_start: 0.7815 (mm) cc_final: 0.7574 (mm) outliers start: 56 outliers final: 42 residues processed: 414 average time/residue: 0.1423 time to fit residues: 84.2097 Evaluate side-chains 428 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 382 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 334 LYS Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 779 MET Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 894 MET Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 340 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 550 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 860 LYS Chi-restraints excluded: chain B residue 904 SER Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1057 TYR Chi-restraints excluded: chain B residue 1096 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 169 optimal weight: 50.0000 chunk 55 optimal weight: 0.0980 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 150 optimal weight: 0.9980 chunk 22 optimal weight: 0.3980 chunk 122 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A 799 ASN B 582 GLN B 613 ASN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.164303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.135087 restraints weight = 23137.388| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.40 r_work: 0.3565 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14830 Z= 0.148 Angle : 0.603 10.487 20191 Z= 0.318 Chirality : 0.042 0.166 2310 Planarity : 0.004 0.058 2416 Dihedral : 17.109 133.583 2308 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.78 % Favored : 95.16 % Rotamer: Outliers : 3.53 % Allowed : 27.16 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.21), residues: 1674 helix: 1.17 (0.18), residues: 814 sheet: -0.76 (0.36), residues: 212 loop : -1.09 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 382 TYR 0.033 0.002 TYR B 334 PHE 0.032 0.002 PHE A 232 TRP 0.008 0.001 TRP B1111 HIS 0.007 0.001 HIS B 984 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (14830) covalent geometry : angle 0.60323 / 0.32 (20191) hydrogen bonds : bond 0.03938 / 2.56 ( 751) hydrogen bonds : angle 4.32446 / 2.99 ( 2087) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 387 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 TYR cc_start: 0.7502 (m-80) cc_final: 0.6994 (m-80) REVERT: A 97 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7460 (mm-40) REVERT: A 119 LEU cc_start: 0.8284 (tp) cc_final: 0.7988 (tp) REVERT: A 160 GLN cc_start: 0.7526 (tt0) cc_final: 0.7109 (tt0) REVERT: A 215 GLN cc_start: 0.7543 (tm-30) cc_final: 0.7023 (tm-30) REVERT: A 254 ASN cc_start: 0.6700 (t0) cc_final: 0.6469 (t0) REVERT: A 261 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7199 (tmm) REVERT: A 298 GLN cc_start: 0.8090 (mt0) cc_final: 0.7758 (mt0) REVERT: A 371 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7768 (mm-30) REVERT: A 430 LYS cc_start: 0.6056 (mmmt) cc_final: 0.5231 (mmmt) REVERT: A 452 GLU cc_start: 0.7116 (pp20) cc_final: 0.6825 (pp20) REVERT: A 515 SER cc_start: 0.8219 (m) cc_final: 0.7943 (t) REVERT: A 530 GLU cc_start: 0.5767 (OUTLIER) cc_final: 0.5405 (mp0) REVERT: A 555 LYS cc_start: 0.8977 (tmmt) cc_final: 0.8746 (tmmt) REVERT: A 562 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7155 (mm-30) REVERT: A 569 GLU cc_start: 0.7510 (tp30) cc_final: 0.6992 (tp30) REVERT: A 658 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7469 (mt-10) REVERT: A 691 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.7855 (pt) REVERT: A 726 MET cc_start: 0.7913 (tpt) cc_final: 0.7631 (tpp) REVERT: A 729 MET cc_start: 0.7832 (mmm) cc_final: 0.7518 (mmm) REVERT: A 850 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7409 (tm-30) REVERT: A 899 MET cc_start: 0.2597 (OUTLIER) cc_final: 0.2068 (tmm) REVERT: B 257 ARG cc_start: 0.8222 (mmm-85) cc_final: 0.7927 (mtm-85) REVERT: B 264 GLU cc_start: 0.7204 (mp0) cc_final: 0.6920 (mp0) REVERT: B 445 SER cc_start: 0.8006 (t) cc_final: 0.7361 (m) REVERT: B 452 ARG cc_start: 0.7576 (ttt-90) cc_final: 0.7261 (ttt-90) REVERT: B 508 LYS cc_start: 0.8012 (ttmm) cc_final: 0.7786 (ttmm) REVERT: B 550 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.7959 (p0) REVERT: B 606 SER cc_start: 0.7805 (m) cc_final: 0.7275 (p) REVERT: B 709 PHE cc_start: 0.7596 (OUTLIER) cc_final: 0.7145 (m-80) REVERT: B 863 ARG cc_start: 0.7981 (mtm-85) cc_final: 0.7728 (ptp90) REVERT: B 899 MET cc_start: 0.6158 (ppp) cc_final: 0.5926 (ppp) REVERT: B 976 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7145 (mt-10) REVERT: B 1063 ILE cc_start: 0.7724 (mm) cc_final: 0.7498 (mm) REVERT: B 1092 GLU cc_start: 0.7521 (tp30) cc_final: 0.7019 (tp30) outliers start: 53 outliers final: 35 residues processed: 418 average time/residue: 0.1431 time to fit residues: 85.7707 Evaluate side-chains 418 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 377 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 894 MET Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 550 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 904 SER Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1057 TYR Chi-restraints excluded: chain B residue 1096 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 153 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 chunk 165 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 140 optimal weight: 0.6980 chunk 99 optimal weight: 0.4980 chunk 129 optimal weight: 0.0170 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN B 582 GLN B 613 ASN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.164109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.133033 restraints weight = 30895.556| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.99 r_work: 0.3506 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14830 Z= 0.164 Angle : 0.627 12.192 20191 Z= 0.331 Chirality : 0.043 0.193 2310 Planarity : 0.004 0.059 2416 Dihedral : 17.102 137.932 2308 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.72 % Favored : 95.22 % Rotamer: Outliers : 2.86 % Allowed : 27.56 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.21), residues: 1674 helix: 1.17 (0.18), residues: 814 sheet: -0.74 (0.36), residues: 212 loop : -1.05 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 382 TYR 0.034 0.002 TYR B 334 PHE 0.031 0.002 PHE A 232 TRP 0.007 0.001 TRP B1111 HIS 0.008 0.001 HIS B 984 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (14830) covalent geometry : angle 0.62710 / 0.33 (20191) hydrogen bonds : bond 0.04032 / 2.60 ( 751) hydrogen bonds : angle 4.31258 / 2.98 ( 2087) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3348 Ramachandran restraints generated. 1674 Oldfield, 0 Emsley, 1674 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 380 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 TYR cc_start: 0.7570 (m-80) cc_final: 0.7039 (m-80) REVERT: A 97 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7518 (mm-40) REVERT: A 119 LEU cc_start: 0.8319 (tp) cc_final: 0.8012 (tp) REVERT: A 160 GLN cc_start: 0.7535 (tt0) cc_final: 0.7140 (tt0) REVERT: A 215 GLN cc_start: 0.7627 (tm-30) cc_final: 0.7094 (tm-30) REVERT: A 237 ILE cc_start: 0.7159 (tp) cc_final: 0.6906 (tp) REVERT: A 254 ASN cc_start: 0.6711 (t0) cc_final: 0.6479 (t0) REVERT: A 261 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7236 (tmm) REVERT: A 298 GLN cc_start: 0.8153 (mt0) cc_final: 0.7840 (mt0) REVERT: A 371 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7863 (mm-30) REVERT: A 430 LYS cc_start: 0.6131 (mmmt) cc_final: 0.5314 (mmmt) REVERT: A 485 MET cc_start: 0.8023 (mmt) cc_final: 0.7804 (mtt) REVERT: A 515 SER cc_start: 0.8243 (m) cc_final: 0.8003 (t) REVERT: A 530 GLU cc_start: 0.5868 (OUTLIER) cc_final: 0.5483 (mp0) REVERT: A 555 LYS cc_start: 0.9005 (tmmt) cc_final: 0.8767 (tmmt) REVERT: A 562 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7247 (mm-30) REVERT: A 569 GLU cc_start: 0.7596 (tp30) cc_final: 0.7063 (tp30) REVERT: A 658 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7508 (mt-10) REVERT: A 691 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.7896 (pt) REVERT: A 726 MET cc_start: 0.7975 (tpt) cc_final: 0.7699 (tpp) REVERT: A 729 MET cc_start: 0.7780 (mmm) cc_final: 0.7468 (mmm) REVERT: A 850 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7438 (tm-30) REVERT: A 899 MET cc_start: 0.2752 (OUTLIER) cc_final: 0.2196 (tmm) REVERT: B 257 ARG cc_start: 0.8273 (mmm-85) cc_final: 0.7983 (mtm-85) REVERT: B 264 GLU cc_start: 0.7312 (mp0) cc_final: 0.7007 (mp0) REVERT: B 445 SER cc_start: 0.7950 (t) cc_final: 0.7294 (m) REVERT: B 452 ARG cc_start: 0.7637 (ttt-90) cc_final: 0.7300 (ttt-90) REVERT: B 508 LYS cc_start: 0.8107 (ttmm) cc_final: 0.7898 (ttmm) REVERT: B 550 ASN cc_start: 0.8279 (OUTLIER) cc_final: 0.7932 (p0) REVERT: B 606 SER cc_start: 0.7865 (m) cc_final: 0.7324 (p) REVERT: B 709 PHE cc_start: 0.7697 (OUTLIER) cc_final: 0.7269 (m-80) REVERT: B 812 GLU cc_start: 0.7776 (tp30) cc_final: 0.7250 (tp30) REVERT: B 860 LYS cc_start: 0.8393 (ptpt) cc_final: 0.8062 (ptmm) REVERT: B 898 ASN cc_start: 0.7814 (t0) cc_final: 0.7374 (t0) REVERT: B 899 MET cc_start: 0.6241 (ppp) cc_final: 0.5987 (ppp) REVERT: B 1063 ILE cc_start: 0.7773 (mm) cc_final: 0.7538 (mm) outliers start: 43 outliers final: 34 residues processed: 406 average time/residue: 0.1378 time to fit residues: 80.5936 Evaluate side-chains 417 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 377 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 404 CYS Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 638 ARG Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 894 MET Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 550 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 709 PHE Chi-restraints excluded: chain B residue 771 VAL Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 904 SER Chi-restraints excluded: chain B residue 1014 VAL Chi-restraints excluded: chain B residue 1057 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 114 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 chunk 33 optimal weight: 0.2980 chunk 20 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 ASN A 671 ASN B 582 GLN B 613 ASN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 880 ASN ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.163853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.134435 restraints weight = 22925.793| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.47 r_work: 0.3552 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3553 r_free = 0.3553 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14830 Z= 0.164 Angle : 0.630 12.339 20191 Z= 0.331 Chirality : 0.043 0.189 2310 Planarity : 0.004 0.059 2416 Dihedral : 17.074 139.668 2308 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.26 % Allowed : 27.36 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.21), residues: 1674 helix: 1.17 (0.18), residues: 814 sheet: -0.69 (0.36), residues: 212 loop : -1.06 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 406 TYR 0.031 0.002 TYR B 334 PHE 0.032 0.002 PHE A 232 TRP 0.008 0.001 TRP B1111 HIS 0.006 0.001 HIS B 984 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (14830) covalent geometry : angle 0.63013 / 0.33 (20191) hydrogen bonds : bond 0.03976 / 2.56 ( 751) hydrogen bonds : angle 4.31540 / 2.98 ( 2087) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4244.50 seconds wall clock time: 73 minutes 25.41 seconds (4405.41 seconds total)