Starting phenix.real_space_refine on Fri Sep 19 04:30:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9arf_43780/09_2025/9arf_43780.cif Found real_map, /net/cci-nas-00/data/ceres_data/9arf_43780/09_2025/9arf_43780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9arf_43780/09_2025/9arf_43780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9arf_43780/09_2025/9arf_43780.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9arf_43780/09_2025/9arf_43780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9arf_43780/09_2025/9arf_43780.map" } resolution = 3.13 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 298 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 14800 2.51 5 N 3810 2.21 5 O 4302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23032 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 5775 Classifications: {'peptide': 796} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 34, 'TRANS': 761} Chain breaks: 2 Unresolved non-hydrogen bonds: 533 Unresolved non-hydrogen angles: 649 Unresolved non-hydrogen dihedrals: 448 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 21, 'HIS:plan': 5, 'GLU:plan': 21, 'GLN:plan1': 10, 'ASN:plan1': 9, 'TYR:plan': 2, 'ASP:plan': 13, 'PHE:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 367 Chain: "B" Number of atoms: 5684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5684 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 27, 'TRANS': 757} Chain breaks: 2 Unresolved non-hydrogen bonds: 541 Unresolved non-hydrogen angles: 662 Unresolved non-hydrogen dihedrals: 471 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 17, 'GLU:plan': 29, 'HIS:plan': 7, 'PHE:plan': 6, 'ARG:plan': 9, 'ASN:plan1': 5, 'GLN:plan1': 9, 'TYR:plan': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 385 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, D, F Time building chain proxies: 8.63, per 1000 atoms: 0.37 Number of scatterers: 23032 At special positions: 0 Unit cell: (126.567, 148.953, 175.644, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 4302 8.00 N 3810 7.00 C 14800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.02 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.02 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG B 901 " - " ASN B 491 " " NAG D 901 " - " ASN D 491 " " NAG E 1 " - " ASN B 688 " " NAG F 1 " - " ASN D 688 " Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 900.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5912 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 28 sheets defined 41.7% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 35 through 51 removed outlier: 3.829A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 86 Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.529A pdb=" N SER A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.556A pdb=" N ASP A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 147 removed outlier: 3.573A pdb=" N GLN A 147 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 158 Processing helix chain 'A' and resid 170 through 186 Processing helix chain 'A' and resid 204 through 212 removed outlier: 4.086A pdb=" N GLU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 236 removed outlier: 3.913A pdb=" N ALA A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 259 removed outlier: 3.883A pdb=" N ALA A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU A 259 " --> pdb=" O GLY A 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 255 through 259' Processing helix chain 'A' and resid 277 through 296 removed outlier: 3.515A pdb=" N SER A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 327 removed outlier: 3.629A pdb=" N VAL A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 470 removed outlier: 3.839A pdb=" N LEU A 463 " --> pdb=" O CYS A 459 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 506 removed outlier: 3.718A pdb=" N LEU A 505 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 525 removed outlier: 3.823A pdb=" N GLN A 525 " --> pdb=" O GLU A 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 522 through 525' Processing helix chain 'A' and resid 559 through 583 removed outlier: 3.877A pdb=" N LEU A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N HIS A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 582 " --> pdb=" O TYR A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 612 Processing helix chain 'A' and resid 628 through 655 removed outlier: 4.236A pdb=" N LEU A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N MET A 634 " --> pdb=" O ARG A 630 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 640 " --> pdb=" O TRP A 636 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET A 641 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 643 " --> pdb=" O PHE A 639 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 653 " --> pdb=" O ALA A 649 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE A 654 " --> pdb=" O ASN A 650 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU A 655 " --> pdb=" O LEU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 689 through 694 Processing helix chain 'A' and resid 699 through 708 removed outlier: 3.940A pdb=" N HIS A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 723 removed outlier: 3.654A pdb=" N ALA A 717 " --> pdb=" O SER A 713 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE A 718 " --> pdb=" O ALA A 714 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 743 removed outlier: 4.394A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 770 removed outlier: 4.248A pdb=" N GLN A 770 " --> pdb=" O PRO A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 777 removed outlier: 3.642A pdb=" N LEU A 777 " --> pdb=" O SER A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 781 removed outlier: 3.574A pdb=" N GLU A 781 " --> pdb=" O LYS A 778 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 778 through 781' Processing helix chain 'A' and resid 783 through 793 removed outlier: 3.898A pdb=" N ASP A 787 " --> pdb=" O GLY A 783 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU A 788 " --> pdb=" O PHE A 784 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TRP A 792 " --> pdb=" O LEU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 812 No H-bonds generated for 'chain 'A' and resid 810 through 812' Processing helix chain 'A' and resid 813 through 841 removed outlier: 4.100A pdb=" N PHE A 817 " --> pdb=" O MET A 813 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL A 820 " --> pdb=" O VAL A 816 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE A 833 " --> pdb=" O PHE A 829 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG A 839 " --> pdb=" O ILE A 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 4.324A pdb=" N GLU B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 removed outlier: 4.176A pdb=" N ARG B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 119 removed outlier: 4.158A pdb=" N GLN B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.597A pdb=" N MET B 132 " --> pdb=" O GLY B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 removed outlier: 3.584A pdb=" N GLN B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 190 Processing helix chain 'B' and resid 212 through 221 removed outlier: 3.605A pdb=" N LYS B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 248 removed outlier: 4.014A pdb=" N SER B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 264 removed outlier: 4.250A pdb=" N ALA B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 310 removed outlier: 3.709A pdb=" N GLU B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 330 removed outlier: 4.417A pdb=" N TYR B 330 " --> pdb=" O LYS B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 339 Processing helix chain 'B' and resid 459 through 472 removed outlier: 3.655A pdb=" N ASP B 463 " --> pdb=" O GLY B 459 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE B 464 " --> pdb=" O PHE B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 503 Processing helix chain 'B' and resid 555 through 577 removed outlier: 4.058A pdb=" N TRP B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET B 565 " --> pdb=" O MET B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 612 removed outlier: 3.562A pdb=" N ALA B 605 " --> pdb=" O THR B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 656 removed outlier: 3.745A pdb=" N SER B 628 " --> pdb=" O LYS B 624 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR B 647 " --> pdb=" O LEU B 643 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 674 through 677 removed outlier: 3.945A pdb=" N PHE B 677 " --> pdb=" O PRO B 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 674 through 677' Processing helix chain 'B' and resid 689 through 699 removed outlier: 3.830A pdb=" N ARG B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN B 698 " --> pdb=" O ASN B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 708 Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 733 through 742 Processing helix chain 'B' and resid 772 through 787 Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.721A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 845 removed outlier: 4.162A pdb=" N PHE B 822 " --> pdb=" O MET B 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 51 removed outlier: 3.829A pdb=" N LYS C 51 " --> pdb=" O ASN C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 86 Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.529A pdb=" N SER C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR C 109 " --> pdb=" O THR C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 130 removed outlier: 3.556A pdb=" N ASP C 130 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 147 removed outlier: 3.573A pdb=" N GLN C 147 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 158 Processing helix chain 'C' and resid 170 through 186 Processing helix chain 'C' and resid 204 through 212 removed outlier: 4.086A pdb=" N GLU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 236 removed outlier: 3.913A pdb=" N ALA C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL C 231 " --> pdb=" O ASP C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 259 removed outlier: 3.883A pdb=" N ALA C 258 " --> pdb=" O SER C 255 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU C 259 " --> pdb=" O GLY C 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 255 through 259' Processing helix chain 'C' and resid 277 through 296 removed outlier: 3.515A pdb=" N SER C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL C 287 " --> pdb=" O ASP C 283 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN C 290 " --> pdb=" O GLY C 286 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA C 291 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU C 294 " --> pdb=" O GLN C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 327 removed outlier: 3.630A pdb=" N VAL C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 470 removed outlier: 3.840A pdb=" N LEU C 463 " --> pdb=" O CYS C 459 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS C 465 " --> pdb=" O ASP C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 506 removed outlier: 3.717A pdb=" N LEU C 505 " --> pdb=" O MET C 501 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU C 506 " --> pdb=" O MET C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 525 removed outlier: 3.824A pdb=" N GLN C 525 " --> pdb=" O GLU C 522 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 522 through 525' Processing helix chain 'C' and resid 559 through 583 removed outlier: 3.877A pdb=" N LEU C 564 " --> pdb=" O SER C 560 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N HIS C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG C 582 " --> pdb=" O TYR C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 612 Processing helix chain 'C' and resid 628 through 655 removed outlier: 4.236A pdb=" N LEU C 632 " --> pdb=" O SER C 628 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET C 634 " --> pdb=" O ARG C 630 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA C 640 " --> pdb=" O TRP C 636 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET C 641 " --> pdb=" O ALA C 637 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE C 642 " --> pdb=" O GLY C 638 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE C 643 " --> pdb=" O PHE C 639 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA C 653 " --> pdb=" O ALA C 649 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE C 654 " --> pdb=" O ASN C 650 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU C 655 " --> pdb=" O LEU C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 689 through 694 Processing helix chain 'C' and resid 699 through 708 removed outlier: 3.940A pdb=" N HIS C 705 " --> pdb=" O THR C 701 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS C 708 " --> pdb=" O ARG C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 723 removed outlier: 3.654A pdb=" N ALA C 717 " --> pdb=" O SER C 713 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN C 719 " --> pdb=" O ALA C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 743 removed outlier: 4.394A pdb=" N PHE C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 766 through 770 removed outlier: 4.248A pdb=" N GLN C 770 " --> pdb=" O PRO C 767 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 777 removed outlier: 3.642A pdb=" N LEU C 777 " --> pdb=" O SER C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 781 removed outlier: 3.575A pdb=" N GLU C 781 " --> pdb=" O LYS C 778 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 778 through 781' Processing helix chain 'C' and resid 783 through 793 removed outlier: 3.898A pdb=" N ASP C 787 " --> pdb=" O GLY C 783 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU C 788 " --> pdb=" O PHE C 784 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TRP C 792 " --> pdb=" O LEU C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 810 through 812 No H-bonds generated for 'chain 'C' and resid 810 through 812' Processing helix chain 'C' and resid 813 through 841 removed outlier: 4.101A pdb=" N PHE C 817 " --> pdb=" O MET C 813 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C 819 " --> pdb=" O GLY C 815 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL C 820 " --> pdb=" O VAL C 816 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE C 833 " --> pdb=" O PHE C 829 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG C 839 " --> pdb=" O ILE C 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 55 removed outlier: 4.324A pdb=" N GLU D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 92 removed outlier: 4.177A pdb=" N ARG D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 119 removed outlier: 4.158A pdb=" N GLN D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 132 removed outlier: 3.597A pdb=" N MET D 132 " --> pdb=" O GLY D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 164 removed outlier: 3.584A pdb=" N GLN D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR D 164 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 190 Processing helix chain 'D' and resid 212 through 221 removed outlier: 3.606A pdb=" N LYS D 221 " --> pdb=" O GLN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 248 removed outlier: 4.014A pdb=" N SER D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL D 247 " --> pdb=" O VAL D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 264 removed outlier: 4.250A pdb=" N ALA D 263 " --> pdb=" O PRO D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 310 removed outlier: 3.710A pdb=" N GLU D 310 " --> pdb=" O ASP D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 330 removed outlier: 4.416A pdb=" N TYR D 330 " --> pdb=" O LYS D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 339 Processing helix chain 'D' and resid 459 through 472 removed outlier: 3.655A pdb=" N ASP D 463 " --> pdb=" O GLY D 459 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE D 464 " --> pdb=" O PHE D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 503 Processing helix chain 'D' and resid 555 through 577 removed outlier: 4.058A pdb=" N TRP D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET D 565 " --> pdb=" O MET D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 612 removed outlier: 3.562A pdb=" N ALA D 605 " --> pdb=" O THR D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 656 removed outlier: 3.745A pdb=" N SER D 628 " --> pdb=" O LYS D 624 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR D 647 " --> pdb=" O LEU D 643 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA D 648 " --> pdb=" O ALA D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 668 through 673 Processing helix chain 'D' and resid 674 through 677 removed outlier: 3.945A pdb=" N PHE D 677 " --> pdb=" O PRO D 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 674 through 677' Processing helix chain 'D' and resid 689 through 699 removed outlier: 3.830A pdb=" N ARG D 693 " --> pdb=" O GLY D 689 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN D 698 " --> pdb=" O ASN D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 708 Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 772 through 787 Processing helix chain 'D' and resid 787 through 797 removed outlier: 3.721A pdb=" N GLU D 791 " --> pdb=" O GLY D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 845 removed outlier: 4.162A pdb=" N PHE D 822 " --> pdb=" O MET D 818 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 63 removed outlier: 3.617A pdb=" N THR A 63 " --> pdb=" O ILE A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 removed outlier: 7.266A pdb=" N ILE A 163 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N LEU A 195 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N SER A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU A 166 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 271 removed outlier: 3.742A pdb=" N TYR A 351 " --> pdb=" O TYR A 367 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASN A 355 " --> pdb=" O GLN A 363 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLN A 363 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLN A 357 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU A 361 " --> pdb=" O GLN A 357 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 366 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 373 " --> pdb=" O ILE A 366 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 476 through 478 removed outlier: 6.034A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL A 401 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N ILE A 513 " --> pdb=" O ARG A 763 " (cutoff:3.500A) removed outlier: 9.287A pdb=" N ARG A 763 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ALA A 515 " --> pdb=" O GLY A 761 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLY A 761 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU A 517 " --> pdb=" O GLY A 759 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 410 through 413 removed outlier: 3.821A pdb=" N GLY A 438 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 487 through 489 removed outlier: 3.615A pdb=" N GLU A 497 " --> pdb=" O GLU A 488 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 681 through 682 removed outlier: 7.029A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.607A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 67 through 73 removed outlier: 3.585A pdb=" N GLU B 69 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLY B 36 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL B 42 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 198 through 199 removed outlier: 7.152A pdb=" N ILE B 168 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N LEU B 229 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER B 170 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N TYR B 231 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL B 172 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL B 258 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N TYR B 282 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU B 362 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LYS B 378 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE B 364 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 408 through 409 removed outlier: 3.608A pdb=" N VAL B 409 " --> pdb=" O MET B 508 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 765 " --> pdb=" O ALA B 509 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 418 through 420 Processing sheet with id=AB3, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AB4, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AB5, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.711A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N ASP B 732 " --> pdb=" O GLY B 684 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 62 through 63 removed outlier: 3.618A pdb=" N THR C 63 " --> pdb=" O ILE C 29 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 193 through 197 removed outlier: 7.267A pdb=" N ILE C 163 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N LEU C 195 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU C 165 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE C 164 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N SER C 222 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU C 166 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 269 through 271 removed outlier: 3.743A pdb=" N TYR C 351 " --> pdb=" O TYR C 367 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASN C 355 " --> pdb=" O GLN C 363 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLN C 363 " --> pdb=" O ASN C 355 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLN C 357 " --> pdb=" O LEU C 361 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LEU C 361 " --> pdb=" O GLN C 357 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 366 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 373 " --> pdb=" O ILE C 366 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 476 through 478 removed outlier: 6.035A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL C 401 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N ILE C 513 " --> pdb=" O ARG C 763 " (cutoff:3.500A) removed outlier: 9.287A pdb=" N ARG C 763 " --> pdb=" O ILE C 513 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ALA C 515 " --> pdb=" O GLY C 761 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N GLY C 761 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU C 517 " --> pdb=" O GLY C 759 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 410 through 413 removed outlier: 3.820A pdb=" N GLY C 438 " --> pdb=" O VAL C 451 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 487 through 489 removed outlier: 3.614A pdb=" N GLU C 497 " --> pdb=" O GLU C 488 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 681 through 682 removed outlier: 7.029A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 9.607A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 67 through 73 removed outlier: 3.586A pdb=" N GLU D 69 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLY D 36 " --> pdb=" O ILE D 94 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL D 42 " --> pdb=" O ALA D 100 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 198 through 199 removed outlier: 7.152A pdb=" N ILE D 168 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N LEU D 229 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER D 170 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N TYR D 231 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL D 172 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N TRP D 256 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N VAL D 280 " --> pdb=" O TRP D 256 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL D 258 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N TYR D 282 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU D 362 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LYS D 378 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE D 364 " --> pdb=" O VAL D 376 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 408 through 409 removed outlier: 3.608A pdb=" N VAL D 409 " --> pdb=" O MET D 508 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA D 765 " --> pdb=" O ALA D 509 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 418 through 420 Processing sheet with id=AC8, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AC9, first strand: chain 'D' and resid 531 through 532 Processing sheet with id=AD1, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.711A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) 898 hydrogen bonds defined for protein. 2598 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.38 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.20: 128 1.20 - 1.35: 7316 1.35 - 1.51: 6822 1.51 - 1.67: 9044 1.67 - 1.82: 202 Bond restraints: 23512 Sorted by residual: bond pdb=" C MET C 512 " pdb=" O MET C 512 " ideal model delta sigma weight residual 1.234 1.038 0.196 1.24e-02 6.50e+03 2.49e+02 bond pdb=" C MET A 512 " pdb=" O MET A 512 " ideal model delta sigma weight residual 1.234 1.038 0.195 1.24e-02 6.50e+03 2.48e+02 bond pdb=" C MET B 508 " pdb=" O MET B 508 " ideal model delta sigma weight residual 1.234 1.044 0.190 1.26e-02 6.30e+03 2.27e+02 bond pdb=" C MET D 508 " pdb=" O MET D 508 " ideal model delta sigma weight residual 1.234 1.044 0.190 1.26e-02 6.30e+03 2.27e+02 bond pdb=" C ALA D 509 " pdb=" O ALA D 509 " ideal model delta sigma weight residual 1.236 1.062 0.174 1.20e-02 6.94e+03 2.09e+02 ... (remaining 23507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.29: 31958 6.29 - 12.58: 150 12.58 - 18.87: 14 18.87 - 25.17: 2 25.17 - 31.46: 2 Bond angle restraints: 32126 Sorted by residual: angle pdb=" C ASN B 495 " pdb=" CA ASN B 495 " pdb=" CB ASN B 495 " ideal model delta sigma weight residual 113.15 81.69 31.46 2.38e+00 1.77e-01 1.75e+02 angle pdb=" C ASN D 495 " pdb=" CA ASN D 495 " pdb=" CB ASN D 495 " ideal model delta sigma weight residual 113.15 81.70 31.45 2.38e+00 1.77e-01 1.75e+02 angle pdb=" C ASP C 690 " pdb=" CA ASP C 690 " pdb=" CB ASP C 690 " ideal model delta sigma weight residual 110.79 89.10 21.69 1.66e+00 3.63e-01 1.71e+02 angle pdb=" C ASP A 690 " pdb=" CA ASP A 690 " pdb=" CB ASP A 690 " ideal model delta sigma weight residual 110.79 89.11 21.68 1.66e+00 3.63e-01 1.71e+02 angle pdb=" C GLU B 500 " pdb=" CA GLU B 500 " pdb=" CB GLU B 500 " ideal model delta sigma weight residual 110.85 95.10 15.75 1.70e+00 3.46e-01 8.59e+01 ... (remaining 32121 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.87: 13448 22.87 - 45.73: 394 45.73 - 68.60: 76 68.60 - 91.46: 8 91.46 - 114.33: 6 Dihedral angle restraints: 13932 sinusoidal: 4774 harmonic: 9158 Sorted by residual: dihedral pdb=" C ASN B 495 " pdb=" N ASN B 495 " pdb=" CA ASN B 495 " pdb=" CB ASN B 495 " ideal model delta harmonic sigma weight residual -122.60 -89.15 -33.45 0 2.50e+00 1.60e-01 1.79e+02 dihedral pdb=" C ASN D 495 " pdb=" N ASN D 495 " pdb=" CA ASN D 495 " pdb=" CB ASN D 495 " ideal model delta harmonic sigma weight residual -122.60 -89.16 -33.44 0 2.50e+00 1.60e-01 1.79e+02 dihedral pdb=" C ASP C 690 " pdb=" N ASP C 690 " pdb=" CA ASP C 690 " pdb=" CB ASP C 690 " ideal model delta harmonic sigma weight residual -122.60 -98.01 -24.59 0 2.50e+00 1.60e-01 9.68e+01 ... (remaining 13929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.175: 3728 0.175 - 0.350: 112 0.350 - 0.525: 22 0.525 - 0.700: 4 0.700 - 0.875: 4 Chirality restraints: 3870 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.53 -0.87 2.00e-02 2.50e+03 1.91e+03 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.53 -0.87 2.00e-02 2.50e+03 1.91e+03 chirality pdb=" CA TYR D 507 " pdb=" N TYR D 507 " pdb=" C TYR D 507 " pdb=" CB TYR D 507 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.36e+01 ... (remaining 3867 not shown) Planarity restraints: 4074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP A 792 " 0.031 2.00e-02 2.50e+03 6.52e-02 4.25e+01 pdb=" C TRP A 792 " -0.113 2.00e-02 2.50e+03 pdb=" O TRP A 792 " 0.043 2.00e-02 2.50e+03 pdb=" N VAL A 793 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP C 792 " 0.031 2.00e-02 2.50e+03 6.51e-02 4.24e+01 pdb=" C TRP C 792 " -0.112 2.00e-02 2.50e+03 pdb=" O TRP C 792 " 0.043 2.00e-02 2.50e+03 pdb=" N VAL C 793 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 500 " 0.026 2.00e-02 2.50e+03 5.45e-02 2.97e+01 pdb=" C GLU D 500 " -0.094 2.00e-02 2.50e+03 pdb=" O GLU D 500 " 0.036 2.00e-02 2.50e+03 pdb=" N VAL D 501 " 0.032 2.00e-02 2.50e+03 ... (remaining 4071 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 136 2.57 - 3.15: 18076 3.15 - 3.73: 32718 3.73 - 4.32: 43831 4.32 - 4.90: 74299 Nonbonded interactions: 169060 Sorted by model distance: nonbonded pdb=" O ILE B 297 " pdb=" CG2 THR B 301 " model vdw 1.985 3.460 nonbonded pdb=" O ILE D 297 " pdb=" CG2 THR D 301 " model vdw 1.986 3.460 nonbonded pdb=" NH1 ARG A 722 " pdb=" OD2 ASP A 745 " model vdw 2.099 3.120 nonbonded pdb=" NH1 ARG C 722 " pdb=" OD2 ASP C 745 " model vdw 2.099 3.120 nonbonded pdb=" OH TYR A 647 " pdb=" CD1 ILE D 641 " model vdw 2.153 3.460 ... (remaining 169055 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 24.380 Find NCS groups from input model: 0.180 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: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.196 23534 Z= 0.760 Angle : 1.168 31.458 32176 Z= 0.758 Chirality : 0.077 0.875 3870 Planarity : 0.007 0.065 4070 Dihedral : 11.195 114.326 7972 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.56 % Favored : 95.32 % Rotamer: Outliers : 5.16 % Allowed : 6.04 % Favored : 88.80 % Cbeta Deviations : 1.42 % 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 aren not related in a simple way. whole: -3.34 (0.13), residues: 3138 helix: -1.25 (0.14), residues: 1202 sheet: -2.19 (0.23), residues: 430 loop : -3.08 (0.13), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 763 TYR 0.064 0.001 TYR D 507 PHE 0.058 0.002 PHE C 529 TRP 0.014 0.001 TRP A 636 HIS 0.005 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.01039 (23512) covalent geometry : angle 1.15659 (32126) SS BOND : bond 0.00450 ( 16) SS BOND : angle 1.24853 ( 32) hydrogen bonds : bond 0.23941 ( 898) hydrogen bonds : angle 7.27617 ( 2598) link_BETA1-4 : bond 0.06442 ( 2) link_BETA1-4 : angle 11.90154 ( 6) link_NAG-ASN : bond 0.00297 ( 4) link_NAG-ASN : angle 1.00585 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 411 time to evaluate : 0.810 Fit side-chains REVERT: B 386 MET cc_start: 0.8867 (mmm) cc_final: 0.8449 (mmm) REVERT: B 513 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.7733 (mt) REVERT: B 515 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8643 (mt) REVERT: B 654 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8524 (mtt) REVERT: D 513 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.7738 (mt) outliers start: 116 outliers final: 66 residues processed: 512 average time/residue: 0.1504 time to fit residues: 119.3072 Evaluate side-chains 361 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 291 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 663 ARG Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 722 ARG Chi-restraints excluded: chain A residue 725 LYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 795 TYR Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 137 LYS Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 437 GLN Chi-restraints excluded: chain B residue 485 LYS Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 515 ILE Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 654 MET Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 663 ARG Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 722 ARG Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 795 TYR Chi-restraints excluded: chain C residue 798 CYS Chi-restraints excluded: chain C residue 819 LEU Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 185 LYS Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 437 GLN Chi-restraints excluded: chain D residue 485 LYS Chi-restraints excluded: chain D residue 504 LYS Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 515 ILE Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 617 SER Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 630 ILE Chi-restraints excluded: chain D residue 642 PHE Chi-restraints excluded: chain D residue 686 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 0.0770 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 30.0000 chunk 298 optimal weight: 3.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 313 ASN A 358 ASN A 471 GLN A 724 ASN B 152 GLN B 192 ASN B 219 GLN B 437 GLN C 146 HIS C 313 ASN C 358 ASN C 471 GLN C 724 ASN D 152 GLN D 192 ASN D 219 GLN D 437 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.217945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.171345 restraints weight = 27451.261| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 2.19 r_work: 0.3710 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23534 Z= 0.131 Angle : 0.559 8.577 32176 Z= 0.292 Chirality : 0.043 0.194 3870 Planarity : 0.004 0.052 4070 Dihedral : 8.150 95.623 3585 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.61 % Favored : 94.33 % Rotamer: Outliers : 2.76 % Allowed : 10.13 % Favored : 87.11 % 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 aren not related in a simple way. whole: -2.17 (0.14), residues: 3138 helix: -0.11 (0.15), residues: 1216 sheet: -1.61 (0.25), residues: 448 loop : -2.59 (0.14), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 540 TYR 0.016 0.001 TYR C 795 PHE 0.019 0.002 PHE D 642 TRP 0.015 0.001 TRP A 636 HIS 0.006 0.001 HIS C 280 Details of bonding type rmsd covalent geometry : bond 0.00276 (23512) covalent geometry : angle 0.55626 (32126) SS BOND : bond 0.01071 ( 16) SS BOND : angle 1.54848 ( 32) hydrogen bonds : bond 0.05334 ( 898) hydrogen bonds : angle 4.95740 ( 2598) link_BETA1-4 : bond 0.00195 ( 2) link_BETA1-4 : angle 1.37532 ( 6) link_NAG-ASN : bond 0.00237 ( 4) link_NAG-ASN : angle 1.60402 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 301 time to evaluate : 0.868 Fit side-chains REVERT: A 128 TYR cc_start: 0.8705 (m-80) cc_final: 0.8498 (m-80) REVERT: B 115 ILE cc_start: 0.8803 (mm) cc_final: 0.8564 (mm) outliers start: 62 outliers final: 39 residues processed: 352 average time/residue: 0.1344 time to fit residues: 76.6288 Evaluate side-chains 313 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 274 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 706 MET Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 437 GLN Chi-restraints excluded: chain B residue 485 LYS Chi-restraints excluded: chain B residue 504 LYS Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 654 MET Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 437 GLN Chi-restraints excluded: chain D residue 504 LYS Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 798 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 56 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 259 optimal weight: 9.9990 chunk 103 optimal weight: 0.8980 chunk 196 optimal weight: 0.0470 chunk 292 optimal weight: 40.0000 chunk 63 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 HIS A 313 ASN A 358 ASN B 192 ASN C 280 HIS C 313 ASN C 358 ASN D 118 GLN D 153 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.216072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.167262 restraints weight = 27405.368| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 2.22 r_work: 0.3699 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23534 Z= 0.115 Angle : 0.528 9.252 32176 Z= 0.273 Chirality : 0.042 0.196 3870 Planarity : 0.004 0.054 4070 Dihedral : 6.878 91.233 3495 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.58 % Allowed : 11.64 % Favored : 85.78 % 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 aren not related in a simple way. whole: -1.67 (0.15), residues: 3138 helix: 0.50 (0.16), residues: 1192 sheet: -1.46 (0.25), residues: 456 loop : -2.40 (0.14), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 540 TYR 0.014 0.001 TYR C 795 PHE 0.015 0.001 PHE D 642 TRP 0.010 0.001 TRP A 636 HIS 0.004 0.001 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00256 (23512) covalent geometry : angle 0.52261 (32126) SS BOND : bond 0.00419 ( 16) SS BOND : angle 2.24720 ( 32) hydrogen bonds : bond 0.04329 ( 898) hydrogen bonds : angle 4.46054 ( 2598) link_BETA1-4 : bond 0.00357 ( 2) link_BETA1-4 : angle 0.96953 ( 6) link_NAG-ASN : bond 0.00157 ( 4) link_NAG-ASN : angle 1.80503 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 284 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.6471 (tpp) cc_final: 0.6192 (mmm) REVERT: B 115 ILE cc_start: 0.8702 (mm) cc_final: 0.8489 (mm) REVERT: B 485 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7879 (mmtp) outliers start: 58 outliers final: 38 residues processed: 327 average time/residue: 0.1319 time to fit residues: 70.2449 Evaluate side-chains 317 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 278 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 706 MET Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 437 GLN Chi-restraints excluded: chain B residue 485 LYS Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 744 CYS Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 372 LYS Chi-restraints excluded: chain D residue 437 GLN Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 798 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 304 optimal weight: 0.0030 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 265 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 95 optimal weight: 8.9990 chunk 200 optimal weight: 0.9990 chunk 171 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 235 optimal weight: 20.0000 chunk 49 optimal weight: 0.6980 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 358 ASN B 153 GLN C 313 ASN C 358 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.214902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.166798 restraints weight = 27465.447| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.14 r_work: 0.3695 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23534 Z= 0.116 Angle : 0.529 10.191 32176 Z= 0.270 Chirality : 0.043 0.179 3870 Planarity : 0.004 0.055 4070 Dihedral : 6.321 84.413 3480 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.11 % Allowed : 11.69 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.15), residues: 3138 helix: 0.76 (0.16), residues: 1194 sheet: -1.54 (0.24), residues: 456 loop : -2.27 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 712 TYR 0.015 0.001 TYR B 179 PHE 0.016 0.001 PHE D 550 TRP 0.010 0.001 TRP B 607 HIS 0.004 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00268 (23512) covalent geometry : angle 0.52571 (32126) SS BOND : bond 0.00364 ( 16) SS BOND : angle 1.32263 ( 32) hydrogen bonds : bond 0.03924 ( 898) hydrogen bonds : angle 4.22012 ( 2598) link_BETA1-4 : bond 0.00216 ( 2) link_BETA1-4 : angle 0.95041 ( 6) link_NAG-ASN : bond 0.00112 ( 4) link_NAG-ASN : angle 2.22547 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 281 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 134 MET cc_start: 0.7356 (tpp) cc_final: 0.7092 (mmm) outliers start: 70 outliers final: 48 residues processed: 339 average time/residue: 0.1204 time to fit residues: 67.9517 Evaluate side-chains 316 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 268 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 706 MET Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 437 GLN Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 744 CYS Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 437 GLN Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 524 ASP Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 654 MET Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 706 MET Chi-restraints excluded: chain D residue 798 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 29 optimal weight: 9.9990 chunk 245 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 269 optimal weight: 1.9990 chunk 276 optimal weight: 8.9990 chunk 224 optimal weight: 2.9990 chunk 215 optimal weight: 20.0000 chunk 72 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN B 153 GLN C 146 HIS C 313 ASN C 358 ASN D 118 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.212609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.162882 restraints weight = 27096.437| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.09 r_work: 0.3683 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23534 Z= 0.165 Angle : 0.583 10.983 32176 Z= 0.297 Chirality : 0.044 0.164 3870 Planarity : 0.004 0.055 4070 Dihedral : 6.219 75.151 3475 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.29 % Allowed : 12.36 % Favored : 84.36 % 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 aren not related in a simple way. whole: -1.36 (0.15), residues: 3138 helix: 0.83 (0.16), residues: 1202 sheet: -1.45 (0.24), residues: 456 loop : -2.24 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 468 TYR 0.017 0.002 TYR D 179 PHE 0.018 0.002 PHE D 550 TRP 0.008 0.001 TRP B 607 HIS 0.005 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00406 (23512) covalent geometry : angle 0.57677 (32126) SS BOND : bond 0.00465 ( 16) SS BOND : angle 2.08452 ( 32) hydrogen bonds : bond 0.04366 ( 898) hydrogen bonds : angle 4.23738 ( 2598) link_BETA1-4 : bond 0.00319 ( 2) link_BETA1-4 : angle 1.10727 ( 6) link_NAG-ASN : bond 0.00163 ( 4) link_NAG-ASN : angle 2.74500 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 281 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.6365 (tpp) cc_final: 0.6106 (mmm) REVERT: A 695 ARG cc_start: 0.8248 (tmm-80) cc_final: 0.7907 (ttm170) REVERT: C 704 ARG cc_start: 0.8094 (mtm-85) cc_final: 0.7852 (mtm110) REVERT: D 134 MET cc_start: 0.7391 (tpp) cc_final: 0.7173 (mmm) outliers start: 74 outliers final: 52 residues processed: 339 average time/residue: 0.1322 time to fit residues: 74.3480 Evaluate side-chains 326 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 274 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 415 MET Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 744 CYS Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 441 ILE Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 524 ASP Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 654 MET Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 706 MET Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 798 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 29 optimal weight: 8.9990 chunk 278 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 72 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 279 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 571 HIS B 153 GLN C 313 ASN C 571 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.214147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.167084 restraints weight = 27315.482| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.12 r_work: 0.3662 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23534 Z= 0.112 Angle : 0.535 10.932 32176 Z= 0.271 Chirality : 0.042 0.173 3870 Planarity : 0.004 0.055 4070 Dihedral : 5.407 54.223 3467 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.22 % Allowed : 12.93 % Favored : 84.84 % 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 aren not related in a simple way. whole: -1.17 (0.15), residues: 3138 helix: 0.97 (0.15), residues: 1214 sheet: -1.36 (0.24), residues: 456 loop : -2.15 (0.15), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 712 TYR 0.034 0.001 TYR D 179 PHE 0.018 0.001 PHE D 550 TRP 0.009 0.001 TRP C 768 HIS 0.003 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00260 (23512) covalent geometry : angle 0.52836 (32126) SS BOND : bond 0.00375 ( 16) SS BOND : angle 1.42358 ( 32) hydrogen bonds : bond 0.03631 ( 898) hydrogen bonds : angle 4.11871 ( 2598) link_BETA1-4 : bond 0.00305 ( 2) link_BETA1-4 : angle 1.08448 ( 6) link_NAG-ASN : bond 0.00171 ( 4) link_NAG-ASN : angle 3.76574 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 286 time to evaluate : 0.924 Fit side-chains REVERT: A 744 CYS cc_start: 0.6424 (OUTLIER) cc_final: 0.6139 (m) REVERT: B 314 ILE cc_start: 0.2759 (OUTLIER) cc_final: 0.2529 (tp) REVERT: C 704 ARG cc_start: 0.8136 (mtm-85) cc_final: 0.7882 (mtm110) REVERT: C 744 CYS cc_start: 0.6348 (OUTLIER) cc_final: 0.6066 (m) REVERT: D 134 MET cc_start: 0.7536 (tpp) cc_final: 0.7320 (mmm) outliers start: 50 outliers final: 43 residues processed: 325 average time/residue: 0.1290 time to fit residues: 69.3482 Evaluate side-chains 314 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 268 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 706 MET Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 744 CYS Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 524 ASP Chi-restraints excluded: chain D residue 654 MET Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 706 MET Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 798 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 161 optimal weight: 5.9990 chunk 256 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 189 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 208 optimal weight: 0.6980 chunk 243 optimal weight: 10.0000 chunk 226 optimal weight: 0.8980 chunk 248 optimal weight: 0.6980 chunk 155 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN C 313 ASN C 358 ASN ** C 363 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 = 0.4409 r_free = 0.4409 target = 0.214227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.166632 restraints weight = 27248.679| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.13 r_work: 0.3676 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3615 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 23534 Z= 0.107 Angle : 0.524 15.059 32176 Z= 0.265 Chirality : 0.042 0.152 3870 Planarity : 0.004 0.055 4070 Dihedral : 4.982 54.370 3467 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.58 % Allowed : 12.58 % Favored : 84.84 % 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 aren not related in a simple way. whole: -1.00 (0.15), residues: 3138 helix: 1.13 (0.16), residues: 1214 sheet: -1.21 (0.25), residues: 468 loop : -2.12 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 540 TYR 0.017 0.001 TYR D 239 PHE 0.030 0.001 PHE B 642 TRP 0.008 0.001 TRP B 635 HIS 0.003 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00250 (23512) covalent geometry : angle 0.51702 (32126) SS BOND : bond 0.00363 ( 16) SS BOND : angle 1.18737 ( 32) hydrogen bonds : bond 0.03469 ( 898) hydrogen bonds : angle 4.05314 ( 2598) link_BETA1-4 : bond 0.00370 ( 2) link_BETA1-4 : angle 1.02758 ( 6) link_NAG-ASN : bond 0.00347 ( 4) link_NAG-ASN : angle 4.18196 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 279 time to evaluate : 0.843 Fit side-chains REVERT: A 695 ARG cc_start: 0.8255 (tmm-80) cc_final: 0.7928 (ttm170) REVERT: A 744 CYS cc_start: 0.6330 (OUTLIER) cc_final: 0.6104 (m) REVERT: B 314 ILE cc_start: 0.2840 (OUTLIER) cc_final: 0.2609 (tp) REVERT: C 704 ARG cc_start: 0.8154 (mtm-85) cc_final: 0.7901 (mtm110) REVERT: C 744 CYS cc_start: 0.6368 (OUTLIER) cc_final: 0.6080 (m) REVERT: D 134 MET cc_start: 0.7479 (tpp) cc_final: 0.7263 (mmm) outliers start: 58 outliers final: 46 residues processed: 323 average time/residue: 0.1209 time to fit residues: 65.1595 Evaluate side-chains 314 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 265 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 439 ARG Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 706 MET Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 744 CYS Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 524 ASP Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 654 MET Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 706 MET Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 798 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 147 optimal weight: 0.0970 chunk 118 optimal weight: 0.0670 chunk 146 optimal weight: 0.0980 chunk 277 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 167 optimal weight: 0.1980 chunk 57 optimal weight: 0.0980 chunk 112 optimal weight: 6.9990 chunk 273 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 3 optimal weight: 40.0000 overall best weight: 0.1116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 313 ASN D 359 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.216763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.162498 restraints weight = 26770.073| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.09 r_work: 0.3633 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 23534 Z= 0.088 Angle : 0.493 14.747 32176 Z= 0.248 Chirality : 0.041 0.152 3870 Planarity : 0.004 0.054 4070 Dihedral : 4.459 48.564 3466 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.00 % Allowed : 12.93 % Favored : 85.07 % 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 aren not related in a simple way. whole: -0.82 (0.15), residues: 3138 helix: 1.30 (0.16), residues: 1216 sheet: -1.23 (0.24), residues: 480 loop : -1.98 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 712 TYR 0.019 0.001 TYR B 179 PHE 0.019 0.001 PHE B 642 TRP 0.009 0.001 TRP A 636 HIS 0.005 0.000 HIS D 359 Details of bonding type rmsd covalent geometry : bond 0.00190 (23512) covalent geometry : angle 0.48778 (32126) SS BOND : bond 0.00272 ( 16) SS BOND : angle 0.72437 ( 32) hydrogen bonds : bond 0.02830 ( 898) hydrogen bonds : angle 3.95646 ( 2598) link_BETA1-4 : bond 0.00410 ( 2) link_BETA1-4 : angle 1.00983 ( 6) link_NAG-ASN : bond 0.00192 ( 4) link_NAG-ASN : angle 3.41376 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 273 time to evaluate : 0.833 Fit side-chains REVERT: A 744 CYS cc_start: 0.6147 (OUTLIER) cc_final: 0.5907 (m) REVERT: B 314 ILE cc_start: 0.2951 (OUTLIER) cc_final: 0.2742 (tp) REVERT: C 704 ARG cc_start: 0.8260 (mtm-85) cc_final: 0.8009 (mtm110) REVERT: C 744 CYS cc_start: 0.6115 (OUTLIER) cc_final: 0.5912 (m) REVERT: D 134 MET cc_start: 0.7515 (tpp) cc_final: 0.7288 (mmm) outliers start: 45 outliers final: 30 residues processed: 308 average time/residue: 0.1151 time to fit residues: 59.5511 Evaluate side-chains 300 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 267 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 744 CYS Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 524 ASP Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 798 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 38 optimal weight: 2.9990 chunk 309 optimal weight: 0.5980 chunk 218 optimal weight: 0.0470 chunk 205 optimal weight: 0.5980 chunk 160 optimal weight: 4.9990 chunk 145 optimal weight: 0.6980 chunk 193 optimal weight: 0.8980 chunk 267 optimal weight: 0.0670 chunk 233 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS C 313 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.215761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.160798 restraints weight = 27010.687| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.15 r_work: 0.3617 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 23534 Z= 0.090 Angle : 0.498 14.832 32176 Z= 0.251 Chirality : 0.041 0.156 3870 Planarity : 0.004 0.054 4070 Dihedral : 4.361 42.572 3466 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.73 % Allowed : 13.51 % Favored : 84.76 % 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 aren not related in a simple way. whole: -0.70 (0.15), residues: 3138 helix: 1.38 (0.15), residues: 1220 sheet: -1.12 (0.24), residues: 480 loop : -1.91 (0.16), residues: 1438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 712 TYR 0.019 0.001 TYR B 179 PHE 0.036 0.001 PHE D 642 TRP 0.008 0.001 TRP B 635 HIS 0.002 0.000 HIS D 703 Details of bonding type rmsd covalent geometry : bond 0.00200 (23512) covalent geometry : angle 0.49459 (32126) SS BOND : bond 0.00252 ( 16) SS BOND : angle 0.84993 ( 32) hydrogen bonds : bond 0.02946 ( 898) hydrogen bonds : angle 3.90981 ( 2598) link_BETA1-4 : bond 0.00310 ( 2) link_BETA1-4 : angle 0.88192 ( 6) link_NAG-ASN : bond 0.00140 ( 4) link_NAG-ASN : angle 2.91776 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 269 time to evaluate : 0.892 Fit side-chains REVERT: C 704 ARG cc_start: 0.8256 (mtm-85) cc_final: 0.8008 (mtm110) REVERT: D 134 MET cc_start: 0.7530 (tpp) cc_final: 0.7311 (mmm) outliers start: 39 outliers final: 32 residues processed: 301 average time/residue: 0.1268 time to fit residues: 63.8841 Evaluate side-chains 292 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 260 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 524 ASP Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 706 MET Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 798 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 290 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 chunk 203 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 chunk 247 optimal weight: 0.8980 chunk 156 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 299 optimal weight: 0.7980 chunk 232 optimal weight: 0.3980 chunk 240 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 313 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.215241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.163611 restraints weight = 27326.719| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.33 r_work: 0.3653 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 23534 Z= 0.103 Angle : 0.519 14.574 32176 Z= 0.262 Chirality : 0.042 0.168 3870 Planarity : 0.004 0.050 4070 Dihedral : 4.361 40.726 3464 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.47 % Allowed : 13.78 % Favored : 84.76 % 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 aren not related in a simple way. whole: -0.65 (0.15), residues: 3138 helix: 1.41 (0.15), residues: 1220 sheet: -0.98 (0.25), residues: 460 loop : -1.91 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 540 TYR 0.022 0.001 TYR B 179 PHE 0.038 0.001 PHE B 642 TRP 0.009 0.001 TRP B 635 HIS 0.003 0.001 HIS A 780 Details of bonding type rmsd covalent geometry : bond 0.00242 (23512) covalent geometry : angle 0.51452 (32126) SS BOND : bond 0.00318 ( 16) SS BOND : angle 1.53077 ( 32) hydrogen bonds : bond 0.03176 ( 898) hydrogen bonds : angle 3.94081 ( 2598) link_BETA1-4 : bond 0.00355 ( 2) link_BETA1-4 : angle 0.91146 ( 6) link_NAG-ASN : bond 0.00095 ( 4) link_NAG-ASN : angle 2.69396 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6276 Ramachandran restraints generated. 3138 Oldfield, 0 Emsley, 3138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 270 time to evaluate : 0.849 Fit side-chains REVERT: C 704 ARG cc_start: 0.8171 (mtm-85) cc_final: 0.7911 (mtm110) REVERT: D 134 MET cc_start: 0.7435 (tpp) cc_final: 0.7221 (mmm) outliers start: 33 outliers final: 33 residues processed: 300 average time/residue: 0.1238 time to fit residues: 62.2747 Evaluate side-chains 295 residues out of total 2750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 262 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 749 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 524 ASP Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 706 MET Chi-restraints excluded: chain D residue 749 VAL Chi-restraints excluded: chain D residue 798 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 129 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 233 optimal weight: 0.8980 chunk 81 optimal weight: 50.0000 chunk 220 optimal weight: 0.0980 chunk 299 optimal weight: 1.9990 chunk 240 optimal weight: 0.0770 chunk 268 optimal weight: 1.9990 chunk 309 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 127 optimal weight: 0.0970 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 358 ASN C 146 HIS C 313 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.215668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.161761 restraints weight = 26933.256| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 2.32 r_work: 0.3498 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 23534 Z= 0.090 Angle : 0.503 14.970 32176 Z= 0.253 Chirality : 0.041 0.154 3870 Planarity : 0.004 0.054 4070 Dihedral : 4.136 41.768 3464 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.60 % Allowed : 13.64 % Favored : 84.76 % 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 aren not related in a simple way. whole: -0.55 (0.15), residues: 3138 helix: 1.49 (0.15), residues: 1220 sheet: -0.91 (0.25), residues: 460 loop : -1.87 (0.16), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 712 TYR 0.023 0.001 TYR B 179 PHE 0.037 0.001 PHE D 642 TRP 0.009 0.001 TRP B 607 HIS 0.002 0.000 HIS C 780 Details of bonding type rmsd covalent geometry : bond 0.00203 (23512) covalent geometry : angle 0.49991 (32126) SS BOND : bond 0.00281 ( 16) SS BOND : angle 1.15320 ( 32) hydrogen bonds : bond 0.02856 ( 898) hydrogen bonds : angle 3.87469 ( 2598) link_BETA1-4 : bond 0.00375 ( 2) link_BETA1-4 : angle 0.94667 ( 6) link_NAG-ASN : bond 0.00050 ( 4) link_NAG-ASN : angle 2.54356 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6010.47 seconds wall clock time: 103 minutes 1.66 seconds (6181.66 seconds total)