Starting phenix.real_space_refine on Tue Apr 7 11:15:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10fd_75127/04_2026/10fd_75127_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/10fd_75127/04_2026/10fd_75127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10fd_75127/04_2026/10fd_75127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10fd_75127/04_2026/10fd_75127.map" model { file = "/net/cci-nas-00/data/ceres_data/10fd_75127/04_2026/10fd_75127_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10fd_75127/04_2026/10fd_75127_neut.cif" } resolution = 3.09 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= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 140 5.16 5 C 17068 2.51 5 N 4517 2.21 5 O 4990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26715 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 6002 Classifications: {'peptide': 791} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 31, 'TRANS': 759} Chain breaks: 2 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 13, 'ASP:plan': 6, 'ARG:plan': 7, 'GLN:plan1': 3, 'ASN:plan1': 6, 'TYR:plan': 1, 'PHE:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 158 Chain: "B" Number of atoms: 5719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 5719 Classifications: {'peptide': 774} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'PTRANS': 28, 'TRANS': 745} Chain breaks: 4 Unresolved non-hydrogen bonds: 409 Unresolved non-hydrogen angles: 520 Unresolved non-hydrogen dihedrals: 340 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'TYR:plan': 7, 'ASP:plan': 13, 'GLU:plan': 14, 'ARG:plan': 5, 'ASN:plan1': 6, 'PHE:plan': 6, 'GLN:plan1': 5, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 257 Chain: "C" Number of atoms: 5814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 5814 Classifications: {'peptide': 791} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PTRANS': 31, 'TRANS': 759} Chain breaks: 2 Unresolved non-hydrogen bonds: 435 Unresolved non-hydrogen angles: 540 Unresolved non-hydrogen dihedrals: 354 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ARG:plan': 12, 'GLU:plan': 15, 'ASP:plan': 13, 'ASN:plan1': 7, 'HIS:plan': 2, 'GLN:plan1': 5, 'TYR:plan': 4, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 262 Chain: "D" Number of atoms: 5582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 5582 Classifications: {'peptide': 771} Incomplete info: {'truncation_to_alanine': 138} Link IDs: {'PTRANS': 27, 'TRANS': 743} Chain breaks: 5 Unresolved non-hydrogen bonds: 523 Unresolved non-hydrogen angles: 665 Unresolved non-hydrogen dihedrals: 431 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'TYR:plan': 6, 'TRP:plan': 2, 'ASP:plan': 15, 'GLU:plan': 18, 'ARG:plan': 8, 'ASN:plan1': 9, 'PHE:plan': 7, 'GLN:plan1': 6, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 320 Chain: "E" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 872 Classifications: {'peptide': 113} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 107} Chain: "F" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 927 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "I" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 872 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "J" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 927 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Time building chain proxies: 5.88, per 1000 atoms: 0.22 Number of scatterers: 26715 At special positions: 0 Unit cell: (136.899, 199.752, 188.559, 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 140 16.00 O 4990 8.00 N 4517 7.00 C 17068 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 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 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=2.03 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 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 1.3 seconds 7094 Ramachandran restraints generated. 3547 Oldfield, 0 Emsley, 3547 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6690 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 46 sheets defined 32.2% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 35 through 53 removed outlier: 3.554A pdb=" N MET A 41 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 82 removed outlier: 3.681A pdb=" N CYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 104 through 111 Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.700A pdb=" N SER A 129 " --> pdb=" O SER A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 148 removed outlier: 3.651A pdb=" N GLN A 147 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER A 148 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 158 removed outlier: 3.600A pdb=" N GLU A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 187 removed outlier: 3.604A pdb=" N LYS A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 235 removed outlier: 3.929A pdb=" N VAL A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 4.136A pdb=" N SER A 255 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 298 removed outlier: 3.647A pdb=" N HIS A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 327 removed outlier: 3.903A pdb=" N ARG A 323 " --> pdb=" O PRO A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 471 removed outlier: 3.959A pdb=" N LYS A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 581 removed outlier: 4.221A pdb=" N HIS A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 615 removed outlier: 4.005A pdb=" N MET A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TRP A 608 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 615 " --> pdb=" O TRP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 657 removed outlier: 3.743A pdb=" N ILE A 631 " --> pdb=" O PHE A 627 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN A 650 " --> pdb=" O SER A 646 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 651 " --> pdb=" O TYR A 647 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA A 652 " --> pdb=" O THR A 648 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA A 653 " --> pdb=" O ALA A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 695 removed outlier: 3.780A pdb=" N ILE A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 698 No H-bonds generated for 'chain 'A' and resid 696 through 698' Processing helix chain 'A' and resid 699 through 707 Processing helix chain 'A' and resid 717 through 723 Processing helix chain 'A' and resid 733 through 743 removed outlier: 3.641A pdb=" N GLU A 737 " --> pdb=" O SER A 733 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 740 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER A 741 " --> pdb=" O GLU A 737 " (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: 4.334A pdb=" N PHE A 817 " --> pdb=" O MET A 813 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 828 " --> pdb=" O ILE A 824 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE A 832 " --> pdb=" O ILE A 828 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE A 833 " --> pdb=" O PHE A 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.752A pdb=" N ASP B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER B 90 " --> pdb=" O CYS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 120 removed outlier: 3.784A pdb=" N ILE B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE B 114 " --> pdb=" O GLN B 110 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA B 117 " --> pdb=" O ASP B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.720A pdb=" N SER B 131 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N MET B 132 " --> pdb=" O GLY B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'B' and resid 155 through 162 removed outlier: 3.877A pdb=" N MET B 161 " --> pdb=" O MET B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 192 removed outlier: 3.552A pdb=" N PHE B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL B 183 " --> pdb=" O TYR B 179 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN B 184 " --> pdb=" O GLN B 180 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS B 185 " --> pdb=" O ASP B 181 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B 186 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 220 removed outlier: 3.525A pdb=" N ASN B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 248 removed outlier: 3.751A pdb=" N SER B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 264 removed outlier: 3.923A pdb=" N ALA B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 295 removed outlier: 3.566A pdb=" N ASP B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 301 removed outlier: 3.951A pdb=" N ILE B 300 " --> pdb=" O GLY B 296 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 301 " --> pdb=" O ILE B 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 296 through 301' Processing helix chain 'B' and resid 330 through 340 removed outlier: 3.524A pdb=" N MET B 334 " --> pdb=" O TYR B 330 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE B 340 " --> pdb=" O ASN B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 469 removed outlier: 3.629A pdb=" N ILE B 464 " --> pdb=" O PHE B 460 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 465 " --> pdb=" O CYS B 461 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 503 removed outlier: 3.592A pdb=" N VAL B 501 " --> pdb=" O MET B 497 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N MET B 503 " --> pdb=" O GLY B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 579 removed outlier: 4.127A pdb=" N VAL B 560 " --> pdb=" O ALA B 556 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 564 " --> pdb=" O VAL B 560 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR B 579 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 614 removed outlier: 3.567A pdb=" N TRP B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 608 " --> pdb=" O LYS B 604 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 656 removed outlier: 3.775A pdb=" N LYS B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE B 630 " --> pdb=" O THR B 626 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N MET B 631 " --> pdb=" O THR B 627 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR B 646 " --> pdb=" O PHE B 642 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR B 647 " --> pdb=" O LEU B 643 " (cutoff:3.500A) removed outlier: 4.353A 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 689 through 699 removed outlier: 3.739A pdb=" N ARG B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 719 removed outlier: 3.519A pdb=" N LEU B 719 " --> pdb=" O ASP B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 785 removed outlier: 3.568A pdb=" N LEU B 783 " --> pdb=" O ALA B 779 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE B 784 " --> pdb=" O ILE B 780 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY B 785 " --> pdb=" O LEU B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 797 removed outlier: 3.891A pdb=" N GLU B 791 " --> pdb=" O GLY B 787 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 792 " --> pdb=" O GLU B 788 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU B 793 " --> pdb=" O MET B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 843 removed outlier: 3.853A pdb=" N LEU B 825 " --> pdb=" O VAL B 821 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY B 826 " --> pdb=" O PHE B 822 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TYR B 843 " --> pdb=" O GLU B 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 53 removed outlier: 3.637A pdb=" N ASN C 50 " --> pdb=" O VAL C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 81 removed outlier: 3.585A pdb=" N MET C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N CYS C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 85 Processing helix chain 'C' and resid 104 through 114 removed outlier: 3.530A pdb=" N THR C 110 " --> pdb=" O PRO C 106 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.890A pdb=" N TYR C 128 " --> pdb=" O MET C 125 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP C 130 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 146 Processing helix chain 'C' and resid 147 through 157 removed outlier: 3.516A pdb=" N GLU C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET C 155 " --> pdb=" O TRP C 151 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG C 156 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 184 removed outlier: 3.740A pdb=" N LYS C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG C 179 " --> pdb=" O ALA C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 211 Processing helix chain 'C' and resid 226 through 238 removed outlier: 3.898A pdb=" N ALA C 236 " --> pdb=" O TYR C 232 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET C 237 " --> pdb=" O ARG C 233 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 259 Processing helix chain 'C' and resid 276 through 298 removed outlier: 3.665A pdb=" N SER C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA C 291 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU C 294 " --> pdb=" O GLN C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 328 removed outlier: 4.322A pdb=" N LEU C 320 " --> pdb=" O LYS C 316 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 471 removed outlier: 3.562A pdb=" N LEU C 463 " --> pdb=" O CYS C 459 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS C 465 " --> pdb=" O ASP C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 584 removed outlier: 3.571A pdb=" N VAL C 566 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLY C 567 " --> pdb=" O TRP C 563 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 568 " --> pdb=" O LEU C 564 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER C 584 " --> pdb=" O LEU C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 614 removed outlier: 3.769A pdb=" N TRP C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER C 610 " --> pdb=" O ALA C 606 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TRP C 611 " --> pdb=" O MET C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 658 removed outlier: 3.508A pdb=" N VAL C 635 " --> pdb=" O ILE C 631 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY C 638 " --> pdb=" O MET C 634 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP C 658 " --> pdb=" O PHE C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 694 removed outlier: 3.721A pdb=" N ILE C 691 " --> pdb=" O SER C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 698 No H-bonds generated for 'chain 'C' and resid 696 through 698' Processing helix chain 'C' and resid 699 through 707 Processing helix chain 'C' and resid 716 through 721 removed outlier: 3.689A pdb=" N VAL C 721 " --> pdb=" O ALA C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 781 removed outlier: 3.500A pdb=" N LYS C 778 " --> pdb=" O LEU C 774 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU C 781 " --> pdb=" O LEU C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 841 removed outlier: 4.009A pdb=" N PHE C 817 " --> pdb=" O MET C 813 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE C 828 " --> pdb=" O ILE C 824 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE C 833 " --> pdb=" O PHE C 829 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LYS C 838 " --> pdb=" O GLU C 834 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N SER C 839 " --> pdb=" O ILE C 835 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG C 840 " --> pdb=" O ALA C 836 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA C 841 " --> pdb=" O TYR C 837 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 57 Processing helix chain 'D' and resid 77 through 92 removed outlier: 3.698A pdb=" N CYS D 86 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU D 88 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET D 89 " --> pdb=" O ILE D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 120 removed outlier: 3.698A pdb=" N ILE D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE D 114 " --> pdb=" O GLN D 110 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE D 115 " --> pdb=" O ILE D 111 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 132 removed outlier: 3.675A pdb=" N SER D 130 " --> pdb=" O HIS D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 158 through 165 removed outlier: 3.710A pdb=" N GLU D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU D 163 " --> pdb=" O ASN D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 191 removed outlier: 3.989A pdb=" N VAL D 183 " --> pdb=" O TYR D 179 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU D 191 " --> pdb=" O ARG D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 221 removed outlier: 4.027A pdb=" N LYS D 221 " --> pdb=" O GLN D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 245 removed outlier: 3.681A pdb=" N TYR D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE D 240 " --> pdb=" O GLU D 236 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL D 243 " --> pdb=" O TYR D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 264 removed outlier: 3.726A pdb=" N ALA D 263 " --> pdb=" O PRO D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 312 removed outlier: 3.601A pdb=" N ARG D 294 " --> pdb=" O PRO D 290 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA D 298 " --> pdb=" O ARG D 294 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE D 300 " --> pdb=" O GLY D 296 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER D 309 " --> pdb=" O SER D 305 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU D 310 " --> pdb=" O ASP D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 333 Processing helix chain 'D' and resid 334 through 339 removed outlier: 4.057A pdb=" N TYR D 338 " --> pdb=" O MET D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 473 removed outlier: 3.671A pdb=" N LEU D 465 " --> pdb=" O CYS D 461 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS D 467 " --> pdb=" O ASP D 463 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS D 470 " --> pdb=" O LYS D 466 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER D 471 " --> pdb=" O LYS D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 522 removed outlier: 3.850A pdb=" N GLU D 521 " --> pdb=" O GLU D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 577 removed outlier: 3.802A pdb=" N TRP D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 560 " --> pdb=" O ALA D 556 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL D 574 " --> pdb=" O SER D 570 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE D 575 " --> pdb=" O ALA D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 614 removed outlier: 3.569A pdb=" N ALA D 605 " --> pdb=" O THR D 601 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP D 607 " --> pdb=" O GLY D 603 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU D 608 " --> pdb=" O LYS D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 656 removed outlier: 3.787A pdb=" N SER D 633 " --> pdb=" O LYS D 629 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE D 638 " --> pdb=" O VAL D 634 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR D 647 " --> pdb=" O LEU D 643 " (cutoff:3.500A) removed outlier: 3.857A 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: 3.959A 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 690 through 698 removed outlier: 3.643A pdb=" N ASN D 694 " --> pdb=" O SER D 690 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE D 695 " --> pdb=" O THR D 691 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG D 696 " --> pdb=" O GLU D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 706 Processing helix chain 'D' and resid 713 through 723 removed outlier: 3.581A pdb=" N LEU D 718 " --> pdb=" O VAL D 714 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 719 " --> pdb=" O ASP D 715 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 786 removed outlier: 3.889A pdb=" N GLN D 782 " --> pdb=" O LEU D 778 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU D 783 " --> pdb=" O ALA D 779 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE D 784 " --> pdb=" O ILE D 780 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY D 785 " --> pdb=" O LEU D 781 " (cutoff:3.500A) Processing helix chain 'D' and resid 791 through 796 removed outlier: 3.581A pdb=" N LEU D 795 " --> pdb=" O GLU D 791 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TRP D 796 " --> pdb=" O LEU D 792 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 791 through 796' Processing helix chain 'D' and resid 814 through 819 Processing helix chain 'D' and resid 820 through 832 Processing helix chain 'D' and resid 833 through 845 removed outlier: 3.828A pdb=" N HIS D 840 " --> pdb=" O PHE D 836 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN D 845 " --> pdb=" O LEU D 841 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.810A pdb=" N SER F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 64 removed outlier: 7.064A pdb=" N VAL A 27 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N THR A 63 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE A 29 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL A 87 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASN A 28 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA A 89 " --> pdb=" O ASN A 28 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N LEU A 119 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197 removed outlier: 6.406A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE A 164 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N SER A 222 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A 166 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 268 Processing sheet with id=AA4, first strand: chain 'A' and resid 365 through 367 Processing sheet with id=AA5, first strand: chain 'A' and resid 473 through 478 removed outlier: 6.720A pdb=" N LEU A 398 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N HIS A 477 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 514 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.765A pdb=" N ILE A 513 " --> pdb=" O ARG A 763 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N ARG A 763 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ALA A 515 " --> pdb=" O GLY A 761 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLY A 761 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU A 517 " --> pdb=" O GLY A 759 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 413 Processing sheet with id=AA7, first strand: chain 'A' and resid 487 through 489 Processing sheet with id=AA8, first strand: chain 'A' and resid 729 through 732 removed outlier: 6.384A pdb=" N LEU A 538 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU A 751 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 65 through 73 removed outlier: 3.635A pdb=" N LEU B 41 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ASP B 101 " --> pdb=" O ILE B 126 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 171 through 173 removed outlier: 3.552A pdb=" N VAL B 280 " --> pdb=" O VAL B 258 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 377 through 379 Processing sheet with id=AB3, first strand: chain 'B' and resid 405 through 410 Processing sheet with id=AB4, first strand: chain 'B' and resid 418 through 420 Processing sheet with id=AB5, first strand: chain 'B' and resid 508 through 509 removed outlier: 3.643A pdb=" N ALA B 765 " --> pdb=" O ALA B 509 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 530 through 532 removed outlier: 4.271A pdb=" N ILE B 530 " --> pdb=" O TYR B 762 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR B 760 " --> pdb=" O THR B 532 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.691A pdb=" N GLY B 684 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N ASP B 732 " --> pdb=" O GLY B 684 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 59 through 66 removed outlier: 6.963A pdb=" N VAL C 27 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N THR C 63 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE C 29 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N VAL C 65 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N VAL C 87 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ASN C 28 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ALA C 89 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY C 30 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 193 through 197 removed outlier: 4.076A pdb=" N LYS C 193 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE C 197 " --> pdb=" O VAL C 167 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 270 through 271 removed outlier: 6.511A pdb=" N TYR C 351 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ILE C 366 " --> pdb=" O TYR C 351 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE C 353 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 473 through 478 removed outlier: 3.847A pdb=" N VAL C 514 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.854A pdb=" N ILE C 513 " --> pdb=" O ARG C 763 " (cutoff:3.500A) removed outlier: 9.348A pdb=" N ARG C 763 " --> pdb=" O ILE C 513 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ALA C 515 " --> pdb=" O GLY C 761 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLY C 761 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU C 517 " --> pdb=" O GLY C 759 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 410 through 413 Processing sheet with id=AC4, first strand: chain 'C' and resid 486 through 489 Processing sheet with id=AC5, first strand: chain 'C' and resid 681 through 682 removed outlier: 7.115A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 9.500A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU C 538 " --> pdb=" O GLU C 751 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU C 751 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 68 through 73 removed outlier: 7.254A pdb=" N ILE D 37 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL D 71 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL D 39 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N MET D 73 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU D 41 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL D 97 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 208 through 209 removed outlier: 7.736A pdb=" N ILE D 171 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL D 280 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU D 362 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LYS D 378 " --> pdb=" O LEU D 362 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE D 364 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER D 383 " --> pdb=" O LYS D 380 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 342 through 344 removed outlier: 3.877A pdb=" N VAL D 342 " --> pdb=" O LEU D 349 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 475 through 478 removed outlier: 3.602A pdb=" N VAL D 409 " --> pdb=" O MET D 508 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 418 through 420 Processing sheet with id=AD2, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AD3, first strand: chain 'D' and resid 524 through 525 Processing sheet with id=AD4, first strand: chain 'D' and resid 683 through 684 removed outlier: 6.396A pdb=" N GLY D 684 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N ASP D 732 " --> pdb=" O GLY D 684 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE D 729 " --> pdb=" O MET D 537 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE D 534 " --> pdb=" O ALA D 758 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ALA D 758 " --> pdb=" O ILE D 534 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 6 through 7 removed outlier: 3.637A pdb=" N SER E 7 " --> pdb=" O SER E 22 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 10 through 13 Processing sheet with id=AD7, first strand: chain 'E' and resid 30 through 31 Processing sheet with id=AD8, first strand: chain 'E' and resid 51 through 54 removed outlier: 6.525A pdb=" N TRP E 41 " --> pdb=" O LEU E 53 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 68 through 69 removed outlier: 3.817A pdb=" N ILE E 69 " --> pdb=" O THR E 80 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N THR E 80 " --> pdb=" O ILE E 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'F' and resid 17 through 23 removed outlier: 3.786A pdb=" N CYS F 22 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR F 78 " --> pdb=" O ASP F 73 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 44 through 47 removed outlier: 4.207A pdb=" N TYR F 108 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 4 through 5 Processing sheet with id=AE4, first strand: chain 'I' and resid 11 through 13 removed outlier: 6.519A pdb=" N LEU I 11 " --> pdb=" O GLU I 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'I' and resid 19 through 22 removed outlier: 3.561A pdb=" N VAL I 19 " --> pdb=" O ILE I 81 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE I 81 " --> pdb=" O VAL I 19 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 59 through 60 removed outlier: 6.794A pdb=" N TRP I 41 " --> pdb=" O LEU I 53 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TYR I 55 " --> pdb=" O LEU I 39 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU I 39 " --> pdb=" O TYR I 55 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 3 through 5 Processing sheet with id=AE8, first strand: chain 'J' and resid 18 through 19 removed outlier: 3.902A pdb=" N VAL J 18 " --> pdb=" O LEU J 83 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 58 through 60 removed outlier: 6.824A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N MET J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N MET J 34 " --> pdb=" O MET J 50 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG J 98 " --> pdb=" O TYR J 108 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N TYR J 108 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 58 through 60 removed outlier: 6.824A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N MET J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N MET J 34 " --> pdb=" O MET J 50 " (cutoff:3.500A) 863 hydrogen bonds defined for protein. 2403 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: 4.97 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8643 1.35 - 1.48: 6902 1.48 - 1.60: 11517 1.60 - 1.73: 0 1.73 - 1.86: 236 Bond restraints: 27298 Sorted by residual: bond pdb=" C TRP B 391 " pdb=" N PRO B 392 " ideal model delta sigma weight residual 1.331 1.397 -0.066 1.20e-02 6.94e+03 3.01e+01 bond pdb=" C SER A 446 " pdb=" N PRO A 447 " ideal model delta sigma weight residual 1.330 1.370 -0.039 1.23e-02 6.61e+03 1.02e+01 bond pdb=" C GLU B 552 " pdb=" N PRO B 553 " ideal model delta sigma weight residual 1.328 1.364 -0.036 1.25e-02 6.40e+03 8.35e+00 bond pdb=" CA VAL C 204 " pdb=" CB VAL C 204 " ideal model delta sigma weight residual 1.527 1.560 -0.034 1.31e-02 5.83e+03 6.55e+00 bond pdb=" CA ASN D 192 " pdb=" CB ASN D 192 " ideal model delta sigma weight residual 1.528 1.561 -0.032 1.39e-02 5.18e+03 5.39e+00 ... (remaining 27293 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 36381 2.57 - 5.14: 612 5.14 - 7.71: 111 7.71 - 10.29: 22 10.29 - 12.86: 9 Bond angle restraints: 37135 Sorted by residual: angle pdb=" N PHE B 169 " pdb=" CA PHE B 169 " pdb=" C PHE B 169 " ideal model delta sigma weight residual 108.34 119.09 -10.75 1.31e+00 5.83e-01 6.73e+01 angle pdb=" N PHE D 169 " pdb=" CA PHE D 169 " pdb=" C PHE D 169 " ideal model delta sigma weight residual 108.34 117.11 -8.77 1.31e+00 5.83e-01 4.48e+01 angle pdb=" CA GLN I 85 " pdb=" CB GLN I 85 " pdb=" CG GLN I 85 " ideal model delta sigma weight residual 114.10 125.66 -11.56 2.00e+00 2.50e-01 3.34e+01 angle pdb=" N LEU B 199 " pdb=" CA LEU B 199 " pdb=" C LEU B 199 " ideal model delta sigma weight residual 110.80 123.06 -12.26 2.13e+00 2.20e-01 3.31e+01 angle pdb=" C SER A 553 " pdb=" CA SER A 553 " pdb=" CB SER A 553 " ideal model delta sigma weight residual 116.54 110.02 6.52 1.15e+00 7.56e-01 3.21e+01 ... (remaining 37130 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 14227 17.88 - 35.75: 1478 35.75 - 53.62: 405 53.62 - 71.50: 53 71.50 - 89.37: 12 Dihedral angle restraints: 16175 sinusoidal: 5801 harmonic: 10374 Sorted by residual: dihedral pdb=" CA THR I 100 " pdb=" C THR I 100 " pdb=" N PRO I 101 " pdb=" CA PRO I 101 " ideal model delta harmonic sigma weight residual -180.00 -121.48 -58.52 0 5.00e+00 4.00e-02 1.37e+02 dihedral pdb=" CB CYS D 86 " pdb=" SG CYS D 86 " pdb=" SG CYS D 321 " pdb=" CB CYS D 321 " ideal model delta sinusoidal sigma weight residual -86.00 -15.33 -70.67 1 1.00e+01 1.00e-02 6.42e+01 dihedral pdb=" CA TYR D 167 " pdb=" C TYR D 167 " pdb=" N PHE D 169 " pdb=" CA PHE D 169 " ideal model delta harmonic sigma weight residual -180.00 -142.49 -37.51 0 5.00e+00 4.00e-02 5.63e+01 ... (remaining 16172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3538 0.063 - 0.125: 647 0.125 - 0.188: 67 0.188 - 0.251: 5 0.251 - 0.314: 2 Chirality restraints: 4259 Sorted by residual: chirality pdb=" CG LEU D 567 " pdb=" CB LEU D 567 " pdb=" CD1 LEU D 567 " pdb=" CD2 LEU D 567 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" CB ILE B 160 " pdb=" CA ILE B 160 " pdb=" CG1 ILE B 160 " pdb=" CG2 ILE B 160 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA LEU B 199 " pdb=" N LEU B 199 " pdb=" C LEU B 199 " pdb=" CB LEU B 199 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 4256 not shown) Planarity restraints: 4737 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR I 100 " -0.071 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO I 101 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO I 101 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO I 101 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 669 " -0.062 5.00e-02 4.00e+02 9.37e-02 1.40e+01 pdb=" N PRO A 670 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO A 670 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 670 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 552 " -0.054 5.00e-02 4.00e+02 8.12e-02 1.06e+01 pdb=" N PRO D 553 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO D 553 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 553 " -0.045 5.00e-02 4.00e+02 ... (remaining 4734 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6324 2.79 - 3.32: 22118 3.32 - 3.84: 41141 3.84 - 4.37: 45250 4.37 - 4.90: 82715 Nonbonded interactions: 197548 Sorted by model distance: nonbonded pdb=" O TYR E 55 " pdb=" OG1 THR E 59 " model vdw 2.259 3.040 nonbonded pdb=" O PRO J 7 " pdb=" OG1 THR J 113 " model vdw 2.271 3.040 nonbonded pdb=" OG SER E 49 " pdb=" O GLY F 110 " model vdw 2.274 3.040 nonbonded pdb=" OG1 THR C 302 " pdb=" OG1 THR C 317 " model vdw 2.288 3.040 nonbonded pdb=" O VAL D 68 " pdb=" OH TYR F 32 " model vdw 2.289 3.040 ... (remaining 197543 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 393 or (resid 394 through 397 and (name N or na \ me CA or name C or name O or name CB )) or resid 398 or (resid 399 and (name N o \ r name CA or name C or name O or name CB )) or resid 400 through 413 or (resid 4 \ 14 through 417 and (name N or name CA or name C or name O or name CB )) or resid \ 418 or (resid 419 and (name N or name CA or name C or name O or name CB )) or r \ esid 420 through 425 or (resid 426 through 427 and (name N or name CA or name C \ or name O or name CB )) or resid 428 through 431 or (resid 432 through 433 and ( \ name N or name CA or name C or name O or name CB )) or resid 434 through 448 or \ (resid 449 and (name N or name CA or name C or name O or name CB )) or resid 450 \ through 460 or (resid 461 and (name N or name CA or name C or name O or name CB \ )) or resid 462 through 464 or (resid 465 and (name N or name CA or name C or n \ ame O or name CB )) or resid 466 through 467 or (resid 468 and (name N or name C \ A or name C or name O or name CB )) or resid 469 through 485 or (resid 486 throu \ gh 492 and (name N or name CA or name C or name O or name CB )) or resid 493 or \ (resid 494 through 497 and (name N or name CA or name C or name O or name CB )) \ or resid 498 through 503 or (resid 504 and (name N or name CA or name C or name \ O or name CB )) or resid 505 through 521 or (resid 522 and (name N or name CA or \ name C or name O or name CB )) or resid 523 through 527 or (resid 528 and (name \ N or name CA or name C or name O or name CB )) or resid 529 through 541 or (res \ id 542 through 545 and (name N or name CA or name C or name O or name CB )) or r \ esid 546 through 547 or (resid 548 through 549 and (name N or name CA or name C \ or name O or name CB )) or resid 550 or (resid 551 through 552 and (name N or na \ me CA or name C or name O or name CB )) or resid 553 through 567 or (resid 568 a \ nd (name N or name CA or name C or name O or name CB )) or resid 569 through 571 \ or (resid 572 and (name N or name CA or name C or name O or name CB )) or resid \ 573 through 580 or (resid 581 through 584 and (name N or name CA or name C or n \ ame O or name CB )) or resid 602 through 603 or (resid 604 and (name N or name C \ A or name C or name O or name CB )) or resid 605 through 618 or (resid 619 and ( \ name N or name CA or name C or name O or name CB )) or resid 620 through 633 or \ (resid 634 and (name N or name CA or name C or name O or name CB )) or resid 635 \ through 656 or (resid 657 and (name N or name CA or name C or name O or name CB \ )) or resid 658 through 666 or (resid 667 through 669 and (name N or name CA or \ name C or name O or name CB )) or resid 670 or (resid 671 through 672 and (name \ N or name CA or name C or name O or name CB )) or resid 673 through 676 or (res \ id 677 through 679 and (name N or name CA or name C or name O or name CB )) or r \ esid 680 through 684 or (resid 685 through 686 and (name N or name CA or name C \ or name O or name CB )) or resid 687 through 689 or (resid 690 and (name N or na \ me CA or name C or name O or name CB )) or resid 691 through 696 or (resid 697 a \ nd (name N or name CA or name C or name O or name CB )) or resid 698 or (resid 6 \ 99 through 709 and (name N or name CA or name C or name O or name CB )) or resid \ 710 or (resid 711 through 718 and (name N or name CA or name C or name O or nam \ e CB )) or resid 719 through 731 or (resid 732 and (name N or name CA or name C \ or name O or name CB )) or resid 733 through 747 or (resid 748 and (name N or na \ me CA or name C or name O or name CB )) or resid 749 through 764 or (resid 765 a \ nd (name N or name CA or name C or name O or name CB )) or resid 766 through 768 \ or (resid 769 and (name N or name CA or name C or name O or name CB )) or resid \ 770 through 792 or (resid 793 through 794 and (name N or name CA or name C or n \ ame O or name CB )) or resid 795 or (resid 796 through 797 and (name N or name C \ A or name C or name O or name CB )) or resid 798 or (resid 799 through 804 and ( \ name N or name CA or name C or name O or name CB )) or resid 805 through 810 or \ (resid 811 through 814 and (name N or name CA or name C or name O or name CB )) \ or resid 815 through 819 or (resid 820 through 821 and (name N or name CA or nam \ e C or name O or name CB )) or resid 822 through 828 or (resid 829 through 841 a \ nd (name N or name CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 25 through 414 or (resid 415 through 417 and (name N or na \ me CA or name C or name O or name CB )) or resid 418 through 482 or (resid 483 a \ nd (name N or name CA or name C or name O or name CB )) or resid 484 through 542 \ or (resid 543 through 545 and (name N or name CA or name C or name O or name CB \ )) or resid 546 through 551 or (resid 552 and (name N or name CA or name C or n \ ame O or name CB )) or resid 553 through 555 or (resid 556 and (name N or name C \ A or name C or name O or name CB )) or resid 557 through 576 or (resid 577 throu \ gh 578 and (name N or name CA or name C or name O or name CB )) or resid 579 thr \ ough 583 or (resid 584 and (name N or name CA or name C or name O or name CB )) \ or resid 602 through 606 or (resid 607 and (name N or name CA or name C or name \ O or name CB )) or resid 608 through 624 or (resid 625 through 626 and (name N o \ r name CA or name C or name O or name CB )) or resid 627 through 667 or (resid 6 \ 68 through 669 and (name N or name CA or name C or name O or name CB )) or resid \ 670 through 694 or (resid 695 and (name N or name CA or name C or name O or nam \ e CB )) or resid 696 through 704 or (resid 705 through 709 and (name N or name C \ A or name C or name O or name CB )) or resid 710 through 715 or (resid 716 throu \ gh 718 and (name N or name CA or name C or name O or name CB )) or resid 719 thr \ ough 736 or (resid 737 and (name N or name CA or name C or name O or name CB )) \ or resid 738 or (resid 739 through 740 and (name N or name CA or name C or name \ O or name CB )) or resid 741 through 743 or (resid 744 through 745 and (name N o \ r name CA or name C or name O or name CB )) or resid 746 through 785 or (resid 7 \ 86 and (name N or name CA or name C or name O or name CB )) or resid 787 through \ 799 or (resid 800 through 804 and (name N or name CA or name C or name O or nam \ e CB )) or resid 805 through 841)) } ncs_group { reference = (chain 'B' and (resid 32 through 390 or (resid 391 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 403 through 404 and (name N or name CA or \ name C or name O or name CB )) or resid 405 through 419 or (resid 420 and (name \ N or name CA or name C or name O or name CB )) or resid 421 or (resid 422 throug \ h 423 and (name N or name CA or name C or name O or name CB )) or resid 424 thro \ ugh 431 or (resid 432 through 434 and (name N or name CA or name C or name O or \ name CB )) or resid 435 through 438 or (resid 439 through 449 and (name N or nam \ e CA or name C or name O or name CB )) or resid 450 through 451 or (resid 452 th \ rough 455 and (name N or name CA or name C or name O or name CB )) or resid 456 \ through 462 or (resid 463 and (name N or name CA or name C or name O or name CB \ )) or resid 464 through 476 or (resid 477 and (name N or name CA or name C or na \ me O or name CB )) or resid 478 through 480 or (resid 481 through 482 and (name \ N or name CA or name C or name O or name CB )) or resid 483 through 492 or (resi \ d 493 and (name N or name CA or name C or name O or name CB )) or resid 494 thro \ ugh 496 or (resid 497 and (name N or name CA or name C or name O or name CB )) o \ r resid 498 through 499 or (resid 500 through 506 and (name N or name CA or name \ C or name O or name CB )) or resid 507 through 515 or resid 517 through 523 or \ (resid 524 and (name N or name CA or name C or name O or name CB )) or resid 525 \ through 535 or (resid 536 through 538 and (name N or name CA or name C or name \ O or name CB )) or resid 539 or (resid 540 and (name N or name CA or name C or n \ ame O or name CB )) or resid 541 or (resid 542 and (name N or name CA or name C \ or name O or name CB )) or resid 543 through 549 or (resid 550 through 552 and ( \ name N or name CA or name C or name O or name CB )) or resid 553 through 556 or \ (resid 557 and (name N or name CA or name C or name O or name CB )) or resid 558 \ through 560 or (resid 561 and (name N or name CA or name C or name O or name CB \ )) or resid 562 through 573 or (resid 574 through 579 and (name N or name CA or \ name C or name O or name CB )) or resid 599 through 600 or (resid 601 through 6 \ 02 and (name N or name CA or name C or name O or name CB )) or resid 603 or (res \ id 604 through 606 and (name N or name CA or name C or name O or name CB )) or r \ esid 607 through 617 or (resid 618 and (name N or name CA or name C or name O or \ name CB )) or resid 619 through 620 or (resid 621 and (name N or name CA or nam \ e C or name O or name CB )) or resid 622 through 623 or (resid 624 and (name N o \ r name CA or name C or name O or name CB )) or resid 625 through 662 or (resid 6 \ 63 and (name N or name CA or name C or name O or name CB )) or resid 664 through \ 665 or (resid 666 and (name N or name CA or name C or name O or name CB )) or r \ esid 667 through 669 or (resid 670 and (name N or name CA or name C or name O or \ name CB )) or resid 671 through 684 or (resid 685 through 686 and (name N or na \ me CA or name C or name O or name CB )) or resid 687 through 691 or (resid 692 a \ nd (name N or name CA or name C or name O or name CB )) or resid 693 through 695 \ or (resid 696 and (name N or name CA or name C or name O or name CB )) or resid \ 697 through 700 or (resid 701 through 706 and (name N or name CA or name C or n \ ame O or name CB )) or (resid 707 through 712 and (name N or name CA or name C o \ r name O or name CB )) or resid 713 through 747 or (resid 748 through 749 and (n \ ame N or name CA or name C or name O or name CB )) or resid 750 through 754 or ( \ resid 755 and (name N or name CA or name C or name O or name CB )) or resid 756 \ through 774 or (resid 775 and (name N or name CA or name C or name O or name CB \ )) or resid 776 or (resid 777 and (name N or name CA or name C or name O or name \ CB )) or resid 778 through 785 or (resid 786 and (name N or name CA or name C o \ r name O or name CB )) or resid 787 or (resid 788 and (name N or name CA or name \ C or name O or name CB )) or resid 789 or (resid 790 through 791 and (name N or \ name CA or name C or name O or name CB )) or resid 792 through 794 or (resid 79 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 796 through \ 811 or (resid 812 and (name N or name CA or name C or name O or name CB )) or re \ sid 813 through 817 or (resid 818 through 819 and (name N or name CA or name C o \ r name O or name CB )) or resid 820 through 835 or (resid 836 and (name N or nam \ e CA or name C or name O or name CB )) or resid 837 through 839 or (resid 840 th \ rough 845 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 32 through 411 or (resid 412 and (name N or name CA or nam \ e C or name O or name CB )) or resid 413 through 422 or (resid 423 and (name N o \ r name CA or name C or name O or name CB )) or resid 424 through 531 or (resid 5 \ 32 and (name N or name CA or name C or name O or name CB )) or resid 533 through \ 545 or (resid 546 and (name N or name CA or name C or name O or name CB )) or r \ esid 547 through 559 or (resid 560 through 561 and (name N or name CA or name C \ or name O or name CB )) or resid 562 or (resid 563 through 564 and (name N or na \ me CA or name C or name O or name CB )) or resid 565 through 567 or (resid 568 a \ nd (name N or name CA or name C or name O or name CB )) or resid 569 or (resid 5 \ 70 through 571 and (name N or name CA or name C or name O or name CB )) or resid \ 572 through 601 or (resid 602 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 603 through 606 and (name N or name CA or name C or name O or \ name CB )) or resid 607 through 661 or (resid 662 through 663 and (name N or nam \ e CA or name C or name O or name CB )) or resid 664 through 668 or (resid 669 th \ rough 670 and (name N or name CA or name C or name O or name CB )) or resid 671 \ through 677 or (resid 678 and (name N or name CA or name C or name O or name CB \ )) or resid 679 through 704 or (resid 705 through 706 and (name N or name CA or \ name C or name O or name CB )) or resid 707 or (resid 708 through 712 and (name \ N or name CA or name C or name O or name CB )) or resid 713 through 714 or (resi \ d 715 through 717 and (name N or name CA or name C or name O or name CB )) or re \ sid 718 through 722 or (resid 723 and (name N or name CA or name C or name O or \ name CB )) or resid 724 through 731 or (resid 732 through 734 and (name N or nam \ e CA or name C or name O or name CB )) or resid 735 through 741 or (resid 742 th \ rough 744 and (name N or name CA or name C or name O or name CB )) or resid 745 \ through 766 or (resid 767 through 769 and (name N or name CA or name C or name O \ or name CB )) or resid 770 through 790 or (resid 791 and (name N or name CA or \ name C or name O or name CB )) or resid 792 or (resid 793 through 795 and (name \ N or name CA or name C or name O or name CB )) or resid 796 through 797 or (resi \ d 798 and (name N or name CA or name C or name O or name CB )) or (resid 799 thr \ ough 812 and (name N or name CA or name C or name O or name CB )) or resid 813 t \ hrough 815 or (resid 816 and (name N or name CA or name C or name O or name CB ) \ ) or resid 817 through 822 or (resid 823 through 824 and (name N or name CA or n \ ame C or name O or name CB )) or resid 825 through 830 or (resid 831 and (name N \ or name CA or name C or name O or name CB )) or resid 832 through 834 or (resid \ 835 through 836 and (name N or name CA or name C or name O or name CB )) or res \ id 837 through 840 or (resid 841 through 845 and (name N or name CA or name C or \ name O or name CB )))) } ncs_group { reference = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'J' } 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: 4.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 24.190 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 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 : 0.004 0.066 27314 Z= 0.196 Angle : 0.870 12.857 37167 Z= 0.495 Chirality : 0.048 0.314 4259 Planarity : 0.007 0.110 4737 Dihedral : 15.700 89.374 9437 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.46 % Favored : 93.06 % Rotamer: Outliers : 3.74 % Allowed : 21.33 % Favored : 74.93 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 3.65 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.35 (0.12), residues: 3547 helix: -2.60 (0.12), residues: 1167 sheet: -0.96 (0.22), residues: 581 loop : -2.38 (0.12), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 156 TYR 0.038 0.002 TYR C 647 PHE 0.047 0.002 PHE A 654 TRP 0.022 0.002 TRP B 635 HIS 0.011 0.001 HIS B 840 Details of bonding type rmsd covalent geometry : bond 0.00374 (27298) covalent geometry : angle 0.87020 (37135) SS BOND : bond 0.00149 ( 16) SS BOND : angle 0.97571 ( 32) hydrogen bonds : bond 0.25913 ( 852) hydrogen bonds : angle 8.22846 ( 2403) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7094 Ramachandran restraints generated. 3547 Oldfield, 0 Emsley, 3547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7094 Ramachandran restraints generated. 3547 Oldfield, 0 Emsley, 3547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 323 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7149 (tmt90) REVERT: A 576 MET cc_start: 0.8207 (tpp) cc_final: 0.7861 (tpt) REVERT: A 603 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7766 (tt) REVERT: A 794 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7997 (ttm-80) REVERT: A 833 ILE cc_start: 0.6805 (OUTLIER) cc_final: 0.6512 (mt) REVERT: B 104 ASP cc_start: 0.8333 (t0) cc_final: 0.8046 (t0) REVERT: B 180 GLN cc_start: 0.8408 (mm-40) cc_final: 0.7996 (tp-100) REVERT: B 252 TYR cc_start: 0.7813 (t80) cc_final: 0.7567 (t80) REVERT: B 311 HIS cc_start: 0.8521 (m90) cc_final: 0.8273 (m90) REVERT: B 380 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7985 (mmtm) REVERT: B 477 ASP cc_start: 0.8212 (t70) cc_final: 0.7832 (m-30) REVERT: B 561 MET cc_start: 0.7812 (tmm) cc_final: 0.7577 (tmm) REVERT: B 600 PHE cc_start: 0.5118 (OUTLIER) cc_final: 0.4019 (m-80) REVERT: B 610 TRP cc_start: 0.7562 (t-100) cc_final: 0.7304 (t-100) REVERT: B 654 MET cc_start: 0.8314 (mtp) cc_final: 0.8077 (mtp) REVERT: C 41 MET cc_start: 0.8636 (tmm) cc_final: 0.8389 (tmm) REVERT: C 113 PHE cc_start: 0.8183 (t80) cc_final: 0.7711 (t80) REVERT: C 125 MET cc_start: 0.7190 (mmt) cc_final: 0.6792 (mmt) REVERT: C 166 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7819 (tt) REVERT: C 326 MET cc_start: 0.7289 (tpp) cc_final: 0.6316 (tmm) REVERT: C 354 MET cc_start: 0.7771 (mmt) cc_final: 0.7535 (mtp) REVERT: C 523 ARG cc_start: 0.9180 (OUTLIER) cc_final: 0.7033 (mtt180) REVERT: C 576 MET cc_start: 0.8211 (tmm) cc_final: 0.7784 (ttt) REVERT: C 781 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.7588 (pt0) REVERT: C 810 PHE cc_start: 0.6617 (OUTLIER) cc_final: 0.5896 (t80) REVERT: D 93 LYS cc_start: 0.7514 (mmtm) cc_final: 0.6680 (mttt) REVERT: D 136 ASP cc_start: 0.8163 (t0) cc_final: 0.7959 (m-30) REVERT: D 175 TYR cc_start: 0.7911 (OUTLIER) cc_final: 0.7317 (t80) REVERT: D 207 MET cc_start: 0.7990 (mtt) cc_final: 0.7613 (mmm) REVERT: D 272 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6272 (mm-30) REVERT: D 329 ILE cc_start: 0.1916 (OUTLIER) cc_final: 0.1040 (mt) REVERT: D 337 ARG cc_start: 0.7733 (ttp-170) cc_final: 0.6720 (ttp-170) REVERT: D 338 TYR cc_start: 0.7064 (m-10) cc_final: 0.6779 (m-10) REVERT: E 21 MET cc_start: 0.2629 (tpt) cc_final: 0.2413 (tpt) REVERT: I 13 MET cc_start: 0.8399 (tpt) cc_final: 0.6048 (mmm) REVERT: I 38 TYR cc_start: 0.8473 (m-80) cc_final: 0.8055 (m-10) REVERT: J 1 GLN cc_start: 0.8080 (mp10) cc_final: 0.7779 (mm-40) REVERT: J 81 MET cc_start: 0.6951 (ppp) cc_final: 0.6611 (ppp) outliers start: 100 outliers final: 76 residues processed: 403 average time/residue: 0.1611 time to fit residues: 106.6189 Evaluate side-chains 408 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 319 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 494 ASN Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 794 ARG Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 542 ASN Chi-restraints excluded: chain B residue 600 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 624 LYS Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 681 PHE Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 523 ARG Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 810 PHE Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 146 PHE Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 287 TYR Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 526 SER Chi-restraints excluded: chain D residue 617 SER Chi-restraints excluded: chain D residue 662 GLN Chi-restraints excluded: chain D residue 750 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 93 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN C 146 HIS D 54 HIS D 224 GLN D 311 HIS D 649 ASN ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN J 5 GLN J 61 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.189447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.121797 restraints weight = 37713.349| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.70 r_work: 0.3293 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27314 Z= 0.135 Angle : 0.596 11.459 37167 Z= 0.320 Chirality : 0.044 0.246 4259 Planarity : 0.005 0.099 4737 Dihedral : 7.651 70.545 3950 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.51 % Favored : 93.12 % Rotamer: Outliers : 4.37 % Allowed : 19.84 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.73 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.13), residues: 3547 helix: -1.23 (0.14), residues: 1162 sheet: -0.94 (0.21), residues: 624 loop : -2.19 (0.13), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 13 TYR 0.025 0.001 TYR B 164 PHE 0.028 0.002 PHE A 458 TRP 0.025 0.001 TRP B 391 HIS 0.007 0.001 HIS B 840 Details of bonding type rmsd covalent geometry : bond 0.00309 (27298) covalent geometry : angle 0.59565 (37135) SS BOND : bond 0.00180 ( 16) SS BOND : angle 1.04348 ( 32) hydrogen bonds : bond 0.04896 ( 852) hydrogen bonds : angle 5.33149 ( 2403) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7094 Ramachandran restraints generated. 3547 Oldfield, 0 Emsley, 3547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7094 Ramachandran restraints generated. 3547 Oldfield, 0 Emsley, 3547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 330 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.6959 (t0) cc_final: 0.6689 (t0) REVERT: A 346 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7189 (tmt90) REVERT: A 576 MET cc_start: 0.8169 (tpp) cc_final: 0.7818 (tpt) REVERT: A 686 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8265 (mt0) REVERT: A 833 ILE cc_start: 0.6615 (OUTLIER) cc_final: 0.6280 (mm) REVERT: B 104 ASP cc_start: 0.8383 (t0) cc_final: 0.7981 (t0) REVERT: B 180 GLN cc_start: 0.8388 (mm-40) cc_final: 0.8009 (tp-100) REVERT: B 252 TYR cc_start: 0.7787 (t80) cc_final: 0.7546 (t80) REVERT: B 380 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7883 (mmtm) REVERT: B 413 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.7781 (tp30) REVERT: B 477 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7826 (m-30) REVERT: B 600 PHE cc_start: 0.4959 (OUTLIER) cc_final: 0.3969 (m-80) REVERT: B 610 TRP cc_start: 0.7213 (t-100) cc_final: 0.6647 (t60) REVERT: C 41 MET cc_start: 0.8721 (tmm) cc_final: 0.8475 (tmm) REVERT: C 74 MET cc_start: 0.8296 (mmm) cc_final: 0.7889 (tpp) REVERT: C 125 MET cc_start: 0.7147 (mmt) cc_final: 0.6794 (mmt) REVERT: C 152 PHE cc_start: 0.8252 (t80) cc_final: 0.7932 (t80) REVERT: C 166 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7870 (tt) REVERT: C 326 MET cc_start: 0.7295 (tpp) cc_final: 0.6268 (tmm) REVERT: C 518 THR cc_start: 0.9170 (OUTLIER) cc_final: 0.8911 (t) REVERT: C 523 ARG cc_start: 0.9272 (OUTLIER) cc_final: 0.7086 (mtt180) REVERT: C 651 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8059 (tt) REVERT: C 694 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.5621 (ttm-80) REVERT: C 780 HIS cc_start: 0.9298 (OUTLIER) cc_final: 0.6906 (m-70) REVERT: C 810 PHE cc_start: 0.6585 (OUTLIER) cc_final: 0.6257 (m-80) REVERT: D 93 LYS cc_start: 0.7650 (mmtm) cc_final: 0.6793 (mttt) REVERT: D 140 SER cc_start: 0.8413 (m) cc_final: 0.7954 (p) REVERT: D 175 TYR cc_start: 0.7832 (OUTLIER) cc_final: 0.7415 (t80) REVERT: D 207 MET cc_start: 0.7945 (mtt) cc_final: 0.7604 (mmm) REVERT: D 220 LEU cc_start: 0.8275 (tt) cc_final: 0.7997 (tp) REVERT: I 38 TYR cc_start: 0.8618 (m-80) cc_final: 0.8054 (m-10) REVERT: J 1 GLN cc_start: 0.8059 (mp10) cc_final: 0.7769 (mm-40) REVERT: J 38 LYS cc_start: 0.7843 (ttmt) cc_final: 0.7555 (tppt) REVERT: J 81 MET cc_start: 0.6737 (ppp) cc_final: 0.6338 (ppp) outliers start: 117 outliers final: 63 residues processed: 432 average time/residue: 0.1641 time to fit residues: 116.5323 Evaluate side-chains 399 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 321 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 686 GLN Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 812 ASN Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 391 TRP Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 600 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 624 LYS Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 681 PHE Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 523 ARG Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 694 ARG Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 749 THR Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 810 PHE Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain J residue 13 ARG Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 64 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 196 optimal weight: 3.9990 chunk 244 optimal weight: 0.7980 chunk 263 optimal weight: 3.9990 chunk 257 optimal weight: 2.9990 chunk 171 optimal weight: 8.9990 chunk 292 optimal weight: 2.9990 chunk 158 optimal weight: 30.0000 chunk 144 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 267 optimal weight: 0.9990 chunk 349 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 GLN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 HIS D 224 GLN D 649 ASN D 737 ASN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 GLN J 6 GLN J 61 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.186678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.122961 restraints weight = 37769.083| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.57 r_work: 0.3244 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 27314 Z= 0.201 Angle : 0.639 12.421 37167 Z= 0.341 Chirality : 0.046 0.290 4259 Planarity : 0.005 0.103 4737 Dihedral : 7.037 72.586 3873 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.58 % Favored : 92.02 % Rotamer: Outliers : 5.72 % Allowed : 19.91 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.73 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.13), residues: 3547 helix: -0.72 (0.15), residues: 1178 sheet: -1.00 (0.21), residues: 626 loop : -2.26 (0.13), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 671 TYR 0.030 0.002 TYR B 164 PHE 0.036 0.002 PHE C 458 TRP 0.024 0.001 TRP B 391 HIS 0.008 0.001 HIS C 404 Details of bonding type rmsd covalent geometry : bond 0.00490 (27298) covalent geometry : angle 0.63837 (37135) SS BOND : bond 0.00228 ( 16) SS BOND : angle 1.25989 ( 32) hydrogen bonds : bond 0.05113 ( 852) hydrogen bonds : angle 5.02462 ( 2403) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7094 Ramachandran restraints generated. 3547 Oldfield, 0 Emsley, 3547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7094 Ramachandran restraints generated. 3547 Oldfield, 0 Emsley, 3547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 325 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 ARG cc_start: 0.8041 (ttp-110) cc_final: 0.7760 (ttp-110) REVERT: A 261 TYR cc_start: 0.8886 (m-10) cc_final: 0.8657 (m-10) REVERT: A 346 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7498 (tmt90) REVERT: A 354 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8519 (mtp) REVERT: A 562 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.6984 (tt) REVERT: A 576 MET cc_start: 0.8170 (tpp) cc_final: 0.7897 (tpt) REVERT: A 833 ILE cc_start: 0.6739 (OUTLIER) cc_final: 0.6396 (mm) REVERT: B 104 ASP cc_start: 0.8479 (t0) cc_final: 0.8137 (t0) REVERT: B 380 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7841 (mmtm) REVERT: B 413 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.7791 (tp30) REVERT: B 477 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.7896 (m-30) REVERT: B 600 PHE cc_start: 0.5047 (OUTLIER) cc_final: 0.4007 (m-80) REVERT: B 610 TRP cc_start: 0.7314 (t-100) cc_final: 0.6680 (t60) REVERT: C 41 MET cc_start: 0.8741 (tmm) cc_final: 0.8453 (tmm) REVERT: C 125 MET cc_start: 0.7278 (mmt) cc_final: 0.6982 (mmt) REVERT: C 152 PHE cc_start: 0.8446 (t80) cc_final: 0.8245 (t80) REVERT: C 166 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.7977 (tt) REVERT: C 225 GLU cc_start: 0.8581 (tt0) cc_final: 0.8247 (tp30) REVERT: C 523 ARG cc_start: 0.9404 (OUTLIER) cc_final: 0.7338 (mtt180) REVERT: C 694 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.5684 (ttm-80) REVERT: C 780 HIS cc_start: 0.9330 (OUTLIER) cc_final: 0.7126 (m-70) REVERT: C 810 PHE cc_start: 0.6516 (OUTLIER) cc_final: 0.6236 (m-80) REVERT: D 93 LYS cc_start: 0.7713 (mmtm) cc_final: 0.6896 (mttt) REVERT: D 140 SER cc_start: 0.8480 (m) cc_final: 0.8016 (p) REVERT: D 142 MET cc_start: 0.7750 (mmt) cc_final: 0.7116 (mmt) REVERT: D 175 TYR cc_start: 0.8017 (OUTLIER) cc_final: 0.7518 (t80) REVERT: D 220 LEU cc_start: 0.8306 (tt) cc_final: 0.8034 (tp) REVERT: D 272 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6249 (mm-30) REVERT: D 329 ILE cc_start: 0.1739 (OUTLIER) cc_final: 0.0983 (mt) REVERT: D 413 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.7679 (tp30) REVERT: D 747 LYS cc_start: 0.7403 (OUTLIER) cc_final: 0.6941 (pttt) REVERT: F 117 VAL cc_start: 0.6059 (OUTLIER) cc_final: 0.5108 (p) REVERT: I 6 GLN cc_start: 0.4674 (OUTLIER) cc_final: 0.4000 (pt0) REVERT: I 23 CYS cc_start: 0.8197 (t) cc_final: 0.7767 (t) REVERT: I 38 TYR cc_start: 0.8649 (m-80) cc_final: 0.7810 (m-10) REVERT: I 96 GLN cc_start: 0.7624 (pp30) cc_final: 0.7401 (pp30) REVERT: J 1 GLN cc_start: 0.8075 (mp10) cc_final: 0.7796 (mm-40) outliers start: 153 outliers final: 91 residues processed: 451 average time/residue: 0.1658 time to fit residues: 121.7057 Evaluate side-chains 427 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 316 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 494 ASN Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 812 ASN Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 391 TRP Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 600 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 624 LYS Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 681 PHE Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 760 THR Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 523 ARG Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 694 ARG Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 749 THR Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 810 PHE Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 634 VAL Chi-restraints excluded: chain D residue 721 LEU Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 742 ARG Chi-restraints excluded: chain D residue 747 LYS Chi-restraints excluded: chain F residue 13 ARG Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain J residue 13 ARG Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 61 ASN Chi-restraints excluded: chain J residue 64 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 349 optimal weight: 0.0070 chunk 127 optimal weight: 0.7980 chunk 259 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 211 optimal weight: 0.0370 chunk 262 optimal weight: 0.0470 chunk 135 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 195 optimal weight: 0.0570 chunk 42 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 overall best weight: 0.1892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 ASN D 224 GLN D 649 ASN D 737 ASN J 5 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.190440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.123405 restraints weight = 37808.881| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.74 r_work: 0.3318 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 27314 Z= 0.096 Angle : 0.536 9.433 37167 Z= 0.285 Chirality : 0.042 0.196 4259 Planarity : 0.005 0.102 4737 Dihedral : 6.415 68.864 3869 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.03 % Favored : 93.60 % Rotamer: Outliers : 4.63 % Allowed : 20.55 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.73 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.14), residues: 3547 helix: -0.34 (0.16), residues: 1179 sheet: -0.89 (0.21), residues: 622 loop : -2.08 (0.13), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 156 TYR 0.021 0.001 TYR I 55 PHE 0.014 0.001 PHE D 642 TRP 0.020 0.001 TRP B 391 HIS 0.006 0.001 HIS B 840 Details of bonding type rmsd covalent geometry : bond 0.00204 (27298) covalent geometry : angle 0.53561 (37135) SS BOND : bond 0.00151 ( 16) SS BOND : angle 0.65113 ( 32) hydrogen bonds : bond 0.03373 ( 852) hydrogen bonds : angle 4.57018 ( 2403) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7094 Ramachandran restraints generated. 3547 Oldfield, 0 Emsley, 3547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7094 Ramachandran restraints generated. 3547 Oldfield, 0 Emsley, 3547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 341 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 PHE cc_start: 0.8063 (t80) cc_final: 0.7793 (t80) REVERT: A 346 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.6987 (tmt90) REVERT: A 354 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8410 (mtp) REVERT: A 562 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6795 (tt) REVERT: A 576 MET cc_start: 0.8050 (tpp) cc_final: 0.7753 (tpt) REVERT: A 603 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7650 (tt) REVERT: A 833 ILE cc_start: 0.6723 (OUTLIER) cc_final: 0.6439 (mt) REVERT: B 104 ASP cc_start: 0.8350 (t0) cc_final: 0.7983 (t0) REVERT: B 252 TYR cc_start: 0.7777 (t80) cc_final: 0.7566 (t80) REVERT: B 311 HIS cc_start: 0.8650 (m90) cc_final: 0.8195 (m90) REVERT: B 380 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7788 (mmtm) REVERT: B 413 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.7783 (tp30) REVERT: B 477 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7833 (m-30) REVERT: B 600 PHE cc_start: 0.5038 (OUTLIER) cc_final: 0.4077 (m-80) REVERT: B 610 TRP cc_start: 0.7153 (t-100) cc_final: 0.6595 (t60) REVERT: B 818 MET cc_start: 0.8712 (mtm) cc_final: 0.8448 (mtm) REVERT: C 41 MET cc_start: 0.8774 (tmm) cc_final: 0.8430 (tmm) REVERT: C 74 MET cc_start: 0.8265 (mmm) cc_final: 0.8045 (mmm) REVERT: C 125 MET cc_start: 0.7128 (mmt) cc_final: 0.6788 (mmt) REVERT: C 166 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7912 (tt) REVERT: C 326 MET cc_start: 0.6864 (mmm) cc_final: 0.5962 (tmm) REVERT: C 523 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.6929 (mtt180) REVERT: C 780 HIS cc_start: 0.9244 (OUTLIER) cc_final: 0.7518 (m170) REVERT: C 810 PHE cc_start: 0.6514 (OUTLIER) cc_final: 0.6091 (m-80) REVERT: D 60 HIS cc_start: 0.7426 (m90) cc_final: 0.7124 (m90) REVERT: D 93 LYS cc_start: 0.7747 (mmtm) cc_final: 0.6983 (mttt) REVERT: D 140 SER cc_start: 0.8427 (m) cc_final: 0.7972 (p) REVERT: D 142 MET cc_start: 0.7559 (mmt) cc_final: 0.6981 (mmt) REVERT: D 175 TYR cc_start: 0.7909 (OUTLIER) cc_final: 0.7436 (t80) REVERT: D 207 MET cc_start: 0.7868 (mtt) cc_final: 0.7186 (pmm) REVERT: D 220 LEU cc_start: 0.8194 (tt) cc_final: 0.7915 (tp) REVERT: D 272 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6218 (mm-30) REVERT: D 747 LYS cc_start: 0.7226 (OUTLIER) cc_final: 0.6764 (pttt) REVERT: F 117 VAL cc_start: 0.5866 (OUTLIER) cc_final: 0.5055 (p) REVERT: I 6 GLN cc_start: 0.4574 (OUTLIER) cc_final: 0.4127 (pt0) REVERT: I 38 TYR cc_start: 0.8330 (m-80) cc_final: 0.7847 (m-10) REVERT: J 1 GLN cc_start: 0.7994 (mp10) cc_final: 0.7720 (mm-40) REVERT: J 30 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8071 (m) outliers start: 124 outliers final: 66 residues processed: 440 average time/residue: 0.1574 time to fit residues: 114.1544 Evaluate side-chains 408 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 323 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 812 ASN Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 391 TRP Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 600 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 624 LYS Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 681 PHE Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 523 ARG Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 810 PHE Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 747 LYS Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain F residue 13 ARG Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain J residue 13 ARG Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 64 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 28 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 228 optimal weight: 1.9990 chunk 155 optimal weight: 20.0000 chunk 347 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 200 optimal weight: 0.7980 chunk 354 optimal weight: 5.9990 chunk 351 optimal weight: 8.9990 chunk 289 optimal weight: 9.9990 chunk 230 optimal weight: 0.8980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 HIS D 737 ASN J 5 GLN J 61 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.187021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.120232 restraints weight = 37514.859| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.44 r_work: 0.3255 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 27314 Z= 0.197 Angle : 0.617 10.914 37167 Z= 0.326 Chirality : 0.046 0.251 4259 Planarity : 0.005 0.109 4737 Dihedral : 6.625 68.920 3861 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.41 % Favored : 92.19 % Rotamer: Outliers : 4.97 % Allowed : 20.58 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.73 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.14), residues: 3547 helix: -0.31 (0.16), residues: 1185 sheet: -0.99 (0.21), residues: 614 loop : -2.14 (0.13), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 671 TYR 0.025 0.001 TYR B 164 PHE 0.035 0.002 PHE A 458 TRP 0.034 0.001 TRP J 47 HIS 0.008 0.001 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00486 (27298) covalent geometry : angle 0.61682 (37135) SS BOND : bond 0.00236 ( 16) SS BOND : angle 1.13328 ( 32) hydrogen bonds : bond 0.04444 ( 852) hydrogen bonds : angle 4.67607 ( 2403) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7094 Ramachandran restraints generated. 3547 Oldfield, 0 Emsley, 3547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7094 Ramachandran restraints generated. 3547 Oldfield, 0 Emsley, 3547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 315 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.6644 (tmt90) REVERT: A 354 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8493 (mtp) REVERT: A 562 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6894 (tt) REVERT: A 576 MET cc_start: 0.8079 (tpp) cc_final: 0.7831 (tpt) REVERT: A 603 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7634 (tt) REVERT: A 727 HIS cc_start: 0.7145 (OUTLIER) cc_final: 0.6541 (t70) REVERT: A 833 ILE cc_start: 0.6716 (OUTLIER) cc_final: 0.6430 (mt) REVERT: B 104 ASP cc_start: 0.8419 (t0) cc_final: 0.8058 (t0) REVERT: B 336 ASN cc_start: 0.8582 (OUTLIER) cc_final: 0.8188 (t0) REVERT: B 361 LYS cc_start: 0.7733 (tppp) cc_final: 0.7352 (ptpt) REVERT: B 380 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7836 (mmtm) REVERT: B 413 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.7760 (tp30) REVERT: B 477 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.7877 (m-30) REVERT: B 600 PHE cc_start: 0.5039 (OUTLIER) cc_final: 0.4107 (m-80) REVERT: B 693 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8307 (tpt170) REVERT: B 818 MET cc_start: 0.8794 (mtm) cc_final: 0.8505 (mtm) REVERT: C 41 MET cc_start: 0.8789 (tmm) cc_final: 0.8384 (tmm) REVERT: C 74 MET cc_start: 0.8245 (mmm) cc_final: 0.7889 (tpp) REVERT: C 125 MET cc_start: 0.7193 (mmt) cc_final: 0.6915 (mmt) REVERT: C 166 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8009 (tt) REVERT: C 523 ARG cc_start: 0.9404 (OUTLIER) cc_final: 0.7066 (mpt-90) REVERT: C 694 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.5613 (ttm-80) REVERT: C 780 HIS cc_start: 0.9333 (OUTLIER) cc_final: 0.7103 (m-70) REVERT: C 810 PHE cc_start: 0.6545 (OUTLIER) cc_final: 0.6089 (m-80) REVERT: D 60 HIS cc_start: 0.7470 (m90) cc_final: 0.7133 (m90) REVERT: D 140 SER cc_start: 0.8404 (m) cc_final: 0.7922 (p) REVERT: D 142 MET cc_start: 0.7615 (mmt) cc_final: 0.6986 (mmt) REVERT: D 175 TYR cc_start: 0.8105 (OUTLIER) cc_final: 0.7610 (t80) REVERT: D 220 LEU cc_start: 0.8218 (tt) cc_final: 0.7939 (tp) REVERT: D 413 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.7633 (tp30) REVERT: D 609 LEU cc_start: 0.7874 (mt) cc_final: 0.7617 (mt) REVERT: D 747 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.6929 (pttt) REVERT: F 117 VAL cc_start: 0.5829 (OUTLIER) cc_final: 0.5029 (p) REVERT: I 38 TYR cc_start: 0.8345 (m-80) cc_final: 0.7830 (m-10) REVERT: J 1 GLN cc_start: 0.7992 (mp10) cc_final: 0.7778 (mm-40) outliers start: 133 outliers final: 83 residues processed: 429 average time/residue: 0.1647 time to fit residues: 115.4584 Evaluate side-chains 413 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 309 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 494 ASN Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 812 ASN Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 391 TRP Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 600 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 624 LYS Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 681 PHE Chi-restraints excluded: chain B residue 693 ARG Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 453 GLN Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 523 ARG Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 694 ARG Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 749 THR Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 810 PHE Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 690 SER Chi-restraints excluded: chain D residue 747 LYS Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain F residue 13 ARG Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain J residue 13 ARG Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 61 ASN Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 93 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 278 optimal weight: 0.0000 chunk 168 optimal weight: 1.9990 chunk 195 optimal weight: 0.0000 chunk 342 optimal weight: 8.9990 chunk 308 optimal weight: 30.0000 chunk 78 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 229 optimal weight: 0.6980 chunk 189 optimal weight: 9.9990 chunk 264 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 HIS I 96 GLN J 5 GLN J 61 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.189605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.122413 restraints weight = 37665.786| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.74 r_work: 0.3296 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 27314 Z= 0.104 Angle : 0.545 8.669 37167 Z= 0.287 Chirality : 0.043 0.193 4259 Planarity : 0.005 0.106 4737 Dihedral : 6.146 59.456 3857 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.34 % Favored : 93.32 % Rotamer: Outliers : 4.33 % Allowed : 21.18 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.73 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.14), residues: 3547 helix: -0.05 (0.16), residues: 1173 sheet: -0.95 (0.21), residues: 633 loop : -2.04 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 24 TYR 0.022 0.001 TYR I 55 PHE 0.020 0.001 PHE A 654 TRP 0.019 0.001 TRP B 391 HIS 0.008 0.001 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00238 (27298) covalent geometry : angle 0.54453 (37135) SS BOND : bond 0.00237 ( 16) SS BOND : angle 0.70469 ( 32) hydrogen bonds : bond 0.03324 ( 852) hydrogen bonds : angle 4.40287 ( 2403) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7094 Ramachandran restraints generated. 3547 Oldfield, 0 Emsley, 3547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7094 Ramachandran restraints generated. 3547 Oldfield, 0 Emsley, 3547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 319 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 PHE cc_start: 0.8327 (t80) cc_final: 0.8112 (t80) REVERT: A 170 ASP cc_start: 0.7287 (t0) cc_final: 0.7061 (t0) REVERT: A 346 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.6246 (tmt90) REVERT: A 354 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8409 (mtp) REVERT: A 562 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.6896 (tt) REVERT: A 576 MET cc_start: 0.8079 (tpp) cc_final: 0.7841 (tpt) REVERT: A 603 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7663 (tt) REVERT: A 727 HIS cc_start: 0.6757 (OUTLIER) cc_final: 0.6403 (t70) REVERT: A 833 ILE cc_start: 0.6786 (OUTLIER) cc_final: 0.6461 (mt) REVERT: B 73 MET cc_start: 0.7671 (ttm) cc_final: 0.7464 (ttm) REVERT: B 104 ASP cc_start: 0.8390 (t0) cc_final: 0.7998 (t0) REVERT: B 380 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7789 (mmtm) REVERT: B 413 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.7845 (tp30) REVERT: B 477 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7868 (m-30) REVERT: B 600 PHE cc_start: 0.5135 (OUTLIER) cc_final: 0.4236 (m-80) REVERT: C 74 MET cc_start: 0.8269 (mmm) cc_final: 0.7912 (tpp) REVERT: C 125 MET cc_start: 0.7219 (mmt) cc_final: 0.6916 (mmt) REVERT: C 166 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8030 (tt) REVERT: C 326 MET cc_start: 0.6901 (mmm) cc_final: 0.6052 (tmm) REVERT: C 523 ARG cc_start: 0.9313 (OUTLIER) cc_final: 0.7188 (mtt180) REVERT: C 780 HIS cc_start: 0.9280 (OUTLIER) cc_final: 0.7913 (m-70) REVERT: C 810 PHE cc_start: 0.6497 (OUTLIER) cc_final: 0.6050 (m-80) REVERT: D 60 HIS cc_start: 0.7481 (m90) cc_final: 0.7169 (m90) REVERT: D 93 LYS cc_start: 0.7778 (mmtm) cc_final: 0.7096 (mttt) REVERT: D 140 SER cc_start: 0.8422 (m) cc_final: 0.7954 (p) REVERT: D 142 MET cc_start: 0.7668 (mmt) cc_final: 0.7065 (mmt) REVERT: D 175 TYR cc_start: 0.7978 (OUTLIER) cc_final: 0.7520 (t80) REVERT: D 609 LEU cc_start: 0.7920 (mt) cc_final: 0.7646 (mt) REVERT: D 747 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.7072 (pttt) REVERT: F 117 VAL cc_start: 0.5748 (OUTLIER) cc_final: 0.4958 (p) REVERT: I 6 GLN cc_start: 0.4265 (OUTLIER) cc_final: 0.3880 (pt0) REVERT: I 38 TYR cc_start: 0.8354 (m-80) cc_final: 0.7871 (m-10) REVERT: I 96 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7800 (pp30) REVERT: J 1 GLN cc_start: 0.7935 (mp10) cc_final: 0.7704 (mm-40) outliers start: 116 outliers final: 72 residues processed: 415 average time/residue: 0.1503 time to fit residues: 103.1451 Evaluate side-chains 402 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 311 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 812 ASN Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 391 TRP Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 437 GLU Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 600 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 624 LYS Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 681 PHE Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 453 GLN Chi-restraints excluded: chain C residue 523 ARG Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 749 THR Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 810 PHE Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 690 SER Chi-restraints excluded: chain D residue 747 LYS Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain I residue 6 GLN Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain J residue 13 ARG Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 64 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 336 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 chunk 290 optimal weight: 9.9990 chunk 253 optimal weight: 1.9990 chunk 268 optimal weight: 4.9990 chunk 319 optimal weight: 30.0000 chunk 230 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 347 optimal weight: 1.9990 chunk 212 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 HIS A 494 ASN C 48 GLN D 311 HIS I 95 GLN J 5 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.186638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.119179 restraints weight = 37517.859| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.61 r_work: 0.3246 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 27314 Z= 0.204 Angle : 0.625 9.944 37167 Z= 0.330 Chirality : 0.047 0.269 4259 Planarity : 0.005 0.105 4737 Dihedral : 6.456 58.764 3856 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.70 % Favored : 91.94 % Rotamer: Outliers : 4.97 % Allowed : 20.58 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.73 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.14), residues: 3547 helix: -0.14 (0.16), residues: 1184 sheet: -0.98 (0.21), residues: 615 loop : -2.12 (0.13), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 671 TYR 0.025 0.002 TYR I 55 PHE 0.034 0.002 PHE C 458 TRP 0.028 0.001 TRP J 47 HIS 0.009 0.001 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00499 (27298) covalent geometry : angle 0.62422 (37135) SS BOND : bond 0.00244 ( 16) SS BOND : angle 1.16492 ( 32) hydrogen bonds : bond 0.04399 ( 852) hydrogen bonds : angle 4.57599 ( 2403) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7094 Ramachandran restraints generated. 3547 Oldfield, 0 Emsley, 3547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7094 Ramachandran restraints generated. 3547 Oldfield, 0 Emsley, 3547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 306 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7454 (t0) cc_final: 0.7231 (t0) REVERT: A 346 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.6651 (tmt90) REVERT: A 354 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8478 (mtp) REVERT: A 562 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.6928 (tt) REVERT: A 576 MET cc_start: 0.8054 (tpp) cc_final: 0.7823 (tpt) REVERT: A 603 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7677 (tt) REVERT: A 727 HIS cc_start: 0.7171 (OUTLIER) cc_final: 0.6705 (t70) REVERT: A 833 ILE cc_start: 0.6752 (OUTLIER) cc_final: 0.6410 (mt) REVERT: B 104 ASP cc_start: 0.8430 (t0) cc_final: 0.8070 (t0) REVERT: B 194 PHE cc_start: 0.6413 (OUTLIER) cc_final: 0.5522 (p90) REVERT: B 361 LYS cc_start: 0.7735 (tppp) cc_final: 0.7411 (ptpt) REVERT: B 380 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7829 (mmtm) REVERT: B 413 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.7763 (tp30) REVERT: B 477 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7907 (m-30) REVERT: B 600 PHE cc_start: 0.5196 (OUTLIER) cc_final: 0.4311 (m-80) REVERT: B 693 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8328 (tpt170) REVERT: C 74 MET cc_start: 0.8295 (mmm) cc_final: 0.7955 (tpp) REVERT: C 125 MET cc_start: 0.7295 (mmt) cc_final: 0.7028 (mmt) REVERT: C 166 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8077 (tt) REVERT: C 523 ARG cc_start: 0.9424 (OUTLIER) cc_final: 0.6912 (mtt90) REVERT: C 694 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.5691 (ttm-80) REVERT: C 780 HIS cc_start: 0.9337 (OUTLIER) cc_final: 0.7159 (m-70) REVERT: D 60 HIS cc_start: 0.7624 (m90) cc_final: 0.7285 (m90) REVERT: D 93 LYS cc_start: 0.7788 (mmtm) cc_final: 0.7196 (mptt) REVERT: D 142 MET cc_start: 0.7764 (mmt) cc_final: 0.7127 (mmt) REVERT: D 175 TYR cc_start: 0.8093 (OUTLIER) cc_final: 0.7629 (t80) REVERT: D 329 ILE cc_start: 0.1681 (OUTLIER) cc_final: 0.1021 (mt) REVERT: D 413 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.7626 (tp30) REVERT: D 609 LEU cc_start: 0.8081 (mt) cc_final: 0.7819 (mt) REVERT: D 747 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.7046 (pttt) REVERT: F 117 VAL cc_start: 0.5658 (OUTLIER) cc_final: 0.4891 (p) REVERT: I 38 TYR cc_start: 0.8491 (m-80) cc_final: 0.7890 (m-10) REVERT: I 48 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8196 (pm20) REVERT: I 94 CYS cc_start: 0.7916 (OUTLIER) cc_final: 0.6609 (p) outliers start: 133 outliers final: 94 residues processed: 419 average time/residue: 0.1629 time to fit residues: 111.4127 Evaluate side-chains 421 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 304 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 494 ASN Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 812 ASN Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain B residue 471 SER Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 600 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 624 LYS Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 681 PHE Chi-restraints excluded: chain B residue 693 ARG Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain B residue 795 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 453 GLN Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 523 ARG Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 694 ARG Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 749 THR Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 810 PHE Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 369 LYS Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 690 SER Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 747 LYS Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain F residue 13 ARG Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 48 GLN Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 94 CYS Chi-restraints excluded: chain J residue 13 ARG Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 64 PHE Chi-restraints excluded: chain J residue 93 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 132 optimal weight: 0.9980 chunk 213 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 274 optimal weight: 0.1980 chunk 238 optimal weight: 8.9990 chunk 321 optimal weight: 7.9990 chunk 275 optimal weight: 0.0670 chunk 236 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 184 optimal weight: 0.0870 chunk 203 optimal weight: 0.9980 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN D 311 HIS J 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.190416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.122692 restraints weight = 37859.076| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.93 r_work: 0.3311 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.082 27314 Z= 0.099 Angle : 0.537 7.643 37167 Z= 0.284 Chirality : 0.043 0.185 4259 Planarity : 0.005 0.104 4737 Dihedral : 5.987 59.721 3856 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.03 % Favored : 93.60 % Rotamer: Outliers : 3.88 % Allowed : 21.82 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.73 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.14), residues: 3547 helix: 0.14 (0.16), residues: 1167 sheet: -0.97 (0.21), residues: 630 loop : -1.96 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 156 TYR 0.029 0.001 TYR I 55 PHE 0.024 0.001 PHE A 654 TRP 0.021 0.001 TRP J 47 HIS 0.009 0.001 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00229 (27298) covalent geometry : angle 0.53734 (37135) SS BOND : bond 0.00181 ( 16) SS BOND : angle 0.66270 ( 32) hydrogen bonds : bond 0.02991 ( 852) hydrogen bonds : angle 4.25574 ( 2403) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7094 Ramachandran restraints generated. 3547 Oldfield, 0 Emsley, 3547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7094 Ramachandran restraints generated. 3547 Oldfield, 0 Emsley, 3547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 319 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7164 (t0) cc_final: 0.6904 (t0) REVERT: A 346 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.6036 (tmt90) REVERT: A 354 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8348 (mtp) REVERT: A 562 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6800 (tt) REVERT: A 576 MET cc_start: 0.7948 (tpp) cc_final: 0.7745 (tpt) REVERT: A 603 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7714 (tt) REVERT: A 634 MET cc_start: 0.7014 (mmm) cc_final: 0.6579 (tpt) REVERT: A 727 HIS cc_start: 0.6586 (OUTLIER) cc_final: 0.6224 (t70) REVERT: A 833 ILE cc_start: 0.6645 (OUTLIER) cc_final: 0.6329 (mt) REVERT: B 104 ASP cc_start: 0.8381 (t0) cc_final: 0.8009 (t0) REVERT: B 194 PHE cc_start: 0.5966 (OUTLIER) cc_final: 0.5688 (p90) REVERT: B 380 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7722 (mmtm) REVERT: B 413 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.7819 (tp30) REVERT: B 477 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7834 (m-30) REVERT: B 600 PHE cc_start: 0.5090 (OUTLIER) cc_final: 0.4220 (m-80) REVERT: C 74 MET cc_start: 0.8216 (mmm) cc_final: 0.7880 (tpp) REVERT: C 125 MET cc_start: 0.7060 (mmt) cc_final: 0.6789 (mmt) REVERT: C 166 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7958 (tt) REVERT: C 326 MET cc_start: 0.6905 (mmm) cc_final: 0.6019 (tmm) REVERT: C 523 ARG cc_start: 0.9243 (OUTLIER) cc_final: 0.6878 (mtt180) REVERT: C 780 HIS cc_start: 0.9258 (OUTLIER) cc_final: 0.7526 (m170) REVERT: C 810 PHE cc_start: 0.6491 (OUTLIER) cc_final: 0.6097 (m-80) REVERT: D 60 HIS cc_start: 0.7569 (m90) cc_final: 0.7225 (m90) REVERT: D 93 LYS cc_start: 0.7762 (mmtm) cc_final: 0.7103 (mttt) REVERT: D 140 SER cc_start: 0.8334 (m) cc_final: 0.7865 (p) REVERT: D 142 MET cc_start: 0.7613 (mmt) cc_final: 0.6950 (mmt) REVERT: D 175 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.7461 (t80) REVERT: D 272 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6179 (mm-30) REVERT: D 747 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.6963 (pttt) REVERT: E 4 MET cc_start: 0.6446 (pmm) cc_final: 0.5921 (pmm) REVERT: F 117 VAL cc_start: 0.5754 (OUTLIER) cc_final: 0.4968 (p) REVERT: I 38 TYR cc_start: 0.8370 (m-80) cc_final: 0.7848 (m-10) outliers start: 104 outliers final: 65 residues processed: 404 average time/residue: 0.1622 time to fit residues: 106.8785 Evaluate side-chains 394 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 310 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 332 ASP Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 812 ASN Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 391 TRP Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 600 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 523 ARG Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 810 PHE Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 747 LYS Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain F residue 13 ARG Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain J residue 13 ARG Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 64 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 297 optimal weight: 0.8980 chunk 271 optimal weight: 0.9990 chunk 130 optimal weight: 30.0000 chunk 331 optimal weight: 30.0000 chunk 125 optimal weight: 3.9990 chunk 265 optimal weight: 7.9990 chunk 177 optimal weight: 5.9990 chunk 248 optimal weight: 0.1980 chunk 335 optimal weight: 0.0980 chunk 339 optimal weight: 7.9990 chunk 140 optimal weight: 0.4980 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 HIS ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 ASN D 224 GLN D 311 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.190593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.124207 restraints weight = 37770.023| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.46 r_work: 0.3331 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 27314 Z= 0.098 Angle : 0.535 8.597 37167 Z= 0.279 Chirality : 0.043 0.182 4259 Planarity : 0.004 0.106 4737 Dihedral : 5.712 59.809 3850 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.34 % Favored : 93.29 % Rotamer: Outliers : 3.77 % Allowed : 21.96 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.73 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.14), residues: 3547 helix: 0.26 (0.16), residues: 1172 sheet: -0.83 (0.21), residues: 611 loop : -1.94 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 156 TYR 0.037 0.001 TYR I 55 PHE 0.031 0.001 PHE D 563 TRP 0.022 0.001 TRP J 47 HIS 0.009 0.001 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00224 (27298) covalent geometry : angle 0.53498 (37135) SS BOND : bond 0.00149 ( 16) SS BOND : angle 0.67929 ( 32) hydrogen bonds : bond 0.02986 ( 852) hydrogen bonds : angle 4.15015 ( 2403) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7094 Ramachandran restraints generated. 3547 Oldfield, 0 Emsley, 3547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7094 Ramachandran restraints generated. 3547 Oldfield, 0 Emsley, 3547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 315 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7195 (t0) cc_final: 0.6967 (t0) REVERT: A 346 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.5967 (tmt90) REVERT: A 354 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8363 (mtp) REVERT: A 562 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6823 (tt) REVERT: A 603 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7692 (tt) REVERT: A 634 MET cc_start: 0.7036 (mmm) cc_final: 0.6561 (tpt) REVERT: A 727 HIS cc_start: 0.6652 (OUTLIER) cc_final: 0.6270 (t70) REVERT: A 833 ILE cc_start: 0.6734 (OUTLIER) cc_final: 0.6442 (mt) REVERT: B 104 ASP cc_start: 0.8337 (t0) cc_final: 0.7959 (t0) REVERT: B 380 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7717 (mmtm) REVERT: B 413 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.7816 (tp30) REVERT: B 477 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7801 (m-30) REVERT: B 600 PHE cc_start: 0.5036 (OUTLIER) cc_final: 0.4243 (m-80) REVERT: C 74 MET cc_start: 0.8213 (mmm) cc_final: 0.7896 (tpp) REVERT: C 125 MET cc_start: 0.7056 (mmt) cc_final: 0.6790 (mmt) REVERT: C 166 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7951 (tt) REVERT: C 326 MET cc_start: 0.6876 (mmm) cc_final: 0.6015 (tmm) REVERT: C 523 ARG cc_start: 0.9233 (OUTLIER) cc_final: 0.7003 (mtt180) REVERT: C 780 HIS cc_start: 0.9295 (OUTLIER) cc_final: 0.7663 (m170) REVERT: C 810 PHE cc_start: 0.6490 (OUTLIER) cc_final: 0.6156 (m-80) REVERT: D 60 HIS cc_start: 0.7591 (m90) cc_final: 0.7216 (m90) REVERT: D 93 LYS cc_start: 0.7768 (mmtm) cc_final: 0.7099 (mttt) REVERT: D 140 SER cc_start: 0.8339 (m) cc_final: 0.7871 (p) REVERT: D 142 MET cc_start: 0.7606 (mmt) cc_final: 0.6955 (mmt) REVERT: D 175 TYR cc_start: 0.7866 (OUTLIER) cc_final: 0.7441 (t80) REVERT: D 233 THR cc_start: 0.5998 (OUTLIER) cc_final: 0.5764 (t) REVERT: D 272 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6180 (mm-30) REVERT: D 337 ARG cc_start: 0.8348 (ttm170) cc_final: 0.7253 (ttp-170) REVERT: D 747 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.6997 (pttt) REVERT: E 4 MET cc_start: 0.6742 (pmm) cc_final: 0.6392 (pmm) REVERT: F 117 VAL cc_start: 0.5670 (OUTLIER) cc_final: 0.4890 (p) REVERT: I 38 TYR cc_start: 0.8399 (m-80) cc_final: 0.7857 (m-10) REVERT: I 48 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8195 (pm20) outliers start: 101 outliers final: 64 residues processed: 394 average time/residue: 0.1615 time to fit residues: 104.5550 Evaluate side-chains 395 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 311 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 494 ASN Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 600 PHE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 523 ARG Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 768 TRP Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 810 PHE Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 690 SER Chi-restraints excluded: chain D residue 747 LYS Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain F residue 13 ARG Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 48 GLN Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain J residue 13 ARG Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 64 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 71 optimal weight: 2.9990 chunk 10 optimal weight: 0.4980 chunk 336 optimal weight: 30.0000 chunk 87 optimal weight: 3.9990 chunk 297 optimal weight: 0.5980 chunk 116 optimal weight: 9.9990 chunk 188 optimal weight: 4.9990 chunk 182 optimal weight: 10.0000 chunk 236 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 HIS ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 ASN D 224 GLN D 311 HIS J 5 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.186689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.121221 restraints weight = 37515.474| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.79 r_work: 0.3228 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 27314 Z= 0.220 Angle : 0.643 9.408 37167 Z= 0.337 Chirality : 0.047 0.333 4259 Planarity : 0.005 0.105 4737 Dihedral : 6.036 59.018 3841 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.84 % Favored : 91.77 % Rotamer: Outliers : 3.55 % Allowed : 22.00 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.73 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.14), residues: 3547 helix: 0.01 (0.16), residues: 1185 sheet: -0.97 (0.21), residues: 618 loop : -2.05 (0.14), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 671 TYR 0.034 0.002 TYR I 55 PHE 0.036 0.002 PHE A 458 TRP 0.026 0.001 TRP B 197 HIS 0.009 0.001 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00546 (27298) covalent geometry : angle 0.64197 (37135) SS BOND : bond 0.00255 ( 16) SS BOND : angle 1.18547 ( 32) hydrogen bonds : bond 0.04340 ( 852) hydrogen bonds : angle 4.44677 ( 2403) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7094 Ramachandran restraints generated. 3547 Oldfield, 0 Emsley, 3547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7094 Ramachandran restraints generated. 3547 Oldfield, 0 Emsley, 3547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 312 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 ASP cc_start: 0.7556 (t0) cc_final: 0.7283 (t0) REVERT: A 192 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8575 (tt0) REVERT: A 346 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.6590 (tmt90) REVERT: A 354 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8469 (mtp) REVERT: A 562 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7037 (tt) REVERT: A 603 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7694 (tt) REVERT: A 634 MET cc_start: 0.7154 (mmm) cc_final: 0.6582 (tpt) REVERT: A 727 HIS cc_start: 0.7220 (OUTLIER) cc_final: 0.6803 (t70) REVERT: A 833 ILE cc_start: 0.6719 (OUTLIER) cc_final: 0.6389 (mt) REVERT: B 104 ASP cc_start: 0.8453 (t0) cc_final: 0.8097 (t0) REVERT: B 194 PHE cc_start: 0.6550 (OUTLIER) cc_final: 0.6157 (p90) REVERT: B 361 LYS cc_start: 0.7751 (tppp) cc_final: 0.7401 (ptpt) REVERT: B 380 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7788 (mmtm) REVERT: B 413 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.7842 (tp30) REVERT: B 477 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7938 (m-30) REVERT: C 74 MET cc_start: 0.8247 (mmm) cc_final: 0.7943 (tpp) REVERT: C 125 MET cc_start: 0.7262 (mmt) cc_final: 0.6996 (mmt) REVERT: C 166 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8129 (tt) REVERT: C 523 ARG cc_start: 0.9439 (OUTLIER) cc_final: 0.6877 (mtm-85) REVERT: C 780 HIS cc_start: 0.9342 (OUTLIER) cc_final: 0.7198 (m-70) REVERT: C 810 PHE cc_start: 0.6565 (OUTLIER) cc_final: 0.6288 (m-80) REVERT: D 60 HIS cc_start: 0.7682 (m90) cc_final: 0.7323 (m90) REVERT: D 93 LYS cc_start: 0.7773 (mmtm) cc_final: 0.7092 (mttt) REVERT: D 175 TYR cc_start: 0.8090 (OUTLIER) cc_final: 0.7651 (t80) REVERT: D 233 THR cc_start: 0.6316 (OUTLIER) cc_final: 0.6088 (t) REVERT: D 272 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6191 (mm-30) REVERT: D 329 ILE cc_start: 0.1610 (OUTLIER) cc_final: 0.0962 (mt) REVERT: D 413 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.7644 (tp30) REVERT: D 747 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7128 (pttt) REVERT: E 4 MET cc_start: 0.6715 (pmm) cc_final: 0.6291 (pmm) REVERT: F 117 VAL cc_start: 0.5610 (OUTLIER) cc_final: 0.4842 (p) REVERT: I 48 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8198 (pm20) REVERT: I 94 CYS cc_start: 0.7851 (OUTLIER) cc_final: 0.6543 (p) outliers start: 95 outliers final: 64 residues processed: 389 average time/residue: 0.1624 time to fit residues: 103.7392 Evaluate side-chains 394 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 306 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 354 MET Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 657 LEU Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 727 HIS Chi-restraints excluded: chain A residue 833 ILE Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 197 TRP Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 380 LYS Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 714 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 386 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 523 ARG Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 810 PHE Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain D residue 61 HIS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 175 TYR Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 653 PHE Chi-restraints excluded: chain D residue 690 SER Chi-restraints excluded: chain D residue 747 LYS Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain F residue 13 ARG Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 48 GLN Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 94 CYS Chi-restraints excluded: chain J residue 13 ARG Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 64 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 256 optimal weight: 7.9990 chunk 174 optimal weight: 0.9980 chunk 310 optimal weight: 10.0000 chunk 255 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 337 optimal weight: 8.9990 chunk 16 optimal weight: 0.0070 chunk 94 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 overall best weight: 1.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 GLN D 311 HIS ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.187382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.120440 restraints weight = 37556.892| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.71 r_work: 0.3250 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 27314 Z= 0.175 Angle : 0.608 14.248 37167 Z= 0.318 Chirality : 0.046 0.275 4259 Planarity : 0.005 0.105 4737 Dihedral : 5.935 58.233 3839 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.27 % Favored : 92.36 % Rotamer: Outliers : 3.66 % Allowed : 22.00 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.73 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.14), residues: 3547 helix: 0.04 (0.16), residues: 1175 sheet: -0.97 (0.21), residues: 615 loop : -2.05 (0.14), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 156 TYR 0.034 0.001 TYR I 55 PHE 0.037 0.002 PHE D 563 TRP 0.022 0.001 TRP J 47 HIS 0.009 0.001 HIS A 293 Details of bonding type rmsd covalent geometry : bond 0.00433 (27298) covalent geometry : angle 0.60710 (37135) SS BOND : bond 0.00248 ( 16) SS BOND : angle 0.98909 ( 32) hydrogen bonds : bond 0.03947 ( 852) hydrogen bonds : angle 4.40034 ( 2403) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11121.29 seconds wall clock time: 189 minutes 10.84 seconds (11350.84 seconds total)