Starting phenix.real_space_refine on Thu Mar 5 18:29:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eor_31228/03_2026/7eor_31228_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eor_31228/03_2026/7eor_31228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7eor_31228/03_2026/7eor_31228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eor_31228/03_2026/7eor_31228.map" model { file = "/net/cci-nas-00/data/ceres_data/7eor_31228/03_2026/7eor_31228_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eor_31228/03_2026/7eor_31228_trim.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 150 5.16 5 C 15544 2.51 5 N 4040 2.21 5 O 4468 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24204 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5886 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 27, 'TRANS': 717} Chain breaks: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 6093 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 770, 6088 Classifications: {'peptide': 770} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 32, 'TRANS': 737} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 770, 6088 Classifications: {'peptide': 770} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 32, 'TRANS': 737} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 6215 Chain: "C" Number of atoms: 5886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 5886 Classifications: {'peptide': 745} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 27, 'TRANS': 717} Chain breaks: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 6093 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 770, 6088 Classifications: {'peptide': 770} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 32, 'TRANS': 737} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 770, 6088 Classifications: {'peptide': 770} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 32, 'TRANS': 737} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 6215 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'6RM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'6RM': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 7.67, per 1000 atoms: 0.32 Number of scatterers: 24204 At special positions: 0 Unit cell: (116.61, 145.002, 185.562, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 150 16.00 F 2 9.00 O 4468 8.00 N 4040 7.00 C 15544 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 320 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 456 " distance=2.03 Simple disulfide: pdb=" SG CYS A 794 " - pdb=" SG CYS D 698 " distance=2.03 Simple disulfide: pdb=" SG CYS B 420 " - pdb=" SG CYS B 454 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 455 " distance=2.03 Simple disulfide: pdb=" SG CYS B 698 " - pdb=" SG CYS C 794 " distance=2.03 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 320 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 420 " - pdb=" SG CYS D 454 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 455 " 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=2, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 687 " " NAG B 901 " - " ASN B 61 " " NAG B 902 " - " ASN B 276 " " NAG B 903 " - " ASN B 239 " " NAG B 904 " - " ASN B 203 " " NAG B 905 " - " ASN B 771 " " NAG B 906 " - " ASN B 471 " " NAG C 901 " - " ASN C 687 " " NAG D 901 " - " ASN D 61 " " NAG D 902 " - " ASN D 276 " " NAG D 903 " - " ASN D 239 " " NAG D 904 " - " ASN D 203 " " NAG D 905 " - " ASN D 771 " " NAG D 906 " - " ASN D 471 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 1.4 seconds 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5676 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 31 sheets defined 45.2% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 45 through 60 removed outlier: 3.747A pdb=" N GLY A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Proline residue: A 57 - end of helix removed outlier: 3.678A pdb=" N ALA A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 113 through 121 removed outlier: 3.676A pdb=" N PHE A 121 " --> pdb=" O SER A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 152 through 165 removed outlier: 4.135A pdb=" N THR A 156 " --> pdb=" O GLN A 152 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 157 " --> pdb=" O GLN A 153 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N MET A 162 " --> pdb=" O MET A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 193 Processing helix chain 'A' and resid 214 through 220 Processing helix chain 'A' and resid 232 through 247 removed outlier: 3.527A pdb=" N SER A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 removed outlier: 3.822A pdb=" N SER A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 310 removed outlier: 3.920A pdb=" N LYS A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 383 removed outlier: 4.157A pdb=" N THR A 382 " --> pdb=" O GLU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 472 removed outlier: 3.565A pdb=" N ARG A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 502 removed outlier: 3.848A pdb=" N TYR A 502 " --> pdb=" O GLY A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 520 removed outlier: 3.871A pdb=" N GLU A 520 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 569 removed outlier: 3.718A pdb=" N LEU A 566 " --> pdb=" O PHE A 562 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 567 " --> pdb=" O VAL A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 580 Processing helix chain 'A' and resid 601 through 612 removed outlier: 4.060A pdb=" N VAL A 612 " --> pdb=" O LEU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 627 No H-bonds generated for 'chain 'A' and resid 625 through 627' Processing helix chain 'A' and resid 628 through 653 removed outlier: 3.698A pdb=" N TRP A 634 " --> pdb=" O MET A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 672 removed outlier: 3.888A pdb=" N GLN A 671 " --> pdb=" O ASP A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 698 removed outlier: 3.677A pdb=" N ASN A 693 " --> pdb=" O SER A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 706 Processing helix chain 'A' and resid 707 through 709 No H-bonds generated for 'chain 'A' and resid 707 through 709' Processing helix chain 'A' and resid 712 through 722 removed outlier: 3.972A pdb=" N ALA A 716 " --> pdb=" O GLY A 712 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU A 717 " --> pdb=" O VAL A 713 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 718 " --> pdb=" O GLU A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 742 through 746 removed outlier: 3.649A pdb=" N CYS A 745 " --> pdb=" O ASP A 742 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LYS A 746 " --> pdb=" O GLU A 743 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 742 through 746' Processing helix chain 'A' and resid 771 through 785 removed outlier: 4.075A pdb=" N LEU A 777 " --> pdb=" O ARG A 773 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 796 removed outlier: 4.175A pdb=" N THR A 793 " --> pdb=" O GLU A 789 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N CYS A 794 " --> pdb=" O GLU A 790 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TRP A 795 " --> pdb=" O LEU A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 837 Processing helix chain 'B' and resid 35 through 53 removed outlier: 3.618A pdb=" N GLU B 39 " --> pdb=" O THR B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 84 removed outlier: 3.693A pdb=" N SER B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 112 removed outlier: 3.693A pdb=" N SER B 108 " --> pdb=" O PRO B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 129 removed outlier: 3.543A pdb=" N TYR B 128 " --> pdb=" O MET B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 159 removed outlier: 3.873A pdb=" N SER B 148 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP B 151 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE B 152 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 185 Processing helix chain 'B' and resid 186 through 188 No H-bonds generated for 'chain 'B' and resid 186 through 188' Processing helix chain 'B' and resid 204 through 213 removed outlier: 3.722A pdb=" N LEU B 208 " --> pdb=" O VAL B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 238 removed outlier: 3.920A pdb=" N MET B 237 " --> pdb=" O ARG B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 255 removed outlier: 4.279A pdb=" N SER B 255 " --> pdb=" O ARG B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 261 removed outlier: 4.147A pdb=" N ARG B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 296 removed outlier: 3.867A pdb=" N GLN B 290 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 291 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 328 removed outlier: 3.540A pdb=" N LYS B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 470 removed outlier: 3.621A pdb=" N LEU B 462 " --> pdb=" O PHE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 507 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 559 through 561 No H-bonds generated for 'chain 'B' and resid 559 through 561' Processing helix chain 'B' and resid 562 through 583 removed outlier: 3.913A pdb=" N VAL B 566 " --> pdb=" O LEU B 562 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY B 567 " --> pdb=" O TRP B 563 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 573 " --> pdb=" O SER B 569 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL B 575 " --> pdb=" O HIS B 571 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET B 576 " --> pdb=" O VAL B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 615 Processing helix chain 'B' and resid 627 through 658 removed outlier: 3.745A pdb=" N VAL B 656 " --> pdb=" O ALA B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 674 removed outlier: 4.244A pdb=" N ARG B 673 " --> pdb=" O ASP B 669 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN B 674 " --> pdb=" O PRO B 670 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 669 through 674' Processing helix chain 'B' and resid 687 through 696 removed outlier: 3.579A pdb=" N ILE B 691 " --> pdb=" O SER B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 701 No H-bonds generated for 'chain 'B' and resid 699 through 701' Processing helix chain 'B' and resid 702 through 710 removed outlier: 5.461A pdb=" N LYS B 708 " --> pdb=" O ARG B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 723 Processing helix chain 'B' and resid 733 through 743 Processing helix chain 'B' and resid 768 through 782 removed outlier: 3.552A pdb=" N VAL B 772 " --> pdb=" O TRP B 768 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER B 775 " --> pdb=" O ASN B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 793 Processing helix chain 'B' and resid 810 through 844 removed outlier: 3.860A pdb=" N ALA B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY B 822 " --> pdb=" O MET B 818 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE B 829 " --> pdb=" O VAL B 825 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 836 " --> pdb=" O PHE B 832 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 60 removed outlier: 3.752A pdb=" N GLY C 56 " --> pdb=" O ARG C 52 " (cutoff:3.500A) Proline residue: C 57 - end of helix removed outlier: 3.684A pdb=" N ALA C 60 " --> pdb=" O GLY C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 113 through 121 removed outlier: 3.594A pdb=" N PHE C 121 " --> pdb=" O SER C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 132 Processing helix chain 'C' and resid 152 through 165 removed outlier: 4.124A pdb=" N THR C 156 " --> pdb=" O GLN C 152 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL C 157 " --> pdb=" O GLN C 153 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET C 162 " --> pdb=" O MET C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 193 Processing helix chain 'C' and resid 214 through 220 Processing helix chain 'C' and resid 232 through 247 removed outlier: 3.528A pdb=" N SER C 245 " --> pdb=" O SER C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 removed outlier: 3.777A pdb=" N SER C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 310 removed outlier: 3.908A pdb=" N LYS C 309 " --> pdb=" O SER C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 338 removed outlier: 4.175A pdb=" N MET C 338 " --> pdb=" O HIS C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 383 removed outlier: 4.180A pdb=" N THR C 382 " --> pdb=" O GLU C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 472 removed outlier: 3.571A pdb=" N ARG C 469 " --> pdb=" O LYS C 465 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR C 470 " --> pdb=" O LYS C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 502 removed outlier: 3.828A pdb=" N TYR C 502 " --> pdb=" O GLY C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 520 removed outlier: 3.865A pdb=" N GLU C 520 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 569 removed outlier: 3.674A pdb=" N LEU C 566 " --> pdb=" O PHE C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 580 Processing helix chain 'C' and resid 600 through 612 removed outlier: 4.110A pdb=" N ALA C 604 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL C 612 " --> pdb=" O LEU C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 653 removed outlier: 3.630A pdb=" N TRP C 634 " --> pdb=" O MET C 630 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET C 653 " --> pdb=" O LEU C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 672 removed outlier: 3.925A pdb=" N GLN C 671 " --> pdb=" O ASP C 667 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 698 removed outlier: 3.670A pdb=" N ASN C 693 " --> pdb=" O SER C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 706 Processing helix chain 'C' and resid 707 through 709 No H-bonds generated for 'chain 'C' and resid 707 through 709' Processing helix chain 'C' and resid 712 through 722 removed outlier: 3.979A pdb=" N ALA C 716 " --> pdb=" O GLY C 712 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU C 717 " --> pdb=" O VAL C 713 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL C 718 " --> pdb=" O GLU C 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 741 removed outlier: 3.594A pdb=" N TYR C 737 " --> pdb=" O ALA C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 746 removed outlier: 3.506A pdb=" N CYS C 745 " --> pdb=" O ASP C 742 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS C 746 " --> pdb=" O GLU C 743 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 742 through 746' Processing helix chain 'C' and resid 771 through 785 removed outlier: 4.121A pdb=" N LEU C 777 " --> pdb=" O ARG C 773 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 786 through 796 removed outlier: 4.177A pdb=" N THR C 793 " --> pdb=" O GLU C 789 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N CYS C 794 " --> pdb=" O GLU C 790 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TRP C 795 " --> pdb=" O LEU C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 837 Processing helix chain 'D' and resid 35 through 53 removed outlier: 3.629A pdb=" N GLU D 39 " --> pdb=" O THR D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 84 removed outlier: 3.853A pdb=" N ALA D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 112 removed outlier: 3.602A pdb=" N SER D 108 " --> pdb=" O PRO D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 129 removed outlier: 3.532A pdb=" N TYR D 128 " --> pdb=" O MET D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 159 removed outlier: 3.873A pdb=" N SER D 148 " --> pdb=" O TYR D 144 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP D 151 " --> pdb=" O GLN D 147 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE D 152 " --> pdb=" O SER D 148 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 157 " --> pdb=" O GLU D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 185 Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 204 through 213 removed outlier: 3.714A pdb=" N LEU D 208 " --> pdb=" O VAL D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 238 removed outlier: 3.917A pdb=" N MET D 237 " --> pdb=" O ARG D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 255 removed outlier: 3.583A pdb=" N GLU D 253 " --> pdb=" O GLY D 250 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER D 255 " --> pdb=" O ARG D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 261 removed outlier: 4.162A pdb=" N ARG D 260 " --> pdb=" O GLY D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 296 removed outlier: 3.867A pdb=" N GLN D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU D 296 " --> pdb=" O VAL D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 328 removed outlier: 3.536A pdb=" N LYS D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 470 removed outlier: 3.635A pdb=" N LEU D 462 " --> pdb=" O PHE D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 507 Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 559 through 561 No H-bonds generated for 'chain 'D' and resid 559 through 561' Processing helix chain 'D' and resid 562 through 583 removed outlier: 3.951A pdb=" N VAL D 566 " --> pdb=" O LEU D 562 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY D 567 " --> pdb=" O TRP D 563 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL D 573 " --> pdb=" O SER D 569 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL D 575 " --> pdb=" O HIS D 571 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET D 576 " --> pdb=" O VAL D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 615 Processing helix chain 'D' and resid 627 through 658 removed outlier: 3.798A pdb=" N VAL D 656 " --> pdb=" O ALA D 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 674 removed outlier: 4.208A pdb=" N ARG D 673 " --> pdb=" O ASP D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 696 removed outlier: 3.568A pdb=" N ILE D 691 " --> pdb=" O SER D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 701 No H-bonds generated for 'chain 'D' and resid 699 through 701' Processing helix chain 'D' and resid 702 through 710 removed outlier: 5.373A pdb=" N LYS D 708 " --> pdb=" O ARG D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 723 Processing helix chain 'D' and resid 733 through 743 Processing helix chain 'D' and resid 768 through 782 removed outlier: 3.564A pdb=" N VAL D 772 " --> pdb=" O TRP D 768 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER D 775 " --> pdb=" O ASN D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 783 through 793 Processing helix chain 'D' and resid 810 through 844 removed outlier: 3.800A pdb=" N ALA D 821 " --> pdb=" O PHE D 817 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY D 822 " --> pdb=" O MET D 818 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE D 829 " --> pdb=" O VAL D 825 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA D 836 " --> pdb=" O PHE D 832 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 3.655A pdb=" N VAL A 99 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU A 98 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 170 removed outlier: 3.524A pdb=" N PHE A 170 " --> pdb=" O ASP A 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 174 removed outlier: 3.554A pdb=" N THR A 174 " --> pdb=" O ILE A 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 228 removed outlier: 3.727A pdb=" N VAL A 279 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 475 through 479 removed outlier: 6.357A pdb=" N LEU A 406 " --> pdb=" O ASP A 476 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N TYR A 478 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ILE A 408 " --> pdb=" O TYR A 478 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N SER A 407 " --> pdb=" O MET A 507 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 508 " --> pdb=" O ALA A 764 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 417 through 419 Processing sheet with id=AA7, first strand: chain 'A' and resid 436 through 440 removed outlier: 3.563A pdb=" N CYS A 436 " --> pdb=" O LYS A 454 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 452 " --> pdb=" O LYS A 438 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 533 through 536 removed outlier: 3.501A pdb=" N SER A 534 " --> pdb=" O TYR A 730 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 730 " --> pdb=" O SER A 534 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET A 536 " --> pdb=" O PHE A 728 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 728 " --> pdb=" O MET A 536 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLY A 683 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 9.068A pdb=" N ASP A 731 " --> pdb=" O GLY A 683 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 60 through 65 removed outlier: 6.917A pdb=" N ASN B 28 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA B 89 " --> pdb=" O ASN B 28 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL B 32 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LEU B 119 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ILE B 90 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL B 118 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 194 through 197 removed outlier: 6.575A pdb=" N LEU B 165 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N PHE B 197 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL B 167 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B 168 " --> pdb=" O SER B 222 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 267 through 270 removed outlier: 6.528A pdb=" N TYR B 351 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE B 366 " --> pdb=" O TYR B 351 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE B 353 " --> pdb=" O VAL B 364 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 397 through 402 removed outlier: 7.399A pdb=" N LEU B 398 " --> pdb=" O GLU B 475 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N HIS B 477 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE B 400 " --> pdb=" O HIS B 477 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ILE B 435 " --> pdb=" O TYR B 474 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL B 476 " --> pdb=" O ILE B 435 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL B 434 " --> pdb=" O CYS B 455 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N CYS B 455 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY B 438 " --> pdb=" O VAL B 451 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 451 " --> pdb=" O GLY B 438 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 487 through 488 removed outlier: 3.574A pdb=" N GLU B 488 " --> pdb=" O GLU B 497 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU B 497 " --> pdb=" O GLU B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 513 through 518 removed outlier: 5.084A pdb=" N ALA B 515 " --> pdb=" O GLY B 759 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLY B 759 " --> pdb=" O ALA B 515 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 681 through 682 removed outlier: 7.296A pdb=" N ALA B 682 " --> pdb=" O ILE B 730 " (cutoff:3.500A) removed outlier: 10.005A pdb=" N ASP B 732 " --> pdb=" O ALA B 682 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TRP B 731 " --> pdb=" O THR B 539 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N LEU B 538 " --> pdb=" O GLU B 751 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N GLU B 751 " --> pdb=" O LEU B 538 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 37 through 40 removed outlier: 3.668A pdb=" N VAL C 99 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU C 98 " --> pdb=" O LEU C 125 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.514A pdb=" N PHE C 170 " --> pdb=" O ASP C 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 173 through 174 removed outlier: 3.569A pdb=" N THR C 174 " --> pdb=" O ILE C 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 226 through 228 removed outlier: 3.644A pdb=" N VAL C 279 " --> pdb=" O VAL C 257 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 475 through 479 removed outlier: 6.387A pdb=" N LEU C 406 " --> pdb=" O ASP C 476 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TYR C 478 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ILE C 408 " --> pdb=" O TYR C 478 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N SER C 407 " --> pdb=" O MET C 507 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA C 508 " --> pdb=" O ALA C 764 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 417 through 419 Processing sheet with id=AC4, first strand: chain 'C' and resid 436 through 440 removed outlier: 3.516A pdb=" N CYS C 436 " --> pdb=" O LYS C 454 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL C 452 " --> pdb=" O LYS C 438 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 533 through 536 removed outlier: 3.546A pdb=" N TYR C 730 " --> pdb=" O SER C 534 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET C 536 " --> pdb=" O PHE C 728 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE C 728 " --> pdb=" O MET C 536 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY C 683 " --> pdb=" O ILE C 729 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N ASP C 731 " --> pdb=" O GLY C 683 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 60 through 65 removed outlier: 6.438A pdb=" N VAL D 27 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N THR D 63 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ILE D 29 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL D 65 " --> pdb=" O ILE D 29 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA D 31 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASN D 28 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA D 89 " --> pdb=" O ASN D 28 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL D 32 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEU D 119 " --> pdb=" O TYR D 88 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ILE D 90 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL D 118 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 194 through 197 removed outlier: 6.575A pdb=" N LEU D 165 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N PHE D 197 " --> pdb=" O LEU D 165 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL D 167 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER D 168 " --> pdb=" O SER D 222 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 267 through 270 removed outlier: 6.539A pdb=" N TYR D 351 " --> pdb=" O ILE D 366 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE D 366 " --> pdb=" O TYR D 351 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE D 353 " --> pdb=" O VAL D 364 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 397 through 402 removed outlier: 7.411A pdb=" N LEU D 398 " --> pdb=" O GLU D 475 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N HIS D 477 " --> pdb=" O LEU D 398 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE D 400 " --> pdb=" O HIS D 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 409 through 412 removed outlier: 3.582A pdb=" N VAL D 451 " --> pdb=" O GLY D 438 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY D 438 " --> pdb=" O VAL D 451 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N CYS D 455 " --> pdb=" O VAL D 434 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL D 434 " --> pdb=" O CYS D 455 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 487 through 488 removed outlier: 3.583A pdb=" N GLU D 488 " --> pdb=" O GLU D 497 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU D 497 " --> pdb=" O GLU D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'D' and resid 513 through 518 removed outlier: 5.071A pdb=" N ALA D 515 " --> pdb=" O GLY D 759 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLY D 759 " --> pdb=" O ALA D 515 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 681 through 682 removed outlier: 7.290A pdb=" N ALA D 682 " --> pdb=" O ILE D 730 " (cutoff:3.500A) removed outlier: 9.983A pdb=" N ASP D 732 " --> pdb=" O ALA D 682 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TRP D 731 " --> pdb=" O THR D 539 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU D 538 " --> pdb=" O GLU D 751 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLU D 751 " --> pdb=" O LEU D 538 " (cutoff:3.500A) 892 hydrogen bonds defined for protein. 2599 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.84 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3908 1.32 - 1.44: 6770 1.44 - 1.56: 13822 1.56 - 1.69: 0 1.69 - 1.81: 258 Bond restraints: 24758 Sorted by residual: bond pdb=" C1 NAG D 905 " pdb=" O5 NAG D 905 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C1 NAG B 905 " pdb=" O5 NAG B 905 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" N 6RM A 902 " pdb=" C2 6RM A 902 " ideal model delta sigma weight residual 1.412 1.371 0.041 2.00e-02 2.50e+03 4.21e+00 bond pdb=" N 6RM C 902 " pdb=" C2 6RM C 902 " ideal model delta sigma weight residual 1.412 1.371 0.041 2.00e-02 2.50e+03 4.13e+00 bond pdb=" C1 NAG B 902 " pdb=" O5 NAG B 902 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.87e+00 ... (remaining 24753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 33171 1.57 - 3.14: 339 3.14 - 4.71: 29 4.71 - 6.28: 19 6.28 - 7.85: 8 Bond angle restraints: 33566 Sorted by residual: angle pdb=" C GLU A 211 " pdb=" N ASP A 212 " pdb=" CA ASP A 212 " ideal model delta sigma weight residual 121.54 126.24 -4.70 1.91e+00 2.74e-01 6.06e+00 angle pdb=" C5 6RM A 902 " pdb=" C7 6RM A 902 " pdb=" O1 6RM A 902 " ideal model delta sigma weight residual 107.46 114.20 -6.74 3.00e+00 1.11e-01 5.05e+00 angle pdb=" C CYS A 399 " pdb=" N GLU A 400 " pdb=" CA GLU A 400 " ideal model delta sigma weight residual 121.80 127.24 -5.44 2.44e+00 1.68e-01 4.96e+00 angle pdb=" C5 6RM C 902 " pdb=" C7 6RM C 902 " pdb=" O1 6RM C 902 " ideal model delta sigma weight residual 107.46 114.13 -6.67 3.00e+00 1.11e-01 4.95e+00 angle pdb=" C CYS C 399 " pdb=" N GLU C 400 " pdb=" CA GLU C 400 " ideal model delta sigma weight residual 121.80 127.22 -5.42 2.44e+00 1.68e-01 4.93e+00 ... (remaining 33561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.44: 14551 24.44 - 48.89: 316 48.89 - 73.33: 17 73.33 - 97.77: 4 97.77 - 122.21: 6 Dihedral angle restraints: 14894 sinusoidal: 6110 harmonic: 8784 Sorted by residual: dihedral pdb=" C2 NAG D 905 " pdb=" C1 NAG D 905 " pdb=" O5 NAG D 905 " pdb=" C5 NAG D 905 " ideal model delta sinusoidal sigma weight residual -62.96 59.25 -122.21 1 3.00e+01 1.11e-03 1.64e+01 dihedral pdb=" C2 NAG B 905 " pdb=" C1 NAG B 905 " pdb=" O5 NAG B 905 " pdb=" C5 NAG B 905 " ideal model delta sinusoidal sigma weight residual -62.96 59.18 -122.14 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" C1 NAG D 905 " pdb=" C5 NAG D 905 " pdb=" O5 NAG D 905 " pdb=" C6 NAG D 905 " ideal model delta sinusoidal sigma weight residual 171.16 -88.80 -100.04 1 3.00e+01 1.11e-03 1.25e+01 ... (remaining 14891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3296 0.058 - 0.116: 503 0.116 - 0.174: 25 0.174 - 0.233: 0 0.233 - 0.291: 2 Chirality restraints: 3826 Sorted by residual: chirality pdb=" C1 NAG D 902 " pdb=" ND2 ASN D 276 " pdb=" C2 NAG D 902 " pdb=" O5 NAG D 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C1 NAG B 902 " pdb=" ND2 ASN B 276 " pdb=" C2 NAG B 902 " pdb=" O5 NAG B 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C1 NAG B 905 " pdb=" ND2 ASN B 771 " pdb=" C2 NAG B 905 " pdb=" O5 NAG B 905 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.05e-01 ... (remaining 3823 not shown) Planarity restraints: 4220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N 6RM C 902 " 0.020 2.00e-02 2.50e+03 5.51e-02 9.87e+01 pdb=" C 6RM C 902 " -0.106 2.00e-02 2.50e+03 pdb=" O 6RM C 902 " -0.065 2.00e-02 2.50e+03 pdb=" C1 6RM C 902 " -0.014 2.00e-02 2.50e+03 pdb=" C14 6RM C 902 " 0.084 2.00e-02 2.50e+03 pdb=" C2 6RM C 902 " 0.011 2.00e-02 2.50e+03 pdb=" C3 6RM C 902 " -0.008 2.00e-02 2.50e+03 pdb=" C4 6RM C 902 " 0.006 2.00e-02 2.50e+03 pdb=" C5 6RM C 902 " 0.029 2.00e-02 2.50e+03 pdb=" C6 6RM C 902 " 0.046 2.00e-02 2.50e+03 pdb=" C7 6RM C 902 " -0.091 2.00e-02 2.50e+03 pdb=" N1 6RM C 902 " 0.065 2.00e-02 2.50e+03 pdb=" S 6RM C 902 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N 6RM A 902 " 0.021 2.00e-02 2.50e+03 5.50e-02 9.84e+01 pdb=" C 6RM A 902 " -0.107 2.00e-02 2.50e+03 pdb=" O 6RM A 902 " -0.064 2.00e-02 2.50e+03 pdb=" C1 6RM A 902 " -0.014 2.00e-02 2.50e+03 pdb=" C14 6RM A 902 " 0.083 2.00e-02 2.50e+03 pdb=" C2 6RM A 902 " 0.011 2.00e-02 2.50e+03 pdb=" C3 6RM A 902 " -0.008 2.00e-02 2.50e+03 pdb=" C4 6RM A 902 " 0.005 2.00e-02 2.50e+03 pdb=" C5 6RM A 902 " 0.029 2.00e-02 2.50e+03 pdb=" C6 6RM A 902 " 0.045 2.00e-02 2.50e+03 pdb=" C7 6RM A 902 " -0.091 2.00e-02 2.50e+03 pdb=" N1 6RM A 902 " 0.065 2.00e-02 2.50e+03 pdb=" S 6RM A 902 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 6RM C 902 " 0.006 2.00e-02 2.50e+03 2.08e-02 8.69e+00 pdb=" C11 6RM C 902 " -0.010 2.00e-02 2.50e+03 pdb=" C12 6RM C 902 " -0.001 2.00e-02 2.50e+03 pdb=" C13 6RM C 902 " 0.024 2.00e-02 2.50e+03 pdb=" C8 6RM C 902 " 0.021 2.00e-02 2.50e+03 pdb=" C9 6RM C 902 " 0.018 2.00e-02 2.50e+03 pdb=" F 6RM C 902 " -0.017 2.00e-02 2.50e+03 pdb=" O1 6RM C 902 " -0.041 2.00e-02 2.50e+03 ... (remaining 4217 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3652 2.76 - 3.30: 23794 3.30 - 3.83: 38636 3.83 - 4.37: 42318 4.37 - 4.90: 73288 Nonbonded interactions: 181688 Sorted by model distance: nonbonded pdb=" O THR B 396 " pdb=" OG1 THR B 473 " model vdw 2.227 3.040 nonbonded pdb=" OG1 THR C 446 " pdb=" OE1 GLU C 448 " model vdw 2.228 3.040 nonbonded pdb=" O THR D 396 " pdb=" OG1 THR D 473 " model vdw 2.229 3.040 nonbonded pdb=" O GLU A 577 " pdb=" OG SER A 580 " model vdw 2.231 3.040 nonbonded pdb=" OG1 THR A 446 " pdb=" OE1 GLU A 448 " model vdw 2.231 3.040 ... (remaining 181683 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 25 through 775 or resid 777 through 906)) selection = (chain 'D' and (resid 25 through 775 or resid 777 through 906)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.150 Find NCS groups from input model: 0.550 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 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 : 0.002 0.076 24784 Z= 0.109 Angle : 0.446 8.792 33628 Z= 0.220 Chirality : 0.041 0.291 3826 Planarity : 0.003 0.055 4206 Dihedral : 9.476 122.215 9188 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.64 % Allowed : 4.72 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.17), residues: 2980 helix: 2.18 (0.16), residues: 1162 sheet: -0.18 (0.32), residues: 344 loop : -0.86 (0.17), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 523 TYR 0.004 0.000 TYR C 761 PHE 0.008 0.001 PHE C 599 TRP 0.005 0.000 TRP A 606 HIS 0.002 0.000 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00211 (24758) covalent geometry : angle 0.43963 (33566) SS BOND : bond 0.00041 ( 10) SS BOND : angle 0.47386 ( 20) hydrogen bonds : bond 0.14639 ( 892) hydrogen bonds : angle 5.67454 ( 2599) Misc. bond : bond 0.00048 ( 2) link_NAG-ASN : bond 0.00559 ( 14) link_NAG-ASN : angle 2.17627 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 546 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.9302 (mt) cc_final: 0.8991 (mm) REVERT: A 99 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.8056 (m) REVERT: A 100 PHE cc_start: 0.7144 (m-10) cc_final: 0.6520 (m-10) REVERT: A 147 PHE cc_start: 0.8232 (m-80) cc_final: 0.7914 (m-80) REVERT: A 188 LYS cc_start: 0.9079 (mmmm) cc_final: 0.8837 (mmmm) REVERT: A 192 ASP cc_start: 0.8844 (m-30) cc_final: 0.8631 (m-30) REVERT: A 255 TRP cc_start: 0.8338 (m100) cc_final: 0.8035 (m100) REVERT: A 455 CYS cc_start: 0.7235 (t) cc_final: 0.6823 (t) REVERT: A 641 PHE cc_start: 0.6585 (t80) cc_final: 0.6371 (t80) REVERT: B 41 MET cc_start: 0.9028 (ptp) cc_final: 0.7765 (ptp) REVERT: B 74 MET cc_start: 0.7495 (ppp) cc_final: 0.6918 (ttt) REVERT: B 90 ILE cc_start: 0.8552 (mm) cc_final: 0.8254 (mm) REVERT: B 116 ILE cc_start: 0.8957 (mm) cc_final: 0.8398 (mt) REVERT: B 127 ILE cc_start: 0.8730 (mt) cc_final: 0.8322 (pt) REVERT: B 136 SER cc_start: 0.8040 (m) cc_final: 0.7410 (p) REVERT: B 163 ILE cc_start: 0.9200 (mt) cc_final: 0.8992 (mp) REVERT: B 226 ASP cc_start: 0.7963 (p0) cc_final: 0.7746 (p0) REVERT: B 254 ILE cc_start: 0.8474 (mm) cc_final: 0.8204 (mm) REVERT: B 724 ASN cc_start: 0.9153 (m-40) cc_final: 0.8882 (m110) REVERT: C 40 LEU cc_start: 0.9286 (mt) cc_final: 0.9034 (mm) REVERT: C 99 VAL cc_start: 0.8424 (OUTLIER) cc_final: 0.7983 (m) REVERT: C 100 PHE cc_start: 0.7156 (m-10) cc_final: 0.6813 (m-10) REVERT: C 188 LYS cc_start: 0.9068 (mmmm) cc_final: 0.8748 (mmmm) REVERT: C 192 ASP cc_start: 0.8866 (m-30) cc_final: 0.8644 (m-30) REVERT: C 255 TRP cc_start: 0.8333 (m100) cc_final: 0.8083 (m100) REVERT: C 455 CYS cc_start: 0.7466 (t) cc_final: 0.7007 (t) REVERT: D 41 MET cc_start: 0.9078 (ptp) cc_final: 0.7828 (ptp) REVERT: D 74 MET cc_start: 0.7836 (ppp) cc_final: 0.6663 (ttp) REVERT: D 136 SER cc_start: 0.7993 (m) cc_final: 0.7400 (p) REVERT: D 818 MET cc_start: -0.0370 (mmt) cc_final: -0.0929 (ttm) outliers start: 43 outliers final: 8 residues processed: 587 average time/residue: 0.1743 time to fit residues: 155.9174 Evaluate side-chains 317 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 307 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 401 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN A 674 HIS ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN B 363 GLN B 477 HIS B 559 GLN ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 ASN C 674 HIS C 774 GLN D 363 GLN D 477 HIS D 650 ASN ** D 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.093814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.070848 restraints weight = 114950.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.072800 restraints weight = 64559.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.074207 restraints weight = 43799.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.075058 restraints weight = 33612.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.075607 restraints weight = 27945.296| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24784 Z= 0.196 Angle : 0.681 10.049 33628 Z= 0.338 Chirality : 0.046 0.283 3826 Planarity : 0.005 0.085 4206 Dihedral : 6.977 109.644 3586 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.13 % Allowed : 11.96 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.16), residues: 2980 helix: 1.68 (0.16), residues: 1192 sheet: -0.49 (0.28), residues: 400 loop : -0.98 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 49 TYR 0.022 0.002 TYR D 692 PHE 0.020 0.002 PHE C 473 TRP 0.026 0.002 TRP C 55 HIS 0.008 0.001 HIS B 477 Details of bonding type rmsd covalent geometry : bond 0.00439 (24758) covalent geometry : angle 0.67564 (33566) SS BOND : bond 0.00376 ( 10) SS BOND : angle 0.73515 ( 20) hydrogen bonds : bond 0.03187 ( 892) hydrogen bonds : angle 4.78382 ( 2599) Misc. bond : bond 0.00076 ( 2) link_NAG-ASN : bond 0.00491 ( 14) link_NAG-ASN : angle 2.49283 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 281 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 VAL cc_start: 0.7967 (OUTLIER) cc_final: 0.7726 (m) REVERT: A 188 LYS cc_start: 0.9270 (mmmm) cc_final: 0.8974 (mmmm) REVERT: A 192 ASP cc_start: 0.9099 (m-30) cc_final: 0.8845 (m-30) REVERT: A 413 GLU cc_start: 0.8255 (tp30) cc_final: 0.7942 (tm-30) REVERT: A 564 MET cc_start: 0.4769 (tmm) cc_final: 0.4399 (tmm) REVERT: A 641 PHE cc_start: 0.6728 (t80) cc_final: 0.6523 (t80) REVERT: A 776 ASP cc_start: 0.8502 (p0) cc_final: 0.8250 (p0) REVERT: B 152 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.8448 (m-80) REVERT: B 254 ILE cc_start: 0.8693 (mm) cc_final: 0.8430 (mm) REVERT: B 679 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.7661 (t80) REVERT: B 785 MET cc_start: 0.9273 (mmt) cc_final: 0.8909 (mpp) REVERT: B 818 MET cc_start: -0.2621 (mtp) cc_final: -0.3115 (ttm) REVERT: C 99 VAL cc_start: 0.8178 (OUTLIER) cc_final: 0.7876 (m) REVERT: C 188 LYS cc_start: 0.9282 (mmmm) cc_final: 0.8982 (mmmm) REVERT: C 192 ASP cc_start: 0.9068 (m-30) cc_final: 0.8827 (m-30) REVERT: C 415 PRO cc_start: 0.7200 (Cg_exo) cc_final: 0.6859 (Cg_endo) REVERT: C 560 MET cc_start: 0.5352 (tmm) cc_final: 0.4691 (ttp) REVERT: C 792 GLU cc_start: 0.8729 (tp30) cc_final: 0.8266 (mm-30) REVERT: D 136 SER cc_start: 0.8349 (m) cc_final: 0.7746 (p) REVERT: D 679 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.7622 (t80) REVERT: D 785 MET cc_start: 0.9260 (mmt) cc_final: 0.8888 (mpp) REVERT: D 818 MET cc_start: -0.0319 (mmt) cc_final: -0.0888 (ttm) outliers start: 56 outliers final: 35 residues processed: 328 average time/residue: 0.1581 time to fit residues: 82.8811 Evaluate side-chains 283 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 243 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 737 TYR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 477 HIS Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 679 PHE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 490 ASN Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 561 MET Chi-restraints excluded: chain C residue 634 TRP Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 477 HIS Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 578 TYR Chi-restraints excluded: chain D residue 679 PHE Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 736 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 150 optimal weight: 10.0000 chunk 252 optimal weight: 5.9990 chunk 256 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 159 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 242 optimal weight: 0.0770 chunk 297 optimal weight: 8.9990 chunk 162 optimal weight: 4.9990 chunk 72 optimal weight: 30.0000 overall best weight: 3.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 HIS B 477 HIS ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 HIS ** D 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.091941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.068386 restraints weight = 117720.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.070232 restraints weight = 66346.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.071436 restraints weight = 45607.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.072413 restraints weight = 35492.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.072893 restraints weight = 29886.517| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24784 Z= 0.174 Angle : 0.642 10.257 33628 Z= 0.314 Chirality : 0.045 0.288 3826 Planarity : 0.004 0.057 4206 Dihedral : 6.819 109.175 3584 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.25 % Allowed : 12.19 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.16), residues: 2980 helix: 1.48 (0.15), residues: 1202 sheet: -0.83 (0.28), residues: 382 loop : -0.97 (0.17), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 692 TYR 0.019 0.001 TYR B 692 PHE 0.030 0.002 PHE A 100 TRP 0.051 0.002 TRP C 55 HIS 0.017 0.001 HIS D 477 Details of bonding type rmsd covalent geometry : bond 0.00389 (24758) covalent geometry : angle 0.63474 (33566) SS BOND : bond 0.00781 ( 10) SS BOND : angle 1.21367 ( 20) hydrogen bonds : bond 0.03025 ( 892) hydrogen bonds : angle 4.54689 ( 2599) Misc. bond : bond 0.00063 ( 2) link_NAG-ASN : bond 0.00425 ( 14) link_NAG-ASN : angle 2.62995 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 252 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LYS cc_start: 0.9331 (mmmm) cc_final: 0.9044 (mmmm) REVERT: A 192 ASP cc_start: 0.9105 (m-30) cc_final: 0.8888 (m-30) REVERT: A 490 ASN cc_start: 0.8712 (OUTLIER) cc_final: 0.8318 (p0) REVERT: A 701 MET cc_start: 0.8819 (mmm) cc_final: 0.8463 (mmm) REVERT: B 152 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.8233 (m-10) REVERT: B 254 ILE cc_start: 0.8754 (mm) cc_final: 0.8469 (mm) REVERT: B 470 MET cc_start: 0.8347 (pmm) cc_final: 0.8072 (pmm) REVERT: B 679 PHE cc_start: 0.8827 (OUTLIER) cc_final: 0.7721 (t80) REVERT: B 818 MET cc_start: -0.2596 (mtp) cc_final: -0.3043 (ttm) REVERT: C 99 VAL cc_start: 0.8516 (OUTLIER) cc_final: 0.8251 (m) REVERT: C 188 LYS cc_start: 0.9348 (mmmm) cc_final: 0.9064 (mmmm) REVERT: C 192 ASP cc_start: 0.9107 (m-30) cc_final: 0.8884 (m-30) REVERT: C 490 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8338 (p0) REVERT: C 701 MET cc_start: 0.8826 (mmm) cc_final: 0.8471 (mmm) REVERT: D 136 SER cc_start: 0.8326 (m) cc_final: 0.7684 (p) REVERT: D 679 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.7837 (t80) REVERT: D 818 MET cc_start: -0.0505 (mmt) cc_final: -0.1173 (ttm) outliers start: 59 outliers final: 41 residues processed: 300 average time/residue: 0.1510 time to fit residues: 74.1326 Evaluate side-chains 275 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 228 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 737 TYR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 679 PHE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 478 TYR Chi-restraints excluded: chain C residue 490 ASN Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 561 MET Chi-restraints excluded: chain C residue 634 TRP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 459 CYS Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 578 TYR Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 679 PHE Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 736 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 201 optimal weight: 4.9990 chunk 230 optimal weight: 7.9990 chunk 277 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 244 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 175 optimal weight: 5.9990 chunk 72 optimal weight: 30.0000 chunk 299 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 GLN C 490 ASN C 736 ASN ** D 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.087825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.064542 restraints weight = 115989.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.066256 restraints weight = 65755.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.067359 restraints weight = 45331.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.068246 restraints weight = 35361.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.068716 restraints weight = 30015.447| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3368 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3368 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 24784 Z= 0.248 Angle : 0.706 9.361 33628 Z= 0.352 Chirality : 0.046 0.285 3826 Planarity : 0.005 0.075 4206 Dihedral : 7.133 110.852 3581 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.05 % Allowed : 12.07 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.16), residues: 2980 helix: 1.17 (0.15), residues: 1212 sheet: -1.02 (0.27), residues: 388 loop : -1.19 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 630 TYR 0.023 0.002 TYR A 230 PHE 0.029 0.002 PHE D 738 TRP 0.052 0.002 TRP A 55 HIS 0.006 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00545 (24758) covalent geometry : angle 0.69772 (33566) SS BOND : bond 0.00323 ( 10) SS BOND : angle 1.74677 ( 20) hydrogen bonds : bond 0.03338 ( 892) hydrogen bonds : angle 4.75762 ( 2599) Misc. bond : bond 0.00068 ( 2) link_NAG-ASN : bond 0.00444 ( 14) link_NAG-ASN : angle 2.86119 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 228 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8269 (pmm) cc_final: 0.7974 (pmm) REVERT: A 164 ASP cc_start: 0.9090 (t0) cc_final: 0.8858 (t0) REVERT: A 180 TYR cc_start: 0.7042 (m-80) cc_final: 0.6640 (m-80) REVERT: A 188 LYS cc_start: 0.9367 (mmmm) cc_final: 0.9112 (mmmm) REVERT: A 473 PHE cc_start: 0.7375 (m-80) cc_final: 0.7144 (m-80) REVERT: A 536 MET cc_start: 0.8696 (tpp) cc_final: 0.8175 (tpt) REVERT: A 701 MET cc_start: 0.8847 (mmm) cc_final: 0.8504 (mmm) REVERT: B 133 ILE cc_start: 0.9256 (OUTLIER) cc_final: 0.8976 (tt) REVERT: B 188 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.8037 (tm-30) REVERT: B 209 MET cc_start: 0.9050 (ptp) cc_final: 0.8832 (mmm) REVERT: B 254 ILE cc_start: 0.8861 (mm) cc_final: 0.8542 (mm) REVERT: B 679 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8102 (t80) REVERT: B 818 MET cc_start: -0.2220 (mtp) cc_final: -0.2660 (ttm) REVERT: C 164 ASP cc_start: 0.9148 (t0) cc_final: 0.8885 (t0) REVERT: C 536 MET cc_start: 0.8654 (tpp) cc_final: 0.7919 (tpp) REVERT: C 560 MET cc_start: 0.5179 (tmm) cc_final: 0.4611 (ttp) REVERT: C 641 PHE cc_start: 0.6733 (t80) cc_final: 0.6528 (t80) REVERT: C 701 MET cc_start: 0.8874 (mmm) cc_final: 0.8540 (mmm) REVERT: D 679 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.8157 (t80) REVERT: D 738 PHE cc_start: 0.7550 (OUTLIER) cc_final: 0.7249 (t80) REVERT: D 818 MET cc_start: -0.0549 (mmt) cc_final: -0.1165 (ttm) outliers start: 80 outliers final: 56 residues processed: 289 average time/residue: 0.1602 time to fit residues: 74.4663 Evaluate side-chains 268 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 207 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TRP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 737 TYR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 474 TYR Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 542 VAL Chi-restraints excluded: chain B residue 679 PHE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain C residue 55 TRP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 478 TYR Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 634 TRP Chi-restraints excluded: chain C residue 737 TYR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 512 MET Chi-restraints excluded: chain D residue 514 VAL Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 578 TYR Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 679 PHE Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 736 LEU Chi-restraints excluded: chain D residue 738 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 147 optimal weight: 9.9990 chunk 149 optimal weight: 50.0000 chunk 251 optimal weight: 10.0000 chunk 275 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 216 optimal weight: 5.9990 chunk 72 optimal weight: 30.0000 chunk 104 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 HIS A 485 HIS ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 GLN C 405 HIS C 485 HIS ** D 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.085061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.061833 restraints weight = 113524.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.063565 restraints weight = 64215.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.064646 restraints weight = 44143.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.065513 restraints weight = 34512.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.065982 restraints weight = 29131.828| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 24784 Z= 0.282 Angle : 0.761 9.703 33628 Z= 0.383 Chirality : 0.048 0.291 3826 Planarity : 0.004 0.056 4206 Dihedral : 7.582 112.691 3580 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.66 % Allowed : 12.64 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.15), residues: 2980 helix: 0.99 (0.15), residues: 1192 sheet: -1.35 (0.26), residues: 402 loop : -1.41 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 181 TYR 0.026 0.002 TYR C 230 PHE 0.035 0.003 PHE B 738 TRP 0.047 0.002 TRP A 55 HIS 0.007 0.001 HIS B 134 Details of bonding type rmsd covalent geometry : bond 0.00619 (24758) covalent geometry : angle 0.75196 (33566) SS BOND : bond 0.00345 ( 10) SS BOND : angle 1.96937 ( 20) hydrogen bonds : bond 0.03696 ( 892) hydrogen bonds : angle 4.89647 ( 2599) Misc. bond : bond 0.00068 ( 2) link_NAG-ASN : bond 0.00461 ( 14) link_NAG-ASN : angle 3.08547 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 209 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8681 (pmm) cc_final: 0.8430 (pmm) REVERT: A 133 MET cc_start: 0.8059 (pmm) cc_final: 0.7751 (pmm) REVERT: A 164 ASP cc_start: 0.9114 (t0) cc_final: 0.8715 (t0) REVERT: A 413 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8136 (tp30) REVERT: B 528 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7811 (tm-30) REVERT: B 679 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8286 (t80) REVERT: B 738 PHE cc_start: 0.7562 (OUTLIER) cc_final: 0.7150 (t80) REVERT: D 528 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7738 (tm-30) REVERT: D 627 PHE cc_start: 0.7073 (OUTLIER) cc_final: 0.6771 (m-80) REVERT: D 679 PHE cc_start: 0.8967 (OUTLIER) cc_final: 0.8335 (t80) REVERT: D 777 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9213 (mm) outliers start: 96 outliers final: 61 residues processed: 287 average time/residue: 0.1570 time to fit residues: 72.6625 Evaluate side-chains 267 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 200 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TRP Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 459 CYS Chi-restraints excluded: chain B residue 474 TYR Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 679 PHE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 738 PHE Chi-restraints excluded: chain C residue 55 TRP Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 115 PHE Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 478 TYR Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 629 ILE Chi-restraints excluded: chain C residue 634 TRP Chi-restraints excluded: chain C residue 737 TYR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 241 THR Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 470 MET Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 578 TYR Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 627 PHE Chi-restraints excluded: chain D residue 679 PHE Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 777 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 111 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 159 optimal weight: 0.0670 chunk 224 optimal weight: 20.0000 chunk 210 optimal weight: 9.9990 chunk 195 optimal weight: 6.9990 chunk 205 optimal weight: 9.9990 chunk 138 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 151 optimal weight: 20.0000 chunk 102 optimal weight: 8.9990 overall best weight: 1.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 HIS ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 GLN C 485 HIS ** D 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.087058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.063846 restraints weight = 112640.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.065676 restraints weight = 62828.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.066823 restraints weight = 42678.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.067730 restraints weight = 32882.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.068246 restraints weight = 27651.813| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.5429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24784 Z= 0.138 Angle : 0.679 12.634 33628 Z= 0.332 Chirality : 0.046 0.335 3826 Planarity : 0.004 0.053 4206 Dihedral : 7.138 110.136 3580 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.02 % Allowed : 15.54 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.16), residues: 2980 helix: 1.14 (0.15), residues: 1210 sheet: -1.28 (0.26), residues: 398 loop : -1.17 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 741 TYR 0.019 0.001 TYR D 692 PHE 0.032 0.002 PHE B 754 TRP 0.052 0.002 TRP A 55 HIS 0.005 0.001 HIS C 42 Details of bonding type rmsd covalent geometry : bond 0.00313 (24758) covalent geometry : angle 0.67058 (33566) SS BOND : bond 0.00331 ( 10) SS BOND : angle 1.75113 ( 20) hydrogen bonds : bond 0.03018 ( 892) hydrogen bonds : angle 4.60459 ( 2599) Misc. bond : bond 0.00062 ( 2) link_NAG-ASN : bond 0.00466 ( 14) link_NAG-ASN : angle 2.90881 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 216 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8657 (pmm) cc_final: 0.8280 (pmm) REVERT: A 701 MET cc_start: 0.8912 (mmm) cc_final: 0.8618 (mmm) REVERT: B 528 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7823 (tm-30) REVERT: B 679 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8221 (t80) REVERT: C 134 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8810 (tt) REVERT: C 135 MET cc_start: 0.7593 (pmm) cc_final: 0.7363 (pmm) REVERT: C 701 MET cc_start: 0.8951 (mmm) cc_final: 0.8642 (mmm) REVERT: D 528 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7751 (tm-30) REVERT: D 679 PHE cc_start: 0.8916 (OUTLIER) cc_final: 0.8296 (t80) outliers start: 53 outliers final: 38 residues processed: 256 average time/residue: 0.1626 time to fit residues: 66.7838 Evaluate side-chains 238 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 197 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 TRP Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 474 TYR Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 679 PHE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain C residue 55 TRP Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 478 TYR Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 634 TRP Chi-restraints excluded: chain C residue 737 TYR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 321 PHE Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 578 TYR Chi-restraints excluded: chain D residue 679 PHE Chi-restraints excluded: chain D residue 736 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 179 optimal weight: 0.0470 chunk 289 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 198 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 180 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 GLN ** D 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.088260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.064601 restraints weight = 113316.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.066501 restraints weight = 62176.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.067795 restraints weight = 41997.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.068574 restraints weight = 32220.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.069196 restraints weight = 26949.818| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3377 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24784 Z= 0.115 Angle : 0.665 11.390 33628 Z= 0.321 Chirality : 0.045 0.340 3826 Planarity : 0.003 0.050 4206 Dihedral : 6.852 108.733 3578 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.90 % Allowed : 15.31 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.16), residues: 2980 helix: 1.30 (0.15), residues: 1198 sheet: -1.14 (0.26), residues: 386 loop : -1.06 (0.17), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 755 TYR 0.016 0.001 TYR B 692 PHE 0.039 0.001 PHE A 641 TRP 0.052 0.001 TRP A 55 HIS 0.005 0.001 HIS C 42 Details of bonding type rmsd covalent geometry : bond 0.00262 (24758) covalent geometry : angle 0.65576 (33566) SS BOND : bond 0.00338 ( 10) SS BOND : angle 2.10119 ( 20) hydrogen bonds : bond 0.02875 ( 892) hydrogen bonds : angle 4.47931 ( 2599) Misc. bond : bond 0.00052 ( 2) link_NAG-ASN : bond 0.00492 ( 14) link_NAG-ASN : angle 2.79879 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 222 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8614 (pmm) cc_final: 0.8201 (pmm) REVERT: A 164 ASP cc_start: 0.9221 (t0) cc_final: 0.8963 (t0) REVERT: A 701 MET cc_start: 0.8915 (mmm) cc_final: 0.8598 (mmm) REVERT: B 41 MET cc_start: 0.8248 (ptt) cc_final: 0.7460 (ptp) REVERT: B 209 MET cc_start: 0.9027 (ptp) cc_final: 0.8776 (mmm) REVERT: B 528 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7813 (tm-30) REVERT: B 679 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8340 (t80) REVERT: C 134 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8829 (tt) REVERT: C 144 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8494 (m-80) REVERT: C 162 MET cc_start: 0.8304 (ttm) cc_final: 0.7440 (ttm) REVERT: C 170 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.6865 (m-80) REVERT: C 701 MET cc_start: 0.8935 (mmm) cc_final: 0.8621 (mmm) REVERT: D 528 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7749 (tm-30) REVERT: D 627 PHE cc_start: 0.7000 (OUTLIER) cc_final: 0.6713 (m-80) REVERT: D 679 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.8351 (t80) REVERT: D 818 MET cc_start: -0.1760 (mmt) cc_final: -0.2567 (mtt) outliers start: 50 outliers final: 33 residues processed: 265 average time/residue: 0.1561 time to fit residues: 66.9438 Evaluate side-chains 248 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 475 TYR Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 474 TYR Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 679 PHE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain C residue 170 PHE Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 520 GLU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 634 TRP Chi-restraints excluded: chain C residue 737 TYR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 436 CYS Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 578 TYR Chi-restraints excluded: chain D residue 627 PHE Chi-restraints excluded: chain D residue 679 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 293 optimal weight: 0.4980 chunk 57 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 243 optimal weight: 9.9990 chunk 282 optimal weight: 20.0000 chunk 207 optimal weight: 20.0000 chunk 198 optimal weight: 0.5980 chunk 78 optimal weight: 20.0000 chunk 296 optimal weight: 0.8980 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS ** D 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.087200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.063244 restraints weight = 115576.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.065002 restraints weight = 66083.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.066091 restraints weight = 45874.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.066962 restraints weight = 36158.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.067454 restraints weight = 30627.862| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.5608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24784 Z= 0.147 Angle : 0.680 12.000 33628 Z= 0.329 Chirality : 0.045 0.329 3826 Planarity : 0.003 0.050 4206 Dihedral : 6.839 109.094 3576 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.17 % Allowed : 15.42 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.16), residues: 2980 helix: 1.29 (0.15), residues: 1202 sheet: -1.10 (0.25), residues: 428 loop : -1.07 (0.18), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 755 TYR 0.017 0.001 TYR B 692 PHE 0.036 0.002 PHE B 754 TRP 0.016 0.001 TRP C 609 HIS 0.004 0.001 HIS C 42 Details of bonding type rmsd covalent geometry : bond 0.00333 (24758) covalent geometry : angle 0.67079 (33566) SS BOND : bond 0.00510 ( 10) SS BOND : angle 2.50927 ( 20) hydrogen bonds : bond 0.02948 ( 892) hydrogen bonds : angle 4.53030 ( 2599) Misc. bond : bond 0.00048 ( 2) link_NAG-ASN : bond 0.00431 ( 14) link_NAG-ASN : angle 2.77156 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 214 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8632 (pmm) cc_final: 0.8189 (pmm) REVERT: A 164 ASP cc_start: 0.9168 (t0) cc_final: 0.8928 (t0) REVERT: A 170 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7272 (m-80) REVERT: A 641 PHE cc_start: 0.7555 (OUTLIER) cc_final: 0.7277 (t80) REVERT: A 701 MET cc_start: 0.8946 (mmm) cc_final: 0.8617 (mmm) REVERT: B 237 MET cc_start: 0.8532 (ppp) cc_final: 0.8319 (ppp) REVERT: B 679 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.8385 (t80) REVERT: C 134 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8795 (tt) REVERT: C 135 MET cc_start: 0.7543 (pmm) cc_final: 0.7237 (pmm) REVERT: C 162 MET cc_start: 0.8408 (ttm) cc_final: 0.7678 (ttm) REVERT: C 170 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.6991 (m-80) REVERT: C 701 MET cc_start: 0.8971 (mmm) cc_final: 0.8641 (mmm) REVERT: D 197 PHE cc_start: 0.7432 (m-80) cc_final: 0.7232 (m-80) REVERT: D 627 PHE cc_start: 0.6897 (OUTLIER) cc_final: 0.6655 (m-80) REVERT: D 679 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8403 (t80) REVERT: D 695 ARG cc_start: 0.8333 (ttp-110) cc_final: 0.8128 (ttm170) REVERT: D 794 ARG cc_start: 0.6719 (ptt-90) cc_final: 0.6451 (ptp-170) outliers start: 57 outliers final: 38 residues processed: 265 average time/residue: 0.1598 time to fit residues: 68.5289 Evaluate side-chains 252 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 207 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 641 PHE Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 474 TYR Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 679 PHE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 170 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 475 TYR Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 634 TRP Chi-restraints excluded: chain C residue 737 TYR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 474 TYR Chi-restraints excluded: chain D residue 578 TYR Chi-restraints excluded: chain D residue 627 PHE Chi-restraints excluded: chain D residue 679 PHE Chi-restraints excluded: chain D residue 733 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 75 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 262 optimal weight: 3.9990 chunk 295 optimal weight: 1.9990 chunk 224 optimal weight: 5.9990 chunk 292 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 chunk 285 optimal weight: 4.9990 chunk 266 optimal weight: 8.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.085998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.061717 restraints weight = 116052.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.063550 restraints weight = 64105.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.064798 restraints weight = 43707.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.065613 restraints weight = 33909.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.066112 restraints weight = 28548.311| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3320 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3320 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.5930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24784 Z= 0.185 Angle : 0.714 13.375 33628 Z= 0.347 Chirality : 0.046 0.322 3826 Planarity : 0.004 0.051 4206 Dihedral : 6.994 109.527 3576 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.83 % Allowed : 16.03 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.16), residues: 2980 helix: 1.25 (0.15), residues: 1202 sheet: -1.26 (0.26), residues: 384 loop : -1.11 (0.17), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 755 TYR 0.037 0.001 TYR D 692 PHE 0.041 0.002 PHE B 754 TRP 0.022 0.002 TRP C 609 HIS 0.004 0.001 HIS C 42 Details of bonding type rmsd covalent geometry : bond 0.00414 (24758) covalent geometry : angle 0.70526 (33566) SS BOND : bond 0.00262 ( 10) SS BOND : angle 2.47297 ( 20) hydrogen bonds : bond 0.03087 ( 892) hydrogen bonds : angle 4.63907 ( 2599) Misc. bond : bond 0.00051 ( 2) link_NAG-ASN : bond 0.00402 ( 14) link_NAG-ASN : angle 2.83357 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 207 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8622 (pmm) cc_final: 0.8183 (pmm) REVERT: A 144 PHE cc_start: 0.8967 (OUTLIER) cc_final: 0.7673 (t80) REVERT: A 162 MET cc_start: 0.8670 (ttm) cc_final: 0.8159 (ttp) REVERT: A 170 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7351 (m-80) REVERT: A 701 MET cc_start: 0.8976 (mmm) cc_final: 0.8776 (mmm) REVERT: B 41 MET cc_start: 0.8208 (ptt) cc_final: 0.7411 (ptp) REVERT: B 74 MET cc_start: 0.8652 (ttt) cc_final: 0.7907 (tmm) REVERT: B 679 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8416 (t80) REVERT: C 162 MET cc_start: 0.8541 (ttm) cc_final: 0.7996 (ttp) REVERT: C 170 PHE cc_start: 0.8267 (OUTLIER) cc_final: 0.7225 (m-80) REVERT: C 182 GLU cc_start: 0.8277 (pm20) cc_final: 0.8071 (pm20) REVERT: C 754 TYR cc_start: 0.7377 (t80) cc_final: 0.7109 (t80) REVERT: D 41 MET cc_start: 0.8274 (ptt) cc_final: 0.7466 (ptp) REVERT: D 627 PHE cc_start: 0.6959 (OUTLIER) cc_final: 0.6685 (m-80) REVERT: D 679 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8454 (t80) outliers start: 48 outliers final: 36 residues processed: 252 average time/residue: 0.1523 time to fit residues: 62.7006 Evaluate side-chains 240 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 198 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 474 TYR Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 679 PHE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 170 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 634 TRP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 578 TYR Chi-restraints excluded: chain D residue 627 PHE Chi-restraints excluded: chain D residue 679 PHE Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 736 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 122 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 184 optimal weight: 0.6980 chunk 141 optimal weight: 4.9990 chunk 301 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 253 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 264 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.086607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.062614 restraints weight = 114848.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.064345 restraints weight = 63996.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.065559 restraints weight = 44015.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.066199 restraints weight = 34064.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.066915 restraints weight = 29121.446| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.5998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24784 Z= 0.148 Angle : 0.710 13.814 33628 Z= 0.344 Chirality : 0.046 0.334 3826 Planarity : 0.004 0.050 4206 Dihedral : 6.922 108.511 3576 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.64 % Allowed : 16.45 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.16), residues: 2980 helix: 1.27 (0.15), residues: 1188 sheet: -1.30 (0.26), residues: 388 loop : -1.04 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 755 TYR 0.049 0.001 TYR D 692 PHE 0.059 0.002 PHE D 583 TRP 0.022 0.001 TRP C 609 HIS 0.005 0.001 HIS C 42 Details of bonding type rmsd covalent geometry : bond 0.00336 (24758) covalent geometry : angle 0.70078 (33566) SS BOND : bond 0.00297 ( 10) SS BOND : angle 2.32505 ( 20) hydrogen bonds : bond 0.02966 ( 892) hydrogen bonds : angle 4.61811 ( 2599) Misc. bond : bond 0.00053 ( 2) link_NAG-ASN : bond 0.00416 ( 14) link_NAG-ASN : angle 2.83505 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5960 Ramachandran restraints generated. 2980 Oldfield, 0 Emsley, 2980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 208 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8654 (pmm) cc_final: 0.8214 (pmm) REVERT: A 170 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7460 (m-80) REVERT: A 701 MET cc_start: 0.8962 (mmm) cc_final: 0.8616 (mmm) REVERT: B 41 MET cc_start: 0.8197 (ptt) cc_final: 0.7413 (ptp) REVERT: B 679 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.8392 (t80) REVERT: C 162 MET cc_start: 0.8491 (ttm) cc_final: 0.7778 (ttm) REVERT: C 170 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7075 (m-80) REVERT: C 701 MET cc_start: 0.8928 (mmm) cc_final: 0.8633 (mmm) REVERT: C 754 TYR cc_start: 0.7419 (t80) cc_final: 0.7215 (t80) REVERT: D 41 MET cc_start: 0.8288 (ptt) cc_final: 0.7479 (ptp) REVERT: D 627 PHE cc_start: 0.6964 (OUTLIER) cc_final: 0.6664 (m-80) REVERT: D 679 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8449 (t80) outliers start: 43 outliers final: 35 residues processed: 249 average time/residue: 0.1629 time to fit residues: 65.2307 Evaluate side-chains 240 residues out of total 2634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 200 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 170 PHE Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 512 MET Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 679 PHE Chi-restraints excluded: chain B residue 684 VAL Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 170 PHE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 605 ILE Chi-restraints excluded: chain C residue 634 TRP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 578 TYR Chi-restraints excluded: chain D residue 627 PHE Chi-restraints excluded: chain D residue 679 PHE Chi-restraints excluded: chain D residue 733 SER Chi-restraints excluded: chain D residue 736 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 71 optimal weight: 0.6980 chunk 217 optimal weight: 0.4980 chunk 119 optimal weight: 9.9990 chunk 80 optimal weight: 0.7980 chunk 275 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 129 optimal weight: 40.0000 chunk 35 optimal weight: 6.9990 chunk 228 optimal weight: 20.0000 chunk 299 optimal weight: 20.0000 chunk 204 optimal weight: 5.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.086495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.062444 restraints weight = 114655.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.064248 restraints weight = 63018.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.065347 restraints weight = 42888.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.066301 restraints weight = 33412.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.066820 restraints weight = 28079.332| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.6103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24784 Z= 0.158 Angle : 0.714 13.931 33628 Z= 0.348 Chirality : 0.046 0.333 3826 Planarity : 0.004 0.051 4206 Dihedral : 6.946 108.773 3576 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.71 % Allowed : 16.26 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.16), residues: 2980 helix: 1.34 (0.15), residues: 1178 sheet: -1.29 (0.26), residues: 388 loop : -1.02 (0.18), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 386 TYR 0.019 0.001 TYR D 692 PHE 0.043 0.002 PHE D 583 TRP 0.024 0.001 TRP C 609 HIS 0.005 0.001 HIS C 42 Details of bonding type rmsd covalent geometry : bond 0.00358 (24758) covalent geometry : angle 0.70580 (33566) SS BOND : bond 0.00282 ( 10) SS BOND : angle 2.33176 ( 20) hydrogen bonds : bond 0.03046 ( 892) hydrogen bonds : angle 4.65965 ( 2599) Misc. bond : bond 0.00049 ( 2) link_NAG-ASN : bond 0.00410 ( 14) link_NAG-ASN : angle 2.82006 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5389.11 seconds wall clock time: 93 minutes 31.84 seconds (5611.84 seconds total)