Starting phenix.real_space_refine on Mon May 4 21:38:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d3c_46531/05_2026/9d3c_46531.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d3c_46531/05_2026/9d3c_46531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9d3c_46531/05_2026/9d3c_46531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d3c_46531/05_2026/9d3c_46531.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d3c_46531/05_2026/9d3c_46531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d3c_46531/05_2026/9d3c_46531.map" } resolution = 3.96 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= 0.012 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 82 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 134 5.16 5 Cl 1 4.86 5 C 15464 2.51 5 N 4073 2.21 5 O 4522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24194 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 779, 6033 Classifications: {'peptide': 779} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 34, 'TRANS': 744} Chain breaks: 4 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 5, 'TYR:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 83 Chain: "B" Number of atoms: 5969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 5969 Classifications: {'peptide': 778} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 27, 'TRANS': 750} Chain breaks: 3 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 5, 'HIS:plan': 4, 'PHE:plan': 5, 'GLN:plan1': 3, 'ARG:plan': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 126 Chain: "C" Number of atoms: 6254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 803, 6254 Classifications: {'peptide': 803} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 35, 'TRANS': 767} Chain breaks: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 56 Chain: "D" Number of atoms: 5752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 755, 5752 Classifications: {'peptide': 755} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 717} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 200 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 7, 'PHE:plan': 4, 'ASP:plan': 1, 'TYR:plan': 3, 'HIS:plan': 1, 'TRP:plan': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 113 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'JC9': 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: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 5.61, per 1000 atoms: 0.23 Number of scatterers: 24194 At special positions: 0 Unit cell: (121.552, 147.232, 183.184, 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) Cl 1 17.00 S 134 16.00 O 4522 8.00 N 4073 7.00 C 15464 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.04 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.04 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 104 " - pdb=" SG CYS D 348 " distance=2.03 Simple disulfide: pdb=" SG CYS D 455 " - pdb=" SG CYS D 483 " distance=2.03 Simple disulfide: pdb=" SG CYS D 462 " - pdb=" SG CYS D 484 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A 902 " - " ASN A 771 " " NAG A 903 " - " ASN A 471 " " NAG A 904 " - " ASN A 203 " " NAG A 905 " - " ASN A 368 " " NAG B 902 " - " ASN B 688 " " NAG C 902 " - " ASN C 771 " " NAG C 903 " - " ASN C 368 " " NAG C 904 " - " ASN C 471 " " NAG E 1 " - " ASN D 715 " Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 1.1 seconds 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5808 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 27 sheets defined 41.4% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 39 through 53 removed outlier: 3.528A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 80 removed outlier: 4.302A pdb=" N CYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 105 through 114 removed outlier: 3.518A pdb=" N THR A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ALA A 111 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N TYR A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 146 Processing helix chain 'A' and resid 147 through 158 removed outlier: 3.971A pdb=" N TRP A 151 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 removed outlier: 3.770A pdb=" N LEU A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 182 " --> pdb=" O LYS A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 210 through 214 removed outlier: 3.551A pdb=" N LEU A 214 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 removed outlier: 3.938A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N MET A 237 " --> pdb=" O ARG A 233 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.522A pdb=" N ILE A 254 " --> pdb=" O GLU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 276 through 296 removed outlier: 3.550A pdb=" N SER A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 327 removed outlier: 3.993A pdb=" N LYS A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 323 " --> pdb=" O PRO A 319 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 325 " --> pdb=" O PHE A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 removed outlier: 3.995A pdb=" N GLU A 385 " --> pdb=" O PRO A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 467 removed outlier: 3.507A pdb=" N LEU A 463 " --> pdb=" O CYS A 459 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.666A pdb=" N GLU A 504 " --> pdb=" O GLY A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.719A pdb=" N GLN A 525 " --> pdb=" O ASN A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 580 removed outlier: 4.002A pdb=" N TRP A 563 " --> pdb=" O GLN A 559 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 570 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N HIS A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N MET A 576 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 577 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 616 removed outlier: 3.548A pdb=" N TRP A 608 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 613 " --> pdb=" O PHE A 609 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 615 " --> pdb=" O TRP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 657 removed outlier: 3.710A pdb=" N LEU A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY A 633 " --> pdb=" O ALA A 629 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL A 635 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA A 637 " --> pdb=" O GLY A 633 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLY A 638 " --> pdb=" O MET A 634 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 640 " --> pdb=" O TRP A 636 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET A 641 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 643 " --> pdb=" O PHE A 639 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR A 648 " --> pdb=" O VAL A 644 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 651 " --> pdb=" O TYR A 647 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 656 " --> pdb=" O ALA A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 688 through 696 removed outlier: 3.764A pdb=" N GLN A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 707 removed outlier: 3.518A pdb=" N HIS A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A 707 " --> pdb=" O TYR A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 722 Processing helix chain 'A' and resid 733 through 744 removed outlier: 3.590A pdb=" N CYS A 744 " --> pdb=" O ALA A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 781 removed outlier: 3.573A pdb=" N LEU A 777 " --> pdb=" O SER A 773 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 779 " --> pdb=" O SER A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 removed outlier: 3.875A pdb=" N ASP A 787 " --> pdb=" O GLY A 783 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 788 " --> pdb=" O PHE A 784 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP A 789 " --> pdb=" O MET A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 827 removed outlier: 3.774A pdb=" N VAL A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY A 827 " --> pdb=" O GLY A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 841 removed outlier: 4.120A pdb=" N ILE A 831 " --> pdb=" O GLY A 827 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A 832 " --> pdb=" O ILE A 828 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ALA A 836 " --> pdb=" O PHE A 832 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TYR A 837 " --> pdb=" O ILE A 833 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG A 839 " --> pdb=" O ILE A 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 57 Processing helix chain 'B' and resid 77 through 92 removed outlier: 3.860A pdb=" N MET B 89 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 119 removed outlier: 3.971A pdb=" N ILE B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 131 Processing helix chain 'B' and resid 149 through 159 removed outlier: 3.877A pdb=" N ALA B 154 " --> pdb=" O ILE B 150 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 191 removed outlier: 4.014A pdb=" N VAL B 183 " --> pdb=" O TYR B 179 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 220 Processing helix chain 'B' and resid 233 through 248 removed outlier: 4.018A pdb=" N THR B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N TYR B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE B 240 " --> pdb=" O GLU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 311 removed outlier: 3.516A pdb=" N ILE B 300 " --> pdb=" O GLY B 296 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASP B 306 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET B 307 " --> pdb=" O ALA B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.892A pdb=" N TYR B 338 " --> pdb=" O MET B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 473 removed outlier: 3.502A pdb=" N ASP B 463 " --> pdb=" O GLY B 459 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 464 " --> pdb=" O PHE B 460 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 465 " --> pdb=" O CYS B 461 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 503 removed outlier: 3.515A pdb=" N VAL B 501 " --> pdb=" O MET B 497 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET B 503 " --> pdb=" O GLY B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 522 removed outlier: 3.850A pdb=" N VAL B 522 " --> pdb=" O ARG B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 577 removed outlier: 3.757A pdb=" N TRP B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N VAL B 564 " --> pdb=" O VAL B 560 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET B 565 " --> pdb=" O MET B 561 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 566 " --> pdb=" O MET B 562 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 567 " --> pdb=" O PHE B 563 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 574 " --> pdb=" O SER B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 614 removed outlier: 4.040A pdb=" N ILE B 606 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N TRP B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE B 614 " --> pdb=" O TRP B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 655 removed outlier: 4.203A pdb=" N ILE B 630 " --> pdb=" O THR B 626 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N MET B 631 " --> pdb=" O THR B 627 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL B 632 " --> pdb=" O SER B 628 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE B 638 " --> pdb=" O VAL B 634 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA B 651 " --> pdb=" O THR B 647 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ALA B 652 " --> pdb=" O ALA B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 673 Processing helix chain 'B' and resid 690 through 699 Processing helix chain 'B' and resid 699 through 706 removed outlier: 4.006A pdb=" N ALA B 704 " --> pdb=" O ALA B 700 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N TYR B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 710 removed outlier: 4.063A pdb=" N ASN B 710 " --> pdb=" O GLY B 707 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 707 through 710' Processing helix chain 'B' and resid 713 through 723 removed outlier: 3.548A pdb=" N LEU B 719 " --> pdb=" O ASP B 715 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER B 720 " --> pdb=" O ASP B 716 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS B 722 " --> pdb=" O LEU B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 742 removed outlier: 4.309A pdb=" N TYR B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 786 removed outlier: 4.040A pdb=" N ASP B 777 " --> pdb=" O LYS B 773 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU B 778 " --> pdb=" O ARG B 774 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE B 784 " --> pdb=" O ILE B 780 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY B 785 " --> pdb=" O LEU B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 797 removed outlier: 4.035A pdb=" N GLU B 793 " --> pdb=" O MET B 789 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ALA B 794 " --> pdb=" O GLU B 790 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 795 " --> pdb=" O GLU B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 845 removed outlier: 3.979A pdb=" N PHE B 822 " --> pdb=" O MET B 818 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU B 825 " --> pdb=" O VAL B 821 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY B 826 " --> pdb=" O PHE B 822 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE B 834 " --> pdb=" O ALA B 830 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 54 removed outlier: 3.891A pdb=" N MET C 41 " --> pdb=" O LYS C 37 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE C 42 " --> pdb=" O HIS C 38 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LYS C 51 " --> pdb=" O ASN C 47 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG C 52 " --> pdb=" O GLN C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 75 removed outlier: 3.842A pdb=" N ALA C 75 " --> pdb=" O ILE C 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 72 through 75' Processing helix chain 'C' and resid 76 through 81 removed outlier: 3.994A pdb=" N ASP C 81 " --> pdb=" O SER C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 85 Processing helix chain 'C' and resid 103 through 114 removed outlier: 4.575A pdb=" N VAL C 107 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 146 removed outlier: 3.580A pdb=" N HIS C 146 " --> pdb=" O PRO C 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 143 through 146' Processing helix chain 'C' and resid 147 through 158 Processing helix chain 'C' and resid 170 through 183 removed outlier: 4.011A pdb=" N ARG C 179 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR C 182 " --> pdb=" O LYS C 178 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU C 183 " --> pdb=" O ARG C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 211 removed outlier: 3.631A pdb=" N ALA C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 237 removed outlier: 3.796A pdb=" N ALA C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET C 237 " --> pdb=" O ARG C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 254 Processing helix chain 'C' and resid 255 through 259 Processing helix chain 'C' and resid 277 through 291 removed outlier: 3.615A pdb=" N VAL C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 296 removed outlier: 3.892A pdb=" N LEU C 296 " --> pdb=" O HIS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 326 removed outlier: 3.505A pdb=" N PHE C 321 " --> pdb=" O THR C 317 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG C 323 " --> pdb=" O PRO C 319 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N VAL C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET C 326 " --> pdb=" O LYS C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 471 removed outlier: 3.907A pdb=" N LYS C 465 " --> pdb=" O ASP C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 508 removed outlier: 3.803A pdb=" N LEU C 506 " --> pdb=" O MET C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 525 Processing helix chain 'C' and resid 545 through 549 Processing helix chain 'C' and resid 559 through 583 removed outlier: 4.089A pdb=" N HIS C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N MET C 576 " --> pdb=" O VAL C 572 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU C 577 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR C 578 " --> pdb=" O ALA C 574 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE C 583 " --> pdb=" O LEU C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 616 removed outlier: 3.648A pdb=" N LEU C 614 " --> pdb=" O SER C 610 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 615 " --> pdb=" O TRP C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 652 removed outlier: 3.866A pdb=" N LEU C 632 " --> pdb=" O SER C 628 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET C 641 " --> pdb=" O ALA C 637 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE C 642 " --> pdb=" O GLY C 638 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE C 643 " --> pdb=" O PHE C 639 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL C 644 " --> pdb=" O ALA C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 656 removed outlier: 3.628A pdb=" N VAL C 656 " --> pdb=" O ALA C 653 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 653 through 656' Processing helix chain 'C' and resid 669 through 674 Processing helix chain 'C' and resid 687 through 694 Processing helix chain 'C' and resid 702 through 707 Processing helix chain 'C' and resid 708 through 710 No H-bonds generated for 'chain 'C' and resid 708 through 710' Processing helix chain 'C' and resid 713 through 723 removed outlier: 3.709A pdb=" N ALA C 717 " --> pdb=" O SER C 713 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN C 719 " --> pdb=" O ALA C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 740 removed outlier: 4.255A pdb=" N PHE C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 774 through 780 removed outlier: 3.780A pdb=" N HIS C 780 " --> pdb=" O ILE C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 791 Processing helix chain 'C' and resid 815 through 838 removed outlier: 3.728A pdb=" N VAL C 820 " --> pdb=" O VAL C 816 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL C 825 " --> pdb=" O ALA C 821 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 826 " --> pdb=" O GLY C 822 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE C 828 " --> pdb=" O ILE C 824 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE C 832 " --> pdb=" O ILE C 828 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS C 838 " --> pdb=" O GLU C 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 61 No H-bonds generated for 'chain 'D' and resid 59 through 61' Processing helix chain 'D' and resid 62 through 77 removed outlier: 4.401A pdb=" N ALA D 67 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY D 70 " --> pdb=" O ALA D 66 " (cutoff:3.500A) Proline residue: D 71 - end of helix Processing helix chain 'D' and resid 95 through 110 Processing helix chain 'D' and resid 125 through 136 removed outlier: 4.488A pdb=" N ILE D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN D 136 " --> pdb=" O PHE D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 150 removed outlier: 3.837A pdb=" N ALA D 149 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU D 150 " --> pdb=" O GLY D 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 146 through 150' Processing helix chain 'D' and resid 167 through 183 Processing helix chain 'D' and resid 198 through 202 removed outlier: 3.572A pdb=" N LEU D 201 " --> pdb=" O ARG D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 208 removed outlier: 3.625A pdb=" N LEU D 207 " --> pdb=" O TYR D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 252 through 262 removed outlier: 3.505A pdb=" N VAL D 256 " --> pdb=" O GLU D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 338 removed outlier: 3.534A pdb=" N ALA D 322 " --> pdb=" O ARG D 318 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL D 327 " --> pdb=" O GLY D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 347 removed outlier: 4.333A pdb=" N ASP D 347 " --> pdb=" O LEU D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 500 removed outlier: 3.591A pdb=" N ASP D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE D 491 " --> pdb=" O PHE D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 529 Processing helix chain 'D' and resid 543 through 548 removed outlier: 3.715A pdb=" N GLU D 548 " --> pdb=" O GLU D 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 584 through 607 removed outlier: 3.897A pdb=" N PHE D 590 " --> pdb=" O TRP D 586 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL D 591 " --> pdb=" O VAL D 587 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU D 594 " --> pdb=" O PHE D 590 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR D 606 " --> pdb=" O PHE D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 639 removed outlier: 3.609A pdb=" N TRP D 634 " --> pdb=" O GLY D 630 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU D 635 " --> pdb=" O LYS D 631 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU D 639 " --> pdb=" O LEU D 635 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 681 removed outlier: 3.758A pdb=" N ILE D 657 " --> pdb=" O THR D 653 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N MET D 658 " --> pdb=" O THR D 654 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL D 659 " --> pdb=" O SER D 655 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA D 678 " --> pdb=" O THR D 674 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE D 680 " --> pdb=" O ASN D 676 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET D 681 " --> pdb=" O LEU D 677 " (cutoff:3.500A) Processing helix chain 'D' and resid 695 through 700 Processing helix chain 'D' and resid 716 through 721 Processing helix chain 'D' and resid 722 through 725 Processing helix chain 'D' and resid 726 through 734 removed outlier: 4.081A pdb=" N TYR D 732 " --> pdb=" O ASP D 728 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL D 734 " --> pdb=" O HIS D 730 " (cutoff:3.500A) Processing helix chain 'D' and resid 735 through 737 No H-bonds generated for 'chain 'D' and resid 735 through 737' Processing helix chain 'D' and resid 741 through 751 removed outlier: 3.645A pdb=" N LEU D 745 " --> pdb=" O VAL D 741 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR D 746 " --> pdb=" O GLU D 742 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN D 747 " --> pdb=" O GLU D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 760 through 767 Processing helix chain 'D' and resid 770 through 773 removed outlier: 3.787A pdb=" N CYS D 773 " --> pdb=" O ASP D 770 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 770 through 773' Processing helix chain 'D' and resid 778 through 782 removed outlier: 3.557A pdb=" N LYS D 782 " --> pdb=" O ILE D 778 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 778 through 782' Processing helix chain 'D' and resid 799 through 813 removed outlier: 3.521A pdb=" N ASP D 813 " --> pdb=" O GLN D 809 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 824 removed outlier: 3.627A pdb=" N MET D 818 " --> pdb=" O ASP D 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 842 through 846 removed outlier: 3.853A pdb=" N ALA D 846 " --> pdb=" O ASP D 843 " (cutoff:3.500A) Processing helix chain 'D' and resid 848 through 864 removed outlier: 3.562A pdb=" N VAL D 862 " --> pdb=" O LEU D 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 870 removed outlier: 4.071A pdb=" N TYR D 870 " --> pdb=" O GLU D 866 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 33 removed outlier: 5.492A pdb=" N ILE A 29 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL A 65 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ALA A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91 removed outlier: 6.665A pdb=" N ILE A 90 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 194 through 197 removed outlier: 6.314A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A 222 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 168 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ILE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 271 removed outlier: 3.550A pdb=" N GLN A 270 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 409 through 413 removed outlier: 3.951A pdb=" N TYR A 456 " --> pdb=" O TYR A 410 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE A 435 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N LEU A 478 " --> pdb=" O ILE A 435 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N THR A 437 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU A 398 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N HIS A 477 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET A 512 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 401 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 487 through 490 removed outlier: 3.784A pdb=" N LYS A 495 " --> pdb=" O VAL A 490 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 681 through 682 removed outlier: 6.861A pdb=" N ALA A 682 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 9.387A pdb=" N ASP A 732 " --> pdb=" O ALA A 682 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TRP A 731 " --> pdb=" O THR A 539 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A 539 " --> pdb=" O TRP A 731 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL A 542 " --> pdb=" O VAL A 747 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 747 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 70 through 73 removed outlier: 3.686A pdb=" N MET B 73 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 98 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL B 97 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE B 123 " --> pdb=" O PHE B 144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 198 through 199 removed outlier: 4.366A pdb=" N PHE B 169 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 9.187A pdb=" N LEU B 203 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 198 through 199 removed outlier: 4.366A pdb=" N PHE B 169 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE B 168 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N LEU B 229 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N SER B 170 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE B 257 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 258 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N TYR B 282 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LEU B 362 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LYS B 378 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE B 364 " --> pdb=" O VAL B 376 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 408 through 410 removed outlier: 3.572A pdb=" N THR B 410 " --> pdb=" O TYR B 479 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU B 478 " --> pdb=" O PRO B 435 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 480 " --> pdb=" O GLN B 437 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 508 through 509 Processing sheet with id=AB4, first strand: chain 'B' and resid 531 through 532 removed outlier: 3.637A pdb=" N THR B 760 " --> pdb=" O THR B 532 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 729 through 732 removed outlier: 3.614A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL B 749 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 64 through 66 removed outlier: 3.775A pdb=" N VAL C 65 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 33 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ASN C 28 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA C 89 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER C 93 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C 119 " --> pdb=" O ILE C 90 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 196 through 197 removed outlier: 7.348A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE C 164 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C 267 " --> pdb=" O TRP C 247 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ILE C 266 " --> pdb=" O LEU C 356 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 398 through 400 removed outlier: 7.188A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N ILE C 435 " --> pdb=" O TYR C 474 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL C 476 " --> pdb=" O ILE C 435 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR C 437 " --> pdb=" O VAL C 476 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N TYR C 456 " --> pdb=" O TYR C 410 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 512 through 513 removed outlier: 3.578A pdb=" N GLU C 528 " --> pdb=" O MET C 762 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 535 through 536 Processing sheet with id=AC2, first strand: chain 'C' and resid 681 through 682 removed outlier: 6.773A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 9.092A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE C 729 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TRP C 731 " --> pdb=" O THR C 539 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL C 747 " --> pdb=" O VAL C 542 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 54 through 57 removed outlier: 3.743A pdb=" N GLU D 118 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL D 115 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 188 through 191 removed outlier: 7.046A pdb=" N ARG D 244 " --> pdb=" O PHE D 273 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE D 305 " --> pdb=" O TRP D 272 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL D 307 " --> pdb=" O MET D 274 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU D 304 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU D 392 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA D 306 " --> pdb=" O ILE D 390 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU D 399 " --> pdb=" O SER D 391 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR D 397 " --> pdb=" O THR D 393 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 368 through 369 Processing sheet with id=AC6, first strand: chain 'D' and resid 431 through 433 removed outlier: 3.805A pdb=" N ASP D 504 " --> pdb=" O LEU D 432 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 444 through 446 Processing sheet with id=AC8, first strand: chain 'D' and resid 757 through 758 removed outlier: 3.512A pdb=" N TYR D 758 " --> pdb=" O SER D 562 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 757 through 758 removed outlier: 3.512A pdb=" N TYR D 758 " --> pdb=" O SER D 562 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR D 559 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N THR D 786 " --> pdb=" O THR D 559 " (cutoff:3.500A) 739 hydrogen bonds defined for protein. 2070 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.49 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3989 1.31 - 1.44: 6594 1.44 - 1.57: 13906 1.57 - 1.70: 1 1.70 - 1.82: 230 Bond restraints: 24720 Sorted by residual: bond pdb=" C3 JC9 B 903 " pdb=" C4 JC9 B 903 " ideal model delta sigma weight residual 1.534 1.473 0.061 2.00e-02 2.50e+03 9.41e+00 bond pdb=" C5 JC9 B 903 " pdb=" C6 JC9 B 903 " ideal model delta sigma weight residual 1.505 1.562 -0.057 2.00e-02 2.50e+03 8.04e+00 bond pdb=" C1 JC9 B 903 " pdb=" N1 JC9 B 903 " ideal model delta sigma weight residual 1.502 1.447 0.055 2.00e-02 2.50e+03 7.65e+00 bond pdb=" C2 JC9 B 903 " pdb=" C3 JC9 B 903 " ideal model delta sigma weight residual 1.531 1.480 0.051 2.00e-02 2.50e+03 6.53e+00 bond pdb=" C8 JC9 B 903 " pdb="CL1 JC9 B 903 " ideal model delta sigma weight residual 1.735 1.782 -0.047 2.00e-02 2.50e+03 5.55e+00 ... (remaining 24715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 33115 2.35 - 4.70: 404 4.70 - 7.05: 48 7.05 - 9.41: 7 9.41 - 11.76: 2 Bond angle restraints: 33576 Sorted by residual: angle pdb=" N PRO D 477 " pdb=" CA PRO D 477 " pdb=" CB PRO D 477 " ideal model delta sigma weight residual 103.00 110.48 -7.48 1.10e+00 8.26e-01 4.62e+01 angle pdb=" C2 JC9 B 903 " pdb=" C1 JC9 B 903 " pdb=" C5 JC9 B 903 " ideal model delta sigma weight residual 106.41 118.17 -11.76 3.00e+00 1.11e-01 1.54e+01 angle pdb=" CB MET A 501 " pdb=" CG MET A 501 " pdb=" SD MET A 501 " ideal model delta sigma weight residual 112.70 100.97 11.73 3.00e+00 1.11e-01 1.53e+01 angle pdb=" CA MET B 561 " pdb=" CB MET B 561 " pdb=" CG MET B 561 " ideal model delta sigma weight residual 114.10 120.35 -6.25 2.00e+00 2.50e-01 9.77e+00 angle pdb=" CB MET C 209 " pdb=" CG MET C 209 " pdb=" SD MET C 209 " ideal model delta sigma weight residual 112.70 121.22 -8.52 3.00e+00 1.11e-01 8.07e+00 ... (remaining 33571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.62: 13831 22.62 - 45.25: 893 45.25 - 67.87: 88 67.87 - 90.50: 38 90.50 - 113.12: 13 Dihedral angle restraints: 14863 sinusoidal: 5859 harmonic: 9004 Sorted by residual: dihedral pdb=" CB CYS B 429 " pdb=" SG CYS B 429 " pdb=" SG CYS B 456 " pdb=" CB CYS B 456 " ideal model delta sinusoidal sigma weight residual -86.00 -124.56 38.56 1 1.00e+01 1.00e-02 2.09e+01 dihedral pdb=" CA PRO C 532 " pdb=" C PRO C 532 " pdb=" N PHE C 533 " pdb=" CA PHE C 533 " ideal model delta harmonic sigma weight residual 180.00 158.29 21.71 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA SER A 132 " pdb=" C SER A 132 " pdb=" N ILE A 133 " pdb=" CA ILE A 133 " ideal model delta harmonic sigma weight residual 180.00 158.42 21.58 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 14860 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3437 0.073 - 0.146: 403 0.146 - 0.218: 1 0.218 - 0.291: 4 0.291 - 0.364: 3 Chirality restraints: 3848 Sorted by residual: chirality pdb=" C1 NAG A 903 " pdb=" ND2 ASN A 471 " pdb=" C2 NAG A 903 " pdb=" O5 NAG A 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CB VAL A 249 " pdb=" CA VAL A 249 " pdb=" CG1 VAL A 249 " pdb=" CG2 VAL A 249 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" C1 NAG A 902 " pdb=" ND2 ASN A 771 " pdb=" C2 NAG A 902 " pdb=" O5 NAG A 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 3845 not shown) Planarity restraints: 4283 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 471 " 0.022 2.00e-02 2.50e+03 2.10e-02 5.50e+00 pdb=" CG ASN C 471 " -0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN C 471 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN C 471 " -0.027 2.00e-02 2.50e+03 pdb=" C1 NAG C 904 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 315 " 0.016 2.00e-02 2.50e+03 1.38e-02 4.78e+00 pdb=" CG TRP C 315 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP C 315 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP C 315 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 315 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 315 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 315 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 315 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 315 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 315 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 766 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.04e+00 pdb=" N PRO A 767 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 767 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 767 " 0.028 5.00e-02 4.00e+02 ... (remaining 4280 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 624 2.69 - 3.24: 25169 3.24 - 3.79: 35561 3.79 - 4.35: 45140 4.35 - 4.90: 72554 Nonbonded interactions: 179048 Sorted by model distance: nonbonded pdb=" O VAL C 684 " pdb=" OG SER C 687 " model vdw 2.134 3.040 nonbonded pdb=" O VAL B 258 " pdb=" OG SER B 279 " model vdw 2.148 3.040 nonbonded pdb=" OD1 ASN C 341 " pdb=" N GLU C 342 " model vdw 2.163 3.120 nonbonded pdb=" O ILE B 115 " pdb=" OG1 THR B 119 " model vdw 2.165 3.040 nonbonded pdb=" ND2 ASN C 28 " pdb=" OG SER C 85 " model vdw 2.189 3.120 ... (remaining 179043 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 25 and (name N or name CA or name C or name O or name CB \ )) or resid 26 through 51 or (resid 52 and (name N or name CA or name C or name \ O or name CB )) or resid 53 through 187 or (resid 188 and (name N or name CA or \ name C or name O or name CB )) or resid 189 through 447 or (resid 448 and (name \ N or name CA or name C or name O or name CB )) or resid 449 through 494 or (resi \ d 495 through 496 and (name N or name CA or name C or name O or name CB )) or re \ sid 497 through 567 or (resid 568 and (name N or name CA or name C or name O or \ name CB )) or resid 569 through 658 or (resid 659 and (name N or name CA or name \ C or name O or name CB )) or resid 660 or (resid 661 through 663 and (name N or \ name CA or name C or name O or name CB )) or resid 664 through 904)) selection = (chain 'C' and (resid 25 through 38 or (resid 39 and (name N or name CA or name \ C or name O or name CB )) or resid 40 through 492 or resid 495 through 544 or (r \ esid 545 and (name N or name CA or name C or name O or name CB )) or resid 546 t \ hrough 548 or resid 552 through 559 or (resid 560 and (name N or name CA or name \ C or name O or name CB )) or resid 561 through 575 or (resid 576 and (name N or \ name CA or name C or name O or name CB )) or resid 577 or (resid 578 and (name \ N or name CA or name C or name O or name CB )) or resid 579 through 582 or (resi \ d 583 and (name N or name CA or name C or name O or name CB )) or resid 584 thro \ ugh 662 or (resid 663 and (name N or name CA or name C or name O or name CB )) o \ r resid 664 through 677 or (resid 678 and (name N or name CA or name C or name O \ or name CB )) or resid 679 through 697 or (resid 698 and (name N or name CA or \ name C or name O or name CB )) or resid 699 through 723 or (resid 724 through 72 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 726 through \ 750 or (resid 751 and (name N or name CA or name C or name O or name CB )) or re \ sid 752 through 798 or (resid 818 and (name N or name CA or name C or name O or \ name CB )) or resid 819 through 823 or (resid 824 through 826 and (name N or nam \ e CA or name C or name O or name CB )) or resid 827 through 828 or (resid 829 th \ rough 831 and (name N or name CA or name C or name O or name CB )) or resid 832 \ or (resid 833 through 841 and (name N or name CA or name C or name O or name CB \ )) or resid 901 through 904)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.770 Find NCS groups from input model: 0.390 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: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 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 : 0.005 0.061 24744 Z= 0.212 Angle : 0.662 11.757 33634 Z= 0.328 Chirality : 0.046 0.364 3848 Planarity : 0.004 0.050 4274 Dihedral : 14.984 113.121 9013 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.09 % Favored : 90.74 % Rotamer: Outliers : 0.04 % Allowed : 0.39 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.15), residues: 3079 helix: -0.49 (0.17), residues: 979 sheet: -1.37 (0.28), residues: 374 loop : -1.83 (0.15), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 440 TYR 0.024 0.002 TYR D 506 PHE 0.018 0.002 PHE D 501 TRP 0.038 0.002 TRP C 315 HIS 0.006 0.001 HIS C 477 Details of bonding type rmsd covalent geometry : bond 0.00487 (24720) covalent geometry : angle 0.64571 (33576) SS BOND : bond 0.00343 ( 14) SS BOND : angle 1.19020 ( 28) hydrogen bonds : bond 0.31151 ( 738) hydrogen bonds : angle 9.14080 ( 2070) link_BETA1-4 : bond 0.00065 ( 1) link_BETA1-4 : angle 5.33207 ( 3) link_NAG-ASN : bond 0.01109 ( 9) link_NAG-ASN : angle 4.70551 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 211 time to evaluate : 0.812 Fit side-chains revert: symmetry clash REVERT: B 99 PHE cc_start: 0.7922 (t80) cc_final: 0.7275 (t80) REVERT: B 184 ASN cc_start: 0.8263 (m-40) cc_final: 0.8042 (t0) REVERT: B 287 TYR cc_start: 0.5191 (t80) cc_final: 0.4847 (t80) REVERT: B 818 MET cc_start: 0.8336 (mpp) cc_final: 0.8117 (mpp) REVERT: C 137 PHE cc_start: 0.6587 (t80) cc_final: 0.6212 (t80) REVERT: C 194 VAL cc_start: 0.8950 (t) cc_final: 0.8690 (t) REVERT: C 315 TRP cc_start: 0.7054 (p-90) cc_final: 0.6172 (p-90) REVERT: D 117 PHE cc_start: 0.7920 (t80) cc_final: 0.7497 (t80) REVERT: D 381 PHE cc_start: 0.6755 (p90) cc_final: 0.6551 (p90) outliers start: 1 outliers final: 0 residues processed: 212 average time/residue: 0.1467 time to fit residues: 51.7169 Evaluate side-chains 181 residues out of total 2675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.0060 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 ASN ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 ASN ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 ASN C 177 GLN C 196 GLN C 650 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.088261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.063707 restraints weight = 104605.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.063908 restraints weight = 65289.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.063900 restraints weight = 52292.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.064328 restraints weight = 49306.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.064700 restraints weight = 42920.912| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24744 Z= 0.149 Angle : 0.630 8.458 33634 Z= 0.322 Chirality : 0.045 0.280 3848 Planarity : 0.004 0.047 4274 Dihedral : 8.823 91.618 3566 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.31 % Favored : 92.53 % Rotamer: Outliers : 0.51 % Allowed : 8.26 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.15), residues: 3079 helix: -0.34 (0.16), residues: 1069 sheet: -1.33 (0.29), residues: 329 loop : -1.85 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 115 TYR 0.018 0.001 TYR D 506 PHE 0.030 0.002 PHE A 42 TRP 0.018 0.001 TRP C 315 HIS 0.004 0.001 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00321 (24720) covalent geometry : angle 0.62125 (33576) SS BOND : bond 0.00239 ( 14) SS BOND : angle 0.90190 ( 28) hydrogen bonds : bond 0.06053 ( 738) hydrogen bonds : angle 6.07332 ( 2070) link_BETA1-4 : bond 0.00350 ( 1) link_BETA1-4 : angle 2.90798 ( 3) link_NAG-ASN : bond 0.00956 ( 9) link_NAG-ASN : angle 3.53268 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 198 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.6853 (ppp) cc_final: 0.6356 (ppp) REVERT: B 99 PHE cc_start: 0.7556 (t80) cc_final: 0.7249 (t80) REVERT: B 287 TYR cc_start: 0.5128 (t80) cc_final: 0.4769 (t80) REVERT: B 809 MET cc_start: 0.7604 (mpp) cc_final: 0.6941 (ppp) REVERT: B 818 MET cc_start: 0.8377 (mpp) cc_final: 0.8141 (mpp) REVERT: C 74 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7510 (ppp) REVERT: C 315 TRP cc_start: 0.6894 (p-90) cc_final: 0.6147 (p-90) REVERT: C 607 MET cc_start: 0.8289 (mmp) cc_final: 0.8087 (mmp) REVERT: D 117 PHE cc_start: 0.8031 (t80) cc_final: 0.7585 (t80) REVERT: D 203 TYR cc_start: 0.7300 (m-10) cc_final: 0.7048 (m-10) outliers start: 13 outliers final: 4 residues processed: 202 average time/residue: 0.1415 time to fit residues: 47.8628 Evaluate side-chains 187 residues out of total 2675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 182 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain D residue 848 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 212 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 302 optimal weight: 3.9990 chunk 87 optimal weight: 0.2980 chunk 56 optimal weight: 2.9990 chunk 138 optimal weight: 0.2980 chunk 150 optimal weight: 2.9990 chunk 303 optimal weight: 0.9990 chunk 252 optimal weight: 20.0000 chunk 256 optimal weight: 20.0000 chunk 124 optimal weight: 0.1980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS A 427 ASN A 650 ASN B 110 GLN B 145 GLN ** B 649 ASN ** 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 = 0.3885 r_free = 0.3885 target = 0.088864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.064465 restraints weight = 105373.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.064635 restraints weight = 68307.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.064328 restraints weight = 58872.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.064727 restraints weight = 53756.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.065978 restraints weight = 46630.118| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24744 Z= 0.115 Angle : 0.572 9.111 33634 Z= 0.288 Chirality : 0.043 0.304 3848 Planarity : 0.003 0.043 4274 Dihedral : 7.465 77.935 3566 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.02 % Favored : 92.82 % Rotamer: Outliers : 0.90 % Allowed : 12.29 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.15), residues: 3079 helix: -0.17 (0.16), residues: 1099 sheet: -1.17 (0.28), residues: 348 loop : -1.88 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 115 TYR 0.018 0.001 TYR B 322 PHE 0.027 0.001 PHE D 680 TRP 0.015 0.001 TRP A 315 HIS 0.005 0.001 HIS C 705 Details of bonding type rmsd covalent geometry : bond 0.00250 (24720) covalent geometry : angle 0.56422 (33576) SS BOND : bond 0.00222 ( 14) SS BOND : angle 0.65141 ( 28) hydrogen bonds : bond 0.04558 ( 738) hydrogen bonds : angle 5.35142 ( 2070) link_BETA1-4 : bond 0.00470 ( 1) link_BETA1-4 : angle 2.76624 ( 3) link_NAG-ASN : bond 0.00751 ( 9) link_NAG-ASN : angle 3.22146 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.7157 (mmm) cc_final: 0.6780 (tpp) REVERT: A 155 MET cc_start: 0.6992 (ppp) cc_final: 0.6392 (ppp) REVERT: B 99 PHE cc_start: 0.7495 (t80) cc_final: 0.7199 (t80) REVERT: B 287 TYR cc_start: 0.4963 (t80) cc_final: 0.4660 (t80) REVERT: B 537 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.7211 (ttt) REVERT: B 809 MET cc_start: 0.7503 (mpp) cc_final: 0.7136 (mmt) REVERT: B 818 MET cc_start: 0.8427 (mpp) cc_final: 0.8221 (mpp) REVERT: C 91 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7447 (tp) REVERT: C 315 TRP cc_start: 0.6721 (p-90) cc_final: 0.5937 (p-90) REVERT: C 706 MET cc_start: 0.7435 (mmm) cc_final: 0.6964 (mmm) REVERT: D 117 PHE cc_start: 0.8007 (t80) cc_final: 0.7572 (t80) REVERT: D 203 TYR cc_start: 0.7115 (m-10) cc_final: 0.6892 (m-10) REVERT: D 524 MET cc_start: 0.7923 (mpp) cc_final: 0.6595 (mtt) outliers start: 23 outliers final: 8 residues processed: 203 average time/residue: 0.1391 time to fit residues: 47.9091 Evaluate side-chains 190 residues out of total 2675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 814 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 77 optimal weight: 30.0000 chunk 252 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 220 optimal weight: 0.0170 chunk 295 optimal weight: 4.9990 chunk 4 optimal weight: 20.0000 chunk 188 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 279 optimal weight: 2.9990 overall best weight: 3.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 ASN B 145 GLN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 699 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.086905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.062471 restraints weight = 104424.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.062200 restraints weight = 67259.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.062230 restraints weight = 55565.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.062581 restraints weight = 56050.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.062677 restraints weight = 45988.783| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 24744 Z= 0.254 Angle : 0.666 8.807 33634 Z= 0.339 Chirality : 0.046 0.291 3848 Planarity : 0.004 0.058 4274 Dihedral : 7.210 64.443 3566 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.74 % Favored : 91.10 % Rotamer: Outliers : 1.53 % Allowed : 14.37 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.15), residues: 3079 helix: -0.21 (0.16), residues: 1096 sheet: -1.27 (0.29), residues: 335 loop : -1.95 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 763 TYR 0.024 0.002 TYR D 506 PHE 0.025 0.002 PHE B 474 TRP 0.018 0.001 TRP C 768 HIS 0.006 0.001 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00600 (24720) covalent geometry : angle 0.65910 (33576) SS BOND : bond 0.00312 ( 14) SS BOND : angle 0.87005 ( 28) hydrogen bonds : bond 0.04839 ( 738) hydrogen bonds : angle 5.47019 ( 2070) link_BETA1-4 : bond 0.00131 ( 1) link_BETA1-4 : angle 2.78711 ( 3) link_NAG-ASN : bond 0.00718 ( 9) link_NAG-ASN : angle 3.38613 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 190 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.7004 (ppp) cc_final: 0.6506 (ppp) REVERT: B 99 PHE cc_start: 0.7499 (t80) cc_final: 0.7231 (t80) REVERT: B 287 TYR cc_start: 0.5336 (t80) cc_final: 0.4880 (t80) REVERT: B 537 MET cc_start: 0.7562 (OUTLIER) cc_final: 0.7272 (ttt) REVERT: C 91 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7534 (tp) REVERT: C 315 TRP cc_start: 0.6810 (p-90) cc_final: 0.6009 (p-90) REVERT: C 607 MET cc_start: 0.8467 (mmp) cc_final: 0.8215 (mmp) REVERT: C 641 MET cc_start: 0.8591 (tpp) cc_final: 0.8382 (tpp) REVERT: C 706 MET cc_start: 0.7596 (mmm) cc_final: 0.6925 (mpp) REVERT: D 117 PHE cc_start: 0.7995 (t80) cc_final: 0.7583 (t80) REVERT: D 187 PHE cc_start: 0.8514 (p90) cc_final: 0.7806 (p90) REVERT: D 203 TYR cc_start: 0.7159 (m-10) cc_final: 0.6923 (m-10) REVERT: D 524 MET cc_start: 0.7955 (mpp) cc_final: 0.6946 (mtt) outliers start: 39 outliers final: 21 residues processed: 216 average time/residue: 0.1404 time to fit residues: 51.1394 Evaluate side-chains 207 residues out of total 2675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain D residue 787 THR Chi-restraints excluded: chain D residue 840 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 36 optimal weight: 7.9990 chunk 172 optimal weight: 4.9990 chunk 216 optimal weight: 0.2980 chunk 218 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 261 optimal weight: 7.9990 chunk 61 optimal weight: 0.0270 chunk 29 optimal weight: 20.0000 chunk 43 optimal weight: 0.8980 chunk 300 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 overall best weight: 1.4440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS A 427 ASN ** A 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN B 357 GLN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.087946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.063574 restraints weight = 104762.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.063680 restraints weight = 67846.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.063558 restraints weight = 52836.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.063878 restraints weight = 56235.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.064260 restraints weight = 46803.315| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24744 Z= 0.129 Angle : 0.580 8.784 33634 Z= 0.290 Chirality : 0.043 0.278 3848 Planarity : 0.003 0.051 4274 Dihedral : 6.689 59.540 3566 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.89 % Favored : 92.98 % Rotamer: Outliers : 1.61 % Allowed : 15.62 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.15), residues: 3079 helix: -0.07 (0.16), residues: 1096 sheet: -1.35 (0.28), residues: 358 loop : -1.87 (0.15), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 821 TYR 0.016 0.001 TYR B 659 PHE 0.030 0.002 PHE C 137 TRP 0.013 0.001 TRP C 768 HIS 0.007 0.001 HIS C 705 Details of bonding type rmsd covalent geometry : bond 0.00296 (24720) covalent geometry : angle 0.57242 (33576) SS BOND : bond 0.00207 ( 14) SS BOND : angle 0.67391 ( 28) hydrogen bonds : bond 0.03827 ( 738) hydrogen bonds : angle 5.05175 ( 2070) link_BETA1-4 : bond 0.00193 ( 1) link_BETA1-4 : angle 2.66546 ( 3) link_NAG-ASN : bond 0.00706 ( 9) link_NAG-ASN : angle 3.17195 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 187 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.7267 (mmm) cc_final: 0.6908 (tpp) REVERT: A 155 MET cc_start: 0.6990 (ppp) cc_final: 0.6528 (ppp) REVERT: B 99 PHE cc_start: 0.7463 (t80) cc_final: 0.7214 (t80) REVERT: B 231 TYR cc_start: 0.6271 (t80) cc_final: 0.6003 (t80) REVERT: B 287 TYR cc_start: 0.5263 (t80) cc_final: 0.4911 (t80) REVERT: B 537 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.7178 (ttt) REVERT: B 568 ILE cc_start: 0.9012 (mt) cc_final: 0.8741 (mm) REVERT: B 809 MET cc_start: 0.7263 (mpp) cc_final: 0.6635 (mmt) REVERT: C 315 TRP cc_start: 0.6717 (p-90) cc_final: 0.5917 (p-90) REVERT: C 607 MET cc_start: 0.8469 (mmp) cc_final: 0.8180 (mmp) REVERT: C 706 MET cc_start: 0.7354 (mmm) cc_final: 0.6742 (mpp) REVERT: C 818 MET cc_start: 0.7663 (mmp) cc_final: 0.7387 (mmp) REVERT: D 117 PHE cc_start: 0.7980 (t80) cc_final: 0.7550 (t80) REVERT: D 187 PHE cc_start: 0.8537 (p90) cc_final: 0.7859 (p90) REVERT: D 203 TYR cc_start: 0.7171 (m-10) cc_final: 0.6947 (m-10) REVERT: D 524 MET cc_start: 0.7915 (mpp) cc_final: 0.6796 (mtt) outliers start: 41 outliers final: 25 residues processed: 217 average time/residue: 0.1437 time to fit residues: 52.8346 Evaluate side-chains 205 residues out of total 2675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 359 HIS Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 705 HIS Chi-restraints excluded: chain C residue 798 CYS Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 814 ASP Chi-restraints excluded: chain D residue 840 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 80 optimal weight: 10.0000 chunk 238 optimal weight: 0.9990 chunk 210 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 190 optimal weight: 6.9990 chunk 175 optimal weight: 0.1980 chunk 126 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 257 optimal weight: 0.5980 chunk 176 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS A 427 ASN A 650 ASN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 705 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.088129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.062994 restraints weight = 105367.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.063240 restraints weight = 68417.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.063540 restraints weight = 52360.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.063907 restraints weight = 46767.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.064136 restraints weight = 40505.282| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24744 Z= 0.133 Angle : 0.580 9.271 33634 Z= 0.289 Chirality : 0.043 0.276 3848 Planarity : 0.003 0.048 4274 Dihedral : 6.407 58.839 3566 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.76 % Favored : 92.11 % Rotamer: Outliers : 1.92 % Allowed : 16.13 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.15), residues: 3079 helix: -0.04 (0.16), residues: 1104 sheet: -1.35 (0.28), residues: 358 loop : -1.88 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 704 TYR 0.013 0.001 TYR C 703 PHE 0.025 0.001 PHE C 102 TRP 0.012 0.001 TRP C 768 HIS 0.004 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00307 (24720) covalent geometry : angle 0.57279 (33576) SS BOND : bond 0.00319 ( 14) SS BOND : angle 0.63063 ( 28) hydrogen bonds : bond 0.03690 ( 738) hydrogen bonds : angle 4.92294 ( 2070) link_BETA1-4 : bond 0.00169 ( 1) link_BETA1-4 : angle 2.45302 ( 3) link_NAG-ASN : bond 0.00671 ( 9) link_NAG-ASN : angle 3.19963 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 186 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 MET cc_start: 0.6961 (ppp) cc_final: 0.6513 (ppp) REVERT: B 99 PHE cc_start: 0.7444 (t80) cc_final: 0.7214 (t80) REVERT: B 231 TYR cc_start: 0.6278 (t80) cc_final: 0.6016 (t80) REVERT: B 287 TYR cc_start: 0.5478 (t80) cc_final: 0.5121 (t80) REVERT: B 537 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.7196 (ttt) REVERT: B 568 ILE cc_start: 0.9002 (mt) cc_final: 0.8739 (mm) REVERT: B 809 MET cc_start: 0.7436 (mpp) cc_final: 0.6729 (mmt) REVERT: C 315 TRP cc_start: 0.6700 (p-90) cc_final: 0.5817 (p-90) REVERT: C 607 MET cc_start: 0.8552 (mmp) cc_final: 0.8262 (mmp) REVERT: C 706 MET cc_start: 0.7327 (mmm) cc_final: 0.7025 (mpp) REVERT: C 818 MET cc_start: 0.7643 (mmp) cc_final: 0.7364 (mmp) REVERT: D 117 PHE cc_start: 0.8018 (t80) cc_final: 0.7590 (t80) REVERT: D 129 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8478 (tp) REVERT: D 187 PHE cc_start: 0.8581 (p90) cc_final: 0.7937 (p90) REVERT: D 190 VAL cc_start: 0.8351 (OUTLIER) cc_final: 0.8143 (m) REVERT: D 203 TYR cc_start: 0.7034 (m-10) cc_final: 0.6830 (m-10) REVERT: D 524 MET cc_start: 0.7892 (mpp) cc_final: 0.6837 (mtt) outliers start: 49 outliers final: 32 residues processed: 222 average time/residue: 0.1399 time to fit residues: 52.6541 Evaluate side-chains 216 residues out of total 2675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 537 MET Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 702 MET Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 798 CYS Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 814 ASP Chi-restraints excluded: chain D residue 840 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 61 optimal weight: 0.0970 chunk 264 optimal weight: 0.2980 chunk 9 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 174 optimal weight: 8.9990 chunk 86 optimal weight: 20.0000 chunk 229 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 175 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS A 427 ASN A 559 GLN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.089566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.063252 restraints weight = 107731.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.065909 restraints weight = 65611.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.066164 restraints weight = 39774.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.066659 restraints weight = 33848.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.066737 restraints weight = 32461.266| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24744 Z= 0.103 Angle : 0.571 10.639 33634 Z= 0.280 Chirality : 0.043 0.275 3848 Planarity : 0.003 0.049 4274 Dihedral : 6.069 58.287 3566 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.02 % Favored : 92.85 % Rotamer: Outliers : 1.49 % Allowed : 16.99 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.15), residues: 3079 helix: 0.08 (0.16), residues: 1101 sheet: -1.21 (0.27), residues: 370 loop : -1.81 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 821 TYR 0.014 0.001 TYR A 681 PHE 0.027 0.001 PHE C 102 TRP 0.014 0.001 TRP A 315 HIS 0.004 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00228 (24720) covalent geometry : angle 0.56374 (33576) SS BOND : bond 0.00175 ( 14) SS BOND : angle 0.58855 ( 28) hydrogen bonds : bond 0.03332 ( 738) hydrogen bonds : angle 4.73551 ( 2070) link_BETA1-4 : bond 0.00189 ( 1) link_BETA1-4 : angle 2.20469 ( 3) link_NAG-ASN : bond 0.00694 ( 9) link_NAG-ASN : angle 3.12072 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.7101 (mmm) cc_final: 0.6430 (mmt) REVERT: A 155 MET cc_start: 0.7030 (ppp) cc_final: 0.6535 (ppp) REVERT: A 373 ILE cc_start: 0.7178 (OUTLIER) cc_final: 0.6854 (mm) REVERT: A 501 MET cc_start: 0.7548 (mtt) cc_final: 0.7246 (mtt) REVERT: B 99 PHE cc_start: 0.7383 (t80) cc_final: 0.7160 (t80) REVERT: B 287 TYR cc_start: 0.5344 (t80) cc_final: 0.5055 (t80) REVERT: B 568 ILE cc_start: 0.8978 (mt) cc_final: 0.8707 (mm) REVERT: B 809 MET cc_start: 0.7345 (mpp) cc_final: 0.6357 (mmm) REVERT: C 315 TRP cc_start: 0.6514 (p-90) cc_final: 0.5684 (p-90) REVERT: C 706 MET cc_start: 0.6990 (mmm) cc_final: 0.6618 (mpp) REVERT: C 818 MET cc_start: 0.7465 (mmp) cc_final: 0.7187 (mmp) REVERT: D 117 PHE cc_start: 0.8026 (t80) cc_final: 0.7605 (t80) REVERT: D 129 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8469 (tp) REVERT: D 187 PHE cc_start: 0.8542 (p90) cc_final: 0.7923 (p90) REVERT: D 190 VAL cc_start: 0.8381 (OUTLIER) cc_final: 0.8169 (m) REVERT: D 203 TYR cc_start: 0.7061 (m-10) cc_final: 0.6843 (m-10) REVERT: D 524 MET cc_start: 0.7886 (mpp) cc_final: 0.6837 (mtt) outliers start: 38 outliers final: 27 residues processed: 213 average time/residue: 0.1405 time to fit residues: 51.3364 Evaluate side-chains 209 residues out of total 2675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 576 MET Chi-restraints excluded: chain C residue 798 CYS Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 787 THR Chi-restraints excluded: chain D residue 814 ASP Chi-restraints excluded: chain D residue 840 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 116 optimal weight: 0.0470 chunk 307 optimal weight: 5.9990 chunk 176 optimal weight: 0.9990 chunk 242 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 132 optimal weight: 0.4980 chunk 229 optimal weight: 0.9990 chunk 30 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 overall best weight: 0.7084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS A 427 ASN A 650 ASN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.089792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.063783 restraints weight = 107609.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.066059 restraints weight = 63556.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.066390 restraints weight = 40381.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.066757 restraints weight = 35025.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.067308 restraints weight = 32140.503| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 24744 Z= 0.099 Angle : 0.568 11.030 33634 Z= 0.275 Chirality : 0.042 0.273 3848 Planarity : 0.003 0.045 4274 Dihedral : 5.814 59.119 3566 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.05 % Favored : 92.82 % Rotamer: Outliers : 1.68 % Allowed : 17.27 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.15), residues: 3079 helix: 0.19 (0.16), residues: 1096 sheet: -1.13 (0.28), residues: 365 loop : -1.79 (0.15), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 440 TYR 0.017 0.001 TYR B 659 PHE 0.027 0.001 PHE C 102 TRP 0.014 0.001 TRP A 315 HIS 0.004 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00223 (24720) covalent geometry : angle 0.56074 (33576) SS BOND : bond 0.00148 ( 14) SS BOND : angle 0.56861 ( 28) hydrogen bonds : bond 0.03090 ( 738) hydrogen bonds : angle 4.59044 ( 2070) link_BETA1-4 : bond 0.00200 ( 1) link_BETA1-4 : angle 1.93826 ( 3) link_NAG-ASN : bond 0.00678 ( 9) link_NAG-ASN : angle 3.10296 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 184 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.7214 (mmm) cc_final: 0.6556 (mmt) REVERT: A 155 MET cc_start: 0.7002 (ppp) cc_final: 0.6537 (ppp) REVERT: A 354 MET cc_start: 0.7627 (tmm) cc_final: 0.7401 (tmm) REVERT: A 373 ILE cc_start: 0.7145 (OUTLIER) cc_final: 0.6826 (mm) REVERT: A 501 MET cc_start: 0.7509 (mtt) cc_final: 0.7151 (mtt) REVERT: B 99 PHE cc_start: 0.7344 (t80) cc_final: 0.7140 (t80) REVERT: B 287 TYR cc_start: 0.5372 (t80) cc_final: 0.5086 (t80) REVERT: B 568 ILE cc_start: 0.8974 (mt) cc_final: 0.8702 (mm) REVERT: C 315 TRP cc_start: 0.6520 (p-90) cc_final: 0.5693 (p-90) REVERT: C 818 MET cc_start: 0.7389 (mmp) cc_final: 0.7156 (mmp) REVERT: D 117 PHE cc_start: 0.8043 (t80) cc_final: 0.7624 (t80) REVERT: D 129 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8475 (tp) REVERT: D 182 TYR cc_start: 0.6780 (OUTLIER) cc_final: 0.6131 (m-80) REVERT: D 187 PHE cc_start: 0.8565 (p90) cc_final: 0.7951 (p90) REVERT: D 190 VAL cc_start: 0.8375 (OUTLIER) cc_final: 0.8167 (m) REVERT: D 203 TYR cc_start: 0.7089 (m-10) cc_final: 0.6874 (m-10) REVERT: D 524 MET cc_start: 0.7841 (mpp) cc_final: 0.6863 (mtt) outliers start: 43 outliers final: 30 residues processed: 214 average time/residue: 0.1369 time to fit residues: 50.1308 Evaluate side-chains 215 residues out of total 2675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 42 PHE Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 798 CYS Chi-restraints excluded: chain C residue 817 PHE Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 787 THR Chi-restraints excluded: chain D residue 814 ASP Chi-restraints excluded: chain D residue 840 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 86 optimal weight: 20.0000 chunk 187 optimal weight: 7.9990 chunk 271 optimal weight: 7.9990 chunk 126 optimal weight: 10.0000 chunk 216 optimal weight: 0.0770 chunk 137 optimal weight: 0.6980 chunk 290 optimal weight: 0.4980 chunk 21 optimal weight: 8.9990 chunk 146 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 overall best weight: 1.3940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS A 427 ASN A 650 ASN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.089372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.065584 restraints weight = 107287.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.065342 restraints weight = 71461.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.065482 restraints weight = 56999.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.065855 restraints weight = 55574.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.066029 restraints weight = 45995.318| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24744 Z= 0.122 Angle : 0.585 12.073 33634 Z= 0.283 Chirality : 0.043 0.278 3848 Planarity : 0.003 0.050 4274 Dihedral : 5.738 59.630 3566 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.44 % Favored : 92.43 % Rotamer: Outliers : 1.84 % Allowed : 17.46 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.15), residues: 3079 helix: 0.22 (0.16), residues: 1093 sheet: -1.22 (0.28), residues: 372 loop : -1.77 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 821 TYR 0.011 0.001 TYR D 506 PHE 0.026 0.001 PHE C 102 TRP 0.014 0.001 TRP A 315 HIS 0.003 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00284 (24720) covalent geometry : angle 0.57812 (33576) SS BOND : bond 0.00154 ( 14) SS BOND : angle 0.60100 ( 28) hydrogen bonds : bond 0.03231 ( 738) hydrogen bonds : angle 4.61027 ( 2070) link_BETA1-4 : bond 0.00043 ( 1) link_BETA1-4 : angle 1.85521 ( 3) link_NAG-ASN : bond 0.00609 ( 9) link_NAG-ASN : angle 3.12141 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 186 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.7339 (mmm) cc_final: 0.6698 (mmt) REVERT: A 155 MET cc_start: 0.6989 (ppp) cc_final: 0.6560 (ppp) REVERT: A 354 MET cc_start: 0.7670 (tmm) cc_final: 0.7410 (tmm) REVERT: A 373 ILE cc_start: 0.7387 (OUTLIER) cc_final: 0.7098 (mm) REVERT: A 501 MET cc_start: 0.7471 (mtt) cc_final: 0.7168 (mtt) REVERT: A 555 MET cc_start: 0.7316 (tpp) cc_final: 0.6621 (tpp) REVERT: B 287 TYR cc_start: 0.5546 (t80) cc_final: 0.5226 (t80) REVERT: B 568 ILE cc_start: 0.8997 (mt) cc_final: 0.8726 (mm) REVERT: B 809 MET cc_start: 0.7137 (mpp) cc_final: 0.6896 (ppp) REVERT: C 315 TRP cc_start: 0.6605 (p-90) cc_final: 0.5778 (p-90) REVERT: C 706 MET cc_start: 0.7265 (mmm) cc_final: 0.7026 (mpp) REVERT: C 818 MET cc_start: 0.7526 (mmp) cc_final: 0.7306 (mmp) REVERT: D 117 PHE cc_start: 0.8012 (t80) cc_final: 0.7618 (t80) REVERT: D 129 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8447 (tp) REVERT: D 182 TYR cc_start: 0.6828 (OUTLIER) cc_final: 0.6178 (m-80) REVERT: D 187 PHE cc_start: 0.8593 (p90) cc_final: 0.7948 (p90) REVERT: D 203 TYR cc_start: 0.7109 (m-10) cc_final: 0.6881 (m-10) REVERT: D 524 MET cc_start: 0.7899 (mpp) cc_final: 0.6920 (mtt) outliers start: 47 outliers final: 35 residues processed: 221 average time/residue: 0.1394 time to fit residues: 52.6198 Evaluate side-chains 221 residues out of total 2675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 798 CYS Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 182 TYR Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 787 THR Chi-restraints excluded: chain D residue 814 ASP Chi-restraints excluded: chain D residue 840 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 52 optimal weight: 0.9990 chunk 250 optimal weight: 3.9990 chunk 228 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 130 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 278 optimal weight: 1.9990 chunk 217 optimal weight: 7.9990 chunk 24 optimal weight: 0.1980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS A 427 ASN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.089746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.063653 restraints weight = 108233.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.065840 restraints weight = 63892.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.066031 restraints weight = 42388.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.066628 restraints weight = 36611.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.066987 restraints weight = 32691.554| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 24744 Z= 0.106 Angle : 0.583 12.244 33634 Z= 0.280 Chirality : 0.042 0.278 3848 Planarity : 0.003 0.050 4274 Dihedral : 5.651 58.654 3566 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.82 % Favored : 93.05 % Rotamer: Outliers : 1.72 % Allowed : 17.74 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.15), residues: 3079 helix: 0.25 (0.16), residues: 1096 sheet: -1.17 (0.28), residues: 360 loop : -1.80 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 821 TYR 0.020 0.001 TYR B 659 PHE 0.028 0.001 PHE C 102 TRP 0.014 0.001 TRP A 315 HIS 0.004 0.000 HIS B 127 Details of bonding type rmsd covalent geometry : bond 0.00241 (24720) covalent geometry : angle 0.57614 (33576) SS BOND : bond 0.00148 ( 14) SS BOND : angle 0.59206 ( 28) hydrogen bonds : bond 0.03081 ( 738) hydrogen bonds : angle 4.55340 ( 2070) link_BETA1-4 : bond 0.00068 ( 1) link_BETA1-4 : angle 1.74071 ( 3) link_NAG-ASN : bond 0.00628 ( 9) link_NAG-ASN : angle 3.06615 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6158 Ramachandran restraints generated. 3079 Oldfield, 0 Emsley, 3079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 187 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.7353 (mmm) cc_final: 0.6712 (mmt) REVERT: A 155 MET cc_start: 0.7020 (ppp) cc_final: 0.6547 (ppp) REVERT: A 354 MET cc_start: 0.7691 (tmm) cc_final: 0.7415 (tmm) REVERT: A 373 ILE cc_start: 0.7209 (OUTLIER) cc_final: 0.6903 (mm) REVERT: A 501 MET cc_start: 0.7527 (mtt) cc_final: 0.7166 (mtt) REVERT: A 555 MET cc_start: 0.7295 (tpp) cc_final: 0.6723 (tpp) REVERT: B 287 TYR cc_start: 0.5421 (t80) cc_final: 0.5119 (t80) REVERT: B 568 ILE cc_start: 0.8985 (mt) cc_final: 0.8715 (mm) REVERT: B 809 MET cc_start: 0.7141 (mpp) cc_final: 0.6746 (ppp) REVERT: C 315 TRP cc_start: 0.6580 (p-90) cc_final: 0.5719 (p-90) REVERT: C 818 MET cc_start: 0.7405 (mmp) cc_final: 0.7185 (mmp) REVERT: D 117 PHE cc_start: 0.8039 (t80) cc_final: 0.7637 (t80) REVERT: D 129 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8436 (tp) REVERT: D 187 PHE cc_start: 0.8520 (p90) cc_final: 0.7883 (p90) REVERT: D 203 TYR cc_start: 0.7101 (m-10) cc_final: 0.6864 (m-10) REVERT: D 524 MET cc_start: 0.7859 (mpp) cc_final: 0.6890 (mtt) outliers start: 44 outliers final: 34 residues processed: 221 average time/residue: 0.1330 time to fit residues: 50.1345 Evaluate side-chains 219 residues out of total 2675 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 237 MET Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 798 CYS Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 194 PHE Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain B residue 312 SER Chi-restraints excluded: chain B residue 433 THR Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 798 CYS Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain D residue 647 VAL Chi-restraints excluded: chain D residue 787 THR Chi-restraints excluded: chain D residue 814 ASP Chi-restraints excluded: chain D residue 840 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 168 optimal weight: 9.9990 chunk 294 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 chunk 285 optimal weight: 0.3980 chunk 209 optimal weight: 6.9990 chunk 225 optimal weight: 0.6980 chunk 104 optimal weight: 20.0000 chunk 66 optimal weight: 0.8980 chunk 173 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS A 427 ASN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.091514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.065508 restraints weight = 111062.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.065092 restraints weight = 73308.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.065911 restraints weight = 58770.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.066539 restraints weight = 45463.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.066529 restraints weight = 42529.128| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24744 Z= 0.107 Angle : 0.601 13.434 33634 Z= 0.286 Chirality : 0.043 0.281 3848 Planarity : 0.003 0.048 4274 Dihedral : 5.579 58.761 3566 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.11 % Favored : 92.76 % Rotamer: Outliers : 1.53 % Allowed : 18.01 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.15), residues: 3079 helix: 0.30 (0.16), residues: 1097 sheet: -1.16 (0.28), residues: 366 loop : -1.80 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 821 TYR 0.012 0.001 TYR C 795 PHE 0.027 0.001 PHE C 102 TRP 0.015 0.001 TRP A 315 HIS 0.003 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00246 (24720) covalent geometry : angle 0.59485 (33576) SS BOND : bond 0.00144 ( 14) SS BOND : angle 0.59111 ( 28) hydrogen bonds : bond 0.03015 ( 738) hydrogen bonds : angle 4.54804 ( 2070) link_BETA1-4 : bond 0.00186 ( 1) link_BETA1-4 : angle 1.67128 ( 3) link_NAG-ASN : bond 0.00609 ( 9) link_NAG-ASN : angle 3.02654 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3857.67 seconds wall clock time: 67 minutes 28.45 seconds (4048.45 seconds total)