Starting phenix.real_space_refine on Fri May 23 14:17:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d38_46527/05_2025/9d38_46527.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d38_46527/05_2025/9d38_46527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d38_46527/05_2025/9d38_46527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d38_46527/05_2025/9d38_46527.map" model { file = "/net/cci-nas-00/data/ceres_data/9d38_46527/05_2025/9d38_46527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d38_46527/05_2025/9d38_46527.cif" } resolution = 3.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.007 sd= 0.038 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: 4 Type Number sf(0) Gaussians S 133 5.16 5 C 15384 2.51 5 N 4046 2.21 5 O 4461 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24024 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 792, 6142 Classifications: {'peptide': 792} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 34, 'TRANS': 757} Chain breaks: 2 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 85 Chain: "B" Number of atoms: 5784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 768, 5784 Classifications: {'peptide': 768} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 26, 'TRANS': 741} Unresolved chain links: 1 Chain breaks: 4 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 304 Unresolved non-hydrogen angles: 375 Unresolved non-hydrogen dihedrals: 264 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 10, 'TYR:plan': 4, 'ASN:plan1': 3, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 14, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 221 Chain: "C" Number of atoms: 6206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6206 Classifications: {'peptide': 796} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 35, 'TRANS': 760} Chain breaks: 2 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 51 Chain: "D" Number of atoms: 5792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 5792 Classifications: {'peptide': 760} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 722} Chain breaks: 4 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 125 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 13.97, per 1000 atoms: 0.58 Number of scatterers: 24024 At special positions: 0 Unit cell: (125.706, 149.814, 190.281, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 133 16.00 O 4461 8.00 N 4046 7.00 C 15384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, 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=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.02 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.03 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.03 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 436 " - pdb=" SG CYS C 455 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.03 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 Simple disulfide: pdb=" SG CYS D 773 " - pdb=" SG CYS D 828 " 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 471 " " NAG B 902 " - " ASN B 688 " " NAG C 902 " - " ASN C 771 " " NAG E 1 " - " ASN A 771 " Time building additional restraints: 5.86 Conformation dependent library (CDL) restraints added in 2.9 seconds 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5806 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 33 sheets defined 41.3% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.00 Creating SS restraints... Processing helix chain 'A' and resid 35 through 53 removed outlier: 4.415A pdb=" N GLU A 44 " --> pdb=" O GLN A 40 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ASN A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 103 through 115 removed outlier: 4.740A pdb=" N VAL A 107 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR A 110 " --> pdb=" O PRO A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.918A pdb=" N ASP A 130 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 145 No H-bonds generated for 'chain 'A' and resid 143 through 145' Processing helix chain 'A' and resid 146 through 157 removed outlier: 4.198A pdb=" N VAL A 150 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET A 154 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N MET A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG A 156 " --> pdb=" O PHE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 182 Processing helix chain 'A' and resid 183 through 188 removed outlier: 3.744A pdb=" N GLU A 186 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 210 removed outlier: 3.880A pdb=" N GLU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 214 Processing helix chain 'A' and resid 224 through 235 removed outlier: 3.583A pdb=" N ALA A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 3.596A pdb=" N ILE A 254 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 250 through 255' Processing helix chain 'A' and resid 276 through 296 removed outlier: 3.948A pdb=" N ILE A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N SER A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY A 286 " --> pdb=" O SER A 282 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A 287 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 292 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N HIS A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 325 Processing helix chain 'A' and resid 457 through 468 removed outlier: 3.503A pdb=" N LYS A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.657A pdb=" N LEU A 506 " --> pdb=" O MET A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 559 through 582 removed outlier: 3.611A pdb=" N TRP A 563 " --> pdb=" O GLN A 559 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL A 570 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N HIS A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A 575 " --> pdb=" O HIS A 571 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N MET A 576 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU A 577 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 615 removed outlier: 3.838A pdb=" N TRP A 608 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N PHE A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP A 611 " --> pdb=" O MET A 607 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 615 " --> pdb=" O TRP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 655 removed outlier: 3.714A pdb=" N ILE A 631 " --> pdb=" O PHE A 627 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY A 638 " --> pdb=" O MET A 634 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 639 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET A 641 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 651 " --> pdb=" O TYR A 647 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ALA A 652 " --> pdb=" O THR A 648 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 653 " --> pdb=" O ALA A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 674 Processing helix chain 'A' and resid 688 through 696 removed outlier: 3.601A pdb=" N GLN A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 707 Processing helix chain 'A' and resid 714 through 723 removed outlier: 3.754A pdb=" N GLN A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 744 removed outlier: 4.211A pdb=" N GLU A 737 " --> pdb=" O SER A 733 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N PHE A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 739 " --> pdb=" O VAL A 735 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS A 743 " --> pdb=" O GLU A 739 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS A 744 " --> pdb=" O ALA A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 782 Processing helix chain 'A' and resid 783 through 793 removed outlier: 3.839A pdb=" N ASP A 787 " --> pdb=" O GLY A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 837 removed outlier: 4.043A pdb=" N MET A 818 " --> pdb=" O ALA A 814 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL A 820 " --> pdb=" O VAL A 816 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE A 829 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE A 832 " --> pdb=" O ILE A 828 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE A 833 " --> pdb=" O PHE A 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.560A pdb=" N LYS B 51 " --> pdb=" O GLU B 47 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP B 52 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 90 removed outlier: 3.751A pdb=" N SER B 90 " --> pdb=" O CYS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 119 removed outlier: 3.658A pdb=" N ILE B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE B 114 " --> pdb=" O GLN B 110 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE B 115 " --> pdb=" O ILE B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 165 removed outlier: 3.777A pdb=" N SER B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE B 160 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU B 163 " --> pdb=" O ASN B 159 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 192 removed outlier: 3.565A pdb=" N ILE B 186 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER B 188 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 removed outlier: 4.137A pdb=" N GLN B 217 " --> pdb=" O ASP B 213 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 248 removed outlier: 4.303A pdb=" N THR B 238 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL B 243 " --> pdb=" O TYR B 239 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER B 246 " --> pdb=" O GLU B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 264 removed outlier: 4.013A pdb=" N ALA B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 304 removed outlier: 3.684A pdb=" N ASP B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY B 296 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR B 301 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA B 304 " --> pdb=" O ILE B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 311 removed outlier: 3.730A pdb=" N LEU B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B 309 " --> pdb=" O SER B 305 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 330 removed outlier: 4.062A pdb=" N ILE B 329 " --> pdb=" O GLU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 460 through 472 removed outlier: 3.644A pdb=" N ILE B 464 " --> pdb=" O PHE B 460 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 465 " --> pdb=" O CYS B 461 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS B 470 " --> pdb=" O LYS B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 503 Processing helix chain 'B' and resid 516 through 523 removed outlier: 4.092A pdb=" N VAL B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 579 removed outlier: 3.933A pdb=" N MET B 561 " --> pdb=" O ASP B 557 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N MET B 562 " --> pdb=" O VAL B 558 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL B 564 " --> pdb=" O VAL B 560 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N MET B 565 " --> pdb=" O MET B 561 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 567 " --> pdb=" O PHE B 563 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 568 " --> pdb=" O VAL B 564 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL B 574 " --> pdb=" O SER B 570 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B 575 " --> pdb=" O ALA B 571 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR B 579 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 614 removed outlier: 3.932A pdb=" N ILE B 606 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TRP B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY B 611 " --> pdb=" O TRP B 607 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LEU B 612 " --> pdb=" O LEU B 608 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE B 614 " --> pdb=" O TRP B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 647 removed outlier: 3.667A pdb=" N SER B 633 " --> pdb=" O LYS B 629 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE B 638 " --> pdb=" O VAL B 634 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B 640 " --> pdb=" O ALA B 636 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 641 " --> pdb=" O PHE B 637 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU B 643 " --> pdb=" O ALA B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 655 Processing helix chain 'B' and resid 668 through 673 removed outlier: 3.878A pdb=" N GLN B 672 " --> pdb=" O ASP B 668 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG B 673 " --> pdb=" O LYS B 669 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 668 through 673' Processing helix chain 'B' and resid 674 through 677 removed outlier: 4.301A pdb=" N PHE B 677 " --> pdb=" O PRO B 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 674 through 677' Processing helix chain 'B' and resid 690 through 699 removed outlier: 3.538A pdb=" N ASN B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN B 698 " --> pdb=" O ASN B 694 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR B 699 " --> pdb=" O ILE B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 707 removed outlier: 3.551A pdb=" N HIS B 703 " --> pdb=" O TYR B 699 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA B 704 " --> pdb=" O ALA B 700 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N TYR B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET B 706 " --> pdb=" O MET B 702 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY B 707 " --> pdb=" O HIS B 703 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 699 through 707' Processing helix chain 'B' and resid 713 through 722 removed outlier: 3.903A pdb=" N LYS B 722 " --> pdb=" O LEU B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 741 Processing helix chain 'B' and resid 742 through 747 removed outlier: 6.313A pdb=" N GLY B 745 " --> pdb=" O ARG B 742 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS B 747 " --> pdb=" O GLU B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 785 removed outlier: 3.665A pdb=" N LEU B 778 " --> pdb=" O ARG B 774 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY B 785 " --> pdb=" O LEU B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 793 Processing helix chain 'B' and resid 794 through 796 No H-bonds generated for 'chain 'B' and resid 794 through 796' Processing helix chain 'B' and resid 818 through 845 removed outlier: 4.037A pdb=" N MET B 829 " --> pdb=" O LEU B 825 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA B 830 " --> pdb=" O GLY B 826 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 838 " --> pdb=" O ILE B 834 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU B 839 " --> pdb=" O THR B 835 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N HIS B 840 " --> pdb=" O PHE B 836 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE B 842 " --> pdb=" O SER B 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 48 Processing helix chain 'C' and resid 70 through 76 Processing helix chain 'C' and resid 104 through 114 Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 146 through 158 removed outlier: 3.793A pdb=" N VAL C 150 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TRP C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG C 156 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 185 removed outlier: 3.611A pdb=" N ARG C 179 " --> pdb=" O ALA C 175 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 removed outlier: 3.623A pdb=" N ALA C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 235 removed outlier: 3.630A pdb=" N ALA C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 260 Processing helix chain 'C' and resid 277 through 296 removed outlier: 3.526A pdb=" N SER C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU C 294 " --> pdb=" O GLN C 290 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 327 removed outlier: 3.631A pdb=" N LYS C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG C 323 " --> pdb=" O PRO C 319 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL C 324 " --> pdb=" O LEU C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 385 removed outlier: 3.533A pdb=" N GLY C 384 " --> pdb=" O TRP C 381 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLU C 385 " --> pdb=" O PRO C 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 381 through 385' Processing helix chain 'C' and resid 458 through 469 removed outlier: 3.543A pdb=" N LEU C 463 " --> pdb=" O CYS C 459 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR C 469 " --> pdb=" O LYS C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 508 removed outlier: 4.087A pdb=" N LEU C 506 " --> pdb=" O MET C 502 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER C 507 " --> pdb=" O GLY C 503 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY C 508 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 560 through 583 removed outlier: 3.566A pdb=" N ALA C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL C 575 " --> pdb=" O HIS C 571 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET C 576 " --> pdb=" O VAL C 572 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU C 577 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR C 578 " --> pdb=" O ALA C 574 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE C 583 " --> pdb=" O LEU C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 615 removed outlier: 4.208A pdb=" N MET C 607 " --> pdb=" O LEU C 603 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU C 614 " --> pdb=" O SER C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 657 removed outlier: 3.687A pdb=" N MET C 634 " --> pdb=" O ARG C 630 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE C 639 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR C 648 " --> pdb=" O VAL C 644 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA C 653 " --> pdb=" O ALA C 649 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 655 " --> pdb=" O LEU C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 674 removed outlier: 3.961A pdb=" N ARG C 673 " --> pdb=" O ASP C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 694 Processing helix chain 'C' and resid 705 through 708 removed outlier: 3.848A pdb=" N LYS C 708 " --> pdb=" O HIS C 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 705 through 708' Processing helix chain 'C' and resid 713 through 723 removed outlier: 3.833A pdb=" N ILE C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN C 719 " --> pdb=" O ALA C 715 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP C 723 " --> pdb=" O GLN C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 743 removed outlier: 3.783A pdb=" N PHE C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU C 739 " --> pdb=" O VAL C 735 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA C 740 " --> pdb=" O LEU C 736 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 782 removed outlier: 3.811A pdb=" N LEU C 774 " --> pdb=" O GLN C 770 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU C 781 " --> pdb=" O LEU C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 793 removed outlier: 3.562A pdb=" N ASP C 787 " --> pdb=" O GLY C 783 " (cutoff:3.500A) Processing helix chain 'C' and resid 812 through 816 removed outlier: 3.503A pdb=" N GLY C 815 " --> pdb=" O ASN C 812 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 826 removed outlier: 3.593A pdb=" N VAL C 825 " --> pdb=" O ALA C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 836 removed outlier: 4.374A pdb=" N PHE C 832 " --> pdb=" O ILE C 828 " (cutoff:3.500A) Processing helix chain 'C' and resid 837 through 839 No H-bonds generated for 'chain 'C' and resid 837 through 839' Processing helix chain 'D' and resid 60 through 75 removed outlier: 4.245A pdb=" N ALA D 64 " --> pdb=" O PRO D 60 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLU D 65 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA D 67 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) Proline residue: D 71 - end of helix removed outlier: 3.621A pdb=" N ALA D 75 " --> pdb=" O PRO D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 109 Processing helix chain 'D' and resid 123 through 125 No H-bonds generated for 'chain 'D' and resid 123 through 125' Processing helix chain 'D' and resid 126 through 135 removed outlier: 3.792A pdb=" N LEU D 130 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP D 131 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU D 133 " --> pdb=" O ILE D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 182 removed outlier: 3.579A pdb=" N GLN D 171 " --> pdb=" O SER D 167 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN D 173 " --> pdb=" O GLU D 169 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL D 174 " --> pdb=" O GLN D 170 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE D 175 " --> pdb=" O GLN D 171 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU D 177 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL D 178 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU D 180 " --> pdb=" O PHE D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 210 removed outlier: 3.781A pdb=" N PHE D 200 " --> pdb=" O GLY D 196 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE D 204 " --> pdb=" O PHE D 200 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU D 205 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL D 206 " --> pdb=" O SER D 202 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 207 " --> pdb=" O TYR D 203 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR D 208 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLY D 210 " --> pdb=" O VAL D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 227 Processing helix chain 'D' and resid 228 through 235 Processing helix chain 'D' and resid 236 through 238 No H-bonds generated for 'chain 'D' and resid 236 through 238' Processing helix chain 'D' and resid 249 through 263 removed outlier: 4.427A pdb=" N GLU D 254 " --> pdb=" O ARG D 250 " (cutoff:3.500A) Proline residue: D 255 - end of helix removed outlier: 3.941A pdb=" N GLU D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA D 263 " --> pdb=" O ALA D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 338 removed outlier: 3.657A pdb=" N GLY D 323 " --> pdb=" O ARG D 319 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL D 324 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL D 327 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASP D 337 " --> pdb=" O ALA D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 347 removed outlier: 4.000A pdb=" N ASP D 347 " --> pdb=" O LEU D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 500 removed outlier: 3.619A pdb=" N ILE D 491 " --> pdb=" O PHE D 487 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS D 493 " --> pdb=" O ILE D 489 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG D 494 " --> pdb=" O ASP D 490 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 495 " --> pdb=" O ILE D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 530 Processing helix chain 'D' and resid 545 through 550 removed outlier: 4.177A pdb=" N ILE D 549 " --> pdb=" O GLU D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 575 through 579 Processing helix chain 'D' and resid 581 through 607 removed outlier: 3.817A pdb=" N VAL D 585 " --> pdb=" O TYR D 581 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TRP D 586 " --> pdb=" O SER D 582 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE D 590 " --> pdb=" O TRP D 586 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL D 591 " --> pdb=" O VAL D 587 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET D 592 " --> pdb=" O MET D 588 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA D 598 " --> pdb=" O LEU D 594 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL D 599 " --> pdb=" O THR D 595 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU D 605 " --> pdb=" O VAL D 601 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TYR D 606 " --> pdb=" O PHE D 602 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU D 607 " --> pdb=" O ILE D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 633 Processing helix chain 'D' and resid 633 through 639 Processing helix chain 'D' and resid 652 through 674 removed outlier: 3.507A pdb=" N MET D 658 " --> pdb=" O THR D 654 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU D 660 " --> pdb=" O LYS D 656 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL D 661 " --> pdb=" O ILE D 657 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE D 665 " --> pdb=" O VAL D 661 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA D 666 " --> pdb=" O TRP D 662 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL D 667 " --> pdb=" O ALA D 663 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA D 671 " --> pdb=" O VAL D 667 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER D 672 " --> pdb=" O ILE D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 679 removed outlier: 3.516A pdb=" N ALA D 678 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA D 679 " --> pdb=" O ASN D 676 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 675 through 679' Processing helix chain 'D' and resid 695 through 700 removed outlier: 3.524A pdb=" N GLN D 699 " --> pdb=" O ASP D 695 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 726 Processing helix chain 'D' and resid 731 through 736 removed outlier: 3.602A pdb=" N VAL D 734 " --> pdb=" O SER D 731 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG D 735 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 750 removed outlier: 3.634A pdb=" N THR D 746 " --> pdb=" O GLU D 742 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU D 748 " --> pdb=" O ALA D 744 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS D 749 " --> pdb=" O LEU D 745 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ALA D 750 " --> pdb=" O THR D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 770 Processing helix chain 'D' and resid 779 through 781 No H-bonds generated for 'chain 'D' and resid 779 through 781' Processing helix chain 'D' and resid 799 through 813 removed outlier: 3.554A pdb=" N ALA D 806 " --> pdb=" O PRO D 802 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN D 809 " --> pdb=" O LEU D 805 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE D 810 " --> pdb=" O ALA D 806 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU D 811 " --> pdb=" O LEU D 807 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 824 removed outlier: 3.509A pdb=" N MET D 818 " --> pdb=" O ASP D 814 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG D 821 " --> pdb=" O GLU D 817 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP D 823 " --> pdb=" O LEU D 819 " (cutoff:3.500A) Processing helix chain 'D' and resid 846 through 872 removed outlier: 4.016A pdb=" N LEU D 852 " --> pdb=" O VAL D 848 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU D 861 " --> pdb=" O GLY D 857 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL D 862 " --> pdb=" O LEU D 858 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N HIS D 867 " --> pdb=" O PHE D 863 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU D 868 " --> pdb=" O ALA D 864 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL D 869 " --> pdb=" O TRP D 865 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 5.675A pdb=" N VAL A 27 " --> pdb=" O ASN A 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 66 removed outlier: 6.375A pdb=" N ALA A 31 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL A 32 " --> pdb=" O LEU A 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA4, first strand: chain 'A' and resid 164 through 168 removed outlier: 6.531A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 218 through 221 removed outlier: 6.588A pdb=" N ILE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 269 through 271 removed outlier: 7.155A pdb=" N TYR A 351 " --> pdb=" O ILE A 366 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ILE A 366 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE A 353 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 476 through 478 removed outlier: 6.125A pdb=" N ILE A 400 " --> pdb=" O HIS A 477 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY A 761 " --> pdb=" O ILE A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 410 through 413 removed outlier: 3.584A pdb=" N TYR A 456 " --> pdb=" O TYR A 410 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY A 438 " --> pdb=" O VAL A 451 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 424 through 425 Processing sheet with id=AB1, first strand: chain 'A' and resid 729 through 732 removed outlier: 3.607A pdb=" N PHE A 729 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP A 731 " --> pdb=" O THR A 539 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL A 542 " --> pdb=" O VAL A 747 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 747 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 66 through 71 removed outlier: 7.189A pdb=" N VAL B 98 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA B 38 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ALA B 100 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE B 40 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASP B 101 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ILE B 123 " --> pdb=" O PHE B 144 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 198 through 203 removed outlier: 7.413A pdb=" N PHE B 169 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N LEU B 203 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE B 171 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ILE B 168 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N LEU B 229 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER B 170 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N TYR B 231 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL B 172 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N TRP B 256 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N VAL B 280 " --> pdb=" O TRP B 256 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL B 258 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N TYR B 282 " --> pdb=" O VAL B 258 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 343 through 344 Processing sheet with id=AB5, first strand: chain 'B' and resid 377 through 379 Processing sheet with id=AB6, first strand: chain 'B' and resid 405 through 410 removed outlier: 3.778A pdb=" N ASP B 477 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE B 408 " --> pdb=" O ASP B 477 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 417 through 421 removed outlier: 3.708A pdb=" N CYS B 436 " --> pdb=" O LYS B 455 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AB9, first strand: chain 'B' and resid 508 through 509 Processing sheet with id=AC1, first strand: chain 'B' and resid 730 through 732 removed outlier: 3.860A pdb=" N TYR B 731 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 535 " --> pdb=" O TYR B 731 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 64 through 65 removed outlier: 8.157A pdb=" N VAL C 65 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA C 31 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASN C 28 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ALA C 89 " --> pdb=" O ASN C 28 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER C 93 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N LEU C 119 " --> pdb=" O TYR C 88 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE C 90 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LEU C 121 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL C 92 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL C 118 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 196 through 197 removed outlier: 7.603A pdb=" N PHE C 197 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL C 167 " --> pdb=" O PHE C 197 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.719A pdb=" N VAL C 362 " --> pdb=" O ASN C 355 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 366 through 367 removed outlier: 4.149A pdb=" N VAL C 372 " --> pdb=" O ILE C 366 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 473 through 478 removed outlier: 7.463A pdb=" N LEU C 398 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N HIS C 477 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ILE C 400 " --> pdb=" O HIS C 477 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET C 512 " --> pdb=" O LYS C 399 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY C 761 " --> pdb=" O ILE C 513 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 409 through 413 removed outlier: 3.636A pdb=" N TYR C 456 " --> pdb=" O TYR C 410 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 439 through 440 removed outlier: 3.662A pdb=" N HIS C 449 " --> pdb=" O ASN C 440 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 710 through 711 removed outlier: 7.784A pdb=" N TYR C 711 " --> pdb=" O TYR C 681 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR C 683 " --> pdb=" O TYR C 711 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ALA C 682 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 9.864A pdb=" N ASP C 732 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 10.856A pdb=" N VAL C 684 " --> pdb=" O ASP C 732 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE C 729 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU C 541 " --> pdb=" O PHE C 729 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TRP C 731 " --> pdb=" O THR C 539 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL C 747 " --> pdb=" O VAL C 542 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 54 through 56 removed outlier: 6.613A pdb=" N ALA D 54 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N GLU D 118 " --> pdb=" O ALA D 54 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N VAL D 56 " --> pdb=" O GLU D 118 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VAL D 115 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL D 144 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N PHE D 117 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE D 141 " --> pdb=" O LEU D 162 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'D' and resid 188 through 189 removed outlier: 6.699A pdb=" N VAL D 188 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG D 244 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE D 273 " --> pdb=" O ARG D 244 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 246 " --> pdb=" O PHE D 273 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N VAL D 307 " --> pdb=" O MET D 274 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU D 304 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU D 387 " --> pdb=" O SER D 403 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N SER D 403 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL D 389 " --> pdb=" O VAL D 401 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR D 397 " --> pdb=" O THR D 393 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 368 through 369 Processing sheet with id=AD4, first strand: chain 'D' and resid 431 through 434 removed outlier: 3.751A pdb=" N ASP D 504 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL D 434 " --> pdb=" O ASP D 504 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU D 505 " --> pdb=" O PRO D 461 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG D 463 " --> pdb=" O LEU D 505 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL D 460 " --> pdb=" O CYS D 484 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS D 484 " --> pdb=" O VAL D 460 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 756 through 759 removed outlier: 3.731A pdb=" N TYR D 758 " --> pdb=" O SER D 562 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL D 776 " --> pdb=" O VAL D 565 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 756 through 759 removed outlier: 3.731A pdb=" N TYR D 758 " --> pdb=" O SER D 562 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ILE D 561 " --> pdb=" O ALA D 785 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ALA D 785 " --> pdb=" O ILE D 561 " (cutoff:3.500A) 683 hydrogen bonds defined for protein. 1932 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: 8.26 Time building geometry restraints manager: 6.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7784 1.35 - 1.46: 5762 1.46 - 1.58: 10779 1.58 - 1.70: 0 1.70 - 1.82: 227 Bond restraints: 24552 Sorted by residual: bond pdb=" C1 NAG C 902 " pdb=" O5 NAG C 902 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.85e+00 bond pdb=" C5 NAG C 902 " pdb=" O5 NAG C 902 " ideal model delta sigma weight residual 1.413 1.441 -0.028 2.00e-02 2.50e+03 1.91e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.429 -0.023 2.00e-02 2.50e+03 1.38e+00 bond pdb=" C ASN B 688 " pdb=" N GLY B 689 " ideal model delta sigma weight residual 1.331 1.313 0.017 1.46e-02 4.69e+03 1.36e+00 bond pdb=" C1 NAG B 902 " pdb=" O5 NAG B 902 " ideal model delta sigma weight residual 1.406 1.429 -0.023 2.00e-02 2.50e+03 1.33e+00 ... (remaining 24547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 32933 2.13 - 4.26: 352 4.26 - 6.40: 56 6.40 - 8.53: 11 8.53 - 10.66: 10 Bond angle restraints: 33362 Sorted by residual: angle pdb=" CB MET B 562 " pdb=" CG MET B 562 " pdb=" SD MET B 562 " ideal model delta sigma weight residual 112.70 123.36 -10.66 3.00e+00 1.11e-01 1.26e+01 angle pdb=" CB MET B 561 " pdb=" CG MET B 561 " pdb=" SD MET B 561 " ideal model delta sigma weight residual 112.70 123.24 -10.54 3.00e+00 1.11e-01 1.23e+01 angle pdb=" CB MET D 274 " pdb=" CG MET D 274 " pdb=" SD MET D 274 " ideal model delta sigma weight residual 112.70 123.12 -10.42 3.00e+00 1.11e-01 1.21e+01 angle pdb=" CB MET A 41 " pdb=" CG MET A 41 " pdb=" SD MET A 41 " ideal model delta sigma weight residual 112.70 123.04 -10.34 3.00e+00 1.11e-01 1.19e+01 angle pdb=" CB MET C 354 " pdb=" CG MET C 354 " pdb=" SD MET C 354 " ideal model delta sigma weight residual 112.70 122.47 -9.77 3.00e+00 1.11e-01 1.06e+01 ... (remaining 33357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.17: 13065 21.17 - 42.34: 1336 42.34 - 63.51: 213 63.51 - 84.68: 31 84.68 - 105.85: 15 Dihedral angle restraints: 14660 sinusoidal: 5658 harmonic: 9002 Sorted by residual: dihedral pdb=" CB CYS C 79 " pdb=" SG CYS C 79 " pdb=" SG CYS C 308 " pdb=" CB CYS C 308 " ideal model delta sinusoidal sigma weight residual 93.00 -176.73 -90.27 1 1.00e+01 1.00e-02 9.64e+01 dihedral pdb=" CB CYS D 455 " pdb=" SG CYS D 455 " pdb=" SG CYS D 483 " pdb=" CB CYS D 483 " ideal model delta sinusoidal sigma weight residual 93.00 166.99 -73.99 1 1.00e+01 1.00e-02 6.95e+01 dihedral pdb=" CB CYS C 744 " pdb=" SG CYS C 744 " pdb=" SG CYS C 798 " pdb=" CB CYS C 798 " ideal model delta sinusoidal sigma weight residual 93.00 150.52 -57.52 1 1.00e+01 1.00e-02 4.45e+01 ... (remaining 14657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3327 0.061 - 0.121: 475 0.121 - 0.182: 21 0.182 - 0.243: 2 0.243 - 0.303: 2 Chirality restraints: 3827 Sorted by residual: chirality pdb=" C1 NAG B 902 " pdb=" ND2 ASN B 688 " pdb=" C2 NAG B 902 " pdb=" O5 NAG B 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CB VAL C 194 " pdb=" CA VAL C 194 " pdb=" CG1 VAL C 194 " pdb=" CG2 VAL C 194 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 771 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 3824 not shown) Planarity restraints: 4249 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 678 " 0.049 5.00e-02 4.00e+02 7.36e-02 8.67e+00 pdb=" N PRO B 679 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 679 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 679 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 637 " -0.023 2.00e-02 2.50e+03 1.71e-02 7.34e+00 pdb=" CG TRP D 637 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP D 637 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP D 637 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 637 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 637 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 637 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 637 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 637 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 637 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 176 " -0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO B 177 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 177 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 177 " -0.026 5.00e-02 4.00e+02 ... (remaining 4246 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 440 2.66 - 3.22: 23661 3.22 - 3.78: 36786 3.78 - 4.34: 47199 4.34 - 4.90: 74600 Nonbonded interactions: 182686 Sorted by model distance: nonbonded pdb=" OG SER B 149 " pdb=" OE1 GLU B 151 " model vdw 2.098 3.040 nonbonded pdb=" N GLU A 737 " pdb=" OE1 GLU A 737 " model vdw 2.199 3.120 nonbonded pdb=" O LYS B 624 " pdb=" OG SER B 628 " model vdw 2.213 3.040 nonbonded pdb=" O PHE D 669 " pdb=" OG SER D 672 " model vdw 2.216 3.040 nonbonded pdb=" O ILE B 115 " pdb=" OG1 THR B 119 " model vdw 2.216 3.040 ... (remaining 182681 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 35 or (resid 36 and (name N or name CA or name C or name \ O or name CB )) or resid 37 through 186 or (resid 187 through 188 and (name N or \ name CA or name C or name O or name CB )) or resid 189 through 447 or (resid 44 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 449 through \ 494 or (resid 495 through 496 and (name N or name CA or name C or name O or name \ CB )) or resid 497 through 545 or (resid 546 and (name N or name CA or name C o \ r name O or name CB )) or resid 547 through 567 or (resid 568 and (name N or nam \ e CA or name C or name O or name CB )) or resid 569 through 624 or (resid 625 an \ d (name N or name CA or name C or name O or name CB )) or resid 626 through 660 \ or (resid 661 through 662 and (name N or name CA or name C or name O or name CB \ )) or resid 663 through 833 or (resid 834 and (name N or name CA or name C or na \ me O or name CB )) or resid 835 through 837 or resid 901 or resid 902)) selection = (chain 'C' and (resid 25 through 259 or (resid 260 and (name N or name CA or nam \ e C or name O or name CB )) or resid 261 through 491 or (resid 492 through 493 a \ nd (name N or name CA or name C or name O or name CB )) or resid 494 through 544 \ or (resid 545 through 546 and (name N or name CA or name C or name O or name CB \ )) or resid 547 through 559 or (resid 560 and (name N or name CA or name C or n \ ame O or name CB )) or resid 561 through 575 or (resid 576 through 578 and (name \ N or name CA or name C or name O or name CB )) or resid 579 through 582 or (res \ id 583 and (name N or name CA or name C or name O or name CB )) or resid 584 thr \ ough 585 or resid 601 through 657 or (resid 658 through 659 and (name N or name \ CA or name C or name O or name CB )) or resid 660 through 677 or (resid 678 and \ (name N or name CA or name C or name O or name CB )) or resid 679 through 694 or \ (resid 695 and (name N or name CA or name C or name O or name CB )) or resid 69 \ 6 through 697 or (resid 698 and (name N or name CA or name C or name O or name C \ B )) or resid 699 through 703 or (resid 704 and (name N or name CA or name C or \ name O or name CB )) or resid 705 through 750 or (resid 751 and (name N or name \ CA or name C or name O or name CB )) or resid 752 through 799 or resid 806 throu \ gh 808 or (resid 809 and (name N or name CA or name C or name O or name CB )) or \ resid 810 or (resid 811 through 812 and (name N or name CA or name C or name O \ or name CB )) or resid 813 through 831 or (resid 832 through 834 and (name N or \ name CA or name C or name O or name CB )) or resid 835 through 836 or (resid 837 \ and (name N or name CA or name C or name O or name CB )) or resid 901 or resid \ 902)) } 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: 3.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 51.550 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 24572 Z= 0.103 Angle : 0.574 10.662 33407 Z= 0.279 Chirality : 0.042 0.303 3827 Planarity : 0.003 0.074 4245 Dihedral : 16.643 105.854 8809 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.27 % Favored : 92.50 % Rotamer: Outliers : 0.12 % Allowed : 27.67 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.15), residues: 3082 helix: -0.55 (0.17), residues: 962 sheet: -1.08 (0.31), residues: 301 loop : -1.61 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP D 637 HIS 0.005 0.001 HIS A 134 PHE 0.011 0.001 PHE A 42 TYR 0.027 0.001 TYR D 419 ARG 0.003 0.000 ARG C 397 Details of bonding type rmsd link_NAG-ASN : bond 0.00947 ( 4) link_NAG-ASN : angle 3.74256 ( 12) link_BETA1-4 : bond 0.00501 ( 1) link_BETA1-4 : angle 0.93000 ( 3) hydrogen bonds : bond 0.33308 ( 680) hydrogen bonds : angle 9.39945 ( 1932) SS BOND : bond 0.00281 ( 15) SS BOND : angle 0.80918 ( 30) covalent geometry : bond 0.00225 (24552) covalent geometry : angle 0.56941 (33362) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 155 time to evaluate : 2.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 824 MET cc_start: 0.8611 (tpt) cc_final: 0.8324 (tpp) REVERT: C 209 MET cc_start: 0.8202 (mmp) cc_final: 0.7783 (ptp) REVERT: C 634 MET cc_start: 0.8898 (tpp) cc_final: 0.8667 (tpt) outliers start: 3 outliers final: 0 residues processed: 156 average time/residue: 0.3117 time to fit residues: 80.8988 Evaluate side-chains 150 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 7.9990 chunk 234 optimal weight: 30.0000 chunk 130 optimal weight: 0.9990 chunk 80 optimal weight: 30.0000 chunk 158 optimal weight: 20.0000 chunk 125 optimal weight: 4.9990 chunk 242 optimal weight: 2.9990 chunk 94 optimal weight: 0.0370 chunk 147 optimal weight: 0.6980 chunk 180 optimal weight: 10.0000 chunk 281 optimal weight: 3.9990 overall best weight: 1.7464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 177 GLN A 358 ASN B 159 ASN B 357 GLN B 385 GLN B 405 HIS B 711 GLN C 311 ASN C 350 ASN C 358 ASN C 650 ASN D 102 GLN D 136 GLN ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.084592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.062076 restraints weight = 145856.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.062547 restraints weight = 92839.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.062383 restraints weight = 74704.786| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24572 Z= 0.145 Angle : 0.604 7.338 33407 Z= 0.313 Chirality : 0.044 0.193 3827 Planarity : 0.004 0.071 4245 Dihedral : 6.311 72.756 3436 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.82 % Favored : 91.95 % Rotamer: Outliers : 3.40 % Allowed : 25.89 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.15), residues: 3082 helix: -0.45 (0.16), residues: 1030 sheet: -0.80 (0.32), residues: 276 loop : -1.65 (0.15), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 637 HIS 0.008 0.001 HIS A 134 PHE 0.019 0.001 PHE C 321 TYR 0.015 0.001 TYR D 419 ARG 0.004 0.000 ARG C 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00595 ( 4) link_NAG-ASN : angle 3.11113 ( 12) link_BETA1-4 : bond 0.00294 ( 1) link_BETA1-4 : angle 1.06009 ( 3) hydrogen bonds : bond 0.06255 ( 680) hydrogen bonds : angle 6.53630 ( 1932) SS BOND : bond 0.00306 ( 15) SS BOND : angle 0.82124 ( 30) covalent geometry : bond 0.00312 (24552) covalent geometry : angle 0.60070 (33362) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 159 time to evaluate : 2.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 ASN cc_start: 0.2920 (OUTLIER) cc_final: 0.2579 (p0) REVERT: B 498 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7679 (mm) REVERT: B 789 MET cc_start: 0.8664 (mpp) cc_final: 0.8162 (mpp) REVERT: C 190 LYS cc_start: 0.7331 (tttm) cc_final: 0.6476 (mtmt) REVERT: C 470 MET cc_start: 0.8627 (mmm) cc_final: 0.8238 (mtt) REVERT: D 274 MET cc_start: 0.5899 (tmm) cc_final: 0.5659 (tmm) outliers start: 86 outliers final: 32 residues processed: 235 average time/residue: 0.2937 time to fit residues: 116.6945 Evaluate side-chains 189 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 151 TRP Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 705 HIS Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 497 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 265 optimal weight: 30.0000 chunk 274 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 187 optimal weight: 20.0000 chunk 267 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 chunk 277 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 283 optimal weight: 4.9990 chunk 258 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN C 61 ASN C 358 ASN ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 ASN ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.082734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.059910 restraints weight = 145307.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.059531 restraints weight = 98638.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.060031 restraints weight = 83822.358| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 24572 Z= 0.299 Angle : 0.707 8.620 33407 Z= 0.367 Chirality : 0.047 0.215 3827 Planarity : 0.005 0.070 4245 Dihedral : 6.097 57.235 3436 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.34 % Favored : 90.43 % Rotamer: Outliers : 6.13 % Allowed : 24.86 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.15), residues: 3082 helix: -0.59 (0.15), residues: 1068 sheet: -1.31 (0.30), residues: 300 loop : -1.85 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 637 HIS 0.008 0.001 HIS A 134 PHE 0.027 0.002 PHE A 533 TYR 0.018 0.002 TYR B 479 ARG 0.004 0.000 ARG C 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00596 ( 4) link_NAG-ASN : angle 4.00342 ( 12) link_BETA1-4 : bond 0.00140 ( 1) link_BETA1-4 : angle 1.42949 ( 3) hydrogen bonds : bond 0.06329 ( 680) hydrogen bonds : angle 6.46032 ( 1932) SS BOND : bond 0.00543 ( 15) SS BOND : angle 1.06144 ( 30) covalent geometry : bond 0.00689 (24552) covalent geometry : angle 0.70236 (33362) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 163 time to evaluate : 2.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 LYS cc_start: 0.9126 (mmmt) cc_final: 0.8907 (mmmt) REVERT: A 461 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7906 (t0) REVERT: B 287 TYR cc_start: 0.7333 (OUTLIER) cc_final: 0.6205 (t80) REVERT: B 551 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8785 (pp) REVERT: B 653 PHE cc_start: 0.6694 (OUTLIER) cc_final: 0.6422 (t80) REVERT: B 681 PHE cc_start: 0.6971 (OUTLIER) cc_final: 0.6356 (t80) REVERT: B 789 MET cc_start: 0.8741 (mpp) cc_final: 0.8155 (mpp) REVERT: C 354 MET cc_start: 0.6635 (tpp) cc_final: 0.6416 (tpp) REVERT: C 415 LEU cc_start: 0.6104 (OUTLIER) cc_final: 0.5589 (pp) REVERT: C 470 MET cc_start: 0.8887 (mmm) cc_final: 0.8686 (mtt) REVERT: D 274 MET cc_start: 0.6129 (tmm) cc_final: 0.5852 (ppp) outliers start: 155 outliers final: 90 residues processed: 305 average time/residue: 0.2834 time to fit residues: 145.9818 Evaluate side-chains 253 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 157 time to evaluate : 2.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 67 HIS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 454 CYS Chi-restraints excluded: chain A residue 461 ASP Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 705 HIS Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 681 PHE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 698 ASN Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 529 PHE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 639 PHE Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 697 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 765 ASP Chi-restraints excluded: chain C residue 775 SER Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 436 THR Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 484 CYS Chi-restraints excluded: chain D residue 497 HIS Chi-restraints excluded: chain D residue 522 ASN Chi-restraints excluded: chain D residue 550 VAL Chi-restraints excluded: chain D residue 561 ILE Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain D residue 752 LYS Chi-restraints excluded: chain D residue 791 ILE Chi-restraints excluded: chain D residue 828 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 229 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 141 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 174 optimal weight: 6.9990 chunk 300 optimal weight: 0.4980 chunk 36 optimal weight: 9.9990 chunk 295 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 263 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 357 GLN ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 ASN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 794 HIS ** 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 = 0.3958 r_free = 0.3958 target = 0.084466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.062140 restraints weight = 146971.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.061946 restraints weight = 95495.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.062375 restraints weight = 77644.069| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 24572 Z= 0.113 Angle : 0.591 12.258 33407 Z= 0.298 Chirality : 0.043 0.212 3827 Planarity : 0.004 0.073 4245 Dihedral : 5.343 59.730 3436 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.56 % Favored : 92.21 % Rotamer: Outliers : 3.83 % Allowed : 26.84 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.15), residues: 3082 helix: -0.32 (0.16), residues: 1048 sheet: -0.86 (0.32), residues: 271 loop : -1.74 (0.15), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 610 HIS 0.008 0.001 HIS A 134 PHE 0.018 0.001 PHE C 321 TYR 0.012 0.001 TYR B 479 ARG 0.003 0.000 ARG C 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00573 ( 4) link_NAG-ASN : angle 3.45621 ( 12) link_BETA1-4 : bond 0.00275 ( 1) link_BETA1-4 : angle 1.34806 ( 3) hydrogen bonds : bond 0.04658 ( 680) hydrogen bonds : angle 5.82926 ( 1932) SS BOND : bond 0.00439 ( 15) SS BOND : angle 1.35814 ( 30) covalent geometry : bond 0.00241 (24552) covalent geometry : angle 0.58666 (33362) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 160 time to evaluate : 2.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 MET cc_start: 0.7609 (mmm) cc_final: 0.6911 (tpp) REVERT: B 281 SER cc_start: 0.7392 (OUTLIER) cc_final: 0.7182 (p) REVERT: B 287 TYR cc_start: 0.7298 (OUTLIER) cc_final: 0.6171 (t80) REVERT: B 537 MET cc_start: 0.7243 (tmm) cc_final: 0.6302 (ttp) REVERT: B 551 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8746 (pp) REVERT: B 669 LYS cc_start: 0.8814 (pptt) cc_final: 0.8518 (tptp) REVERT: B 681 PHE cc_start: 0.6989 (OUTLIER) cc_final: 0.6158 (t80) REVERT: B 789 MET cc_start: 0.8585 (mpp) cc_final: 0.8247 (mpp) REVERT: C 190 LYS cc_start: 0.7367 (tttm) cc_final: 0.6508 (mtmt) REVERT: C 209 MET cc_start: 0.8021 (mmp) cc_final: 0.7487 (ptp) REVERT: C 354 MET cc_start: 0.7117 (tpp) cc_final: 0.6869 (tpp) REVERT: C 415 LEU cc_start: 0.6263 (OUTLIER) cc_final: 0.5759 (pp) REVERT: C 470 MET cc_start: 0.8753 (mmm) cc_final: 0.8390 (mtt) REVERT: D 274 MET cc_start: 0.6298 (tmm) cc_final: 0.6024 (ppp) outliers start: 97 outliers final: 59 residues processed: 245 average time/residue: 0.2939 time to fit residues: 119.9212 Evaluate side-chains 216 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 152 time to evaluate : 2.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 705 HIS Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 461 CYS Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 681 PHE Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 632 LEU Chi-restraints excluded: chain C residue 639 PHE Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 716 GLU Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 484 CYS Chi-restraints excluded: chain D residue 497 HIS Chi-restraints excluded: chain D residue 548 GLU Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain D residue 752 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 65 optimal weight: 0.2980 chunk 39 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 287 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 247 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 225 optimal weight: 0.3980 chunk 2 optimal weight: 10.0000 chunk 109 optimal weight: 0.3980 chunk 172 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 357 GLN B 437 GLN ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 794 HIS ** 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 = 0.3971 r_free = 0.3971 target = 0.084921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.062435 restraints weight = 146451.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.062588 restraints weight = 91515.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.063089 restraints weight = 71972.744| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 24572 Z= 0.105 Angle : 0.579 9.382 33407 Z= 0.289 Chirality : 0.043 0.246 3827 Planarity : 0.004 0.073 4245 Dihedral : 4.895 53.589 3436 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.40 % Favored : 92.38 % Rotamer: Outliers : 4.07 % Allowed : 26.05 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.15), residues: 3082 helix: -0.19 (0.16), residues: 1049 sheet: -0.87 (0.32), residues: 281 loop : -1.67 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 607 HIS 0.007 0.001 HIS A 134 PHE 0.023 0.001 PHE C 321 TYR 0.011 0.001 TYR B 479 ARG 0.004 0.000 ARG A 124 Details of bonding type rmsd link_NAG-ASN : bond 0.00612 ( 4) link_NAG-ASN : angle 3.27737 ( 12) link_BETA1-4 : bond 0.00124 ( 1) link_BETA1-4 : angle 1.23737 ( 3) hydrogen bonds : bond 0.04057 ( 680) hydrogen bonds : angle 5.47633 ( 1932) SS BOND : bond 0.00341 ( 15) SS BOND : angle 1.11868 ( 30) covalent geometry : bond 0.00223 (24552) covalent geometry : angle 0.57536 (33362) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 160 time to evaluate : 2.653 Fit side-chains REVERT: A 311 ASN cc_start: 0.3533 (OUTLIER) cc_final: 0.2777 (p0) REVERT: A 354 MET cc_start: 0.7637 (mmm) cc_final: 0.6939 (tpp) REVERT: A 654 PHE cc_start: 0.8773 (t80) cc_final: 0.8569 (t80) REVERT: B 171 ILE cc_start: 0.8496 (mp) cc_final: 0.7969 (tp) REVERT: B 287 TYR cc_start: 0.7185 (OUTLIER) cc_final: 0.6080 (t80) REVERT: B 653 PHE cc_start: 0.6761 (OUTLIER) cc_final: 0.6535 (t80) REVERT: C 42 PHE cc_start: 0.7601 (t80) cc_final: 0.7360 (t80) REVERT: C 190 LYS cc_start: 0.7329 (tttm) cc_final: 0.6493 (mtmt) REVERT: C 354 MET cc_start: 0.7258 (tpp) cc_final: 0.6916 (tpp) REVERT: C 415 LEU cc_start: 0.6247 (OUTLIER) cc_final: 0.5822 (pp) REVERT: C 470 MET cc_start: 0.8707 (mmm) cc_final: 0.8316 (mtt) REVERT: C 647 TYR cc_start: 0.8059 (t80) cc_final: 0.7858 (t80) REVERT: D 274 MET cc_start: 0.6201 (tmm) cc_final: 0.5904 (ppp) REVERT: D 462 CYS cc_start: 0.5729 (OUTLIER) cc_final: 0.5186 (p) REVERT: D 867 HIS cc_start: 0.4986 (OUTLIER) cc_final: 0.4713 (p-80) outliers start: 103 outliers final: 68 residues processed: 250 average time/residue: 0.2996 time to fit residues: 125.3327 Evaluate side-chains 226 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 152 time to evaluate : 2.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 681 TYR Chi-restraints excluded: chain A residue 705 HIS Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 437 GLN Chi-restraints excluded: chain B residue 460 PHE Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 535 SER Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 639 PHE Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 462 CYS Chi-restraints excluded: chain D residue 497 HIS Chi-restraints excluded: chain D residue 524 MET Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain D residue 828 CYS Chi-restraints excluded: chain D residue 851 MET Chi-restraints excluded: chain D residue 867 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 133 optimal weight: 0.6980 chunk 146 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 243 optimal weight: 0.1980 chunk 24 optimal weight: 6.9990 chunk 290 optimal weight: 2.9990 chunk 111 optimal weight: 0.2980 chunk 307 optimal weight: 10.0000 chunk 258 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 70 ASN ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 794 HIS ** 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 = 0.3960 r_free = 0.3960 target = 0.084498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.061845 restraints weight = 145777.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.061665 restraints weight = 92665.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.062472 restraints weight = 77639.443| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24572 Z= 0.124 Angle : 0.590 9.177 33407 Z= 0.292 Chirality : 0.043 0.230 3827 Planarity : 0.004 0.072 4245 Dihedral : 4.847 54.433 3436 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.59 % Favored : 92.18 % Rotamer: Outliers : 4.31 % Allowed : 25.89 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.15), residues: 3082 helix: -0.08 (0.16), residues: 1044 sheet: -0.88 (0.32), residues: 283 loop : -1.67 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 563 HIS 0.008 0.001 HIS A 134 PHE 0.025 0.001 PHE A 639 TYR 0.011 0.001 TYR B 479 ARG 0.007 0.000 ARG D 821 Details of bonding type rmsd link_NAG-ASN : bond 0.00454 ( 4) link_NAG-ASN : angle 3.34628 ( 12) link_BETA1-4 : bond 0.00192 ( 1) link_BETA1-4 : angle 1.29856 ( 3) hydrogen bonds : bond 0.04050 ( 680) hydrogen bonds : angle 5.37850 ( 1932) SS BOND : bond 0.00432 ( 15) SS BOND : angle 1.41441 ( 30) covalent geometry : bond 0.00282 (24552) covalent geometry : angle 0.58557 (33362) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 156 time to evaluate : 2.534 Fit side-chains REVERT: A 354 MET cc_start: 0.7667 (mmm) cc_final: 0.6952 (tpp) REVERT: B 287 TYR cc_start: 0.7125 (OUTLIER) cc_final: 0.6009 (t80) REVERT: B 653 PHE cc_start: 0.6698 (OUTLIER) cc_final: 0.6492 (t80) REVERT: B 669 LYS cc_start: 0.8766 (pptt) cc_final: 0.8472 (tptp) REVERT: C 42 PHE cc_start: 0.7598 (t80) cc_final: 0.7389 (t80) REVERT: C 190 LYS cc_start: 0.7326 (tttm) cc_final: 0.6478 (mtmt) REVERT: C 209 MET cc_start: 0.8018 (mmp) cc_final: 0.7245 (ptp) REVERT: C 354 MET cc_start: 0.7363 (tpp) cc_final: 0.6972 (tpp) REVERT: C 415 LEU cc_start: 0.6176 (OUTLIER) cc_final: 0.5746 (pp) REVERT: D 183 ASP cc_start: 0.8793 (t0) cc_final: 0.8553 (m-30) REVERT: D 274 MET cc_start: 0.6262 (tmm) cc_final: 0.5977 (ppp) REVERT: D 867 HIS cc_start: 0.4979 (OUTLIER) cc_final: 0.4679 (p-80) outliers start: 109 outliers final: 76 residues processed: 253 average time/residue: 0.2841 time to fit residues: 121.6479 Evaluate side-chains 232 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 152 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 611 TRP Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 705 HIS Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 535 SER Chi-restraints excluded: chain B residue 607 TRP Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 639 PHE Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 716 GLU Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 497 HIS Chi-restraints excluded: chain D residue 524 MET Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain D residue 752 LYS Chi-restraints excluded: chain D residue 828 CYS Chi-restraints excluded: chain D residue 851 MET Chi-restraints excluded: chain D residue 867 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 39 optimal weight: 7.9990 chunk 277 optimal weight: 9.9990 chunk 260 optimal weight: 40.0000 chunk 268 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 150 optimal weight: 0.4980 chunk 264 optimal weight: 40.0000 chunk 202 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 152 optimal weight: 0.3980 chunk 200 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 311 HIS B 437 GLN ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 812 ASN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 794 HIS ** 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 = 0.3954 r_free = 0.3954 target = 0.084312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.061465 restraints weight = 147402.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.062058 restraints weight = 91074.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.061983 restraints weight = 74695.044| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24572 Z= 0.136 Angle : 0.599 9.385 33407 Z= 0.298 Chirality : 0.043 0.240 3827 Planarity : 0.004 0.072 4245 Dihedral : 4.851 54.929 3436 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.59 % Favored : 92.18 % Rotamer: Outliers : 4.15 % Allowed : 26.25 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.15), residues: 3082 helix: -0.03 (0.16), residues: 1034 sheet: -0.90 (0.32), residues: 284 loop : -1.66 (0.15), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 607 HIS 0.010 0.001 HIS B 311 PHE 0.022 0.001 PHE C 321 TYR 0.011 0.001 TYR B 479 ARG 0.005 0.000 ARG D 821 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 4) link_NAG-ASN : angle 3.41301 ( 12) link_BETA1-4 : bond 0.00236 ( 1) link_BETA1-4 : angle 1.35242 ( 3) hydrogen bonds : bond 0.03966 ( 680) hydrogen bonds : angle 5.34767 ( 1932) SS BOND : bond 0.00472 ( 15) SS BOND : angle 1.76217 ( 30) covalent geometry : bond 0.00313 (24552) covalent geometry : angle 0.59375 (33362) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 158 time to evaluate : 2.701 Fit side-chains REVERT: A 354 MET cc_start: 0.7477 (mmm) cc_final: 0.6766 (tpp) REVERT: B 287 TYR cc_start: 0.7113 (OUTLIER) cc_final: 0.6079 (t80) REVERT: B 653 PHE cc_start: 0.6661 (OUTLIER) cc_final: 0.6424 (t80) REVERT: B 669 LYS cc_start: 0.8996 (pptt) cc_final: 0.8631 (tptp) REVERT: B 681 PHE cc_start: 0.6781 (OUTLIER) cc_final: 0.6054 (t80) REVERT: C 42 PHE cc_start: 0.7647 (t80) cc_final: 0.7437 (t80) REVERT: C 190 LYS cc_start: 0.7310 (tttm) cc_final: 0.6504 (mtmt) REVERT: C 354 MET cc_start: 0.7308 (tpp) cc_final: 0.7106 (tpp) REVERT: C 415 LEU cc_start: 0.6089 (OUTLIER) cc_final: 0.5634 (pp) REVERT: D 183 ASP cc_start: 0.8808 (t0) cc_final: 0.8578 (m-30) REVERT: D 274 MET cc_start: 0.6301 (tmm) cc_final: 0.6004 (ppp) outliers start: 105 outliers final: 89 residues processed: 253 average time/residue: 0.2958 time to fit residues: 126.1895 Evaluate side-chains 247 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 154 time to evaluate : 2.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 151 TRP Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 611 TRP Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 705 HIS Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 437 GLN Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 535 SER Chi-restraints excluded: chain B residue 607 TRP Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 653 PHE Chi-restraints excluded: chain B residue 681 PHE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 716 GLU Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 497 HIS Chi-restraints excluded: chain D residue 524 MET Chi-restraints excluded: chain D residue 548 GLU Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain D residue 717 SER Chi-restraints excluded: chain D residue 752 LYS Chi-restraints excluded: chain D residue 828 CYS Chi-restraints excluded: chain D residue 851 MET Chi-restraints excluded: chain D residue 867 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 189 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 237 optimal weight: 20.0000 chunk 102 optimal weight: 0.6980 chunk 298 optimal weight: 6.9990 chunk 186 optimal weight: 0.5980 chunk 290 optimal weight: 3.9990 chunk 95 optimal weight: 20.0000 chunk 173 optimal weight: 10.0000 chunk 256 optimal weight: 8.9990 chunk 217 optimal weight: 20.0000 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN B 437 GLN ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.083843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.060972 restraints weight = 146549.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.061422 restraints weight = 95488.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.061429 restraints weight = 72392.420| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24572 Z= 0.175 Angle : 0.621 9.788 33407 Z= 0.311 Chirality : 0.044 0.251 3827 Planarity : 0.004 0.071 4245 Dihedral : 4.997 55.855 3436 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.27 % Favored : 91.53 % Rotamer: Outliers : 4.43 % Allowed : 26.25 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.15), residues: 3082 helix: 0.01 (0.16), residues: 1023 sheet: -0.96 (0.31), residues: 284 loop : -1.70 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 611 HIS 0.008 0.001 HIS A 134 PHE 0.019 0.001 PHE A 533 TYR 0.011 0.001 TYR B 479 ARG 0.006 0.000 ARG B 439 Details of bonding type rmsd link_NAG-ASN : bond 0.00419 ( 4) link_NAG-ASN : angle 3.58687 ( 12) link_BETA1-4 : bond 0.00197 ( 1) link_BETA1-4 : angle 1.40943 ( 3) hydrogen bonds : bond 0.04155 ( 680) hydrogen bonds : angle 5.40032 ( 1932) SS BOND : bond 0.00354 ( 15) SS BOND : angle 1.48856 ( 30) covalent geometry : bond 0.00406 (24552) covalent geometry : angle 0.61544 (33362) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 158 time to evaluate : 2.658 Fit side-chains REVERT: B 287 TYR cc_start: 0.7177 (OUTLIER) cc_final: 0.6067 (t80) REVERT: B 669 LYS cc_start: 0.8904 (pptt) cc_final: 0.8612 (tptp) REVERT: B 681 PHE cc_start: 0.7097 (OUTLIER) cc_final: 0.6380 (t80) REVERT: C 190 LYS cc_start: 0.7329 (tttm) cc_final: 0.6489 (mtmt) REVERT: C 209 MET cc_start: 0.8010 (mmp) cc_final: 0.7310 (ptp) REVERT: C 415 LEU cc_start: 0.6134 (OUTLIER) cc_final: 0.5636 (pp) REVERT: D 183 ASP cc_start: 0.8791 (t0) cc_final: 0.8561 (m-30) REVERT: D 274 MET cc_start: 0.6510 (tmm) cc_final: 0.5971 (ppp) outliers start: 112 outliers final: 93 residues processed: 257 average time/residue: 0.2902 time to fit residues: 126.5633 Evaluate side-chains 251 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 155 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 611 TRP Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 705 HIS Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 760 ILE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 535 SER Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 681 PHE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 716 GLU Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 497 HIS Chi-restraints excluded: chain D residue 524 MET Chi-restraints excluded: chain D residue 548 GLU Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain D residue 717 SER Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 752 LYS Chi-restraints excluded: chain D residue 828 CYS Chi-restraints excluded: chain D residue 851 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 187 optimal weight: 9.9990 chunk 136 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 106 optimal weight: 0.0070 chunk 88 optimal weight: 20.0000 chunk 150 optimal weight: 2.9990 chunk 246 optimal weight: 5.9990 chunk 241 optimal weight: 0.5980 chunk 124 optimal weight: 0.3980 chunk 96 optimal weight: 30.0000 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 650 ASN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.084408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.061564 restraints weight = 146936.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.062102 restraints weight = 90845.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.062427 restraints weight = 64288.640| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24572 Z= 0.122 Angle : 0.611 10.185 33407 Z= 0.301 Chirality : 0.043 0.261 3827 Planarity : 0.004 0.071 4245 Dihedral : 4.860 55.051 3436 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.62 % Favored : 92.18 % Rotamer: Outliers : 3.99 % Allowed : 26.92 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.15), residues: 3082 helix: 0.07 (0.16), residues: 1023 sheet: -0.91 (0.31), residues: 289 loop : -1.66 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 610 HIS 0.007 0.001 HIS A 134 PHE 0.024 0.001 PHE C 321 TYR 0.011 0.001 TYR B 479 ARG 0.004 0.000 ARG D 821 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 4) link_NAG-ASN : angle 3.47708 ( 12) link_BETA1-4 : bond 0.00244 ( 1) link_BETA1-4 : angle 1.43245 ( 3) hydrogen bonds : bond 0.03807 ( 680) hydrogen bonds : angle 5.26633 ( 1932) SS BOND : bond 0.00349 ( 15) SS BOND : angle 1.33118 ( 30) covalent geometry : bond 0.00279 (24552) covalent geometry : angle 0.60686 (33362) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 157 time to evaluate : 2.784 Fit side-chains REVERT: A 354 MET cc_start: 0.7611 (mmm) cc_final: 0.6905 (tpp) REVERT: B 187 ARG cc_start: 0.9350 (mpp80) cc_final: 0.9006 (mpp80) REVERT: B 287 TYR cc_start: 0.7123 (OUTLIER) cc_final: 0.6031 (t80) REVERT: B 537 MET cc_start: 0.7418 (tmm) cc_final: 0.6361 (ttp) REVERT: B 669 LYS cc_start: 0.8846 (pptt) cc_final: 0.8523 (tptp) REVERT: B 681 PHE cc_start: 0.7018 (OUTLIER) cc_final: 0.6219 (t80) REVERT: C 190 LYS cc_start: 0.7295 (tttm) cc_final: 0.6471 (mtmt) REVERT: C 209 MET cc_start: 0.8024 (mmp) cc_final: 0.7344 (ptp) REVERT: C 415 LEU cc_start: 0.6169 (OUTLIER) cc_final: 0.5676 (pp) REVERT: D 183 ASP cc_start: 0.8835 (t0) cc_final: 0.8617 (m-30) REVERT: D 274 MET cc_start: 0.6546 (tmm) cc_final: 0.6262 (ppp) outliers start: 101 outliers final: 87 residues processed: 250 average time/residue: 0.2957 time to fit residues: 125.5950 Evaluate side-chains 246 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 156 time to evaluate : 2.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 611 TRP Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 705 HIS Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 535 SER Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 681 PHE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 639 PHE Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 716 GLU Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 497 HIS Chi-restraints excluded: chain D residue 524 MET Chi-restraints excluded: chain D residue 548 GLU Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 640 VAL Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain D residue 717 SER Chi-restraints excluded: chain D residue 752 LYS Chi-restraints excluded: chain D residue 828 CYS Chi-restraints excluded: chain D residue 851 MET Chi-restraints excluded: chain D residue 867 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 21 optimal weight: 10.0000 chunk 261 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 296 optimal weight: 7.9990 chunk 169 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 157 optimal weight: 0.0770 chunk 251 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 overall best weight: 1.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.084359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.062176 restraints weight = 146711.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.062338 restraints weight = 94165.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.062169 restraints weight = 72552.532| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24572 Z= 0.130 Angle : 0.620 10.747 33407 Z= 0.305 Chirality : 0.043 0.262 3827 Planarity : 0.004 0.071 4245 Dihedral : 4.847 55.140 3436 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.88 % Favored : 91.89 % Rotamer: Outliers : 3.99 % Allowed : 27.08 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.15), residues: 3082 helix: 0.10 (0.16), residues: 1023 sheet: -0.93 (0.31), residues: 284 loop : -1.65 (0.15), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP D 637 HIS 0.007 0.001 HIS A 134 PHE 0.017 0.001 PHE C 321 TYR 0.011 0.001 TYR B 479 ARG 0.003 0.000 ARG D 821 Details of bonding type rmsd link_NAG-ASN : bond 0.00468 ( 4) link_NAG-ASN : angle 3.48476 ( 12) link_BETA1-4 : bond 0.00209 ( 1) link_BETA1-4 : angle 1.41994 ( 3) hydrogen bonds : bond 0.03750 ( 680) hydrogen bonds : angle 5.23620 ( 1932) SS BOND : bond 0.00328 ( 15) SS BOND : angle 1.30935 ( 30) covalent geometry : bond 0.00300 (24552) covalent geometry : angle 0.61548 (33362) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6164 Ramachandran restraints generated. 3082 Oldfield, 0 Emsley, 3082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 158 time to evaluate : 2.671 Fit side-chains REVERT: A 354 MET cc_start: 0.7680 (mmm) cc_final: 0.6980 (tpp) REVERT: B 187 ARG cc_start: 0.9363 (mpp80) cc_final: 0.9017 (mpp80) REVERT: B 287 TYR cc_start: 0.7120 (OUTLIER) cc_final: 0.6032 (t80) REVERT: B 537 MET cc_start: 0.7344 (tmm) cc_final: 0.6371 (ttp) REVERT: B 669 LYS cc_start: 0.8889 (pptt) cc_final: 0.8554 (tptp) REVERT: B 681 PHE cc_start: 0.7063 (OUTLIER) cc_final: 0.6299 (t80) REVERT: C 190 LYS cc_start: 0.7265 (tttm) cc_final: 0.6487 (mtmt) REVERT: C 209 MET cc_start: 0.7983 (mmp) cc_final: 0.7299 (ptp) REVERT: C 271 LEU cc_start: 0.6384 (mm) cc_final: 0.6051 (mm) REVERT: C 354 MET cc_start: 0.6785 (tpp) cc_final: 0.6005 (tpp) REVERT: C 415 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.5696 (pp) REVERT: C 702 MET cc_start: 0.7998 (pmm) cc_final: 0.7738 (pmm) REVERT: D 183 ASP cc_start: 0.8833 (t0) cc_final: 0.8619 (m-30) REVERT: D 274 MET cc_start: 0.6558 (tmm) cc_final: 0.6249 (ppp) outliers start: 101 outliers final: 90 residues processed: 250 average time/residue: 0.2947 time to fit residues: 124.5601 Evaluate side-chains 250 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 157 time to evaluate : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 611 TRP Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 705 HIS Chi-restraints excluded: chain A residue 744 CYS Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 407 SER Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 498 ILE Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 535 SER Chi-restraints excluded: chain B residue 538 VAL Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 681 PHE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain B residue 784 PHE Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 507 SER Chi-restraints excluded: chain C residue 527 ILE Chi-restraints excluded: chain C residue 561 THR Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 716 GLU Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 444 ILE Chi-restraints excluded: chain D residue 497 HIS Chi-restraints excluded: chain D residue 524 MET Chi-restraints excluded: chain D residue 548 GLU Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain D residue 717 SER Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 752 LYS Chi-restraints excluded: chain D residue 828 CYS Chi-restraints excluded: chain D residue 851 MET Chi-restraints excluded: chain D residue 867 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 275 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 199 optimal weight: 0.0050 chunk 208 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 272 optimal weight: 3.9990 chunk 17 optimal weight: 0.0980 chunk 257 optimal weight: 20.0000 chunk 221 optimal weight: 9.9990 chunk 195 optimal weight: 4.9990 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 794 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.084765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.062038 restraints weight = 146607.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.062310 restraints weight = 91181.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.062663 restraints weight = 78177.440| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 24572 Z= 0.110 Angle : 0.609 11.083 33407 Z= 0.297 Chirality : 0.043 0.269 3827 Planarity : 0.003 0.072 4245 Dihedral : 4.679 54.531 3436 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.56 % Favored : 92.21 % Rotamer: Outliers : 3.75 % Allowed : 27.23 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.15), residues: 3082 helix: 0.11 (0.16), residues: 1036 sheet: -0.87 (0.31), residues: 289 loop : -1.63 (0.15), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 637 HIS 0.007 0.001 HIS A 134 PHE 0.024 0.001 PHE C 321 TYR 0.011 0.001 TYR B 479 ARG 0.003 0.000 ARG D 821 Details of bonding type rmsd link_NAG-ASN : bond 0.00528 ( 4) link_NAG-ASN : angle 3.39825 ( 12) link_BETA1-4 : bond 0.00334 ( 1) link_BETA1-4 : angle 1.40923 ( 3) hydrogen bonds : bond 0.03450 ( 680) hydrogen bonds : angle 5.10552 ( 1932) SS BOND : bond 0.00291 ( 15) SS BOND : angle 1.20149 ( 30) covalent geometry : bond 0.00250 (24552) covalent geometry : angle 0.60443 (33362) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7567.78 seconds wall clock time: 133 minutes 49.89 seconds (8029.89 seconds total)