Starting phenix.real_space_refine on Fri Sep 19 07:43:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d38_46527/09_2025/9d38_46527.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d38_46527/09_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_46527/09_2025/9d38_46527.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d38_46527/09_2025/9d38_46527.map" model { file = "/net/cci-nas-00/data/ceres_data/9d38_46527/09_2025/9d38_46527.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d38_46527/09_2025/9d38_46527.cif" } resolution = 3.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ARG:plan': 6, 'ASN:plan1': 2, 'GLU:plan': 5, 'TYR:plan': 2, 'PHE:plan': 2, 'ASP:plan': 1} 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: {'ASP:plan': 10, 'GLU:plan': 14, 'HIS:plan': 4, 'PHE:plan': 5, 'ASN:plan1': 3, 'ARG:plan': 4, 'GLN:plan1': 7, 'TYR: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: {'ARG:plan': 7, 'GLU:plan': 4} 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: {'ARG:plan': 7, 'GLU:plan': 5, 'ASP:plan': 1, 'TYR:plan': 4, 'PHE:plan': 3, 'HIS:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'TRP:plan': 1} 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: 5.44, per 1000 atoms: 0.23 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: 1.91 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.97 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: 4.68 Time building geometry restraints manager: 2.56 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 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 through 9 \ 02)) } 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: 4.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.130 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.680 ------------------------------------------------------------------------------- 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 : 11.24 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (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 ARG 0.003 0.000 ARG C 397 TYR 0.027 0.001 TYR D 419 PHE 0.011 0.001 PHE A 42 TRP 0.046 0.001 TRP D 637 HIS 0.005 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00225 (24552) covalent geometry : angle 0.56941 (33362) SS BOND : bond 0.00281 ( 15) SS BOND : angle 0.80918 ( 30) hydrogen bonds : bond 0.33308 ( 680) hydrogen bonds : angle 9.39945 ( 1932) link_BETA1-4 : bond 0.00501 ( 1) link_BETA1-4 : angle 0.93000 ( 3) link_NAG-ASN : bond 0.00947 ( 4) link_NAG-ASN : angle 3.74256 ( 12) *********************** 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 : 0.951 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: 0.1474 time to fit residues: 38.3496 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 : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 A 521 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 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.083558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.061155 restraints weight = 146474.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.060633 restraints weight = 94585.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.061195 restraints weight = 82697.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.061267 restraints weight = 61534.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.061310 restraints weight = 60192.465| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 24572 Z= 0.230 Angle : 0.657 7.276 33407 Z= 0.345 Chirality : 0.045 0.190 3827 Planarity : 0.004 0.070 4245 Dihedral : 6.647 77.236 3436 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.89 % Favored : 90.88 % Rotamer: Outliers : 4.03 % Allowed : 26.21 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.15), residues: 3082 helix: -0.55 (0.16), residues: 1047 sheet: -0.97 (0.32), residues: 276 loop : -1.71 (0.15), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 306 TYR 0.014 0.001 TYR D 419 PHE 0.019 0.002 PHE A 458 TRP 0.019 0.001 TRP D 637 HIS 0.007 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00520 (24552) covalent geometry : angle 0.65347 (33362) SS BOND : bond 0.00420 ( 15) SS BOND : angle 0.88164 ( 30) hydrogen bonds : bond 0.07282 ( 680) hydrogen bonds : angle 6.85048 ( 1932) link_BETA1-4 : bond 0.00484 ( 1) link_BETA1-4 : angle 1.24610 ( 3) link_NAG-ASN : bond 0.00472 ( 4) link_NAG-ASN : angle 3.51997 ( 12) *********************** 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 262 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 160 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 461 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7433 (t0) REVERT: A 731 TRP cc_start: 0.8373 (OUTLIER) cc_final: 0.7952 (t-100) REVERT: B 175 TYR cc_start: 0.6654 (m-10) cc_final: 0.6252 (m-80) REVERT: B 204 LEU cc_start: 0.6503 (OUTLIER) cc_final: 0.6088 (mm) REVERT: B 681 PHE cc_start: 0.7004 (OUTLIER) cc_final: 0.6345 (t80) REVERT: B 789 MET cc_start: 0.8662 (mpp) cc_final: 0.8103 (mpp) REVERT: C 190 LYS cc_start: 0.7362 (tttm) cc_final: 0.6522 (mtmt) REVERT: C 459 CYS cc_start: 0.7432 (OUTLIER) cc_final: 0.7211 (t) REVERT: C 470 MET cc_start: 0.8747 (mmm) cc_final: 0.8369 (mtt) outliers start: 102 outliers final: 40 residues processed: 248 average time/residue: 0.1392 time to fit residues: 58.4739 Evaluate side-chains 197 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 152 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 414 THR Chi-restraints excluded: chain A residue 461 ASP 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 731 TRP 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 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 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 681 PHE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 727 ASP 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 437 THR Chi-restraints excluded: chain C residue 459 CYS 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 776 ILE Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain D residue 497 HIS Chi-restraints excluded: chain D residue 635 LEU Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 752 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 163 optimal weight: 8.9990 chunk 301 optimal weight: 0.9990 chunk 151 optimal weight: 20.0000 chunk 261 optimal weight: 6.9990 chunk 123 optimal weight: 0.6980 chunk 227 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 7 optimal weight: 0.0050 chunk 253 optimal weight: 20.0000 chunk 5 optimal weight: 0.9980 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 521 ASN B 357 GLN C 358 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.084796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.062358 restraints weight = 146173.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.062227 restraints weight = 94876.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.062584 restraints weight = 80526.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.062834 restraints weight = 63308.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.062863 restraints weight = 55436.217| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 24572 Z= 0.114 Angle : 0.578 7.996 33407 Z= 0.294 Chirality : 0.043 0.198 3827 Planarity : 0.004 0.072 4245 Dihedral : 5.626 54.385 3436 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.07 % Favored : 92.70 % Rotamer: Outliers : 3.60 % Allowed : 26.28 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.15), residues: 3082 helix: -0.42 (0.16), residues: 1065 sheet: -0.92 (0.32), residues: 270 loop : -1.67 (0.15), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 306 TYR 0.012 0.001 TYR B 479 PHE 0.022 0.001 PHE C 321 TRP 0.010 0.001 TRP D 637 HIS 0.007 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00241 (24552) covalent geometry : angle 0.57409 (33362) SS BOND : bond 0.00359 ( 15) SS BOND : angle 0.83674 ( 30) hydrogen bonds : bond 0.05368 ( 680) hydrogen bonds : angle 6.07255 ( 1932) link_BETA1-4 : bond 0.00273 ( 1) link_BETA1-4 : angle 1.21113 ( 3) link_NAG-ASN : bond 0.00554 ( 4) link_NAG-ASN : angle 3.20374 ( 12) *********************** 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 256 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 165 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 MET cc_start: 0.7573 (mmm) cc_final: 0.6896 (tpp) REVERT: B 175 TYR cc_start: 0.6591 (m-10) cc_final: 0.6190 (m-80) REVERT: B 204 LEU cc_start: 0.6461 (OUTLIER) cc_final: 0.6113 (mm) REVERT: B 287 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.6232 (t80) REVERT: B 498 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7612 (mm) REVERT: B 789 MET cc_start: 0.8675 (mpp) cc_final: 0.8295 (mpp) REVERT: C 42 PHE cc_start: 0.7659 (t80) cc_final: 0.7438 (t80) REVERT: C 190 LYS cc_start: 0.7372 (tttm) cc_final: 0.6530 (mtmt) REVERT: C 209 MET cc_start: 0.8016 (mmp) cc_final: 0.7573 (ptp) REVERT: C 354 MET cc_start: 0.6814 (tpp) cc_final: 0.6594 (tpp) REVERT: C 415 LEU cc_start: 0.6232 (OUTLIER) cc_final: 0.5868 (pp) REVERT: C 470 MET cc_start: 0.8640 (mmm) cc_final: 0.8217 (mtt) REVERT: C 634 MET cc_start: 0.8685 (tpt) cc_final: 0.8416 (tpt) outliers start: 91 outliers final: 46 residues processed: 247 average time/residue: 0.1431 time to fit residues: 59.6212 Evaluate side-chains 206 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 156 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 TRP Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 449 HIS 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 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 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 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 825 LEU 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 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 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 680 ILE Chi-restraints excluded: chain C residue 703 TYR 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 207 LEU Chi-restraints excluded: chain D residue 388 VAL 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 645 VAL Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain D residue 791 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 185 optimal weight: 30.0000 chunk 268 optimal weight: 30.0000 chunk 225 optimal weight: 1.9990 chunk 97 optimal weight: 40.0000 chunk 222 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 16 optimal weight: 0.0770 chunk 172 optimal weight: 20.0000 overall best weight: 3.2146 ------------------------------------------------------------------------------- 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** C 61 ASN 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 = 0.3937 r_free = 0.3937 target = 0.083632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.060938 restraints weight = 146318.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.060952 restraints weight = 100825.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.061211 restraints weight = 78540.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.061434 restraints weight = 65876.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.061456 restraints weight = 58105.192| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 24572 Z= 0.198 Angle : 0.633 8.548 33407 Z= 0.321 Chirality : 0.044 0.208 3827 Planarity : 0.004 0.071 4245 Dihedral : 5.412 57.388 3436 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.40 % Favored : 91.37 % Rotamer: Outliers : 4.90 % Allowed : 25.81 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.15), residues: 3082 helix: -0.34 (0.16), residues: 1058 sheet: -0.93 (0.32), residues: 271 loop : -1.74 (0.15), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 124 TYR 0.013 0.001 TYR B 479 PHE 0.020 0.002 PHE A 533 TRP 0.010 0.001 TRP C 563 HIS 0.008 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00455 (24552) covalent geometry : angle 0.62745 (33362) SS BOND : bond 0.00680 ( 15) SS BOND : angle 1.67053 ( 30) hydrogen bonds : bond 0.05055 ( 680) hydrogen bonds : angle 5.95500 ( 1932) link_BETA1-4 : bond 0.00134 ( 1) link_BETA1-4 : angle 1.34657 ( 3) link_NAG-ASN : bond 0.00407 ( 4) link_NAG-ASN : angle 3.56443 ( 12) *********************** 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 286 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 162 time to evaluate : 1.092 Fit side-chains revert: symmetry clash REVERT: A 461 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7421 (t0) REVERT: A 634 MET cc_start: 0.8397 (tpt) cc_final: 0.8058 (tpt) REVERT: A 818 MET cc_start: 0.7871 (ptp) cc_final: 0.7529 (ptt) REVERT: B 175 TYR cc_start: 0.6552 (m-10) cc_final: 0.6187 (m-80) REVERT: B 204 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.6116 (mm) REVERT: B 281 SER cc_start: 0.7388 (OUTLIER) cc_final: 0.7172 (p) REVERT: B 287 TYR cc_start: 0.7241 (OUTLIER) cc_final: 0.6086 (t80) REVERT: B 653 PHE cc_start: 0.6834 (OUTLIER) cc_final: 0.6575 (t80) REVERT: B 681 PHE cc_start: 0.7009 (OUTLIER) cc_final: 0.6257 (t80) REVERT: B 789 MET cc_start: 0.8631 (mpp) cc_final: 0.8248 (mpp) REVERT: C 42 PHE cc_start: 0.7654 (t80) cc_final: 0.7399 (t80) REVERT: C 354 MET cc_start: 0.7247 (tpp) cc_final: 0.6953 (tpp) REVERT: C 415 LEU cc_start: 0.6219 (OUTLIER) cc_final: 0.5712 (pp) REVERT: C 470 MET cc_start: 0.8767 (mmm) cc_final: 0.8503 (mtt) outliers start: 124 outliers final: 83 residues processed: 271 average time/residue: 0.1294 time to fit residues: 60.2329 Evaluate side-chains 245 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 155 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 288 VAL 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 461 ASP 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 667 ILE 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 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 428 THR Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 460 PHE 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 503 MET Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 538 VAL 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 698 ASN 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 195 LEU 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 527 ILE 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 680 ILE Chi-restraints excluded: chain C residue 703 TYR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 762 MET 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 212 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 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 562 SER 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 198 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 288 optimal weight: 5.9990 chunk 197 optimal weight: 8.9990 chunk 88 optimal weight: 0.0670 chunk 128 optimal weight: 0.7980 chunk 236 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 274 optimal weight: 5.9990 chunk 217 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 overall best weight: 2.1724 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.084075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.061441 restraints weight = 145822.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.061610 restraints weight = 95401.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.061798 restraints weight = 72807.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.061969 restraints weight = 65844.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.062015 restraints weight = 56172.667| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.1753 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= 0.145 Angle : 0.600 11.320 33407 Z= 0.302 Chirality : 0.043 0.217 3827 Planarity : 0.004 0.072 4245 Dihedral : 5.166 54.839 3436 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.56 % Favored : 92.21 % Rotamer: Outliers : 4.94 % Allowed : 25.89 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.15), residues: 3082 helix: -0.25 (0.16), residues: 1054 sheet: -1.01 (0.32), residues: 267 loop : -1.70 (0.15), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 124 TYR 0.012 0.001 TYR B 479 PHE 0.022 0.001 PHE C 321 TRP 0.009 0.001 TRP A 768 HIS 0.008 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00331 (24552) covalent geometry : angle 0.59562 (33362) SS BOND : bond 0.00449 ( 15) SS BOND : angle 1.40587 ( 30) hydrogen bonds : bond 0.04452 ( 680) hydrogen bonds : angle 5.66532 ( 1932) link_BETA1-4 : bond 0.00233 ( 1) link_BETA1-4 : angle 1.34613 ( 3) link_NAG-ASN : bond 0.00469 ( 4) link_NAG-ASN : angle 3.47038 ( 12) *********************** 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 280 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 155 time to evaluate : 1.026 Fit side-chains REVERT: A 311 ASN cc_start: 0.2873 (OUTLIER) cc_final: 0.2190 (p0) REVERT: A 354 MET cc_start: 0.7445 (mmm) cc_final: 0.6758 (tpp) REVERT: A 818 MET cc_start: 0.7762 (ptp) cc_final: 0.7481 (ptt) REVERT: B 171 ILE cc_start: 0.8568 (mp) cc_final: 0.8089 (tp) REVERT: B 287 TYR cc_start: 0.7194 (OUTLIER) cc_final: 0.6097 (t80) REVERT: B 653 PHE cc_start: 0.6737 (OUTLIER) cc_final: 0.6467 (t80) REVERT: B 681 PHE cc_start: 0.6909 (OUTLIER) cc_final: 0.6186 (t80) REVERT: B 789 MET cc_start: 0.8615 (mpp) cc_final: 0.8217 (mpp) REVERT: C 209 MET cc_start: 0.8202 (mmp) cc_final: 0.7526 (ptp) REVERT: C 354 MET cc_start: 0.7325 (tpp) cc_final: 0.6932 (tpp) REVERT: C 415 LEU cc_start: 0.6154 (OUTLIER) cc_final: 0.5667 (pp) REVERT: C 470 MET cc_start: 0.8768 (mmm) cc_final: 0.8557 (mtt) REVERT: C 634 MET cc_start: 0.8735 (tpt) cc_final: 0.8392 (tpt) REVERT: D 183 ASP cc_start: 0.8882 (t0) cc_final: 0.8352 (m-30) REVERT: D 867 HIS cc_start: 0.4877 (OUTLIER) cc_final: 0.4631 (p-80) outliers start: 125 outliers final: 86 residues processed: 268 average time/residue: 0.1350 time to fit residues: 61.8857 Evaluate side-chains 246 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 154 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 288 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 449 HIS 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 667 ILE 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 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 123 ILE Chi-restraints excluded: chain B residue 150 ILE 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 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 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 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 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 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 632 LEU Chi-restraints excluded: chain C residue 639 PHE Chi-restraints excluded: chain C residue 644 VAL 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 776 ILE Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 212 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 436 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 561 ILE Chi-restraints excluded: chain D residue 562 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 248 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 143 optimal weight: 6.9990 chunk 266 optimal weight: 40.0000 chunk 279 optimal weight: 2.9990 chunk 79 optimal weight: 0.3980 chunk 84 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 177 optimal weight: 10.0000 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.083356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.060857 restraints weight = 145696.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.060633 restraints weight = 96720.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.060804 restraints weight = 78288.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.061037 restraints weight = 67387.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.061098 restraints weight = 59247.895| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 24572 Z= 0.209 Angle : 0.646 8.756 33407 Z= 0.328 Chirality : 0.044 0.220 3827 Planarity : 0.004 0.071 4245 Dihedral : 5.342 56.371 3436 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.79 % Favored : 90.98 % Rotamer: Outliers : 5.81 % Allowed : 25.77 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.15), residues: 3082 helix: -0.27 (0.16), residues: 1050 sheet: -1.11 (0.32), residues: 267 loop : -1.78 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 124 TYR 0.013 0.001 TYR B 479 PHE 0.024 0.002 PHE A 533 TRP 0.012 0.001 TRP A 611 HIS 0.009 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00484 (24552) covalent geometry : angle 0.64028 (33362) SS BOND : bond 0.00691 ( 15) SS BOND : angle 1.64161 ( 30) hydrogen bonds : bond 0.04693 ( 680) hydrogen bonds : angle 5.72084 ( 1932) link_BETA1-4 : bond 0.00120 ( 1) link_BETA1-4 : angle 1.47642 ( 3) link_NAG-ASN : bond 0.00422 ( 4) link_NAG-ASN : angle 3.76725 ( 12) *********************** 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 305 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 158 time to evaluate : 0.647 Fit side-chains REVERT: A 311 ASN cc_start: 0.3440 (OUTLIER) cc_final: 0.2746 (p0) REVERT: B 281 SER cc_start: 0.7251 (OUTLIER) cc_final: 0.6981 (p) REVERT: B 287 TYR cc_start: 0.7244 (OUTLIER) cc_final: 0.6096 (t80) REVERT: B 653 PHE cc_start: 0.6655 (OUTLIER) cc_final: 0.6435 (t80) REVERT: B 669 LYS cc_start: 0.8895 (pptt) cc_final: 0.8635 (tptp) REVERT: B 681 PHE cc_start: 0.7115 (OUTLIER) cc_final: 0.6397 (t80) REVERT: B 789 MET cc_start: 0.8545 (mpp) cc_final: 0.8222 (mpp) REVERT: C 354 MET cc_start: 0.7586 (tpp) cc_final: 0.7111 (tpp) REVERT: C 415 LEU cc_start: 0.6049 (OUTLIER) cc_final: 0.5488 (pp) REVERT: C 634 MET cc_start: 0.8634 (tpt) cc_final: 0.8279 (tpt) REVERT: D 867 HIS cc_start: 0.5066 (OUTLIER) cc_final: 0.4773 (p-80) outliers start: 147 outliers final: 103 residues processed: 291 average time/residue: 0.1184 time to fit residues: 59.0148 Evaluate side-chains 264 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 154 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 272 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 311 ASN 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 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 667 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 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 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 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 437 GLN Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 523 VAL Chi-restraints excluded: chain B residue 530 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 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 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 195 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 507 SER 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 619 ILE 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 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 772 VAL 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 212 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 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 524 MET 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 600 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 730 HIS Chi-restraints excluded: chain D residue 752 LYS Chi-restraints excluded: chain D residue 828 CYS 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 206 optimal weight: 0.9980 chunk 96 optimal weight: 0.4980 chunk 269 optimal weight: 9.9990 chunk 231 optimal weight: 10.0000 chunk 201 optimal weight: 0.0270 chunk 309 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 chunk 91 optimal weight: 0.0570 chunk 285 optimal weight: 8.9990 chunk 141 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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** ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 812 ASN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 ASN ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 794 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.084756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.061951 restraints weight = 146232.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.062538 restraints weight = 90065.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.062749 restraints weight = 64422.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.063007 restraints weight = 58331.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.062926 restraints weight = 51940.332| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2006 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= 0.105 Angle : 0.599 9.242 33407 Z= 0.297 Chirality : 0.043 0.238 3827 Planarity : 0.004 0.073 4245 Dihedral : 4.873 54.040 3436 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.17 % Favored : 92.60 % Rotamer: Outliers : 4.19 % Allowed : 27.19 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.58 (0.15), residues: 3082 helix: -0.08 (0.16), residues: 1042 sheet: -0.92 (0.32), residues: 286 loop : -1.72 (0.15), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 439 TYR 0.011 0.001 TYR B 479 PHE 0.020 0.001 PHE C 321 TRP 0.010 0.001 TRP A 768 HIS 0.007 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00226 (24552) covalent geometry : angle 0.59420 (33362) SS BOND : bond 0.00584 ( 15) SS BOND : angle 1.50066 ( 30) hydrogen bonds : bond 0.03827 ( 680) hydrogen bonds : angle 5.35074 ( 1932) link_BETA1-4 : bond 0.00303 ( 1) link_BETA1-4 : angle 1.44635 ( 3) link_NAG-ASN : bond 0.00602 ( 4) link_NAG-ASN : angle 3.38560 ( 12) *********************** 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 264 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 158 time to evaluate : 0.936 Fit side-chains REVERT: A 311 ASN cc_start: 0.3124 (OUTLIER) cc_final: 0.2457 (p0) REVERT: A 354 MET cc_start: 0.7550 (mmm) cc_final: 0.6841 (tpp) REVERT: B 281 SER cc_start: 0.7408 (OUTLIER) cc_final: 0.7172 (p) REVERT: B 287 TYR cc_start: 0.7187 (OUTLIER) cc_final: 0.6131 (t80) REVERT: B 537 MET cc_start: 0.7450 (tmm) cc_final: 0.6932 (tmm) REVERT: B 669 LYS cc_start: 0.8984 (pptt) cc_final: 0.8627 (tptp) REVERT: B 789 MET cc_start: 0.8529 (mpp) cc_final: 0.8219 (mpp) REVERT: C 190 LYS cc_start: 0.7344 (tttm) cc_final: 0.6514 (mtmt) REVERT: C 209 MET cc_start: 0.8063 (mmp) cc_final: 0.7372 (ptp) REVERT: C 354 MET cc_start: 0.7473 (tpp) cc_final: 0.7015 (tpp) REVERT: C 415 LEU cc_start: 0.6075 (OUTLIER) cc_final: 0.5577 (pp) REVERT: D 183 ASP cc_start: 0.8846 (t0) cc_final: 0.8353 (m-30) REVERT: D 274 MET cc_start: 0.6082 (tmm) cc_final: 0.5761 (tmm) outliers start: 106 outliers final: 72 residues processed: 252 average time/residue: 0.1243 time to fit residues: 53.8246 Evaluate side-chains 230 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 154 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 449 HIS 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 776 ILE Chi-restraints excluded: chain A residue 780 HIS Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 150 ILE 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 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 460 PHE 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 650 LEU Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain B residue 784 PHE 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 296 LEU Chi-restraints excluded: chain C residue 415 LEU 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 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 752 LEU 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 484 CYS Chi-restraints excluded: chain D residue 497 HIS Chi-restraints excluded: chain D residue 522 ASN 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 670 LEU Chi-restraints excluded: chain D residue 681 MET Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain D residue 828 CYS Chi-restraints excluded: chain D residue 851 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 245 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 201 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 247 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.083315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.060811 restraints weight = 146453.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.060494 restraints weight = 95047.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.061061 restraints weight = 77916.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.061196 restraints weight = 59958.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.061207 restraints weight = 55653.043| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 24572 Z= 0.232 Angle : 0.673 10.776 33407 Z= 0.340 Chirality : 0.045 0.245 3827 Planarity : 0.004 0.071 4245 Dihedral : 5.283 56.700 3436 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.63 % Favored : 91.14 % Rotamer: Outliers : 4.35 % Allowed : 27.35 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.15), residues: 3082 helix: -0.16 (0.16), residues: 1037 sheet: -1.05 (0.32), residues: 271 loop : -1.82 (0.14), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 124 TYR 0.012 0.001 TYR B 479 PHE 0.026 0.002 PHE A 533 TRP 0.020 0.001 TRP D 521 HIS 0.008 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00534 (24552) covalent geometry : angle 0.66721 (33362) SS BOND : bond 0.00563 ( 15) SS BOND : angle 1.76355 ( 30) hydrogen bonds : bond 0.04535 ( 680) hydrogen bonds : angle 5.61835 ( 1932) link_BETA1-4 : bond 0.00010 ( 1) link_BETA1-4 : angle 1.49625 ( 3) link_NAG-ASN : bond 0.00438 ( 4) link_NAG-ASN : angle 3.79358 ( 12) *********************** 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 267 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 157 time to evaluate : 0.772 Fit side-chains REVERT: A 354 MET cc_start: 0.7700 (mmm) cc_final: 0.7009 (tpp) REVERT: A 472 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.7667 (m-10) REVERT: B 281 SER cc_start: 0.7276 (OUTLIER) cc_final: 0.7014 (p) REVERT: B 287 TYR cc_start: 0.7191 (OUTLIER) cc_final: 0.6067 (t80) REVERT: B 551 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8746 (pp) REVERT: B 669 LYS cc_start: 0.8896 (pptt) cc_final: 0.8637 (tptp) REVERT: B 681 PHE cc_start: 0.7079 (OUTLIER) cc_final: 0.6358 (t80) REVERT: C 209 MET cc_start: 0.7957 (mmp) cc_final: 0.7267 (ptp) REVERT: C 354 MET cc_start: 0.7621 (tpp) cc_final: 0.7123 (tpp) REVERT: C 415 LEU cc_start: 0.6017 (OUTLIER) cc_final: 0.5456 (pp) REVERT: D 183 ASP cc_start: 0.8864 (t0) cc_final: 0.8358 (m-30) REVERT: D 273 PHE cc_start: 0.7318 (t80) cc_final: 0.7115 (t80) outliers start: 110 outliers final: 89 residues processed: 257 average time/residue: 0.1310 time to fit residues: 57.2919 Evaluate side-chains 246 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 151 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 184 LEU Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 449 HIS Chi-restraints excluded: chain A residue 472 PHE 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 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 150 ILE 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 407 SER 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 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 538 VAL Chi-restraints excluded: chain B residue 551 LEU 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 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 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 632 LEU Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 680 ILE Chi-restraints excluded: chain C residue 699 LEU 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 772 VAL 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 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 484 CYS Chi-restraints excluded: chain D residue 497 HIS 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 37 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 281 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 248 optimal weight: 6.9990 chunk 223 optimal weight: 8.9990 chunk 251 optimal weight: 6.9990 chunk 225 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 chunk 228 optimal weight: 0.8980 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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** C 650 ASN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 522 ASN ** D 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.084688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.061911 restraints weight = 145883.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.062369 restraints weight = 90253.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.062661 restraints weight = 66226.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.062843 restraints weight = 58260.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.062851 restraints weight = 51974.722| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2177 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= 0.109 Angle : 0.619 10.216 33407 Z= 0.304 Chirality : 0.043 0.260 3827 Planarity : 0.004 0.072 4245 Dihedral : 4.892 54.389 3436 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.11 % Favored : 92.67 % Rotamer: Outliers : 3.79 % Allowed : 27.59 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.15), residues: 3082 helix: -0.06 (0.16), residues: 1043 sheet: -0.94 (0.32), residues: 276 loop : -1.69 (0.15), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 439 TYR 0.011 0.001 TYR B 479 PHE 0.021 0.001 PHE C 321 TRP 0.011 0.001 TRP C 563 HIS 0.007 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00244 (24552) covalent geometry : angle 0.61378 (33362) SS BOND : bond 0.00445 ( 15) SS BOND : angle 1.56056 ( 30) hydrogen bonds : bond 0.03666 ( 680) hydrogen bonds : angle 5.28080 ( 1932) link_BETA1-4 : bond 0.00374 ( 1) link_BETA1-4 : angle 1.44856 ( 3) link_NAG-ASN : bond 0.00600 ( 4) link_NAG-ASN : angle 3.43600 ( 12) *********************** 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 253 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 157 time to evaluate : 0.918 Fit side-chains REVERT: A 354 MET cc_start: 0.7798 (mmm) cc_final: 0.7087 (tpp) REVERT: B 123 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7659 (pt) REVERT: B 187 ARG cc_start: 0.9375 (mpp80) cc_final: 0.9091 (mpp80) REVERT: B 281 SER cc_start: 0.7492 (OUTLIER) cc_final: 0.7275 (p) REVERT: B 287 TYR cc_start: 0.7236 (OUTLIER) cc_final: 0.6143 (t80) REVERT: B 473 LYS cc_start: 0.8673 (pptt) cc_final: 0.8416 (pttp) REVERT: B 537 MET cc_start: 0.7354 (tmm) cc_final: 0.6413 (tmm) REVERT: B 551 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8771 (pp) REVERT: B 565 MET cc_start: 0.8598 (ttt) cc_final: 0.8244 (ppp) REVERT: B 669 LYS cc_start: 0.8823 (pptt) cc_final: 0.8527 (tptp) REVERT: C 190 LYS cc_start: 0.7243 (tttm) cc_final: 0.6480 (mtmt) REVERT: C 209 MET cc_start: 0.7985 (mmp) cc_final: 0.7334 (ptp) REVERT: C 354 MET cc_start: 0.7590 (tpp) cc_final: 0.7107 (tpp) REVERT: C 415 LEU cc_start: 0.6170 (OUTLIER) cc_final: 0.5663 (pp) REVERT: D 183 ASP cc_start: 0.8892 (t0) cc_final: 0.8397 (m-30) REVERT: D 273 PHE cc_start: 0.7331 (t80) cc_final: 0.7098 (t80) REVERT: D 274 MET cc_start: 0.6035 (tmm) cc_final: 0.5834 (tmm) outliers start: 96 outliers final: 77 residues processed: 242 average time/residue: 0.1254 time to fit residues: 51.5201 Evaluate side-chains 238 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 156 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 437 THR Chi-restraints excluded: chain A residue 449 HIS 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 683 THR 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 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 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 530 ILE Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 535 SER Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 650 LEU 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 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 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 607 MET Chi-restraints excluded: chain C residue 619 ILE Chi-restraints excluded: chain C residue 632 LEU 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 776 ILE Chi-restraints excluded: chain C residue 780 HIS 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 484 CYS Chi-restraints excluded: chain D residue 497 HIS Chi-restraints excluded: chain D residue 522 ASN 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 752 LYS Chi-restraints excluded: chain D residue 828 CYS 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 297 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 179 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 137 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 133 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 GLN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.084086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.061542 restraints weight = 146879.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.061715 restraints weight = 95455.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.061721 restraints weight = 72888.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.061957 restraints weight = 67803.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.061989 restraints weight = 58353.095| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24572 Z= 0.152 Angle : 0.639 10.503 33407 Z= 0.314 Chirality : 0.043 0.267 3827 Planarity : 0.004 0.071 4245 Dihedral : 4.958 55.283 3436 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.62 % Favored : 92.15 % Rotamer: Outliers : 3.28 % Allowed : 28.34 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.15), residues: 3082 helix: 0.01 (0.16), residues: 1036 sheet: -1.04 (0.31), residues: 286 loop : -1.69 (0.15), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 306 TYR 0.012 0.001 TYR B 479 PHE 0.016 0.001 PHE A 533 TRP 0.044 0.001 TRP D 637 HIS 0.008 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00352 (24552) covalent geometry : angle 0.63419 (33362) SS BOND : bond 0.00412 ( 15) SS BOND : angle 1.47227 ( 30) hydrogen bonds : bond 0.03892 ( 680) hydrogen bonds : angle 5.33291 ( 1932) link_BETA1-4 : bond 0.00165 ( 1) link_BETA1-4 : angle 1.44008 ( 3) link_NAG-ASN : bond 0.00406 ( 4) link_NAG-ASN : angle 3.55386 ( 12) ********************** 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 237 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 154 time to evaluate : 0.986 Fit side-chains REVERT: B 123 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7620 (pt) REVERT: B 187 ARG cc_start: 0.9350 (mpp80) cc_final: 0.9041 (mpp80) REVERT: B 281 SER cc_start: 0.7347 (OUTLIER) cc_final: 0.7092 (p) REVERT: B 287 TYR cc_start: 0.7171 (OUTLIER) cc_final: 0.6100 (t80) REVERT: B 537 MET cc_start: 0.7487 (tmm) cc_final: 0.6566 (ttp) REVERT: B 669 LYS cc_start: 0.9034 (pptt) cc_final: 0.8725 (tptp) REVERT: C 354 MET cc_start: 0.7557 (tpp) cc_final: 0.7050 (tpp) REVERT: C 415 LEU cc_start: 0.6098 (OUTLIER) cc_final: 0.5589 (pp) REVERT: C 554 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.6434 (p90) REVERT: D 183 ASP cc_start: 0.8877 (t0) cc_final: 0.8371 (m-30) REVERT: D 273 PHE cc_start: 0.7411 (t80) cc_final: 0.7174 (t80) outliers start: 83 outliers final: 71 residues processed: 230 average time/residue: 0.1348 time to fit residues: 52.8973 Evaluate side-chains 227 residues out of total 2674 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 151 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 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 683 THR 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 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 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 498 ILE Chi-restraints excluded: chain B residue 532 THR Chi-restraints excluded: chain B residue 535 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 686 VAL 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 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 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 554 PHE 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 632 LEU 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 776 ILE Chi-restraints excluded: chain C residue 780 HIS 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 484 CYS Chi-restraints excluded: chain D residue 497 HIS Chi-restraints excluded: chain D residue 524 MET 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 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 153 optimal weight: 0.0870 chunk 268 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 228 optimal weight: 0.9980 chunk 275 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 267 optimal weight: 10.0000 chunk 165 optimal weight: 0.0980 chunk 194 optimal weight: 4.9990 chunk 218 optimal weight: 0.3980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 GLN D 522 ASN D 649 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.085062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.062352 restraints weight = 145824.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.062909 restraints weight = 90156.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.062971 restraints weight = 65643.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.063353 restraints weight = 59264.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.063279 restraints weight = 52961.734| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2272 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= 0.106 Angle : 0.641 12.842 33407 Z= 0.310 Chirality : 0.043 0.266 3827 Planarity : 0.004 0.072 4245 Dihedral : 4.719 54.260 3436 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.07 % Favored : 92.70 % Rotamer: Outliers : 3.08 % Allowed : 28.81 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.15), residues: 3082 helix: 0.00 (0.16), residues: 1040 sheet: -0.89 (0.32), residues: 284 loop : -1.64 (0.15), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 439 TYR 0.011 0.001 TYR B 479 PHE 0.024 0.001 PHE C 321 TRP 0.027 0.001 TRP D 637 HIS 0.007 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00232 (24552) covalent geometry : angle 0.63688 (33362) SS BOND : bond 0.00285 ( 15) SS BOND : angle 1.24777 ( 30) hydrogen bonds : bond 0.03516 ( 680) hydrogen bonds : angle 5.16192 ( 1932) link_BETA1-4 : bond 0.00281 ( 1) link_BETA1-4 : angle 1.35404 ( 3) link_NAG-ASN : bond 0.00642 ( 4) link_NAG-ASN : angle 3.39324 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4246.14 seconds wall clock time: 73 minutes 55.62 seconds (4435.62 seconds total)