Starting phenix.real_space_refine on Thu Mar 5 21:25:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lzh_23606/03_2026/7lzh_23606.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lzh_23606/03_2026/7lzh_23606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lzh_23606/03_2026/7lzh_23606.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lzh_23606/03_2026/7lzh_23606.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lzh_23606/03_2026/7lzh_23606.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lzh_23606/03_2026/7lzh_23606.map" } resolution = 3.57 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= 0.014 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 16214 2.51 5 N 4234 2.21 5 O 4748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25306 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 6251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 798, 6251 Classifications: {'peptide': 798} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 38, 'TRANS': 759} Chain breaks: 3 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 6174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 6174 Classifications: {'peptide': 788} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 38, 'TRANS': 749} Chain breaks: 4 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 6251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 798, 6251 Classifications: {'peptide': 798} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 38, 'TRANS': 759} Chain breaks: 3 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 6174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 6174 Classifications: {'peptide': 788} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 38, 'TRANS': 749} Chain breaks: 4 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 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: "F" 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: "G" 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: "H" 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: "I" 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: "J" 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: "K" 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: "L" 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: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'GSH': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'GSH': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'GSH': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 48 Unusual residues: {'GSH': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.82, per 1000 atoms: 0.23 Number of scatterers: 25306 At special positions: 0 Unit cell: (110.39, 166.83, 189.24, 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 110 16.00 O 4748 8.00 N 4234 7.00 C 16214 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 786 " - pdb=" SG CYS A 841 " distance=2.03 Simple disulfide: pdb=" SG CYS B 786 " - pdb=" SG CYS B 841 " distance=2.03 Simple disulfide: pdb=" SG CYS C 786 " - pdb=" SG CYS C 841 " distance=2.03 Simple disulfide: pdb=" SG CYS D 786 " - pdb=" SG CYS D 841 " 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=4, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1002 " - " ASN A 108 " " NAG A1003 " - " ASN A 404 " " NAG B1002 " - " ASN B 108 " " NAG B1003 " - " ASN B 404 " " NAG C1002 " - " ASN C 108 " " NAG C1003 " - " ASN C 404 " " NAG D1002 " - " ASN D 108 " " NAG D1003 " - " ASN D 404 " " NAG E 1 " - " ASN A 443 " " NAG F 1 " - " ASN A 576 " " NAG G 1 " - " ASN B 443 " " NAG H 1 " - " ASN B 576 " " NAG I 1 " - " ASN C 443 " " NAG J 1 " - " ASN C 576 " " NAG K 1 " - " ASN D 443 " " NAG L 1 " - " ASN D 576 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 1.2 seconds 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5928 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 34 sheets defined 43.4% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 73 through 89 Proline residue: A 79 - end of helix Processing helix chain 'A' and resid 91 through 96 removed outlier: 3.803A pdb=" N LYS A 96 " --> pdb=" O GLN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 124 removed outlier: 3.744A pdb=" N THR A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 145 removed outlier: 3.807A pdb=" N MET A 140 " --> pdb=" O GLY A 136 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 192 removed outlier: 3.606A pdb=" N ALA A 185 " --> pdb=" O MET A 181 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 220 removed outlier: 3.643A pdb=" N ASN A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER A 211 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 212 " --> pdb=" O ASN A 208 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 219 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 248 removed outlier: 3.845A pdb=" N SER A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 248 " --> pdb=" O VAL A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 272 removed outlier: 4.293A pdb=" N PHE A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 294 Processing helix chain 'A' and resid 301 through 306 Processing helix chain 'A' and resid 319 through 333 Processing helix chain 'A' and resid 340 through 363 removed outlier: 3.537A pdb=" N TYR A 344 " --> pdb=" O SER A 340 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP A 350 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG A 361 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 402 removed outlier: 3.737A pdb=" N ILE A 400 " --> pdb=" O PHE A 396 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 402 " --> pdb=" O LYS A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 457 removed outlier: 3.679A pdb=" N TYR A 456 " --> pdb=" O GLU A 453 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER A 457 " --> pdb=" O THR A 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 453 through 457' Processing helix chain 'A' and resid 520 through 530 removed outlier: 3.725A pdb=" N GLU A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 561 removed outlier: 3.878A pdb=" N GLU A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 581 Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 613 through 623 removed outlier: 3.640A pdb=" N ALA A 618 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 621 " --> pdb=" O TRP A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 635 removed outlier: 3.559A pdb=" N VAL A 631 " --> pdb=" O VAL A 627 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TRP A 632 " --> pdb=" O GLY A 628 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 633 " --> pdb=" O ALA A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 655 removed outlier: 3.720A pdb=" N TRP A 655 " --> pdb=" O THR A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 701 removed outlier: 3.520A pdb=" N ILE A 687 " --> pdb=" O PHE A 683 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER A 690 " --> pdb=" O LEU A 686 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA A 694 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER A 698 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 699 " --> pdb=" O SER A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 718 removed outlier: 3.697A pdb=" N THR A 717 " --> pdb=" O ASP A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 735 removed outlier: 3.593A pdb=" N ILE A 735 " --> pdb=" O ARG A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 757 Processing helix chain 'A' and resid 774 through 784 removed outlier: 4.100A pdb=" N VAL A 779 " --> pdb=" O PRO A 775 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 824 removed outlier: 3.552A pdb=" N ASP A 813 " --> pdb=" O PRO A 809 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR A 816 " --> pdb=" O VAL A 812 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU A 824 " --> pdb=" O GLN A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 830 Processing helix chain 'A' and resid 830 through 835 removed outlier: 3.671A pdb=" N TRP A 834 " --> pdb=" O ILE A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 886 removed outlier: 3.589A pdb=" N ILE A 864 " --> pdb=" O GLY A 860 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A 881 " --> pdb=" O PHE A 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 91 Proline residue: B 79 - end of helix removed outlier: 3.669A pdb=" N ASN B 89 " --> pdb=" O MET B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 124 removed outlier: 4.021A pdb=" N GLY B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 145 removed outlier: 4.086A pdb=" N MET B 140 " --> pdb=" O GLY B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 192 removed outlier: 4.222A pdb=" N ALA B 183 " --> pdb=" O PHE B 179 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 220 removed outlier: 3.526A pdb=" N GLY B 209 " --> pdb=" O CYS B 205 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B 212 " --> pdb=" O ASN B 208 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS B 219 " --> pdb=" O ASP B 215 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS B 220 " --> pdb=" O VAL B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 248 removed outlier: 3.922A pdb=" N SER B 245 " --> pdb=" O ASP B 241 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 248 " --> pdb=" O VAL B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 273 removed outlier: 4.490A pdb=" N PHE B 267 " --> pdb=" O GLY B 263 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 Processing helix chain 'B' and resid 319 through 333 removed outlier: 3.609A pdb=" N ASN B 331 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B 332 " --> pdb=" O ARG B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 363 removed outlier: 3.809A pdb=" N VAL B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TRP B 350 " --> pdb=" O TYR B 346 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B 352 " --> pdb=" O SER B 348 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 402 removed outlier: 3.540A pdb=" N ILE B 399 " --> pdb=" O LYS B 395 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE B 400 " --> pdb=" O PHE B 396 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 401 " --> pdb=" O MET B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 456 removed outlier: 3.538A pdb=" N LEU B 455 " --> pdb=" O PRO B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 531 removed outlier: 3.527A pdb=" N ALA B 527 " --> pdb=" O ASP B 523 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU B 530 " --> pdb=" O GLU B 526 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU B 531 " --> pdb=" O ALA B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 561 removed outlier: 3.602A pdb=" N ASN B 557 " --> pdb=" O ASP B 553 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 559 " --> pdb=" O LEU B 555 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B 561 " --> pdb=" O ASN B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 581 removed outlier: 3.945A pdb=" N TYR B 580 " --> pdb=" O ASN B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 608 Processing helix chain 'B' and resid 613 through 616 Processing helix chain 'B' and resid 617 through 634 removed outlier: 3.566A pdb=" N LEU B 625 " --> pdb=" O GLY B 621 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET B 630 " --> pdb=" O PHE B 626 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL B 631 " --> pdb=" O VAL B 627 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TRP B 632 " --> pdb=" O GLY B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 655 removed outlier: 3.629A pdb=" N PHE B 654 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 697 removed outlier: 3.920A pdb=" N VAL B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU B 678 " --> pdb=" O GLY B 674 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE B 679 " --> pdb=" O ARG B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 705 Processing helix chain 'B' and resid 712 through 717 removed outlier: 3.578A pdb=" N THR B 717 " --> pdb=" O ASP B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 735 removed outlier: 4.075A pdb=" N ILE B 735 " --> pdb=" O ARG B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 760 removed outlier: 3.806A pdb=" N LEU B 755 " --> pdb=" O GLU B 751 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 757 " --> pdb=" O GLN B 753 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU B 758 " --> pdb=" O TYR B 754 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 784 removed outlier: 4.257A pdb=" N VAL B 779 " --> pdb=" O PRO B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 824 removed outlier: 3.964A pdb=" N ASP B 813 " --> pdb=" O PRO B 809 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU B 824 " --> pdb=" O GLN B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 835 removed outlier: 3.935A pdb=" N LYS B 829 " --> pdb=" O GLY B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 884 removed outlier: 3.589A pdb=" N ILE B 864 " --> pdb=" O GLY B 860 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N CYS B 869 " --> pdb=" O CYS B 865 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR B 874 " --> pdb=" O PHE B 870 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 89 Proline residue: C 79 - end of helix Processing helix chain 'C' and resid 91 through 96 removed outlier: 3.803A pdb=" N LYS C 96 " --> pdb=" O GLN C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 124 removed outlier: 3.745A pdb=" N THR C 115 " --> pdb=" O GLY C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 145 removed outlier: 3.809A pdb=" N MET C 140 " --> pdb=" O GLY C 136 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 192 removed outlier: 3.605A pdb=" N ALA C 185 " --> pdb=" O MET C 181 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 220 removed outlier: 3.642A pdb=" N ASN C 208 " --> pdb=" O GLU C 204 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER C 211 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 212 " --> pdb=" O ASN C 208 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA C 218 " --> pdb=" O GLY C 214 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS C 219 " --> pdb=" O ASP C 215 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS C 220 " --> pdb=" O VAL C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 248 removed outlier: 3.845A pdb=" N SER C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU C 248 " --> pdb=" O VAL C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 272 removed outlier: 4.293A pdb=" N PHE C 267 " --> pdb=" O GLY C 263 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL C 269 " --> pdb=" O ASN C 265 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER C 272 " --> pdb=" O SER C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 294 Processing helix chain 'C' and resid 301 through 306 Processing helix chain 'C' and resid 319 through 333 Processing helix chain 'C' and resid 340 through 363 removed outlier: 3.536A pdb=" N TYR C 344 " --> pdb=" O SER C 340 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL C 349 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP C 350 " --> pdb=" O TYR C 346 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE C 360 " --> pdb=" O LEU C 356 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG C 361 " --> pdb=" O ASP C 357 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU C 362 " --> pdb=" O VAL C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 402 removed outlier: 3.738A pdb=" N ILE C 400 " --> pdb=" O PHE C 396 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY C 402 " --> pdb=" O LYS C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 457 removed outlier: 3.680A pdb=" N TYR C 456 " --> pdb=" O GLU C 453 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER C 457 " --> pdb=" O THR C 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 453 through 457' Processing helix chain 'C' and resid 520 through 530 removed outlier: 3.724A pdb=" N GLU C 530 " --> pdb=" O GLU C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 561 removed outlier: 3.878A pdb=" N GLU C 558 " --> pdb=" O ASN C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 581 Processing helix chain 'C' and resid 604 through 609 Processing helix chain 'C' and resid 613 through 623 removed outlier: 3.640A pdb=" N ALA C 618 " --> pdb=" O ILE C 614 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY C 621 " --> pdb=" O TRP C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 635 removed outlier: 3.558A pdb=" N VAL C 631 " --> pdb=" O VAL C 627 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TRP C 632 " --> pdb=" O GLY C 628 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 633 " --> pdb=" O ALA C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 655 removed outlier: 3.720A pdb=" N TRP C 655 " --> pdb=" O THR C 652 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 701 removed outlier: 3.520A pdb=" N ILE C 687 " --> pdb=" O PHE C 683 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER C 690 " --> pdb=" O LEU C 686 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA C 694 " --> pdb=" O SER C 690 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER C 698 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE C 699 " --> pdb=" O SER C 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 711 through 718 removed outlier: 3.697A pdb=" N THR C 717 " --> pdb=" O ASP C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 735 removed outlier: 3.593A pdb=" N ILE C 735 " --> pdb=" O ARG C 731 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 757 Processing helix chain 'C' and resid 774 through 784 removed outlier: 4.100A pdb=" N VAL C 779 " --> pdb=" O PRO C 775 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR C 782 " --> pdb=" O GLU C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 809 through 824 removed outlier: 3.551A pdb=" N ASP C 813 " --> pdb=" O PRO C 809 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR C 816 " --> pdb=" O VAL C 812 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU C 823 " --> pdb=" O LEU C 819 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU C 824 " --> pdb=" O GLN C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 825 through 830 Processing helix chain 'C' and resid 830 through 835 removed outlier: 3.671A pdb=" N TRP C 834 " --> pdb=" O ILE C 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 886 removed outlier: 3.591A pdb=" N ILE C 864 " --> pdb=" O GLY C 860 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C 881 " --> pdb=" O PHE C 877 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 91 Proline residue: D 79 - end of helix removed outlier: 3.669A pdb=" N ASN D 89 " --> pdb=" O MET D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 124 removed outlier: 4.021A pdb=" N GLY D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 145 removed outlier: 4.086A pdb=" N MET D 140 " --> pdb=" O GLY D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 192 removed outlier: 4.222A pdb=" N ALA D 183 " --> pdb=" O PHE D 179 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER D 189 " --> pdb=" O ALA D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 220 removed outlier: 3.526A pdb=" N GLY D 209 " --> pdb=" O CYS D 205 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL D 212 " --> pdb=" O ASN D 208 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU D 213 " --> pdb=" O GLY D 209 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA D 218 " --> pdb=" O GLY D 214 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS D 220 " --> pdb=" O VAL D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 removed outlier: 3.922A pdb=" N SER D 245 " --> pdb=" O ASP D 241 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU D 248 " --> pdb=" O VAL D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 273 removed outlier: 4.489A pdb=" N PHE D 267 " --> pdb=" O GLY D 263 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER D 272 " --> pdb=" O SER D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 319 through 333 removed outlier: 3.609A pdb=" N ASN D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU D 332 " --> pdb=" O ARG D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 363 removed outlier: 3.810A pdb=" N VAL D 349 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TRP D 350 " --> pdb=" O TYR D 346 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL D 352 " --> pdb=" O SER D 348 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG D 361 " --> pdb=" O ASP D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 402 removed outlier: 3.540A pdb=" N ILE D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE D 400 " --> pdb=" O PHE D 396 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 401 " --> pdb=" O MET D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 456 removed outlier: 3.539A pdb=" N LEU D 455 " --> pdb=" O PRO D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 531 removed outlier: 3.527A pdb=" N ALA D 527 " --> pdb=" O ASP D 523 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU D 530 " --> pdb=" O GLU D 526 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU D 531 " --> pdb=" O ALA D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 561 removed outlier: 3.602A pdb=" N ASN D 557 " --> pdb=" O ASP D 553 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL D 559 " --> pdb=" O LEU D 555 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 561 " --> pdb=" O ASN D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.945A pdb=" N TYR D 580 " --> pdb=" O ASN D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 608 Processing helix chain 'D' and resid 613 through 616 Processing helix chain 'D' and resid 617 through 634 removed outlier: 3.565A pdb=" N LEU D 625 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET D 630 " --> pdb=" O PHE D 626 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL D 631 " --> pdb=" O VAL D 627 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TRP D 632 " --> pdb=" O GLY D 628 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 655 removed outlier: 3.629A pdb=" N PHE D 654 " --> pdb=" O LEU D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 697 removed outlier: 3.921A pdb=" N VAL D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU D 678 " --> pdb=" O GLY D 674 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE D 679 " --> pdb=" O ARG D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 705 Processing helix chain 'D' and resid 712 through 717 removed outlier: 3.577A pdb=" N THR D 717 " --> pdb=" O ASP D 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 730 through 735 removed outlier: 4.075A pdb=" N ILE D 735 " --> pdb=" O ARG D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 751 through 760 removed outlier: 3.806A pdb=" N LEU D 755 " --> pdb=" O GLU D 751 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA D 757 " --> pdb=" O GLN D 753 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU D 758 " --> pdb=" O TYR D 754 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG D 760 " --> pdb=" O SER D 756 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 784 removed outlier: 4.257A pdb=" N VAL D 779 " --> pdb=" O PRO D 775 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 824 removed outlier: 3.964A pdb=" N ASP D 813 " --> pdb=" O PRO D 809 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU D 824 " --> pdb=" O GLN D 820 " (cutoff:3.500A) Processing helix chain 'D' and resid 825 through 835 removed outlier: 3.935A pdb=" N LYS D 829 " --> pdb=" O GLY D 825 " (cutoff:3.500A) Processing helix chain 'D' and resid 859 through 884 removed outlier: 3.589A pdb=" N ILE D 864 " --> pdb=" O GLY D 860 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N CYS D 869 " --> pdb=" O CYS D 865 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR D 874 " --> pdb=" O PHE D 870 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 101 through 102 removed outlier: 3.869A pdb=" N VAL A 63 " --> pdb=" O ASN A 101 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ASN A 62 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ILE A 130 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLY A 64 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ALA A 129 " --> pdb=" O LEU A 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 223 through 224 removed outlier: 8.043A pdb=" N ALA A 228 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ALA A 198 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE A 230 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE A 200 " --> pdb=" O ILE A 230 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 4.881A pdb=" N VAL A 253 " --> pdb=" O GLN A 195 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 255 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE A 254 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N TRP A 282 " --> pdb=" O VAL A 310 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 367 through 368 removed outlier: 4.498A pdb=" N THR A 367 " --> pdb=" O ASN A 391 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 406 through 407 removed outlier: 3.740A pdb=" N GLY A 410 " --> pdb=" O GLY A 407 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 424 through 425 Processing sheet with id=AA7, first strand: chain 'A' and resid 494 through 498 removed outlier: 5.895A pdb=" N LEU A 494 " --> pdb=" O THR A 539 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE A 541 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE A 496 " --> pdb=" O ILE A 541 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 508 through 510 Processing sheet with id=AA9, first strand: chain 'A' and resid 566 through 567 removed outlier: 3.906A pdb=" N ASP A 582 " --> pdb=" O PHE A 804 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 745 through 746 removed outlier: 6.438A pdb=" N ILE A 722 " --> pdb=" O VAL A 746 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 772 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 596 " --> pdb=" O ARG A 789 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 99 through 105 removed outlier: 6.434A pdb=" N VAL B 61 " --> pdb=" O ASN B 101 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE B 103 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 63 " --> pdb=" O ILE B 103 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLN B 105 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ALA B 65 " --> pdb=" O GLN B 105 " (cutoff:3.500A) removed outlier: 10.560A pdb=" N ALA B 128 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ASN B 62 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N ILE B 130 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLY B 64 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA B 129 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU B 152 " --> pdb=" O LEU B 171 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 223 through 224 removed outlier: 4.567A pdb=" N VAL B 253 " --> pdb=" O GLN B 195 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N TRP B 282 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N PHE B 312 " --> pdb=" O TRP B 282 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ALA B 284 " --> pdb=" O PHE B 312 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N HIS B 314 " --> pdb=" O ALA B 284 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 228 through 230 removed outlier: 7.819A pdb=" N ALA B 228 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ALA B 198 " --> pdb=" O ALA B 228 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE B 230 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N PHE B 200 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL B 253 " --> pdb=" O GLN B 195 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N TRP B 282 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N PHE B 312 " --> pdb=" O TRP B 282 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ALA B 284 " --> pdb=" O PHE B 312 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N HIS B 314 " --> pdb=" O ALA B 284 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 367 through 369 removed outlier: 4.446A pdb=" N THR B 367 " --> pdb=" O ASN B 391 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 406 through 407 Processing sheet with id=AB7, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.005A pdb=" N LEU B 494 " --> pdb=" O THR B 539 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE B 541 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE B 496 " --> pdb=" O ILE B 541 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL B 566 " --> pdb=" O ARG B 495 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE B 804 " --> pdb=" O ASP B 582 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 745 through 746 removed outlier: 6.933A pdb=" N GLY B 723 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N GLU B 773 " --> pdb=" O GLY B 723 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 101 through 102 removed outlier: 3.869A pdb=" N VAL C 63 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ASN C 62 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ILE C 130 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLY C 64 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ALA C 129 " --> pdb=" O LEU C 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 223 through 224 removed outlier: 8.043A pdb=" N ALA C 228 " --> pdb=" O VAL C 196 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ALA C 198 " --> pdb=" O ALA C 228 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE C 230 " --> pdb=" O ALA C 198 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE C 200 " --> pdb=" O ILE C 230 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 223 through 224 removed outlier: 4.881A pdb=" N VAL C 253 " --> pdb=" O GLN C 195 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL C 255 " --> pdb=" O ILE C 197 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N PHE C 254 " --> pdb=" O ILE C 283 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N TRP C 282 " --> pdb=" O VAL C 310 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 367 through 368 removed outlier: 4.498A pdb=" N THR C 367 " --> pdb=" O ASN C 391 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 406 through 407 removed outlier: 3.740A pdb=" N GLY C 410 " --> pdb=" O GLY C 407 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 424 through 425 Processing sheet with id=AC6, first strand: chain 'C' and resid 494 through 498 removed outlier: 5.896A pdb=" N LEU C 494 " --> pdb=" O THR C 539 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE C 541 " --> pdb=" O LEU C 494 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE C 496 " --> pdb=" O ILE C 541 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 508 through 510 Processing sheet with id=AC8, first strand: chain 'C' and resid 566 through 567 removed outlier: 3.906A pdb=" N ASP C 582 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 745 through 746 removed outlier: 6.439A pdb=" N ILE C 722 " --> pdb=" O VAL C 746 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP C 772 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA C 596 " --> pdb=" O ARG C 789 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 99 through 105 removed outlier: 6.435A pdb=" N VAL D 61 " --> pdb=" O ASN D 101 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ILE D 103 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL D 63 " --> pdb=" O ILE D 103 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLN D 105 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ALA D 65 " --> pdb=" O GLN D 105 " (cutoff:3.500A) removed outlier: 10.560A pdb=" N ALA D 128 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ASN D 62 " --> pdb=" O ALA D 128 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ILE D 130 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLY D 64 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA D 129 " --> pdb=" O LEU D 153 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU D 152 " --> pdb=" O LEU D 171 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'D' and resid 223 through 224 removed outlier: 4.568A pdb=" N VAL D 253 " --> pdb=" O GLN D 195 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N TRP D 282 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N PHE D 312 " --> pdb=" O TRP D 282 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ALA D 284 " --> pdb=" O PHE D 312 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N HIS D 314 " --> pdb=" O ALA D 284 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 228 through 230 removed outlier: 7.819A pdb=" N ALA D 228 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ALA D 198 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE D 230 " --> pdb=" O ALA D 198 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N PHE D 200 " --> pdb=" O ILE D 230 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL D 253 " --> pdb=" O GLN D 195 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N TRP D 282 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N PHE D 312 " --> pdb=" O TRP D 282 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ALA D 284 " --> pdb=" O PHE D 312 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N HIS D 314 " --> pdb=" O ALA D 284 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 367 through 369 removed outlier: 4.445A pdb=" N THR D 367 " --> pdb=" O ASN D 391 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 406 through 407 Processing sheet with id=AD6, first strand: chain 'D' and resid 538 through 542 removed outlier: 6.006A pdb=" N LEU D 494 " --> pdb=" O THR D 539 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE D 541 " --> pdb=" O LEU D 494 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE D 496 " --> pdb=" O ILE D 541 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL D 566 " --> pdb=" O ARG D 495 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE D 804 " --> pdb=" O ASP D 582 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 745 through 746 removed outlier: 6.933A pdb=" N GLY D 723 " --> pdb=" O VAL D 771 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N GLU D 773 " --> pdb=" O GLY D 723 " (cutoff:3.500A) 830 hydrogen bonds defined for protein. 2394 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: 5.15 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4113 1.30 - 1.43: 7190 1.43 - 1.57: 14405 1.57 - 1.70: 0 1.70 - 1.83: 188 Bond restraints: 25896 Sorted by residual: bond pdb=" CD1 GSH A1004 " pdb=" N2 GSH A1004 " ideal model delta sigma weight residual 1.336 1.451 -0.115 1.20e-02 6.94e+03 9.17e+01 bond pdb=" CD1 GSH C1004 " pdb=" N2 GSH C1004 " ideal model delta sigma weight residual 1.336 1.450 -0.114 1.20e-02 6.94e+03 9.10e+01 bond pdb=" CD1 GSH B1004 " pdb=" N2 GSH B1004 " ideal model delta sigma weight residual 1.336 1.446 -0.110 1.20e-02 6.94e+03 8.43e+01 bond pdb=" CD1 GSH D1004 " pdb=" N2 GSH D1004 " ideal model delta sigma weight residual 1.336 1.446 -0.110 1.20e-02 6.94e+03 8.39e+01 bond pdb=" C2 GSH A1004 " pdb=" N3 GSH A1004 " ideal model delta sigma weight residual 1.333 1.449 -0.116 1.30e-02 5.92e+03 7.97e+01 ... (remaining 25891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.09: 34915 4.09 - 8.19: 285 8.19 - 12.28: 15 12.28 - 16.37: 0 16.37 - 20.47: 1 Bond angle restraints: 35216 Sorted by residual: angle pdb=" C ASN A 108 " pdb=" CA ASN A 108 " pdb=" CB ASN A 108 " ideal model delta sigma weight residual 111.22 90.75 20.47 1.23e+00 6.61e-01 2.77e+02 angle pdb=" N VAL A 449 " pdb=" CA VAL A 449 " pdb=" C VAL A 449 " ideal model delta sigma weight residual 113.71 107.58 6.13 9.50e-01 1.11e+00 4.16e+01 angle pdb=" N VAL C 449 " pdb=" CA VAL C 449 " pdb=" C VAL C 449 " ideal model delta sigma weight residual 113.71 107.69 6.02 9.50e-01 1.11e+00 4.01e+01 angle pdb=" N ASN B 108 " pdb=" CA ASN B 108 " pdb=" C ASN B 108 " ideal model delta sigma weight residual 111.81 103.81 8.00 1.54e+00 4.22e-01 2.70e+01 angle pdb=" CG1 GSH D1004 " pdb=" CD1 GSH D1004 " pdb=" N2 GSH D1004 " ideal model delta sigma weight residual 115.92 121.06 -5.14 1.00e+00 1.00e+00 2.64e+01 ... (remaining 35211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.69: 14807 20.69 - 41.39: 636 41.39 - 62.08: 97 62.08 - 82.78: 33 82.78 - 103.47: 55 Dihedral angle restraints: 15628 sinusoidal: 6430 harmonic: 9198 Sorted by residual: dihedral pdb=" C ASN A 108 " pdb=" N ASN A 108 " pdb=" CA ASN A 108 " pdb=" CB ASN A 108 " ideal model delta harmonic sigma weight residual -122.60 -98.38 -24.22 0 2.50e+00 1.60e-01 9.39e+01 dihedral pdb=" CA THR A 575 " pdb=" C THR A 575 " pdb=" N ASN A 576 " pdb=" CA ASN A 576 " ideal model delta harmonic sigma weight residual 180.00 151.25 28.75 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA THR C 575 " pdb=" C THR C 575 " pdb=" N ASN C 576 " pdb=" CA ASN C 576 " ideal model delta harmonic sigma weight residual 180.00 151.32 28.68 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 15625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.988: 4019 0.988 - 1.976: 0 1.976 - 2.964: 0 2.964 - 3.952: 0 3.952 - 4.940: 3 Chirality restraints: 4022 Sorted by residual: chirality pdb=" C1 NAG D1002 " pdb=" ND2 ASN D 108 " pdb=" C2 NAG D1002 " pdb=" O5 NAG D1002 " both_signs ideal model delta sigma weight residual False -2.40 2.54 -4.94 2.00e-01 2.50e+01 6.10e+02 chirality pdb=" C1 NAG B1002 " pdb=" ND2 ASN B 108 " pdb=" C2 NAG B1002 " pdb=" O5 NAG B1002 " both_signs ideal model delta sigma weight residual False -2.40 2.45 -4.85 2.00e-01 2.50e+01 5.87e+02 chirality pdb=" C1 NAG C1002 " pdb=" ND2 ASN C 108 " pdb=" C2 NAG C1002 " pdb=" O5 NAG C1002 " both_signs ideal model delta sigma weight residual False -2.40 2.06 -4.46 2.00e-01 2.50e+01 4.97e+02 ... (remaining 4019 not shown) Planarity restraints: 4504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1002 " 0.352 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG C1002 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG C1002 " 0.151 2.00e-02 2.50e+03 pdb=" N2 NAG C1002 " -0.537 2.00e-02 2.50e+03 pdb=" O7 NAG C1002 " 0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1002 " -0.234 2.00e-02 2.50e+03 1.94e-01 4.72e+02 pdb=" C7 NAG B1002 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG B1002 " -0.165 2.00e-02 2.50e+03 pdb=" N2 NAG B1002 " 0.321 2.00e-02 2.50e+03 pdb=" O7 NAG B1002 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D1002 " 0.209 2.00e-02 2.50e+03 1.75e-01 3.81e+02 pdb=" C7 NAG D1002 " -0.053 2.00e-02 2.50e+03 pdb=" C8 NAG D1002 " 0.148 2.00e-02 2.50e+03 pdb=" N2 NAG D1002 " -0.289 2.00e-02 2.50e+03 pdb=" O7 NAG D1002 " -0.015 2.00e-02 2.50e+03 ... (remaining 4501 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 5377 2.77 - 3.30: 23313 3.30 - 3.83: 40589 3.83 - 4.37: 48169 4.37 - 4.90: 80579 Nonbonded interactions: 198027 Sorted by model distance: nonbonded pdb=" OH TYR B 534 " pdb=" OD2 ASP B 813 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR D 534 " pdb=" OD2 ASP D 813 " model vdw 2.232 3.040 nonbonded pdb=" OE2 GLU B 526 " pdb=" OH TYR B 540 " model vdw 2.244 3.040 nonbonded pdb=" OE2 GLU D 526 " pdb=" OH TYR D 540 " model vdw 2.244 3.040 nonbonded pdb=" OE2 GLU A 526 " pdb=" OH TYR A 540 " model vdw 2.253 3.040 ... (remaining 198022 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 56 through 842 or resid 853 through 1004)) selection = chain 'B' selection = (chain 'C' and (resid 56 through 842 or resid 853 through 1004)) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 4.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 23.690 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 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 : 0.010 0.353 25928 Z= 0.611 Angle : 1.063 20.468 35296 Z= 0.581 Chirality : 0.145 4.940 4022 Planarity : 0.010 0.302 4488 Dihedral : 14.007 103.472 9688 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 0.67 % Allowed : 4.81 % Favored : 94.53 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.49 (0.10), residues: 3136 helix: -4.20 (0.06), residues: 1386 sheet: -3.42 (0.20), residues: 420 loop : -2.85 (0.14), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 172 TYR 0.037 0.003 TYR D 474 PHE 0.027 0.003 PHE C 612 TRP 0.034 0.003 TRP C 193 HIS 0.008 0.002 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00904 (25896) covalent geometry : angle 1.03576 (35216) SS BOND : bond 0.00201 ( 4) SS BOND : angle 2.46062 ( 8) hydrogen bonds : bond 0.29689 ( 806) hydrogen bonds : angle 10.33790 ( 2394) Misc. bond : bond 0.34927 ( 4) link_BETA1-4 : bond 0.01443 ( 8) link_BETA1-4 : angle 2.98725 ( 24) link_NAG-ASN : bond 0.01903 ( 16) link_NAG-ASN : angle 6.13571 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 424 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 MET cc_start: 0.9110 (tpt) cc_final: 0.8884 (tpp) REVERT: A 422 ASN cc_start: 0.8220 (m-40) cc_final: 0.7457 (p0) REVERT: A 609 LEU cc_start: 0.8935 (mt) cc_final: 0.8608 (pt) REVERT: B 468 ARG cc_start: 0.8183 (ttp-110) cc_final: 0.7876 (ptp-110) REVERT: B 562 ASP cc_start: 0.7440 (t0) cc_final: 0.7178 (t0) REVERT: B 582 ASP cc_start: 0.8105 (m-30) cc_final: 0.7809 (p0) REVERT: B 616 MET cc_start: 0.5635 (mmt) cc_final: 0.5086 (tpp) REVERT: B 772 ASP cc_start: 0.8043 (m-30) cc_final: 0.7795 (m-30) REVERT: C 397 MET cc_start: 0.9107 (tpt) cc_final: 0.8857 (tpt) REVERT: C 403 MET cc_start: 0.7847 (tpp) cc_final: 0.7627 (tpp) REVERT: C 422 ASN cc_start: 0.8030 (m-40) cc_final: 0.7390 (p0) REVERT: C 616 MET cc_start: 0.7412 (tpp) cc_final: 0.7139 (tpt) REVERT: C 754 TYR cc_start: 0.8209 (m-10) cc_final: 0.7795 (m-10) REVERT: D 141 ILE cc_start: 0.9095 (mm) cc_final: 0.8543 (mm) REVERT: D 468 ARG cc_start: 0.8022 (ttp-110) cc_final: 0.7639 (ptp-110) REVERT: D 562 ASP cc_start: 0.7671 (t0) cc_final: 0.7451 (t0) REVERT: D 582 ASP cc_start: 0.8066 (m-30) cc_final: 0.7717 (p0) REVERT: D 616 MET cc_start: 0.4925 (mmt) cc_final: 0.4606 (mtm) REVERT: D 722 ILE cc_start: 0.8156 (mt) cc_final: 0.7880 (mp) REVERT: D 772 ASP cc_start: 0.8245 (m-30) cc_final: 0.7987 (m-30) outliers start: 18 outliers final: 4 residues processed: 436 average time/residue: 0.1772 time to fit residues: 118.7852 Evaluate side-chains 226 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 222 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 853 LEU Chi-restraints excluded: chain C residue 273 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 175 GLN A 182 HIS A 331 ASN A 365 ASN A 391 ASN ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 ASN A 557 ASN A 689 ASN A 704 GLN A 725 GLN A 732 ASN A 736 ASN A 805 GLN A 831 HIS B 89 ASN B 180 GLN B 182 HIS B 257 HIS B 307 GLN B 331 ASN B 365 ASN B 383 GLN B 391 ASN B 451 HIS B 466 ASN B 554 ASN B 557 ASN B 732 ASN B 831 HIS C 89 ASN C 175 GLN C 182 HIS C 365 ASN C 391 ASN ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 ASN C 557 ASN C 689 ASN C 704 GLN C 725 GLN C 736 ASN C 831 HIS C 839 HIS D 89 ASN D 180 GLN D 182 HIS D 257 HIS D 307 GLN D 331 ASN D 365 ASN D 391 ASN D 554 ASN D 557 ASN D 732 ASN D 831 HIS Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.131296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.098849 restraints weight = 49284.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.099111 restraints weight = 31631.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.100093 restraints weight = 29621.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.101094 restraints weight = 21005.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.102626 restraints weight = 18489.157| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25928 Z= 0.142 Angle : 0.710 17.185 35296 Z= 0.355 Chirality : 0.055 1.216 4022 Planarity : 0.006 0.053 4488 Dihedral : 11.683 75.430 4018 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.26 % Allowed : 8.62 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.92 (0.12), residues: 3136 helix: -2.64 (0.10), residues: 1410 sheet: -2.83 (0.22), residues: 410 loop : -2.26 (0.15), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 436 TYR 0.025 0.002 TYR A 456 PHE 0.024 0.002 PHE C 396 TRP 0.015 0.001 TRP C 800 HIS 0.008 0.001 HIS A 839 Details of bonding type rmsd covalent geometry : bond 0.00307 (25896) covalent geometry : angle 0.67863 (35216) SS BOND : bond 0.00119 ( 4) SS BOND : angle 1.11494 ( 8) hydrogen bonds : bond 0.04564 ( 806) hydrogen bonds : angle 5.49225 ( 2394) Misc. bond : bond 0.00229 ( 4) link_BETA1-4 : bond 0.00827 ( 8) link_BETA1-4 : angle 2.63597 ( 24) link_NAG-ASN : bond 0.00928 ( 16) link_NAG-ASN : angle 5.36676 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 276 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8368 (tt) cc_final: 0.8065 (mt) REVERT: A 169 TYR cc_start: 0.8848 (m-80) cc_final: 0.8363 (m-10) REVERT: A 276 MET cc_start: 0.8510 (ttm) cc_final: 0.8300 (mtp) REVERT: A 397 MET cc_start: 0.9180 (tpt) cc_final: 0.8971 (tpp) REVERT: A 553 ASP cc_start: 0.8123 (t0) cc_final: 0.7778 (t70) REVERT: A 609 LEU cc_start: 0.9060 (mt) cc_final: 0.8767 (tp) REVERT: A 683 PHE cc_start: 0.7062 (m-10) cc_final: 0.6803 (t80) REVERT: A 820 GLN cc_start: 0.7777 (tm-30) cc_final: 0.7478 (tm-30) REVERT: B 307 GLN cc_start: 0.7099 (OUTLIER) cc_final: 0.6522 (tm130) REVERT: B 468 ARG cc_start: 0.8228 (ttp-110) cc_final: 0.7972 (ptp-110) REVERT: B 562 ASP cc_start: 0.7511 (t0) cc_final: 0.7108 (t0) REVERT: B 616 MET cc_start: 0.5755 (mmt) cc_final: 0.5305 (tpp) REVERT: B 861 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7481 (tm) REVERT: C 297 HIS cc_start: 0.6376 (p-80) cc_final: 0.5930 (p-80) REVERT: C 403 MET cc_start: 0.7963 (tpp) cc_final: 0.7523 (tpp) REVERT: C 422 ASN cc_start: 0.8080 (m-40) cc_final: 0.7234 (p0) REVERT: C 553 ASP cc_start: 0.7872 (t70) cc_final: 0.7422 (t70) REVERT: C 630 MET cc_start: 0.7732 (tpp) cc_final: 0.7286 (tmm) REVERT: C 675 ARG cc_start: 0.4459 (mtt180) cc_final: 0.3887 (mtp180) REVERT: C 683 PHE cc_start: 0.6808 (m-10) cc_final: 0.6554 (t80) REVERT: C 754 TYR cc_start: 0.8429 (m-10) cc_final: 0.7708 (m-80) REVERT: C 820 GLN cc_start: 0.7847 (tm-30) cc_final: 0.7525 (tm-30) REVERT: D 307 GLN cc_start: 0.7000 (OUTLIER) cc_final: 0.6460 (tm130) REVERT: D 468 ARG cc_start: 0.8079 (ttp-110) cc_final: 0.7737 (ptp-110) REVERT: D 562 ASP cc_start: 0.7545 (t0) cc_final: 0.7194 (t0) REVERT: D 616 MET cc_start: 0.5235 (mmt) cc_final: 0.4495 (mpp) REVERT: D 625 LEU cc_start: 0.9319 (mt) cc_final: 0.9114 (mt) REVERT: D 722 ILE cc_start: 0.8073 (mt) cc_final: 0.7781 (mp) REVERT: D 828 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7651 (pm20) outliers start: 61 outliers final: 28 residues processed: 324 average time/residue: 0.1680 time to fit residues: 85.5659 Evaluate side-chains 241 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 209 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 568 VAL Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 732 ASN Chi-restraints excluded: chain C residue 865 CYS Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 307 GLN Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 828 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 207 optimal weight: 5.9990 chunk 257 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 246 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 192 optimal weight: 0.4980 chunk 308 optimal weight: 8.9990 chunk 114 optimal weight: 8.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 ASN A 725 GLN B 307 GLN ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 ASN C 725 GLN D 307 GLN D 466 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.118876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.079750 restraints weight = 50344.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.081159 restraints weight = 31537.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.082234 restraints weight = 21948.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.083921 restraints weight = 19222.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.084076 restraints weight = 16538.670| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 25928 Z= 0.273 Angle : 0.743 13.556 35296 Z= 0.375 Chirality : 0.052 0.533 4022 Planarity : 0.005 0.064 4488 Dihedral : 9.884 68.821 4016 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.44 % Allowed : 10.17 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.13), residues: 3136 helix: -1.67 (0.12), residues: 1398 sheet: -2.60 (0.23), residues: 384 loop : -2.17 (0.16), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 675 TYR 0.021 0.002 TYR B 178 PHE 0.027 0.002 PHE A 623 TRP 0.017 0.002 TRP C 193 HIS 0.005 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00638 (25896) covalent geometry : angle 0.71865 (35216) SS BOND : bond 0.00060 ( 4) SS BOND : angle 1.10441 ( 8) hydrogen bonds : bond 0.04150 ( 806) hydrogen bonds : angle 5.22612 ( 2394) Misc. bond : bond 0.00025 ( 4) link_BETA1-4 : bond 0.00749 ( 8) link_BETA1-4 : angle 2.95584 ( 24) link_NAG-ASN : bond 0.00678 ( 16) link_NAG-ASN : angle 4.78843 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 216 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8378 (tt) cc_final: 0.8162 (mt) REVERT: A 169 TYR cc_start: 0.8857 (m-80) cc_final: 0.8267 (m-10) REVERT: A 181 MET cc_start: 0.7791 (mpp) cc_final: 0.7556 (tpp) REVERT: A 305 LEU cc_start: 0.8011 (mp) cc_final: 0.7688 (mp) REVERT: A 553 ASP cc_start: 0.8332 (t0) cc_final: 0.7886 (t70) REVERT: A 609 LEU cc_start: 0.9062 (mt) cc_final: 0.8825 (tp) REVERT: A 630 MET cc_start: 0.7978 (mmt) cc_final: 0.7229 (tmm) REVERT: A 683 PHE cc_start: 0.6803 (m-10) cc_final: 0.6561 (t80) REVERT: A 804 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7590 (m-10) REVERT: A 820 GLN cc_start: 0.7853 (tm-30) cc_final: 0.7372 (tm-30) REVERT: B 140 MET cc_start: 0.7062 (tpt) cc_final: 0.6827 (tpt) REVERT: B 307 GLN cc_start: 0.7124 (OUTLIER) cc_final: 0.6498 (tm130) REVERT: B 468 ARG cc_start: 0.8212 (ttp-110) cc_final: 0.7846 (ptp-110) REVERT: B 562 ASP cc_start: 0.7947 (t0) cc_final: 0.7665 (t0) REVERT: B 616 MET cc_start: 0.5644 (mmt) cc_final: 0.4838 (tpp) REVERT: C 295 MET cc_start: 0.6960 (mmm) cc_final: 0.6551 (mtt) REVERT: C 297 HIS cc_start: 0.6601 (p-80) cc_final: 0.6244 (p-80) REVERT: C 422 ASN cc_start: 0.8166 (m-40) cc_final: 0.7185 (p0) REVERT: C 553 ASP cc_start: 0.8228 (t70) cc_final: 0.7736 (t70) REVERT: C 630 MET cc_start: 0.7889 (tpp) cc_final: 0.7658 (tmm) REVERT: C 676 PHE cc_start: 0.7508 (t80) cc_final: 0.7250 (t80) REVERT: C 683 PHE cc_start: 0.6680 (m-10) cc_final: 0.6352 (t80) REVERT: C 754 TYR cc_start: 0.8372 (m-10) cc_final: 0.7705 (m-80) REVERT: C 820 GLN cc_start: 0.7952 (tm-30) cc_final: 0.7448 (tm-30) REVERT: D 307 GLN cc_start: 0.7068 (OUTLIER) cc_final: 0.6428 (tm130) REVERT: D 468 ARG cc_start: 0.8147 (ttp-110) cc_final: 0.7745 (ptp-110) REVERT: D 562 ASP cc_start: 0.7920 (t0) cc_final: 0.7713 (t0) REVERT: D 616 MET cc_start: 0.5246 (mmt) cc_final: 0.4317 (mpp) REVERT: D 683 PHE cc_start: 0.8224 (t80) cc_final: 0.7950 (t80) REVERT: D 722 ILE cc_start: 0.7814 (mt) cc_final: 0.7495 (mp) REVERT: D 828 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7819 (pm20) outliers start: 93 outliers final: 61 residues processed: 292 average time/residue: 0.1481 time to fit residues: 71.2695 Evaluate side-chains 265 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 200 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 842 SER Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 783 ASN Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 878 TRP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain C residue 582 ASP Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 682 LEU Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain C residue 865 CYS Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 307 GLN Chi-restraints excluded: chain D residue 317 ILE Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 570 ASP Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 767 VAL Chi-restraints excluded: chain D residue 798 THR Chi-restraints excluded: chain D residue 828 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 283 optimal weight: 0.7980 chunk 194 optimal weight: 6.9990 chunk 101 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 226 optimal weight: 9.9990 chunk 130 optimal weight: 0.9980 chunk 245 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 227 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 196 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 GLN B 307 GLN B 736 ASN ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 725 GLN D 307 GLN D 451 HIS D 736 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.122973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.084069 restraints weight = 49490.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.085619 restraints weight = 30260.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.086570 restraints weight = 21232.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.087218 restraints weight = 18956.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.087804 restraints weight = 17276.848| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25928 Z= 0.115 Angle : 0.607 13.374 35296 Z= 0.301 Chirality : 0.046 0.390 4022 Planarity : 0.004 0.048 4488 Dihedral : 8.616 67.251 4016 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.44 % Allowed : 12.39 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.14), residues: 3136 helix: -1.09 (0.13), residues: 1402 sheet: -2.30 (0.24), residues: 384 loop : -1.93 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 221 TYR 0.020 0.001 TYR B 440 PHE 0.025 0.001 PHE C 623 TRP 0.014 0.001 TRP A 193 HIS 0.002 0.000 HIS A 831 Details of bonding type rmsd covalent geometry : bond 0.00257 (25896) covalent geometry : angle 0.58319 (35216) SS BOND : bond 0.00096 ( 4) SS BOND : angle 0.76856 ( 8) hydrogen bonds : bond 0.03218 ( 806) hydrogen bonds : angle 4.70039 ( 2394) Misc. bond : bond 0.00017 ( 4) link_BETA1-4 : bond 0.00857 ( 8) link_BETA1-4 : angle 2.85668 ( 24) link_NAG-ASN : bond 0.00777 ( 16) link_NAG-ASN : angle 4.16656 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 211 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8393 (tt) cc_final: 0.8142 (mt) REVERT: A 169 TYR cc_start: 0.8839 (m-80) cc_final: 0.8293 (m-10) REVERT: A 275 MET cc_start: 0.7709 (mtp) cc_final: 0.7501 (mtp) REVERT: A 553 ASP cc_start: 0.8143 (t0) cc_final: 0.7754 (t70) REVERT: A 630 MET cc_start: 0.8090 (mmt) cc_final: 0.7375 (tmm) REVERT: A 683 PHE cc_start: 0.6892 (m-10) cc_final: 0.6582 (t80) REVERT: A 804 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.7365 (m-10) REVERT: A 820 GLN cc_start: 0.7802 (tm-30) cc_final: 0.7349 (tm-30) REVERT: B 137 ILE cc_start: 0.8988 (mt) cc_final: 0.8668 (mm) REVERT: B 468 ARG cc_start: 0.8216 (ttp-110) cc_final: 0.7922 (ptp-110) REVERT: B 562 ASP cc_start: 0.7913 (t0) cc_final: 0.7707 (t0) REVERT: B 616 MET cc_start: 0.5529 (mmt) cc_final: 0.4867 (tpp) REVERT: B 772 ASP cc_start: 0.7803 (m-30) cc_final: 0.7541 (m-30) REVERT: C 159 ASP cc_start: 0.8292 (OUTLIER) cc_final: 0.8050 (m-30) REVERT: C 403 MET cc_start: 0.7999 (tpp) cc_final: 0.7701 (tpp) REVERT: C 422 ASN cc_start: 0.8166 (m-40) cc_final: 0.7183 (p0) REVERT: C 485 TRP cc_start: 0.8277 (t-100) cc_final: 0.8077 (t60) REVERT: C 553 ASP cc_start: 0.8030 (t70) cc_final: 0.7600 (t70) REVERT: C 676 PHE cc_start: 0.7463 (t80) cc_final: 0.7220 (t80) REVERT: C 683 PHE cc_start: 0.6765 (m-10) cc_final: 0.6357 (t80) REVERT: C 754 TYR cc_start: 0.8335 (m-10) cc_final: 0.7741 (m-80) REVERT: C 804 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7428 (m-10) REVERT: C 820 GLN cc_start: 0.7859 (tm-30) cc_final: 0.7372 (tm-30) REVERT: D 468 ARG cc_start: 0.8157 (ttp-110) cc_final: 0.7824 (ptp-110) REVERT: D 562 ASP cc_start: 0.7873 (t0) cc_final: 0.7672 (t0) REVERT: D 616 MET cc_start: 0.5100 (mmt) cc_final: 0.4266 (mpp) REVERT: D 683 PHE cc_start: 0.8184 (t80) cc_final: 0.7969 (t80) REVERT: D 722 ILE cc_start: 0.7823 (mt) cc_final: 0.7497 (mp) REVERT: D 772 ASP cc_start: 0.8003 (m-30) cc_final: 0.7749 (m-30) outliers start: 66 outliers final: 47 residues processed: 265 average time/residue: 0.1514 time to fit residues: 66.1713 Evaluate side-chains 242 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 192 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 496 ILE Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 614 ILE Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 783 ASN Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 682 LEU Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 725 GLN Chi-restraints excluded: chain C residue 804 PHE Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain C residue 865 CYS Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 609 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 234 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 197 optimal weight: 8.9990 chunk 212 optimal weight: 0.0470 chunk 185 optimal weight: 5.9990 chunk 224 optimal weight: 0.3980 chunk 72 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 284 optimal weight: 10.0000 chunk 223 optimal weight: 1.9990 chunk 201 optimal weight: 10.0000 overall best weight: 1.6884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 GLN B 383 GLN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 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 = 0.3871 r_free = 0.3871 target = 0.122095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.083454 restraints weight = 49223.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.084823 restraints weight = 29783.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.086021 restraints weight = 20930.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.087747 restraints weight = 18156.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.087851 restraints weight = 15700.317| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25928 Z= 0.150 Angle : 0.612 13.458 35296 Z= 0.303 Chirality : 0.046 0.348 4022 Planarity : 0.004 0.047 4488 Dihedral : 8.052 62.979 4016 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.77 % Allowed : 12.65 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.14), residues: 3136 helix: -0.72 (0.13), residues: 1388 sheet: -2.05 (0.25), residues: 388 loop : -1.89 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 501 TYR 0.014 0.001 TYR D 178 PHE 0.024 0.001 PHE A 623 TRP 0.048 0.001 TRP A 485 HIS 0.003 0.001 HIS D 451 Details of bonding type rmsd covalent geometry : bond 0.00351 (25896) covalent geometry : angle 0.58935 (35216) SS BOND : bond 0.00132 ( 4) SS BOND : angle 0.56031 ( 8) hydrogen bonds : bond 0.03178 ( 806) hydrogen bonds : angle 4.59860 ( 2394) Misc. bond : bond 0.00023 ( 4) link_BETA1-4 : bond 0.00808 ( 8) link_BETA1-4 : angle 2.82573 ( 24) link_NAG-ASN : bond 0.00648 ( 16) link_NAG-ASN : angle 4.05418 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 203 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.8320 (tt) cc_final: 0.8081 (mt) REVERT: A 169 TYR cc_start: 0.8825 (m-80) cc_final: 0.8256 (m-10) REVERT: A 335 ASN cc_start: 0.8313 (t0) cc_final: 0.8080 (t0) REVERT: A 553 ASP cc_start: 0.8198 (t0) cc_final: 0.7813 (t70) REVERT: A 630 MET cc_start: 0.8110 (mmt) cc_final: 0.7420 (tmm) REVERT: A 683 PHE cc_start: 0.6888 (m-10) cc_final: 0.6584 (t80) REVERT: A 804 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7446 (m-10) REVERT: A 820 GLN cc_start: 0.7840 (tm-30) cc_final: 0.7365 (tm-30) REVERT: B 307 GLN cc_start: 0.7098 (OUTLIER) cc_final: 0.6823 (tm-30) REVERT: B 433 THR cc_start: 0.7832 (m) cc_final: 0.7467 (t) REVERT: B 468 ARG cc_start: 0.8214 (ttp-110) cc_final: 0.7919 (ptp-110) REVERT: B 616 MET cc_start: 0.5501 (mmt) cc_final: 0.4760 (tpp) REVERT: B 772 ASP cc_start: 0.7816 (m-30) cc_final: 0.7502 (m-30) REVERT: C 422 ASN cc_start: 0.8172 (m-40) cc_final: 0.7151 (p0) REVERT: C 553 ASP cc_start: 0.8109 (t70) cc_final: 0.7672 (t70) REVERT: C 683 PHE cc_start: 0.6877 (m-10) cc_final: 0.6595 (t80) REVERT: C 754 TYR cc_start: 0.8356 (m-10) cc_final: 0.7745 (m-80) REVERT: C 804 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7433 (m-10) REVERT: C 820 GLN cc_start: 0.7839 (tm-30) cc_final: 0.7347 (tm-30) REVERT: D 307 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.6472 (tm130) REVERT: D 468 ARG cc_start: 0.8162 (ttp-110) cc_final: 0.7840 (ptp-110) REVERT: D 616 MET cc_start: 0.5057 (mmt) cc_final: 0.4281 (mpp) REVERT: D 722 ILE cc_start: 0.7815 (mt) cc_final: 0.7494 (mp) outliers start: 75 outliers final: 52 residues processed: 264 average time/residue: 0.1480 time to fit residues: 65.0886 Evaluate side-chains 246 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 190 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 686 LEU Chi-restraints excluded: chain B residue 783 ASN Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 878 TRP Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 419 ASN Chi-restraints excluded: chain C residue 566 VAL Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 682 LEU Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 804 PHE Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 845 ILE Chi-restraints excluded: chain C residue 865 CYS Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 307 GLN Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 570 ASP Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 798 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 196 optimal weight: 0.0170 chunk 102 optimal weight: 0.9990 chunk 176 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 269 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 140 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 HIS A 725 GLN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 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 = 0.4123 r_free = 0.4123 target = 0.133209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.101556 restraints weight = 49612.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.101097 restraints weight = 32050.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.101970 restraints weight = 32875.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.102965 restraints weight = 22579.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.103766 restraints weight = 19959.116| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 25928 Z= 0.102 Angle : 0.569 13.196 35296 Z= 0.282 Chirality : 0.044 0.360 4022 Planarity : 0.004 0.046 4488 Dihedral : 7.187 58.990 4016 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.44 % Allowed : 13.24 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.15), residues: 3136 helix: -0.29 (0.14), residues: 1384 sheet: -1.78 (0.26), residues: 386 loop : -1.77 (0.16), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 501 TYR 0.010 0.001 TYR D 504 PHE 0.031 0.001 PHE A 623 TRP 0.030 0.001 TRP C 681 HIS 0.002 0.000 HIS B 444 Details of bonding type rmsd covalent geometry : bond 0.00230 (25896) covalent geometry : angle 0.54761 (35216) SS BOND : bond 0.00953 ( 4) SS BOND : angle 0.55016 ( 8) hydrogen bonds : bond 0.02836 ( 806) hydrogen bonds : angle 4.32735 ( 2394) Misc. bond : bond 0.00025 ( 4) link_BETA1-4 : bond 0.00731 ( 8) link_BETA1-4 : angle 2.72832 ( 24) link_NAG-ASN : bond 0.00674 ( 16) link_NAG-ASN : angle 3.81517 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 208 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: A 169 TYR cc_start: 0.8740 (m-80) cc_final: 0.8382 (m-10) REVERT: A 553 ASP cc_start: 0.7978 (t0) cc_final: 0.7768 (t70) REVERT: A 630 MET cc_start: 0.8127 (mmt) cc_final: 0.7514 (tmm) REVERT: A 683 PHE cc_start: 0.7172 (m-10) cc_final: 0.6914 (t80) REVERT: A 804 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7781 (m-10) REVERT: A 820 GLN cc_start: 0.7793 (tm-30) cc_final: 0.7459 (tm-30) REVERT: B 137 ILE cc_start: 0.8915 (mt) cc_final: 0.8655 (mm) REVERT: B 616 MET cc_start: 0.5702 (mmt) cc_final: 0.5205 (mpp) REVERT: B 772 ASP cc_start: 0.7755 (m-30) cc_final: 0.7522 (m-30) REVERT: B 814 MET cc_start: 0.8628 (tpp) cc_final: 0.8127 (ttm) REVERT: C 422 ASN cc_start: 0.8065 (m-40) cc_final: 0.7237 (p0) REVERT: C 553 ASP cc_start: 0.7858 (t70) cc_final: 0.7595 (t70) REVERT: C 754 TYR cc_start: 0.8471 (m-10) cc_final: 0.7851 (m-80) REVERT: C 804 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.7668 (m-10) REVERT: C 820 GLN cc_start: 0.7814 (tm-30) cc_final: 0.7468 (tm-30) REVERT: D 616 MET cc_start: 0.5207 (mmt) cc_final: 0.4455 (mpp) REVERT: D 722 ILE cc_start: 0.8140 (mt) cc_final: 0.7837 (mp) REVERT: D 772 ASP cc_start: 0.7798 (m-30) cc_final: 0.7590 (m-30) outliers start: 66 outliers final: 45 residues processed: 260 average time/residue: 0.1484 time to fit residues: 64.2283 Evaluate side-chains 232 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 185 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 725 GLN Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 783 ASN Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 878 TRP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 804 PHE Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 865 CYS Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 819 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 154 optimal weight: 7.9990 chunk 57 optimal weight: 50.0000 chunk 219 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 160 optimal weight: 0.7980 chunk 222 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 GLN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.129498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.091864 restraints weight = 49531.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.093336 restraints weight = 28472.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.094277 restraints weight = 21748.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.094772 restraints weight = 19900.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.094821 restraints weight = 18294.061| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25928 Z= 0.128 Angle : 0.583 13.270 35296 Z= 0.287 Chirality : 0.045 0.342 4022 Planarity : 0.004 0.046 4488 Dihedral : 6.951 59.026 4016 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.03 % Allowed : 13.24 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.15), residues: 3136 helix: -0.02 (0.14), residues: 1378 sheet: -1.56 (0.27), residues: 372 loop : -1.75 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 468 TYR 0.011 0.001 TYR D 178 PHE 0.025 0.001 PHE C 683 TRP 0.049 0.001 TRP C 485 HIS 0.002 0.001 HIS D 444 Details of bonding type rmsd covalent geometry : bond 0.00300 (25896) covalent geometry : angle 0.56210 (35216) SS BOND : bond 0.00044 ( 4) SS BOND : angle 0.32406 ( 8) hydrogen bonds : bond 0.02867 ( 806) hydrogen bonds : angle 4.28230 ( 2394) Misc. bond : bond 0.00021 ( 4) link_BETA1-4 : bond 0.00736 ( 8) link_BETA1-4 : angle 2.71741 ( 24) link_NAG-ASN : bond 0.00639 ( 16) link_NAG-ASN : angle 3.79924 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 196 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 140 MET cc_start: 0.7775 (mmm) cc_final: 0.6940 (mtt) REVERT: A 169 TYR cc_start: 0.8794 (m-80) cc_final: 0.8317 (m-10) REVERT: A 553 ASP cc_start: 0.8149 (t0) cc_final: 0.7830 (t70) REVERT: A 610 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8219 (mmmt) REVERT: A 630 MET cc_start: 0.8189 (mmt) cc_final: 0.7567 (tmm) REVERT: A 804 PHE cc_start: 0.8290 (OUTLIER) cc_final: 0.7690 (m-10) REVERT: B 150 VAL cc_start: 0.9228 (t) cc_final: 0.8969 (m) REVERT: B 307 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.6781 (tm-30) REVERT: B 616 MET cc_start: 0.5600 (mmt) cc_final: 0.5052 (mpp) REVERT: C 422 ASN cc_start: 0.8131 (m-40) cc_final: 0.7180 (p0) REVERT: C 468 ARG cc_start: 0.7479 (mtm110) cc_final: 0.7260 (mtm-85) REVERT: C 553 ASP cc_start: 0.8062 (t70) cc_final: 0.7678 (t70) REVERT: C 570 ASP cc_start: 0.7127 (t0) cc_final: 0.6782 (t70) REVERT: C 754 TYR cc_start: 0.8457 (m-10) cc_final: 0.7841 (m-80) REVERT: C 820 GLN cc_start: 0.7835 (tm-30) cc_final: 0.7407 (tm-30) REVERT: D 616 MET cc_start: 0.5126 (mmt) cc_final: 0.4331 (mpp) REVERT: D 630 MET cc_start: 0.8377 (mmt) cc_final: 0.7955 (mtt) REVERT: D 722 ILE cc_start: 0.7849 (mt) cc_final: 0.7533 (mp) outliers start: 82 outliers final: 57 residues processed: 261 average time/residue: 0.1427 time to fit residues: 62.6845 Evaluate side-chains 245 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 185 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 610 LYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 783 ASN Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain B residue 878 TRP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 865 CYS Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 523 ASP Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 798 THR Chi-restraints excluded: chain D residue 818 ILE Chi-restraints excluded: chain D residue 819 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 259 optimal weight: 2.9990 chunk 281 optimal weight: 0.6980 chunk 118 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 190 optimal weight: 6.9990 chunk 253 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 226 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 36 optimal weight: 0.0050 overall best weight: 1.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN ** C 429 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 = 0.4050 r_free = 0.4050 target = 0.129038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.091850 restraints weight = 49816.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.093101 restraints weight = 28985.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.093733 restraints weight = 23147.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.094174 restraints weight = 21444.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.094345 restraints weight = 18941.623| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25928 Z= 0.140 Angle : 0.591 13.281 35296 Z= 0.291 Chirality : 0.045 0.339 4022 Planarity : 0.004 0.047 4488 Dihedral : 6.734 59.253 4016 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.07 % Allowed : 13.57 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.15), residues: 3136 helix: 0.19 (0.14), residues: 1378 sheet: -1.60 (0.27), residues: 378 loop : -1.64 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 468 TYR 0.012 0.001 TYR D 178 PHE 0.024 0.001 PHE B 683 TRP 0.028 0.001 TRP C 485 HIS 0.004 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00327 (25896) covalent geometry : angle 0.57115 (35216) SS BOND : bond 0.00073 ( 4) SS BOND : angle 0.33030 ( 8) hydrogen bonds : bond 0.02867 ( 806) hydrogen bonds : angle 4.23065 ( 2394) Misc. bond : bond 0.00024 ( 4) link_BETA1-4 : bond 0.00778 ( 8) link_BETA1-4 : angle 2.65374 ( 24) link_NAG-ASN : bond 0.00645 ( 16) link_NAG-ASN : angle 3.78817 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 192 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: A 140 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6946 (mtt) REVERT: A 169 TYR cc_start: 0.8785 (m-80) cc_final: 0.8358 (m-10) REVERT: A 335 ASN cc_start: 0.8281 (t0) cc_final: 0.8044 (t0) REVERT: A 553 ASP cc_start: 0.8118 (t0) cc_final: 0.7815 (t70) REVERT: A 630 MET cc_start: 0.8189 (mmt) cc_final: 0.7670 (mtt) REVERT: A 804 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7674 (m-10) REVERT: B 150 VAL cc_start: 0.9273 (t) cc_final: 0.8971 (m) REVERT: B 307 GLN cc_start: 0.7013 (OUTLIER) cc_final: 0.6769 (tm-30) REVERT: B 616 MET cc_start: 0.5614 (mmt) cc_final: 0.5144 (mtt) REVERT: B 772 ASP cc_start: 0.7722 (m-30) cc_final: 0.7493 (m-30) REVERT: C 295 MET cc_start: 0.6525 (mpp) cc_final: 0.6319 (mpp) REVERT: C 422 ASN cc_start: 0.8128 (m-40) cc_final: 0.7199 (p0) REVERT: C 553 ASP cc_start: 0.8052 (t70) cc_final: 0.7691 (t70) REVERT: C 570 ASP cc_start: 0.7253 (t0) cc_final: 0.6935 (t70) REVERT: C 754 TYR cc_start: 0.8525 (m-10) cc_final: 0.7863 (m-80) REVERT: C 820 GLN cc_start: 0.7836 (tm-30) cc_final: 0.7426 (tm-30) REVERT: D 307 GLN cc_start: 0.6996 (OUTLIER) cc_final: 0.6743 (tm-30) REVERT: D 616 MET cc_start: 0.5265 (mmt) cc_final: 0.4672 (mpp) REVERT: D 623 PHE cc_start: 0.7729 (m-10) cc_final: 0.6452 (t80) REVERT: D 630 MET cc_start: 0.8346 (mmt) cc_final: 0.8098 (mtt) REVERT: D 722 ILE cc_start: 0.7974 (mt) cc_final: 0.7663 (mp) outliers start: 83 outliers final: 58 residues processed: 258 average time/residue: 0.1427 time to fit residues: 61.9086 Evaluate side-chains 247 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 185 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 783 ASN Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 865 CYS Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 307 GLN Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 433 THR Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 798 THR Chi-restraints excluded: chain D residue 818 ILE Chi-restraints excluded: chain D residue 819 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 144 optimal weight: 0.2980 chunk 2 optimal weight: 6.9990 chunk 287 optimal weight: 0.8980 chunk 195 optimal weight: 10.0000 chunk 235 optimal weight: 8.9990 chunk 269 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 312 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 170 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 ASN B 383 GLN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS C 554 ASN D 405 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.130210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.097543 restraints weight = 49641.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.098026 restraints weight = 30709.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.098908 restraints weight = 29003.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.099870 restraints weight = 21029.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.101278 restraints weight = 18543.894| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25928 Z= 0.110 Angle : 0.568 13.198 35296 Z= 0.278 Chirality : 0.044 0.349 4022 Planarity : 0.004 0.047 4488 Dihedral : 6.480 58.548 4016 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.74 % Allowed : 14.02 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.15), residues: 3136 helix: 0.40 (0.14), residues: 1378 sheet: -1.56 (0.27), residues: 370 loop : -1.62 (0.16), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 468 TYR 0.018 0.001 TYR B 504 PHE 0.016 0.001 PHE C 626 TRP 0.022 0.001 TRP C 485 HIS 0.004 0.000 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00256 (25896) covalent geometry : angle 0.54745 (35216) SS BOND : bond 0.00046 ( 4) SS BOND : angle 0.40070 ( 8) hydrogen bonds : bond 0.02718 ( 806) hydrogen bonds : angle 4.13849 ( 2394) Misc. bond : bond 0.00022 ( 4) link_BETA1-4 : bond 0.00770 ( 8) link_BETA1-4 : angle 2.54625 ( 24) link_NAG-ASN : bond 0.00655 ( 16) link_NAG-ASN : angle 3.72452 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 193 time to evaluate : 0.933 Fit side-chains REVERT: A 140 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.7086 (mtt) REVERT: A 169 TYR cc_start: 0.8808 (m-80) cc_final: 0.8361 (m-10) REVERT: A 553 ASP cc_start: 0.8050 (t0) cc_final: 0.7753 (t70) REVERT: A 630 MET cc_start: 0.8185 (mmt) cc_final: 0.7637 (mtt) REVERT: A 804 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7657 (m-10) REVERT: B 150 VAL cc_start: 0.9258 (t) cc_final: 0.8928 (m) REVERT: B 523 ASP cc_start: 0.7821 (t0) cc_final: 0.7225 (m-30) REVERT: B 616 MET cc_start: 0.5613 (mmt) cc_final: 0.5333 (mpp) REVERT: B 772 ASP cc_start: 0.7676 (m-30) cc_final: 0.7382 (m-30) REVERT: C 422 ASN cc_start: 0.8076 (m-40) cc_final: 0.7142 (p0) REVERT: C 468 ARG cc_start: 0.7386 (mtm-85) cc_final: 0.7076 (mtm-85) REVERT: C 553 ASP cc_start: 0.7984 (t70) cc_final: 0.7586 (t70) REVERT: C 820 GLN cc_start: 0.7770 (tm-30) cc_final: 0.7362 (tm-30) REVERT: D 307 GLN cc_start: 0.6913 (OUTLIER) cc_final: 0.6681 (tm-30) REVERT: D 616 MET cc_start: 0.5248 (mmt) cc_final: 0.4726 (mpp) REVERT: D 623 PHE cc_start: 0.7754 (m-10) cc_final: 0.6507 (t80) REVERT: D 630 MET cc_start: 0.8312 (mmt) cc_final: 0.8071 (mtt) REVERT: D 722 ILE cc_start: 0.7990 (mt) cc_final: 0.7686 (mp) outliers start: 74 outliers final: 59 residues processed: 251 average time/residue: 0.1431 time to fit residues: 60.9890 Evaluate side-chains 252 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 190 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 710 GLU Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 570 ASP Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 783 ASN Chi-restraints excluded: chain B residue 786 CYS Chi-restraints excluded: chain B residue 798 THR Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 779 VAL Chi-restraints excluded: chain C residue 814 MET Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 865 CYS Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 307 GLN Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 437 THR Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 570 ASP Chi-restraints excluded: chain D residue 608 PHE Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 786 CYS Chi-restraints excluded: chain D residue 798 THR Chi-restraints excluded: chain D residue 818 ILE Chi-restraints excluded: chain D residue 819 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 159 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 61 optimal weight: 0.0980 chunk 218 optimal weight: 0.0170 chunk 294 optimal weight: 0.0170 chunk 22 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 274 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 251 optimal weight: 2.9990 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 GLN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 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 = 0.4091 r_free = 0.4091 target = 0.132167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.099585 restraints weight = 49252.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.100351 restraints weight = 29443.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.101028 restraints weight = 28629.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.102364 restraints weight = 20514.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.102967 restraints weight = 17914.435| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25928 Z= 0.094 Angle : 0.559 13.105 35296 Z= 0.273 Chirality : 0.043 0.359 4022 Planarity : 0.004 0.046 4488 Dihedral : 6.146 59.827 4014 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.00 % Allowed : 14.72 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.15), residues: 3136 helix: 0.64 (0.14), residues: 1366 sheet: -1.35 (0.28), residues: 356 loop : -1.66 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 501 TYR 0.016 0.001 TYR B 504 PHE 0.027 0.001 PHE B 683 TRP 0.018 0.001 TRP C 485 HIS 0.004 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00208 (25896) covalent geometry : angle 0.53926 (35216) SS BOND : bond 0.00075 ( 4) SS BOND : angle 0.40446 ( 8) hydrogen bonds : bond 0.02577 ( 806) hydrogen bonds : angle 4.04036 ( 2394) Misc. bond : bond 0.00019 ( 4) link_BETA1-4 : bond 0.00823 ( 8) link_BETA1-4 : angle 2.46164 ( 24) link_NAG-ASN : bond 0.00659 ( 16) link_NAG-ASN : angle 3.63715 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 210 time to evaluate : 0.866 Fit side-chains REVERT: A 140 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.7018 (mtt) REVERT: A 169 TYR cc_start: 0.8745 (m-80) cc_final: 0.8341 (m-10) REVERT: A 553 ASP cc_start: 0.7991 (t0) cc_final: 0.7683 (t70) REVERT: A 630 MET cc_start: 0.8170 (mmt) cc_final: 0.7618 (tmm) REVERT: A 820 GLN cc_start: 0.7724 (tm-30) cc_final: 0.7330 (tm-30) REVERT: B 137 ILE cc_start: 0.8962 (mt) cc_final: 0.8676 (mm) REVERT: B 523 ASP cc_start: 0.7628 (t0) cc_final: 0.7376 (m-30) REVERT: B 616 MET cc_start: 0.5511 (mmt) cc_final: 0.5235 (mpp) REVERT: B 772 ASP cc_start: 0.7517 (m-30) cc_final: 0.7273 (m-30) REVERT: C 422 ASN cc_start: 0.8022 (m-40) cc_final: 0.7090 (p0) REVERT: C 468 ARG cc_start: 0.7353 (mtm-85) cc_final: 0.7023 (mtm-85) REVERT: C 553 ASP cc_start: 0.7864 (t70) cc_final: 0.7472 (t70) REVERT: C 820 GLN cc_start: 0.7655 (tm-30) cc_final: 0.7374 (tm-30) REVERT: D 169 TYR cc_start: 0.8054 (m-10) cc_final: 0.7594 (m-10) REVERT: D 403 MET cc_start: 0.8372 (mmm) cc_final: 0.8032 (mmm) REVERT: D 509 SER cc_start: 0.8564 (p) cc_final: 0.7794 (m) REVERT: D 616 MET cc_start: 0.5118 (mmt) cc_final: 0.4662 (mtm) REVERT: D 623 PHE cc_start: 0.7648 (m-10) cc_final: 0.6500 (t80) REVERT: D 630 MET cc_start: 0.8271 (mmt) cc_final: 0.8069 (mtt) REVERT: D 722 ILE cc_start: 0.7940 (mt) cc_final: 0.7641 (mp) outliers start: 54 outliers final: 44 residues processed: 252 average time/residue: 0.1519 time to fit residues: 63.6540 Evaluate side-chains 241 residues out of total 2756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 196 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 419 ASN Chi-restraints excluded: chain A residue 608 PHE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 865 CYS Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 786 CYS Chi-restraints excluded: chain B residue 819 LEU Chi-restraints excluded: chain B residue 863 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 697 THR Chi-restraints excluded: chain C residue 814 MET Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 109 CYS Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 430 LEU Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain D residue 609 LEU Chi-restraints excluded: chain D residue 786 CYS Chi-restraints excluded: chain D residue 798 THR Chi-restraints excluded: chain D residue 819 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 102 optimal weight: 0.9980 chunk 265 optimal weight: 5.9990 chunk 223 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 124 optimal weight: 0.0010 chunk 207 optimal weight: 5.9990 chunk 36 optimal weight: 0.0040 chunk 72 optimal weight: 4.9990 chunk 209 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 HIS ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.131951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.099305 restraints weight = 49325.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.100312 restraints weight = 29150.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.101127 restraints weight = 26649.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.102029 restraints weight = 19970.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.102933 restraints weight = 17790.821| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 25928 Z= 0.098 Angle : 0.562 13.105 35296 Z= 0.274 Chirality : 0.044 0.344 4022 Planarity : 0.004 0.046 4488 Dihedral : 6.031 59.289 4014 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.03 % Allowed : 14.94 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.15), residues: 3136 helix: 0.77 (0.15), residues: 1354 sheet: -1.41 (0.28), residues: 378 loop : -1.58 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 501 TYR 0.019 0.001 TYR B 504 PHE 0.019 0.001 PHE A 804 TRP 0.036 0.001 TRP C 681 HIS 0.005 0.001 HIS B 314 Details of bonding type rmsd covalent geometry : bond 0.00224 (25896) covalent geometry : angle 0.54281 (35216) SS BOND : bond 0.00062 ( 4) SS BOND : angle 0.42559 ( 8) hydrogen bonds : bond 0.02572 ( 806) hydrogen bonds : angle 4.01050 ( 2394) Misc. bond : bond 0.00018 ( 4) link_BETA1-4 : bond 0.00728 ( 8) link_BETA1-4 : angle 2.39013 ( 24) link_NAG-ASN : bond 0.00646 ( 16) link_NAG-ASN : angle 3.62346 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3756.20 seconds wall clock time: 65 minutes 44.48 seconds (3944.48 seconds total)