Starting phenix.real_space_refine on Thu Mar 5 21:01:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mzi_48757/03_2026/9mzi_48757.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mzi_48757/03_2026/9mzi_48757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mzi_48757/03_2026/9mzi_48757.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mzi_48757/03_2026/9mzi_48757.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mzi_48757/03_2026/9mzi_48757.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mzi_48757/03_2026/9mzi_48757.map" } resolution = 3.83 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= 0.003 sd= 0.030 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 136 5.16 5 C 15721 2.51 5 N 4021 2.21 5 O 4704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 24582 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 5966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 757, 5966 Classifications: {'peptide': 757} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 28, 'TRANS': 728} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 5995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 5995 Classifications: {'peptide': 761} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 28, 'TRANS': 732} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 5995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 5995 Classifications: {'peptide': 761} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 28, 'TRANS': 732} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 5977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 758, 5977 Classifications: {'peptide': 758} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 28, 'TRANS': 729} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} 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: "M" 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: "N" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" 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: "Q" 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: "R" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" 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: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.99, per 1000 atoms: 0.24 Number of scatterers: 24582 At special positions: 0 Unit cell: (130.38, 159, 182.32, 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 136 16.00 O 4704 8.00 N 4021 7.00 C 15721 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 804 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.03 Simple disulfide: pdb=" SG CYS B 750 " - pdb=" SG CYS B 804 " distance=2.04 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.03 Simple disulfide: pdb=" SG CYS C 750 " - pdb=" SG CYS C 804 " distance=2.03 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 804 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " NAG E 3 " " NAG F 1 " - " BMA F 2 " " BMA F 2 " - " NAG F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " NAG H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " BMA K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " NAG N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " NAG R 3 " NAG-ASN " NAG A1001 " - " ASN A 546 " " NAG A1002 " - " ASN A 423 " " NAG A1003 " - " ASN A 751 " " NAG B1001 " - " ASN B 275 " " NAG B1002 " - " ASN B 751 " " NAG B1003 " - " ASN B 546 " " NAG B1004 " - " ASN B 412 " " NAG C1001 " - " ASN C 546 " " NAG C1002 " - " ASN C 751 " " NAG D1001 " - " ASN D 751 " " NAG D1002 " - " ASN D 546 " " NAG D1003 " - " ASN D 275 " " NAG D1004 " - " ASN D 412 " " NAG E 1 " - " ASN A 378 " " NAG F 1 " - " ASN A 67 " " NAG G 1 " - " ASN A 412 " " NAG H 1 " - " ASN A 275 " " NAG I 1 " - " ASN A 430 " " NAG J 1 " - " ASN B 378 " " NAG K 1 " - " ASN B 67 " " NAG L 1 " - " ASN C 67 " " NAG M 1 " - " ASN C 412 " " NAG N 1 " - " ASN C 378 " " NAG O 1 " - " ASN C 275 " " NAG P 1 " - " ASN C 430 " " NAG Q 1 " - " ASN D 378 " " NAG R 1 " - " ASN D 67 " Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 983.2 milliseconds 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5658 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 32 sheets defined 45.7% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 87 through 101 removed outlier: 3.539A pdb=" N ALA A 91 " --> pdb=" O ASP A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 126 Processing helix chain 'A' and resid 152 through 168 removed outlier: 4.121A pdb=" N ARG A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 185 removed outlier: 3.937A pdb=" N LEU A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 removed outlier: 3.631A pdb=" N LYS A 190 " --> pdb=" O GLN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 removed outlier: 4.078A pdb=" N ARG A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 222 removed outlier: 3.542A pdb=" N GLU A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 removed outlier: 4.192A pdb=" N GLY A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 300 Processing helix chain 'A' and resid 317 through 337 removed outlier: 3.618A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 365 removed outlier: 3.734A pdb=" N SER A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 475 removed outlier: 3.515A pdb=" N ILE A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 520 through 527 removed outlier: 3.564A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 554 Processing helix chain 'A' and resid 560 through 579 Processing helix chain 'A' and resid 631 through 665 removed outlier: 4.210A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 677 removed outlier: 4.498A pdb=" N CYS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN A 677 " --> pdb=" O ASP A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 695 Processing helix chain 'A' and resid 700 through 710 removed outlier: 4.369A pdb=" N PHE A 708 " --> pdb=" O LYS A 704 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N MET A 709 " --> pdb=" O MET A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 730 removed outlier: 3.738A pdb=" N GLN A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 749 Processing helix chain 'A' and resid 773 through 788 removed outlier: 4.162A pdb=" N LYS A 777 " --> pdb=" O PRO A 773 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU A 788 " --> pdb=" O GLN A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 799 Processing helix chain 'A' and resid 817 through 833 removed outlier: 3.960A pdb=" N GLY A 822 " --> pdb=" O GLN A 818 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ILE A 823 " --> pdb=" O ASN A 819 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 824 " --> pdb=" O ILE A 820 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 87 through 101 removed outlier: 3.732A pdb=" N LEU B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 126 removed outlier: 3.541A pdb=" N ILE B 121 " --> pdb=" O ALA B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 168 removed outlier: 4.633A pdb=" N ARG B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 184 Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 190 through 195 removed outlier: 3.907A pdb=" N ARG B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 221 Processing helix chain 'B' and resid 231 through 245 removed outlier: 3.581A pdb=" N MET B 245 " --> pdb=" O GLN B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 270 Processing helix chain 'B' and resid 286 through 298 removed outlier: 4.071A pdb=" N MET B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 317 through 336 removed outlier: 3.634A pdb=" N GLN B 336 " --> pdb=" O VAL B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 364 removed outlier: 3.902A pdb=" N SER B 361 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B 362 " --> pdb=" O ARG B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 417 No H-bonds generated for 'chain 'B' and resid 415 through 417' Processing helix chain 'B' and resid 461 through 474 removed outlier: 3.737A pdb=" N ILE B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 507 removed outlier: 3.573A pdb=" N GLU B 504 " --> pdb=" O GLY B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 526 removed outlier: 3.554A pdb=" N VAL B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 583 removed outlier: 3.610A pdb=" N TRP B 564 " --> pdb=" O SER B 560 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 569 " --> pdb=" O MET B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 663 removed outlier: 3.879A pdb=" N VAL B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 696 removed outlier: 3.796A pdb=" N PHE B 694 " --> pdb=" O THR B 690 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS B 696 " --> pdb=" O THR B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 712 removed outlier: 3.614A pdb=" N MET B 709 " --> pdb=" O MET B 705 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG B 712 " --> pdb=" O PHE B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 717 Processing helix chain 'B' and resid 720 through 731 Processing helix chain 'B' and resid 738 through 749 removed outlier: 3.506A pdb=" N GLN B 747 " --> pdb=" O GLU B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 789 removed outlier: 3.937A pdb=" N ASP B 776 " --> pdb=" O SER B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 797 removed outlier: 4.005A pdb=" N MET B 793 " --> pdb=" O GLY B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 839 removed outlier: 3.514A pdb=" N VAL B 839 " --> pdb=" O VAL B 835 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 67 Processing helix chain 'C' and resid 87 through 101 Processing helix chain 'C' and resid 111 through 125 removed outlier: 4.703A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 168 removed outlier: 4.212A pdb=" N ARG C 158 " --> pdb=" O SER C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 removed outlier: 3.693A pdb=" N ARG C 184 " --> pdb=" O THR C 180 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU C 185 " --> pdb=" O GLY C 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 180 through 185' Processing helix chain 'C' and resid 185 through 190 removed outlier: 3.681A pdb=" N LYS C 190 " --> pdb=" O GLN C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 195 removed outlier: 4.383A pdb=" N ARG C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 221 Processing helix chain 'C' and resid 231 through 245 removed outlier: 3.568A pdb=" N ALA C 244 " --> pdb=" O LYS C 240 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET C 245 " --> pdb=" O GLN C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 264 Processing helix chain 'C' and resid 266 through 271 removed outlier: 4.263A pdb=" N TYR C 271 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 301 removed outlier: 4.011A pdb=" N MET C 298 " --> pdb=" O GLU C 294 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU C 299 " --> pdb=" O LYS C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 336 removed outlier: 3.676A pdb=" N GLN C 336 " --> pdb=" O VAL C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 366 removed outlier: 3.634A pdb=" N SER C 361 " --> pdb=" O THR C 357 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU C 362 " --> pdb=" O ARG C 358 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C 363 " --> pdb=" O PHE C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 457 No H-bonds generated for 'chain 'C' and resid 455 through 457' Processing helix chain 'C' and resid 461 through 474 Processing helix chain 'C' and resid 500 through 507 Processing helix chain 'C' and resid 520 through 527 removed outlier: 3.594A pdb=" N LYS C 525 " --> pdb=" O TYR C 521 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL C 526 " --> pdb=" O VAL C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 557 Processing helix chain 'C' and resid 560 through 583 removed outlier: 3.527A pdb=" N TYR C 566 " --> pdb=" O ASP C 562 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG C 583 " --> pdb=" O PHE C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 665 removed outlier: 3.992A pdb=" N VAL C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY C 637 " --> pdb=" O THR C 633 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE C 648 " --> pdb=" O THR C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 677 removed outlier: 3.832A pdb=" N LEU C 674 " --> pdb=" O SER C 670 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN C 677 " --> pdb=" O ASP C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 697 removed outlier: 3.606A pdb=" N PHE C 694 " --> pdb=" O THR C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 712 Processing helix chain 'C' and resid 721 through 731 Processing helix chain 'C' and resid 739 through 749 removed outlier: 3.510A pdb=" N PHE C 744 " --> pdb=" O THR C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 789 removed outlier: 4.437A pdb=" N ASP C 776 " --> pdb=" O SER C 772 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS C 777 " --> pdb=" O PRO C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 800 removed outlier: 3.902A pdb=" N MET C 794 " --> pdb=" O LYS C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 835 removed outlier: 3.590A pdb=" N VAL C 826 " --> pdb=" O GLY C 822 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 831 " --> pdb=" O LEU C 827 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 87 through 101 Processing helix chain 'D' and resid 111 through 126 Processing helix chain 'D' and resid 152 through 168 Processing helix chain 'D' and resid 179 through 185 removed outlier: 4.131A pdb=" N ILE D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG D 184 " --> pdb=" O THR D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 190 through 195 removed outlier: 4.304A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 210 Processing helix chain 'D' and resid 211 through 221 Processing helix chain 'D' and resid 231 through 245 removed outlier: 3.989A pdb=" N GLY D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 264 Processing helix chain 'D' and resid 286 through 298 removed outlier: 3.972A pdb=" N MET D 298 " --> pdb=" O GLU D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 337 removed outlier: 3.676A pdb=" N MET D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE D 337 " --> pdb=" O ALA D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 364 removed outlier: 3.675A pdb=" N LEU D 362 " --> pdb=" O ARG D 358 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE D 363 " --> pdb=" O PHE D 359 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS D 364 " --> pdb=" O MET D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 418 Processing helix chain 'D' and resid 461 through 474 Processing helix chain 'D' and resid 500 through 507 removed outlier: 3.608A pdb=" N GLU D 504 " --> pdb=" O GLY D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 560 through 580 Processing helix chain 'D' and resid 631 through 664 Processing helix chain 'D' and resid 688 through 697 removed outlier: 3.548A pdb=" N THR D 692 " --> pdb=" O GLY D 688 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE D 693 " --> pdb=" O ALA D 689 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS D 696 " --> pdb=" O THR D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 712 Processing helix chain 'D' and resid 712 through 717 Processing helix chain 'D' and resid 720 through 731 Processing helix chain 'D' and resid 738 through 749 removed outlier: 4.077A pdb=" N ILE D 742 " --> pdb=" O GLU D 738 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU D 743 " --> pdb=" O SER D 739 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN D 747 " --> pdb=" O GLU D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 773 through 788 removed outlier: 3.817A pdb=" N GLU D 788 " --> pdb=" O GLN D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 820 through 829 removed outlier: 4.387A pdb=" N PHE D 824 " --> pdb=" O ILE D 820 " (cutoff:3.500A) Processing helix chain 'D' and resid 830 through 836 removed outlier: 4.434A pdb=" N LEU D 833 " --> pdb=" O GLY D 830 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL D 835 " --> pdb=" O VAL D 832 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 83 removed outlier: 6.401A pdb=" N LEU A 36 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ASP A 79 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N PHE A 38 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N GLN A 81 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 40 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE A 83 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N PHE A 42 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N VAL A 103 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ARG A 37 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA A 105 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N ILE A 130 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE A 106 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 203 removed outlier: 3.741A pdb=" N TYR A 176 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N TYR A 254 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N PHE A 279 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N PHE A 256 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A 403 " --> pdb=" O VAL A 391 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N SER A 393 " --> pdb=" O LYS A 401 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LYS A 401 " --> pdb=" O SER A 393 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LYS A 395 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LEU A 399 " --> pdb=" O LYS A 395 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 369 through 370 removed outlier: 3.564A pdb=" N GLY A 373 " --> pdb=" O GLY A 370 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 432 through 436 removed outlier: 3.809A pdb=" N GLU A 479 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 481 " --> pdb=" O VAL A 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA6, first strand: chain 'A' and resid 490 through 492 Processing sheet with id=AA7, first strand: chain 'A' and resid 528 through 529 Processing sheet with id=AA8, first strand: chain 'A' and resid 534 through 535 removed outlier: 3.774A pdb=" N MET A 534 " --> pdb=" O TYR A 764 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 682 through 683 removed outlier: 6.911A pdb=" N GLY A 683 " --> pdb=" O LEU A 736 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N GLU A 738 " --> pdb=" O GLY A 683 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 75 through 83 removed outlier: 6.028A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASP B 79 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N PHE B 38 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLN B 81 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLY B 40 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE B 83 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE B 42 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE B 106 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N HIS B 129 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 200 through 203 removed outlier: 6.001A pdb=" N VAL B 174 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N THR B 173 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ASP B 229 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL B 175 " --> pdb=" O ASP B 229 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N TYR B 254 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N PHE B 279 " --> pdb=" O TYR B 254 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N PHE B 256 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG B 280 " --> pdb=" O ASP B 390 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 368 through 369 removed outlier: 3.583A pdb=" N TRP B 368 " --> pdb=" O ILE B 375 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 403 through 406 Processing sheet with id=AB5, first strand: chain 'B' and resid 435 through 437 removed outlier: 3.899A pdb=" N ARG B 481 " --> pdb=" O VAL B 435 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 490 through 492 removed outlier: 3.582A pdb=" N ASP B 492 " --> pdb=" O GLN B 497 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN B 497 " --> pdb=" O ASP B 492 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 527 through 528 removed outlier: 4.036A pdb=" N ASP B 528 " --> pdb=" O THR B 768 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N THR B 768 " --> pdb=" O ASP B 528 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 534 through 536 Processing sheet with id=AB9, first strand: chain 'B' and resid 541 through 542 removed outlier: 6.389A pdb=" N GLU B 681 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LEU B 736 " --> pdb=" O GLU B 681 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N GLY B 683 " --> pdb=" O LEU B 736 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 75 through 83 removed outlier: 6.091A pdb=" N LEU C 36 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP C 79 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N PHE C 38 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N GLN C 81 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLY C 40 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE C 83 " --> pdb=" O GLY C 40 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N PHE C 42 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N VAL C 103 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ARG C 37 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA C 105 " --> pdb=" O ARG C 37 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C 41 " --> pdb=" O PHE C 107 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N ILE C 130 " --> pdb=" O ALA C 104 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE C 106 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 198 through 203 removed outlier: 3.526A pdb=" N TYR C 176 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N HIS C 225 " --> pdb=" O THR C 171 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE C 279 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY C 403 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N SER C 393 " --> pdb=" O LYS C 401 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LYS C 401 " --> pdb=" O SER C 393 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 435 through 437 removed outlier: 6.046A pdb=" N VAL C 435 " --> pdb=" O ARG C 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'C' and resid 445 through 446 Processing sheet with id=AC5, first strand: chain 'C' and resid 490 through 491 removed outlier: 3.528A pdb=" N ALA C 490 " --> pdb=" O ASN C 499 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 528 through 529 removed outlier: 3.505A pdb=" N ASP C 528 " --> pdb=" O THR C 768 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 682 through 684 Processing sheet with id=AC8, first strand: chain 'D' and resid 77 through 78 removed outlier: 4.248A pdb=" N ALA D 105 " --> pdb=" O ARG D 37 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE D 106 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 200 through 203 removed outlier: 6.395A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N TYR D 254 " --> pdb=" O THR D 277 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N PHE D 279 " --> pdb=" O TYR D 254 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N PHE D 256 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N VAL D 391 " --> pdb=" O ILE D 402 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 368 through 370 Processing sheet with id=AD2, first strand: chain 'D' and resid 434 through 436 Processing sheet with id=AD3, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AD4, first strand: chain 'D' and resid 490 through 492 Processing sheet with id=AD5, first strand: chain 'D' and resid 682 through 684 removed outlier: 6.814A pdb=" N GLY D 683 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET D 737 " --> pdb=" O SER D 539 " (cutoff:3.500A) 994 hydrogen bonds defined for protein. 2850 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.68 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7693 1.34 - 1.46: 5949 1.46 - 1.58: 11230 1.58 - 1.70: 1 1.70 - 1.82: 232 Bond restraints: 25105 Sorted by residual: bond pdb=" CA ASP C 140 " pdb=" CB ASP C 140 " ideal model delta sigma weight residual 1.531 1.606 -0.075 3.12e-02 1.03e+03 5.78e+00 bond pdb=" N MET B 664 " pdb=" CA MET B 664 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.47e-02 4.63e+03 4.68e+00 bond pdb=" N MET A 664 " pdb=" CA MET A 664 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.66e+00 bond pdb=" N MET C 664 " pdb=" CA MET C 664 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.23e-02 6.61e+03 4.21e+00 bond pdb=" N MET D 664 " pdb=" CA MET D 664 " ideal model delta sigma weight residual 1.454 1.478 -0.024 1.21e-02 6.83e+03 4.04e+00 ... (remaining 25100 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 33587 2.15 - 4.29: 332 4.29 - 6.44: 62 6.44 - 8.58: 15 8.58 - 10.73: 7 Bond angle restraints: 34003 Sorted by residual: angle pdb=" N MET B 664 " pdb=" CA MET B 664 " pdb=" C MET B 664 " ideal model delta sigma weight residual 108.54 115.59 -7.05 1.41e+00 5.03e-01 2.50e+01 angle pdb=" CA MET D 664 " pdb=" C MET D 664 " pdb=" O MET D 664 " ideal model delta sigma weight residual 121.72 117.47 4.25 1.18e+00 7.18e-01 1.30e+01 angle pdb=" CB MET D 247 " pdb=" CG MET D 247 " pdb=" SD MET D 247 " ideal model delta sigma weight residual 112.70 123.43 -10.73 3.00e+00 1.11e-01 1.28e+01 angle pdb=" CA GLY D 500 " pdb=" C GLY D 500 " pdb=" N MET D 501 " ideal model delta sigma weight residual 114.85 118.07 -3.22 9.50e-01 1.11e+00 1.15e+01 angle pdb=" N GLY D 246 " pdb=" CA GLY D 246 " pdb=" C GLY D 246 " ideal model delta sigma weight residual 115.34 109.86 5.48 1.67e+00 3.59e-01 1.08e+01 ... (remaining 33998 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.81: 13638 19.81 - 39.61: 1546 39.61 - 59.42: 332 59.42 - 79.23: 56 79.23 - 99.04: 19 Dihedral angle restraints: 15591 sinusoidal: 6792 harmonic: 8799 Sorted by residual: dihedral pdb=" CB CYS B 96 " pdb=" SG CYS B 96 " pdb=" SG CYS B 347 " pdb=" CB CYS B 347 " ideal model delta sinusoidal sigma weight residual 93.00 29.15 63.85 1 1.00e+01 1.00e-02 5.37e+01 dihedral pdb=" CB CYS B 750 " pdb=" SG CYS B 750 " pdb=" SG CYS B 804 " pdb=" CB CYS B 804 " ideal model delta sinusoidal sigma weight residual 93.00 30.02 62.98 1 1.00e+01 1.00e-02 5.24e+01 dihedral pdb=" CB CYS A 750 " pdb=" SG CYS A 750 " pdb=" SG CYS A 804 " pdb=" CB CYS A 804 " ideal model delta sinusoidal sigma weight residual -86.00 -134.51 48.51 1 1.00e+01 1.00e-02 3.24e+01 ... (remaining 15588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 3558 0.064 - 0.129: 392 0.129 - 0.193: 16 0.193 - 0.258: 3 0.258 - 0.322: 1 Chirality restraints: 3970 Sorted by residual: chirality pdb=" C1 NAG B1003 " pdb=" ND2 ASN B 546 " pdb=" C2 NAG B1003 " pdb=" O5 NAG B1003 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN C 67 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN C 412 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 3967 not shown) Planarity restraints: 4263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 706 " -0.016 2.00e-02 2.50e+03 1.54e-02 5.95e+00 pdb=" CG TRP A 706 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP A 706 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 706 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 706 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 706 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 706 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 706 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 706 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 706 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 799 " 0.013 2.00e-02 2.50e+03 1.25e-02 3.92e+00 pdb=" CG TRP D 799 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP D 799 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP D 799 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP D 799 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 799 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 799 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 799 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 799 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 799 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 451 " -0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO B 452 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 452 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 452 " -0.024 5.00e-02 4.00e+02 ... (remaining 4260 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 8306 2.84 - 3.36: 25176 3.36 - 3.87: 41305 3.87 - 4.39: 46093 4.39 - 4.90: 74718 Nonbonded interactions: 195598 Sorted by model distance: nonbonded pdb=" O ASP C 140 " pdb=" OD1 ASP C 140 " model vdw 2.327 3.040 nonbonded pdb=" O4 NAG F 1 " pdb=" O2 BMA F 2 " model vdw 2.414 2.432 nonbonded pdb=" C4 BMA F 2 " pdb=" O5 NAG F 3 " model vdw 2.447 2.776 nonbonded pdb=" C4 NAG K 1 " pdb=" O5 BMA K 2 " model vdw 2.471 2.776 nonbonded pdb=" C4 NAG J 1 " pdb=" O5 NAG J 2 " model vdw 2.493 2.776 ... (remaining 195593 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 835 or resid 1002 through 1003)) selection = (chain 'B' and (resid 33 through 835 or resid 1003 through 1004)) selection = (chain 'C' and (resid 33 through 835 or resid 1001 through 1002)) selection = (chain 'D' and (resid 33 through 835 or resid 1003 through 1004)) } ncs_group { reference = (chain 'E' and resid 1) selection = (chain 'F' and resid 1) selection = (chain 'H' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'R' and resid 1) } ncs_group { reference = (chain 'G' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'K' and resid 1) selection = (chain 'L' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) } 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: 1.080 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: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.800 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 25159 Z= 0.109 Angle : 0.589 10.726 34158 Z= 0.284 Chirality : 0.041 0.322 3970 Planarity : 0.003 0.043 4236 Dihedral : 16.802 99.037 9912 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.40 % Allowed : 27.11 % Favored : 69.48 % 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: 3021 helix: 0.34 (0.15), residues: 1240 sheet: -1.52 (0.30), residues: 334 loop : -1.46 (0.16), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 198 TYR 0.023 0.001 TYR C 176 PHE 0.015 0.001 PHE D 359 TRP 0.042 0.001 TRP A 706 HIS 0.004 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00241 (25105) covalent geometry : angle 0.57331 (34003) SS BOND : bond 0.00252 ( 7) SS BOND : angle 0.95665 ( 14) hydrogen bonds : bond 0.23530 ( 994) hydrogen bonds : angle 7.81368 ( 2850) link_BETA1-4 : bond 0.00729 ( 20) link_BETA1-4 : angle 2.26877 ( 60) link_NAG-ASN : bond 0.00338 ( 27) link_NAG-ASN : angle 2.09723 ( 81) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 253 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 CYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8536 (t) REVERT: A 171 THR cc_start: 0.8621 (OUTLIER) cc_final: 0.8145 (t) REVERT: A 186 GLN cc_start: 0.8799 (tp40) cc_final: 0.8392 (tp40) REVERT: A 247 MET cc_start: 0.9039 (mmm) cc_final: 0.8347 (tpp) REVERT: A 360 MET cc_start: 0.8587 (mmt) cc_final: 0.8296 (mmt) REVERT: A 441 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7677 (tm-30) REVERT: A 442 PRO cc_start: 0.7939 (Cg_endo) cc_final: 0.7030 (Cg_exo) REVERT: A 654 ASN cc_start: 0.9042 (t0) cc_final: 0.8617 (t0) REVERT: A 664 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8333 (tmm) REVERT: A 672 ASP cc_start: 0.7707 (p0) cc_final: 0.7335 (p0) REVERT: B 122 CYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8114 (t) REVERT: B 262 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.8615 (m-80) REVERT: B 316 MET cc_start: 0.8723 (mtp) cc_final: 0.8231 (tpp) REVERT: B 362 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9119 (pp) REVERT: B 417 GLN cc_start: 0.5676 (OUTLIER) cc_final: 0.4936 (mp10) REVERT: B 521 TYR cc_start: 0.8341 (t80) cc_final: 0.7813 (t80) REVERT: B 533 PHE cc_start: 0.8600 (p90) cc_final: 0.7974 (p90) REVERT: B 538 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8522 (mt) REVERT: B 673 ASP cc_start: 0.8414 (m-30) cc_final: 0.7599 (m-30) REVERT: B 737 MET cc_start: 0.8274 (ptp) cc_final: 0.7560 (ptp) REVERT: C 55 LEU cc_start: 0.8802 (mt) cc_final: 0.8382 (mt) REVERT: C 178 ASP cc_start: 0.8676 (t70) cc_final: 0.8447 (t0) REVERT: C 264 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9112 (mm) REVERT: C 505 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9074 (tt) REVERT: C 740 THR cc_start: 0.9105 (p) cc_final: 0.8715 (t) REVERT: C 778 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8949 (tt) REVERT: C 795 LYS cc_start: 0.9434 (tptt) cc_final: 0.9136 (tptp) REVERT: C 802 CYS cc_start: 0.7455 (p) cc_final: 0.6621 (m) REVERT: D 53 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8163 (mm-30) REVERT: D 218 MET cc_start: 0.9112 (mmm) cc_final: 0.8796 (mtt) REVERT: D 517 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8322 (mm) REVERT: D 568 LEU cc_start: 0.9651 (tp) cc_final: 0.9373 (mt) REVERT: D 646 ILE cc_start: 0.9578 (mt) cc_final: 0.9156 (mt) REVERT: D 649 SER cc_start: 0.9467 (t) cc_final: 0.9075 (p) REVERT: D 654 ASN cc_start: 0.8442 (t0) cc_final: 0.7907 (t0) REVERT: D 764 TYR cc_start: 0.6139 (OUTLIER) cc_final: 0.4326 (t80) outliers start: 89 outliers final: 66 residues processed: 324 average time/residue: 0.1348 time to fit residues: 75.7373 Evaluate side-chains 321 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 242 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 664 MET Chi-restraints excluded: chain A residue 676 CYS Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 417 GLN Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 501 MET Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 705 MET Chi-restraints excluded: chain B residue 715 SER Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 764 TYR Chi-restraints excluded: chain B residue 770 MET Chi-restraints excluded: chain B residue 791 LEU Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 302 GLN Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 566 TYR Chi-restraints excluded: chain C residue 705 MET Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 764 TYR Chi-restraints excluded: chain D residue 766 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.093253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.072255 restraints weight = 76871.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.072183 restraints weight = 41263.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.072986 restraints weight = 37045.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.073600 restraints weight = 29424.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.073835 restraints weight = 26943.310| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.0756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25159 Z= 0.125 Angle : 0.577 9.345 34158 Z= 0.286 Chirality : 0.041 0.321 3970 Planarity : 0.004 0.046 4236 Dihedral : 8.022 97.945 4392 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.94 % Allowed : 26.92 % Favored : 69.14 % 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: -0.63 (0.16), residues: 3021 helix: 0.91 (0.15), residues: 1272 sheet: -1.48 (0.29), residues: 356 loop : -1.37 (0.17), residues: 1393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 184 TYR 0.009 0.001 TYR A 252 PHE 0.016 0.001 PHE B 166 TRP 0.025 0.001 TRP A 706 HIS 0.004 0.001 HIS D 232 Details of bonding type rmsd covalent geometry : bond 0.00271 (25105) covalent geometry : angle 0.56033 (34003) SS BOND : bond 0.00241 ( 7) SS BOND : angle 1.26196 ( 14) hydrogen bonds : bond 0.05444 ( 994) hydrogen bonds : angle 5.43074 ( 2850) link_BETA1-4 : bond 0.00750 ( 20) link_BETA1-4 : angle 2.25640 ( 60) link_NAG-ASN : bond 0.00309 ( 27) link_NAG-ASN : angle 2.12860 ( 81) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 263 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLN cc_start: 0.8823 (tp40) cc_final: 0.8376 (tp40) REVERT: A 360 MET cc_start: 0.8533 (mmt) cc_final: 0.8185 (mmt) REVERT: A 441 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7622 (tm-30) REVERT: A 442 PRO cc_start: 0.7871 (Cg_endo) cc_final: 0.6931 (Cg_exo) REVERT: A 664 MET cc_start: 0.8596 (ttm) cc_final: 0.8229 (tmm) REVERT: A 672 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7254 (p0) REVERT: B 360 MET cc_start: 0.8812 (mmp) cc_final: 0.8552 (mmp) REVERT: B 521 TYR cc_start: 0.8139 (t80) cc_final: 0.7678 (t80) REVERT: B 533 PHE cc_start: 0.8573 (p90) cc_final: 0.7903 (p90) REVERT: B 673 ASP cc_start: 0.8335 (m-30) cc_final: 0.7566 (m-30) REVERT: B 695 LYS cc_start: 0.8487 (mmmm) cc_final: 0.8116 (mmmm) REVERT: C 55 LEU cc_start: 0.8829 (mt) cc_final: 0.8441 (tp) REVERT: C 90 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8186 (mm-30) REVERT: C 173 THR cc_start: 0.9548 (OUTLIER) cc_final: 0.9018 (p) REVERT: C 178 ASP cc_start: 0.8653 (t70) cc_final: 0.8428 (t0) REVERT: C 264 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9078 (mm) REVERT: C 316 MET cc_start: 0.8802 (tpt) cc_final: 0.8496 (tpt) REVERT: C 740 THR cc_start: 0.9050 (p) cc_final: 0.8623 (t) REVERT: C 768 THR cc_start: 0.7729 (OUTLIER) cc_final: 0.7505 (p) REVERT: C 778 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8927 (tt) REVERT: C 795 LYS cc_start: 0.9494 (tptt) cc_final: 0.9203 (tptp) REVERT: D 218 MET cc_start: 0.9065 (mmm) cc_final: 0.8850 (mtt) REVERT: D 359 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8594 (t80) REVERT: D 646 ILE cc_start: 0.9625 (mt) cc_final: 0.9244 (mt) REVERT: D 649 SER cc_start: 0.9411 (t) cc_final: 0.9087 (p) REVERT: D 654 ASN cc_start: 0.8380 (t0) cc_final: 0.7926 (t0) REVERT: D 669 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8296 (p0) REVERT: D 764 TYR cc_start: 0.6098 (OUTLIER) cc_final: 0.4279 (t80) outliers start: 103 outliers final: 57 residues processed: 345 average time/residue: 0.1360 time to fit residues: 81.1507 Evaluate side-chains 307 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 241 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 682 TYR Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 566 TYR Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 762 LYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 764 TYR Chi-restraints excluded: chain D residue 833 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 91 optimal weight: 3.9990 chunk 291 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 chunk 6 optimal weight: 0.0270 chunk 297 optimal weight: 4.9990 chunk 249 optimal weight: 3.9990 chunk 276 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 chunk 268 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 overall best weight: 2.7444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 GLN ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.091654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.070872 restraints weight = 77404.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.070860 restraints weight = 41136.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.070989 restraints weight = 45943.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.071821 restraints weight = 32912.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.072358 restraints weight = 28627.303| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25159 Z= 0.174 Angle : 0.596 9.441 34158 Z= 0.293 Chirality : 0.042 0.317 3970 Planarity : 0.003 0.049 4236 Dihedral : 7.307 97.921 4297 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.74 % Allowed : 26.54 % Favored : 68.72 % 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: -0.58 (0.16), residues: 3021 helix: 1.08 (0.15), residues: 1270 sheet: -1.55 (0.29), residues: 349 loop : -1.46 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 384 TYR 0.012 0.001 TYR A 478 PHE 0.019 0.001 PHE B 166 TRP 0.024 0.001 TRP A 706 HIS 0.004 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00396 (25105) covalent geometry : angle 0.57926 (34003) SS BOND : bond 0.00294 ( 7) SS BOND : angle 1.21858 ( 14) hydrogen bonds : bond 0.04227 ( 994) hydrogen bonds : angle 5.03323 ( 2850) link_BETA1-4 : bond 0.00639 ( 20) link_BETA1-4 : angle 2.25965 ( 60) link_NAG-ASN : bond 0.00333 ( 27) link_NAG-ASN : angle 2.23283 ( 81) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 245 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 171 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8154 (t) REVERT: A 186 GLN cc_start: 0.8821 (tp40) cc_final: 0.8350 (tp40) REVERT: A 331 SER cc_start: 0.8984 (m) cc_final: 0.8705 (p) REVERT: A 360 MET cc_start: 0.8622 (mmt) cc_final: 0.8240 (mmt) REVERT: A 441 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7655 (tm-30) REVERT: A 442 PRO cc_start: 0.7874 (Cg_endo) cc_final: 0.6918 (Cg_exo) REVERT: A 654 ASN cc_start: 0.9109 (t0) cc_final: 0.8732 (t0) REVERT: B 122 CYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8183 (t) REVERT: B 362 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9252 (pp) REVERT: B 417 GLN cc_start: 0.5771 (OUTLIER) cc_final: 0.5016 (mp10) REVERT: B 521 TYR cc_start: 0.8144 (t80) cc_final: 0.7678 (t80) REVERT: B 533 PHE cc_start: 0.8611 (p90) cc_final: 0.7771 (p90) REVERT: B 659 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9175 (mm) REVERT: C 55 LEU cc_start: 0.8824 (mt) cc_final: 0.8431 (mt) REVERT: C 90 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8290 (mp0) REVERT: C 316 MET cc_start: 0.8911 (tpt) cc_final: 0.8639 (tpt) REVERT: C 413 MET cc_start: 0.7833 (ptp) cc_final: 0.7445 (ppp) REVERT: C 740 THR cc_start: 0.9091 (p) cc_final: 0.8666 (t) REVERT: C 778 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.8994 (tt) REVERT: D 153 PHE cc_start: 0.8985 (OUTLIER) cc_final: 0.8410 (t80) REVERT: D 359 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.8529 (t80) REVERT: D 649 SER cc_start: 0.9425 (t) cc_final: 0.9056 (p) REVERT: D 654 ASN cc_start: 0.8452 (t0) cc_final: 0.8043 (t0) REVERT: D 669 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.8325 (p0) REVERT: D 764 TYR cc_start: 0.6257 (OUTLIER) cc_final: 0.4327 (t80) outliers start: 124 outliers final: 77 residues processed: 342 average time/residue: 0.1273 time to fit residues: 75.2395 Evaluate side-chains 319 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 231 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 802 CYS Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 417 GLN Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 566 TYR Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 733 TYR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 762 LYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 355 PHE Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 404 THR Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 764 TYR Chi-restraints excluded: chain D residue 766 VAL Chi-restraints excluded: chain D residue 833 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 257 optimal weight: 20.0000 chunk 298 optimal weight: 0.8980 chunk 268 optimal weight: 4.9990 chunk 241 optimal weight: 2.9990 chunk 205 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 247 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.091943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.071023 restraints weight = 76564.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.071241 restraints weight = 40378.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.071694 restraints weight = 39669.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.072216 restraints weight = 29585.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.072720 restraints weight = 26749.033| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25159 Z= 0.148 Angle : 0.582 10.154 34158 Z= 0.284 Chirality : 0.042 0.321 3970 Planarity : 0.003 0.049 4236 Dihedral : 7.277 98.171 4294 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.86 % Allowed : 26.92 % Favored : 68.22 % 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: -0.55 (0.16), residues: 3021 helix: 1.12 (0.15), residues: 1279 sheet: -1.47 (0.29), residues: 358 loop : -1.49 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 384 TYR 0.014 0.001 TYR A 252 PHE 0.024 0.001 PHE C 377 TRP 0.028 0.001 TRP D 799 HIS 0.004 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00338 (25105) covalent geometry : angle 0.56441 (34003) SS BOND : bond 0.00449 ( 7) SS BOND : angle 1.22581 ( 14) hydrogen bonds : bond 0.03815 ( 994) hydrogen bonds : angle 4.82094 ( 2850) link_BETA1-4 : bond 0.00692 ( 20) link_BETA1-4 : angle 2.26362 ( 60) link_NAG-ASN : bond 0.00320 ( 27) link_NAG-ASN : angle 2.19485 ( 81) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 252 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8175 (t) REVERT: A 186 GLN cc_start: 0.8811 (tp40) cc_final: 0.8360 (tp40) REVERT: A 331 SER cc_start: 0.8880 (m) cc_final: 0.8648 (p) REVERT: A 360 MET cc_start: 0.8549 (mmt) cc_final: 0.8173 (mmt) REVERT: A 441 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7577 (tm-30) REVERT: A 442 PRO cc_start: 0.7958 (Cg_endo) cc_final: 0.7008 (Cg_exo) REVERT: A 672 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7403 (p0) REVERT: B 122 CYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8161 (t) REVERT: B 202 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.8807 (ptp-110) REVERT: B 362 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9236 (pp) REVERT: B 417 GLN cc_start: 0.5760 (OUTLIER) cc_final: 0.5014 (mp10) REVERT: B 521 TYR cc_start: 0.8149 (t80) cc_final: 0.7622 (t80) REVERT: B 533 PHE cc_start: 0.8476 (p90) cc_final: 0.7628 (p90) REVERT: B 538 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8633 (mt) REVERT: B 775 ARG cc_start: 0.9325 (OUTLIER) cc_final: 0.8818 (ptm-80) REVERT: C 55 LEU cc_start: 0.8822 (mt) cc_final: 0.8473 (tp) REVERT: C 90 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8196 (mp0) REVERT: C 264 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9082 (mm) REVERT: C 316 MET cc_start: 0.8995 (tpt) cc_final: 0.8746 (tpt) REVERT: C 413 MET cc_start: 0.7861 (ptp) cc_final: 0.7595 (ppp) REVERT: C 740 THR cc_start: 0.9049 (p) cc_final: 0.8809 (p) REVERT: C 778 ILE cc_start: 0.9255 (OUTLIER) cc_final: 0.8973 (tt) REVERT: D 153 PHE cc_start: 0.8951 (OUTLIER) cc_final: 0.8400 (t80) REVERT: D 248 MET cc_start: 0.9147 (tpp) cc_final: 0.8861 (mmm) REVERT: D 359 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8541 (t80) REVERT: D 517 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8316 (mm) REVERT: D 646 ILE cc_start: 0.9606 (OUTLIER) cc_final: 0.9198 (mt) REVERT: D 649 SER cc_start: 0.9363 (t) cc_final: 0.9124 (p) REVERT: D 654 ASN cc_start: 0.8448 (t0) cc_final: 0.8027 (t0) REVERT: D 664 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.8193 (ptp) REVERT: D 669 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8327 (p0) REVERT: D 682 TYR cc_start: 0.8899 (p90) cc_final: 0.8248 (p90) REVERT: D 691 MET cc_start: 0.8261 (tmm) cc_final: 0.7902 (tmm) REVERT: D 764 TYR cc_start: 0.6134 (OUTLIER) cc_final: 0.4247 (t80) outliers start: 127 outliers final: 77 residues processed: 354 average time/residue: 0.1357 time to fit residues: 82.4948 Evaluate side-chains 331 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 236 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 802 CYS Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 417 GLN Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 775 ARG Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 566 TYR Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 733 TYR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 762 LYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 355 PHE Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 431 ARG Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 664 MET Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 764 TYR Chi-restraints excluded: chain D residue 766 VAL Chi-restraints excluded: chain D residue 833 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 263 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 202 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 218 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 181 optimal weight: 0.9980 chunk 186 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.092132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.070953 restraints weight = 77022.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.072447 restraints weight = 41255.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.072202 restraints weight = 41408.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.072959 restraints weight = 30274.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.073762 restraints weight = 26203.453| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25159 Z= 0.141 Angle : 0.583 11.428 34158 Z= 0.283 Chirality : 0.042 0.322 3970 Planarity : 0.003 0.048 4236 Dihedral : 7.299 99.266 4293 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 5.12 % Allowed : 26.65 % Favored : 68.22 % 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: -0.51 (0.16), residues: 3021 helix: 1.16 (0.15), residues: 1279 sheet: -1.45 (0.29), residues: 358 loop : -1.48 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 184 TYR 0.012 0.001 TYR A 702 PHE 0.018 0.001 PHE C 555 TRP 0.031 0.001 TRP D 799 HIS 0.005 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00323 (25105) covalent geometry : angle 0.56629 (34003) SS BOND : bond 0.00372 ( 7) SS BOND : angle 1.25016 ( 14) hydrogen bonds : bond 0.03583 ( 994) hydrogen bonds : angle 4.68731 ( 2850) link_BETA1-4 : bond 0.00667 ( 20) link_BETA1-4 : angle 2.25851 ( 60) link_NAG-ASN : bond 0.00317 ( 27) link_NAG-ASN : angle 2.16959 ( 81) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 247 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8186 (t) REVERT: A 186 GLN cc_start: 0.8777 (tp40) cc_final: 0.8340 (tp40) REVERT: A 331 SER cc_start: 0.8798 (m) cc_final: 0.8596 (p) REVERT: A 360 MET cc_start: 0.8514 (mmt) cc_final: 0.8130 (mmt) REVERT: A 441 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7552 (tm-30) REVERT: A 442 PRO cc_start: 0.7963 (Cg_endo) cc_final: 0.7002 (Cg_exo) REVERT: A 672 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7355 (p0) REVERT: B 122 CYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8119 (t) REVERT: B 202 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8824 (ptp-110) REVERT: B 362 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9226 (pp) REVERT: B 417 GLN cc_start: 0.5807 (OUTLIER) cc_final: 0.4978 (mp10) REVERT: B 521 TYR cc_start: 0.8157 (t80) cc_final: 0.7640 (t80) REVERT: B 533 PHE cc_start: 0.8424 (p90) cc_final: 0.7617 (p90) REVERT: B 538 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8649 (mt) REVERT: B 775 ARG cc_start: 0.9337 (OUTLIER) cc_final: 0.8837 (ptm-80) REVERT: B 820 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7533 (tp) REVERT: C 55 LEU cc_start: 0.8832 (mt) cc_final: 0.8454 (tp) REVERT: C 90 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8208 (mp0) REVERT: C 264 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9086 (mm) REVERT: C 413 MET cc_start: 0.7889 (ptp) cc_final: 0.7686 (ppp) REVERT: C 740 THR cc_start: 0.9033 (p) cc_final: 0.8790 (p) REVERT: C 778 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.8992 (tt) REVERT: D 153 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8461 (t80) REVERT: D 248 MET cc_start: 0.9079 (tpp) cc_final: 0.8830 (mmm) REVERT: D 346 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7078 (pp30) REVERT: D 359 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8492 (t80) REVERT: D 649 SER cc_start: 0.9375 (t) cc_final: 0.9149 (p) REVERT: D 654 ASN cc_start: 0.8480 (t0) cc_final: 0.8033 (t0) REVERT: D 664 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8355 (ptt) REVERT: D 669 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8317 (p0) REVERT: D 682 TYR cc_start: 0.8891 (p90) cc_final: 0.8236 (p90) REVERT: D 691 MET cc_start: 0.8315 (tmm) cc_final: 0.7950 (tmm) REVERT: D 764 TYR cc_start: 0.6141 (OUTLIER) cc_final: 0.5916 (m-80) outliers start: 134 outliers final: 92 residues processed: 351 average time/residue: 0.1333 time to fit residues: 80.5280 Evaluate side-chains 340 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 230 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain A residue 750 CYS Chi-restraints excluded: chain A residue 802 CYS Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 417 GLN Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 775 ARG Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 302 GLN Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 566 TYR Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 733 TYR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 762 LYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 778 ILE Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain D residue 355 PHE Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 431 ARG Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 664 MET Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 764 TYR Chi-restraints excluded: chain D residue 766 VAL Chi-restraints excluded: chain D residue 833 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 212 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 chunk 203 optimal weight: 0.9980 chunk 201 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.092967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.072074 restraints weight = 76666.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.072150 restraints weight = 40205.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.072470 restraints weight = 41950.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.073233 restraints weight = 30855.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.073690 restraints weight = 26923.662| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25159 Z= 0.121 Angle : 0.586 11.205 34158 Z= 0.283 Chirality : 0.042 0.324 3970 Planarity : 0.003 0.047 4236 Dihedral : 7.243 99.996 4292 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.78 % Allowed : 27.15 % Favored : 68.07 % 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: -0.45 (0.16), residues: 3021 helix: 1.18 (0.15), residues: 1279 sheet: -1.39 (0.29), residues: 362 loop : -1.42 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 184 TYR 0.009 0.001 TYR B 252 PHE 0.024 0.001 PHE A 643 TRP 0.032 0.001 TRP D 799 HIS 0.004 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00277 (25105) covalent geometry : angle 0.56930 (34003) SS BOND : bond 0.00412 ( 7) SS BOND : angle 1.70048 ( 14) hydrogen bonds : bond 0.03445 ( 994) hydrogen bonds : angle 4.56654 ( 2850) link_BETA1-4 : bond 0.00684 ( 20) link_BETA1-4 : angle 2.25220 ( 60) link_NAG-ASN : bond 0.00316 ( 27) link_NAG-ASN : angle 2.10197 ( 81) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 251 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8115 (t) REVERT: A 186 GLN cc_start: 0.8745 (tp40) cc_final: 0.8331 (tp40) REVERT: A 360 MET cc_start: 0.8463 (mmt) cc_final: 0.8063 (mmt) REVERT: A 441 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7500 (tm-30) REVERT: A 442 PRO cc_start: 0.7877 (Cg_endo) cc_final: 0.6930 (Cg_exo) REVERT: A 672 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7345 (p0) REVERT: B 122 CYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8105 (t) REVERT: B 202 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8781 (ptp-110) REVERT: B 362 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9190 (pp) REVERT: B 521 TYR cc_start: 0.8127 (t80) cc_final: 0.7456 (t80) REVERT: B 538 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8565 (mt) REVERT: B 576 CYS cc_start: 0.8961 (m) cc_final: 0.8586 (p) REVERT: B 775 ARG cc_start: 0.9349 (OUTLIER) cc_final: 0.8857 (ptm-80) REVERT: C 55 LEU cc_start: 0.8798 (mt) cc_final: 0.8442 (tp) REVERT: C 90 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8153 (mp0) REVERT: C 264 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9072 (mm) REVERT: C 709 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8456 (mmt) REVERT: C 740 THR cc_start: 0.8991 (p) cc_final: 0.8748 (p) REVERT: C 802 CYS cc_start: 0.7418 (p) cc_final: 0.6537 (m) REVERT: D 153 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.8509 (t80) REVERT: D 346 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7152 (pp30) REVERT: D 359 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8468 (t80) REVERT: D 646 ILE cc_start: 0.9582 (OUTLIER) cc_final: 0.9221 (mt) REVERT: D 649 SER cc_start: 0.9300 (t) cc_final: 0.9091 (p) REVERT: D 654 ASN cc_start: 0.8388 (t0) cc_final: 0.7967 (t0) REVERT: D 664 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.7919 (ptp) REVERT: D 669 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.8256 (p0) REVERT: D 682 TYR cc_start: 0.8908 (p90) cc_final: 0.8391 (p90) REVERT: D 691 MET cc_start: 0.8220 (tmm) cc_final: 0.7836 (tmm) REVERT: D 764 TYR cc_start: 0.6011 (OUTLIER) cc_final: 0.4207 (t80) outliers start: 125 outliers final: 84 residues processed: 349 average time/residue: 0.1340 time to fit residues: 80.3626 Evaluate side-chains 339 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 238 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 802 CYS Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 643 PHE Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 676 CYS Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 775 ARG Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 302 GLN Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 566 TYR Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 733 TYR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain D residue 355 PHE Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 431 ARG Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 664 MET Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 764 TYR Chi-restraints excluded: chain D residue 793 MET Chi-restraints excluded: chain D residue 833 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 30 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 223 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 7 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 185 optimal weight: 0.7980 chunk 249 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.091585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.070524 restraints weight = 77242.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.071689 restraints weight = 42665.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.071589 restraints weight = 42291.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.072460 restraints weight = 31017.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.072680 restraints weight = 26807.995| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25159 Z= 0.176 Angle : 0.622 12.764 34158 Z= 0.302 Chirality : 0.042 0.320 3970 Planarity : 0.003 0.046 4236 Dihedral : 7.241 100.605 4287 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 5.09 % Allowed : 27.00 % Favored : 67.92 % 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: -0.48 (0.16), residues: 3021 helix: 1.20 (0.15), residues: 1279 sheet: -1.51 (0.29), residues: 335 loop : -1.47 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 184 TYR 0.016 0.001 TYR A 478 PHE 0.030 0.001 PHE D 555 TRP 0.033 0.001 TRP D 799 HIS 0.005 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00403 (25105) covalent geometry : angle 0.60591 (34003) SS BOND : bond 0.00298 ( 7) SS BOND : angle 1.61441 ( 14) hydrogen bonds : bond 0.03469 ( 994) hydrogen bonds : angle 4.61814 ( 2850) link_BETA1-4 : bond 0.00631 ( 20) link_BETA1-4 : angle 2.27135 ( 60) link_NAG-ASN : bond 0.00357 ( 27) link_NAG-ASN : angle 2.21865 ( 81) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 237 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 THR cc_start: 0.8689 (OUTLIER) cc_final: 0.8214 (t) REVERT: A 186 GLN cc_start: 0.8774 (tp40) cc_final: 0.8402 (tp40) REVERT: A 223 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7588 (pm20) REVERT: A 360 MET cc_start: 0.8515 (mmt) cc_final: 0.8167 (mmt) REVERT: A 441 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7837 (tm-30) REVERT: A 672 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7315 (p0) REVERT: B 122 CYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8117 (t) REVERT: B 202 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8852 (ptp-110) REVERT: B 362 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9253 (pp) REVERT: B 521 TYR cc_start: 0.8210 (t80) cc_final: 0.7627 (t80) REVERT: B 533 PHE cc_start: 0.8482 (p90) cc_final: 0.8091 (p90) REVERT: B 538 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8635 (mt) REVERT: B 775 ARG cc_start: 0.9340 (OUTLIER) cc_final: 0.8852 (ptm-80) REVERT: B 820 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7585 (tp) REVERT: C 55 LEU cc_start: 0.8813 (mt) cc_final: 0.8475 (tp) REVERT: C 90 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8188 (mp0) REVERT: C 264 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9091 (mm) REVERT: C 709 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8512 (mmt) REVERT: C 740 THR cc_start: 0.9046 (p) cc_final: 0.8808 (p) REVERT: D 153 PHE cc_start: 0.8951 (OUTLIER) cc_final: 0.8565 (t80) REVERT: D 323 MET cc_start: 0.8650 (ttm) cc_final: 0.8386 (ttm) REVERT: D 346 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7088 (pp30) REVERT: D 359 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8548 (t80) REVERT: D 397 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7704 (mm-30) REVERT: D 649 SER cc_start: 0.9376 (t) cc_final: 0.9144 (p) REVERT: D 654 ASN cc_start: 0.8424 (t0) cc_final: 0.8003 (t0) REVERT: D 664 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7904 (ptp) REVERT: D 669 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8334 (p0) REVERT: D 682 TYR cc_start: 0.8962 (p90) cc_final: 0.8761 (p90) REVERT: D 691 MET cc_start: 0.8339 (tmm) cc_final: 0.7992 (tmm) REVERT: D 764 TYR cc_start: 0.6282 (OUTLIER) cc_final: 0.5764 (m-80) outliers start: 133 outliers final: 97 residues processed: 339 average time/residue: 0.1339 time to fit residues: 77.8617 Evaluate side-chains 345 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 229 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 802 CYS Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 643 PHE Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 664 MET Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 676 CYS Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 775 ARG Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 302 GLN Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 566 TYR Chi-restraints excluded: chain C residue 567 ILE Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 733 TYR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 762 LYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 835 VAL Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain D residue 355 PHE Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 431 ARG Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 664 MET Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 753 THR Chi-restraints excluded: chain D residue 764 TYR Chi-restraints excluded: chain D residue 766 VAL Chi-restraints excluded: chain D residue 793 MET Chi-restraints excluded: chain D residue 833 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 46 optimal weight: 10.0000 chunk 219 optimal weight: 2.9990 chunk 298 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 21 optimal weight: 0.0970 chunk 83 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 226 optimal weight: 6.9990 chunk 44 optimal weight: 0.0870 chunk 198 optimal weight: 7.9990 chunk 13 optimal weight: 0.1980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.094251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.073400 restraints weight = 76465.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.073255 restraints weight = 40557.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.073798 restraints weight = 39812.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.074036 restraints weight = 31658.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.074518 restraints weight = 29741.862| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 25159 Z= 0.107 Angle : 0.608 13.168 34158 Z= 0.289 Chirality : 0.042 0.326 3970 Planarity : 0.003 0.046 4236 Dihedral : 7.108 101.286 4286 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.75 % Allowed : 28.57 % Favored : 67.69 % 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: -0.47 (0.16), residues: 3021 helix: 1.16 (0.15), residues: 1281 sheet: -1.34 (0.30), residues: 350 loop : -1.46 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 712 TYR 0.011 0.001 TYR A 733 PHE 0.016 0.001 PHE A 642 TRP 0.032 0.001 TRP A 706 HIS 0.004 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00241 (25105) covalent geometry : angle 0.59265 (34003) SS BOND : bond 0.00349 ( 7) SS BOND : angle 1.44337 ( 14) hydrogen bonds : bond 0.03244 ( 994) hydrogen bonds : angle 4.43177 ( 2850) link_BETA1-4 : bond 0.00720 ( 20) link_BETA1-4 : angle 2.24961 ( 60) link_NAG-ASN : bond 0.00388 ( 27) link_NAG-ASN : angle 2.03319 ( 81) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 266 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.8101 (t) REVERT: A 186 GLN cc_start: 0.8751 (tp40) cc_final: 0.8347 (tp40) REVERT: A 340 MET cc_start: 0.8659 (tmm) cc_final: 0.8411 (tmm) REVERT: A 360 MET cc_start: 0.8439 (mmt) cc_final: 0.8065 (mmt) REVERT: A 441 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7460 (tm-30) REVERT: A 442 PRO cc_start: 0.7821 (Cg_endo) cc_final: 0.6878 (Cg_exo) REVERT: A 672 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7221 (p0) REVERT: B 122 CYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8021 (t) REVERT: B 202 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8713 (ptp-110) REVERT: B 362 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9211 (pp) REVERT: B 521 TYR cc_start: 0.8203 (t80) cc_final: 0.7615 (t80) REVERT: B 538 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8522 (mt) REVERT: B 576 CYS cc_start: 0.8932 (m) cc_final: 0.8550 (p) REVERT: B 695 LYS cc_start: 0.8383 (mmmm) cc_final: 0.7955 (mmmm) REVERT: B 737 MET cc_start: 0.7691 (ptp) cc_final: 0.7484 (ptp) REVERT: B 770 MET cc_start: 0.6658 (tpt) cc_final: 0.6327 (tpp) REVERT: B 775 ARG cc_start: 0.9309 (OUTLIER) cc_final: 0.8851 (ptm-80) REVERT: C 55 LEU cc_start: 0.8838 (mt) cc_final: 0.8446 (tp) REVERT: C 90 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8056 (mm-30) REVERT: C 264 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9072 (mm) REVERT: C 413 MET cc_start: 0.8224 (ptp) cc_final: 0.7886 (ppp) REVERT: C 646 ILE cc_start: 0.9662 (tp) cc_final: 0.9243 (tp) REVERT: C 740 THR cc_start: 0.8884 (p) cc_final: 0.8627 (p) REVERT: C 802 CYS cc_start: 0.7500 (p) cc_final: 0.6585 (m) REVERT: D 153 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.8458 (t80) REVERT: D 323 MET cc_start: 0.8565 (ttm) cc_final: 0.8297 (ttm) REVERT: D 346 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7141 (pp30) REVERT: D 359 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8512 (t80) REVERT: D 646 ILE cc_start: 0.9582 (OUTLIER) cc_final: 0.9204 (mt) REVERT: D 649 SER cc_start: 0.9351 (t) cc_final: 0.9046 (p) REVERT: D 654 ASN cc_start: 0.8360 (t0) cc_final: 0.7868 (t0) REVERT: D 664 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.7917 (ptt) REVERT: D 669 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8320 (p0) REVERT: D 682 TYR cc_start: 0.8876 (p90) cc_final: 0.8341 (p90) REVERT: D 691 MET cc_start: 0.8293 (tmm) cc_final: 0.7851 (tmm) REVERT: D 764 TYR cc_start: 0.5783 (OUTLIER) cc_final: 0.4033 (t80) outliers start: 98 outliers final: 65 residues processed: 340 average time/residue: 0.1376 time to fit residues: 79.7547 Evaluate side-chains 324 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 243 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 802 CYS Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 676 CYS Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 775 ARG Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 302 GLN Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 566 TYR Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 733 TYR Chi-restraints excluded: chain C residue 762 LYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain D residue 355 PHE Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 664 MET Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 764 TYR Chi-restraints excluded: chain D residue 793 MET Chi-restraints excluded: chain D residue 833 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 221 optimal weight: 1.9990 chunk 239 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 280 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 150 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 188 optimal weight: 4.9990 chunk 112 optimal weight: 0.0770 overall best weight: 1.4944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 ASN ** B 677 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 = 0.3633 r_free = 0.3633 target = 0.093188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.072399 restraints weight = 76786.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.072778 restraints weight = 39846.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.073210 restraints weight = 39208.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.073717 restraints weight = 29307.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.074224 restraints weight = 26300.194| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 25159 Z= 0.128 Angle : 0.623 12.972 34158 Z= 0.296 Chirality : 0.042 0.323 3970 Planarity : 0.003 0.047 4236 Dihedral : 7.023 101.378 4282 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.79 % Allowed : 28.64 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.16), residues: 3021 helix: 1.20 (0.15), residues: 1284 sheet: -1.47 (0.30), residues: 339 loop : -1.42 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 374 TYR 0.011 0.001 TYR A 702 PHE 0.054 0.001 PHE C 377 TRP 0.034 0.001 TRP D 799 HIS 0.004 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00302 (25105) covalent geometry : angle 0.60846 (34003) SS BOND : bond 0.00261 ( 7) SS BOND : angle 1.39175 ( 14) hydrogen bonds : bond 0.03242 ( 994) hydrogen bonds : angle 4.40897 ( 2850) link_BETA1-4 : bond 0.00666 ( 20) link_BETA1-4 : angle 2.22571 ( 60) link_NAG-ASN : bond 0.00323 ( 27) link_NAG-ASN : angle 2.07222 ( 81) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 244 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8092 (t) REVERT: A 186 GLN cc_start: 0.8743 (tp40) cc_final: 0.8365 (tp40) REVERT: A 340 MET cc_start: 0.8543 (tmm) cc_final: 0.8273 (tmm) REVERT: A 360 MET cc_start: 0.8335 (mmt) cc_final: 0.7967 (mmt) REVERT: A 441 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7452 (tm-30) REVERT: A 442 PRO cc_start: 0.7801 (Cg_endo) cc_final: 0.6850 (Cg_exo) REVERT: A 672 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7213 (p0) REVERT: B 122 CYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8042 (t) REVERT: B 202 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8743 (ptp-110) REVERT: B 362 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9179 (pp) REVERT: B 521 TYR cc_start: 0.8105 (t80) cc_final: 0.7555 (t80) REVERT: B 538 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8549 (mt) REVERT: B 576 CYS cc_start: 0.8885 (m) cc_final: 0.8471 (p) REVERT: B 695 LYS cc_start: 0.8336 (mmmm) cc_final: 0.7951 (mmmm) REVERT: B 705 MET cc_start: 0.8394 (ttp) cc_final: 0.8049 (ttt) REVERT: B 770 MET cc_start: 0.6491 (tpt) cc_final: 0.6162 (tpp) REVERT: B 775 ARG cc_start: 0.9387 (OUTLIER) cc_final: 0.8927 (ptm-80) REVERT: B 820 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7610 (tp) REVERT: C 55 LEU cc_start: 0.8783 (mt) cc_final: 0.8425 (tp) REVERT: C 90 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7972 (mm-30) REVERT: C 264 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9101 (mm) REVERT: C 413 MET cc_start: 0.8173 (ptp) cc_final: 0.7746 (ppp) REVERT: C 740 THR cc_start: 0.8858 (p) cc_final: 0.8614 (p) REVERT: D 153 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8490 (t80) REVERT: D 323 MET cc_start: 0.8575 (ttm) cc_final: 0.8328 (ttm) REVERT: D 346 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7148 (pp30) REVERT: D 359 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.8470 (t80) REVERT: D 397 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7626 (mm-30) REVERT: D 646 ILE cc_start: 0.9583 (OUTLIER) cc_final: 0.9211 (mt) REVERT: D 649 SER cc_start: 0.9304 (t) cc_final: 0.9071 (p) REVERT: D 654 ASN cc_start: 0.8415 (t0) cc_final: 0.7956 (t0) REVERT: D 664 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8082 (ptt) REVERT: D 669 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8239 (p0) REVERT: D 682 TYR cc_start: 0.8911 (p90) cc_final: 0.8348 (p90) REVERT: D 691 MET cc_start: 0.8244 (tmm) cc_final: 0.7833 (tmm) REVERT: D 764 TYR cc_start: 0.5917 (OUTLIER) cc_final: 0.4110 (t80) outliers start: 99 outliers final: 71 residues processed: 321 average time/residue: 0.1403 time to fit residues: 76.8391 Evaluate side-chains 330 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 241 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 802 CYS Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 676 CYS Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 775 ARG Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 302 GLN Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 566 TYR Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 733 TYR Chi-restraints excluded: chain C residue 762 LYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain D residue 355 PHE Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 431 ARG Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 646 ILE Chi-restraints excluded: chain D residue 664 MET Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 764 TYR Chi-restraints excluded: chain D residue 793 MET Chi-restraints excluded: chain D residue 833 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 60 optimal weight: 7.9990 chunk 169 optimal weight: 1.9990 chunk 267 optimal weight: 0.9990 chunk 278 optimal weight: 9.9990 chunk 219 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 239 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.093127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.072085 restraints weight = 76055.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.072659 restraints weight = 41066.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.074047 restraints weight = 33166.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.074129 restraints weight = 26369.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.074337 restraints weight = 25188.713| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 25159 Z= 0.137 Angle : 0.628 11.805 34158 Z= 0.299 Chirality : 0.042 0.322 3970 Planarity : 0.003 0.048 4236 Dihedral : 7.085 103.403 4282 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.90 % Allowed : 28.30 % Favored : 67.80 % 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: -0.44 (0.16), residues: 3021 helix: 1.21 (0.15), residues: 1283 sheet: -1.43 (0.29), residues: 354 loop : -1.43 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 184 TYR 0.013 0.001 TYR A 478 PHE 0.048 0.001 PHE C 377 TRP 0.036 0.001 TRP D 799 HIS 0.004 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00322 (25105) covalent geometry : angle 0.61403 (34003) SS BOND : bond 0.00307 ( 7) SS BOND : angle 1.34727 ( 14) hydrogen bonds : bond 0.03216 ( 994) hydrogen bonds : angle 4.40653 ( 2850) link_BETA1-4 : bond 0.00654 ( 20) link_BETA1-4 : angle 2.22763 ( 60) link_NAG-ASN : bond 0.00327 ( 27) link_NAG-ASN : angle 2.07656 ( 81) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6042 Ramachandran restraints generated. 3021 Oldfield, 0 Emsley, 3021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 245 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8149 (t) REVERT: A 186 GLN cc_start: 0.8782 (tp40) cc_final: 0.8432 (tp40) REVERT: A 340 MET cc_start: 0.8580 (tmm) cc_final: 0.8340 (tmm) REVERT: A 360 MET cc_start: 0.8381 (mmt) cc_final: 0.8024 (mmt) REVERT: A 441 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7466 (tm-30) REVERT: A 442 PRO cc_start: 0.7857 (Cg_endo) cc_final: 0.6901 (Cg_exo) REVERT: A 672 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7269 (p0) REVERT: B 122 CYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8061 (t) REVERT: B 202 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8821 (ptp-110) REVERT: B 362 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9226 (pp) REVERT: B 521 TYR cc_start: 0.8122 (t80) cc_final: 0.7547 (t80) REVERT: B 538 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8531 (mt) REVERT: B 576 CYS cc_start: 0.8906 (m) cc_final: 0.8482 (p) REVERT: B 695 LYS cc_start: 0.8406 (mmmm) cc_final: 0.7982 (mmmm) REVERT: B 770 MET cc_start: 0.6551 (tpt) cc_final: 0.6205 (tpp) REVERT: B 775 ARG cc_start: 0.9364 (OUTLIER) cc_final: 0.8904 (ptm-80) REVERT: B 820 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7658 (tp) REVERT: C 55 LEU cc_start: 0.8798 (mt) cc_final: 0.8465 (tp) REVERT: C 90 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8018 (mm-30) REVERT: C 264 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9099 (mm) REVERT: C 413 MET cc_start: 0.8224 (ptp) cc_final: 0.7698 (ppp) REVERT: C 709 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8403 (mmt) REVERT: C 740 THR cc_start: 0.8908 (p) cc_final: 0.8642 (p) REVERT: C 802 CYS cc_start: 0.7397 (p) cc_final: 0.6516 (m) REVERT: D 153 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.8514 (t80) REVERT: D 194 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6692 (mtt-85) REVERT: D 323 MET cc_start: 0.8642 (ttm) cc_final: 0.8388 (ttm) REVERT: D 346 GLN cc_start: 0.7788 (OUTLIER) cc_final: 0.7137 (pp30) REVERT: D 359 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8505 (t80) REVERT: D 397 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7732 (mm-30) REVERT: D 649 SER cc_start: 0.9402 (t) cc_final: 0.9112 (p) REVERT: D 654 ASN cc_start: 0.8440 (t0) cc_final: 0.7997 (t0) REVERT: D 664 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8275 (ptt) REVERT: D 669 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8281 (p0) REVERT: D 682 TYR cc_start: 0.8951 (p90) cc_final: 0.8365 (p90) REVERT: D 691 MET cc_start: 0.8301 (tmm) cc_final: 0.7858 (tmm) REVERT: D 764 TYR cc_start: 0.5989 (OUTLIER) cc_final: 0.4136 (t80) outliers start: 102 outliers final: 77 residues processed: 321 average time/residue: 0.1351 time to fit residues: 73.2719 Evaluate side-chains 337 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 241 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 672 ASP Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 802 CYS Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 202 ARG Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 463 CYS Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 643 PHE Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 668 ILE Chi-restraints excluded: chain B residue 676 CYS Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 703 ASP Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain B residue 775 ARG Chi-restraints excluded: chain B residue 820 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 302 GLN Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 566 TYR Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 716 VAL Chi-restraints excluded: chain C residue 733 TYR Chi-restraints excluded: chain C residue 762 LYS Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 122 CYS Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 194 ARG Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 276 MET Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain D residue 355 PHE Chi-restraints excluded: chain D residue 359 PHE Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 431 ARG Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 664 MET Chi-restraints excluded: chain D residue 669 ASP Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 764 TYR Chi-restraints excluded: chain D residue 793 MET Chi-restraints excluded: chain D residue 833 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 302 random chunks: chunk 141 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 286 optimal weight: 9.9990 chunk 28 optimal weight: 0.0370 chunk 85 optimal weight: 1.9990 chunk 127 optimal weight: 0.0870 chunk 300 optimal weight: 10.0000 chunk 230 optimal weight: 0.0000 chunk 74 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 overall best weight: 0.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 819 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.095283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.074572 restraints weight = 77330.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.075210 restraints weight = 41433.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.075350 restraints weight = 42978.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.076158 restraints weight = 30896.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.076395 restraints weight = 27003.670| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 25159 Z= 0.109 Angle : 0.637 14.235 34158 Z= 0.298 Chirality : 0.042 0.324 3970 Planarity : 0.003 0.050 4236 Dihedral : 6.964 102.854 4282 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.40 % Allowed : 28.95 % Favored : 67.65 % 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: -0.45 (0.16), residues: 3021 helix: 1.19 (0.15), residues: 1272 sheet: -1.28 (0.30), residues: 330 loop : -1.46 (0.16), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 133 TYR 0.011 0.001 TYR A 733 PHE 0.043 0.001 PHE A 315 TRP 0.034 0.001 TRP A 706 HIS 0.003 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00250 (25105) covalent geometry : angle 0.62333 (34003) SS BOND : bond 0.00266 ( 7) SS BOND : angle 1.33746 ( 14) hydrogen bonds : bond 0.03111 ( 994) hydrogen bonds : angle 4.30755 ( 2850) link_BETA1-4 : bond 0.00740 ( 20) link_BETA1-4 : angle 2.22421 ( 60) link_NAG-ASN : bond 0.00380 ( 27) link_NAG-ASN : angle 1.97332 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3517.52 seconds wall clock time: 62 minutes 10.63 seconds (3730.63 seconds total)