Starting phenix.real_space_refine on Sun Jul 5 09:07:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z7x_14539/07_2026/7z7x_14539.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z7x_14539/07_2026/7z7x_14539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z7x_14539/07_2026/7z7x_14539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z7x_14539/07_2026/7z7x_14539.map" model { file = "/net/cci-nas-00/data/ceres_data/7z7x_14539/07_2026/7z7x_14539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z7x_14539/07_2026/7z7x_14539.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7z7x_14539/07_2026/7z7x_14539.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z7x_14539/07_2026/7z7x_14539.cif" } resolution = 3.3 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= 0.000 sd= 0.003 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 123 5.16 5 C 17129 2.51 5 N 4411 2.21 5 O 5243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26906 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 7646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7646 Classifications: {'peptide': 987} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 49, 'TRANS': 937} Chain breaks: 9 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 5, 'ASN:plan1': 4, 'GLU:plan': 4, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 7677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 992, 7677 Classifications: {'peptide': 992} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 49, 'TRANS': 942} Chain breaks: 8 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 3, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 55 Chain: "C" Number of atoms: 7659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7659 Classifications: {'peptide': 990} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 49, 'TRANS': 940} Chain breaks: 7 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 3, 'GLU:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 48 Chain: "F" Number of atoms: 1000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Conformer: "B" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} bond proxies already assigned to first conformer: 997 Chain: "D" Number of atoms: 1000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Conformer: "B" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} bond proxies already assigned to first conformer: 997 Chain: "E" Number of atoms: 1000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Conformer: "B" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} bond proxies already assigned to first conformer: 997 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 chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 chiralities: 2 Chain: "N" 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 chiralities: 2 Chain: "O" 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 chiralities: 2 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 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 chiralities: 2 Chain: "R" 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 chiralities: 2 Chain: "S" 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 chiralities: 2 Chain: "T" 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 chiralities: 2 Chain: "U" 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 chiralities: 2 Chain: "V" 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 chiralities: 2 Chain: "W" 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 chiralities: 2 Chain: "X" 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 chiralities: 2 Chain: "Y" 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 chiralities: 2 Chain: "Z" 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 chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.60, per 1000 atoms: 0.25 Number of scatterers: 26906 At special positions: 0 Unit cell: (139.92, 128.26, 219.42, 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 123 16.00 O 5243 8.00 N 4411 7.00 C 17129 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG ACYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG BCYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG ACYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG BCYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG ACYS E 96 " distance=2.05 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG BCYS E 96 " 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 165 " " NAG A1308 " - " ASN A 343 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 343 " " NAG C1401 " - " ASN C 343 " " NAG C1402 " - " ASN C 61 " " NAG C1403 " - " ASN C 234 " " NAG C1404 " - " ASN C 331 " " NAG C1405 " - " ASN C 603 " " NAG C1406 " - " ASN C 616 " " NAG C1407 " - " ASN C 657 " " NAG C1408 " - " ASN C 165 " " NAG G 1 " - " ASN A 122 " " NAG H 1 " - " ASN A 234 " " NAG I 1 " - " ASN A 282 " " NAG J 1 " - " ASN A 331 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1098 " " NAG R 1 " - " ASN B1134 " " NAG S 1 " - " ASN C 122 " " NAG T 1 " - " ASN C 282 " " NAG U 1 " - " ASN C 709 " " NAG V 1 " - " ASN C 717 " " NAG W 1 " - " ASN C 801 " " NAG X 1 " - " ASN C1074 " " NAG Y 1 " - " ASN C1098 " " NAG Z 1 " - " ASN C1134 " Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.4 seconds 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6266 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 54 sheets defined 25.4% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.898A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.900A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.050A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.138A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.140A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.592A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.917A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.727A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.695A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.623A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.892A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 4.299A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.941A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.746A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.516A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.102A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.631A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.573A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.413A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.790A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.501A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.799A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 384 through 390 removed outlier: 3.720A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 4.012A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.578A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.711A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.120A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.550A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.814A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.748A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 105 through 111 Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.723A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 107 through 111 Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.967A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 105 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.763A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.194A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.766A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.618A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.167A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 327 removed outlier: 5.354A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.017A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.580A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 703 through 704 removed outlier: 7.153A pdb=" N ASN A 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.591A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.152A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.733A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.668A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.796A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.918A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.941A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.985A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.950A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.933A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.122A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 787 through 790 removed outlier: 5.888A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.476A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.076A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.519A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.802A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN C 125 " --> pdb=" O ASN C 122 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.356A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.553A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.601A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.729A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.967A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.711A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.950A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.286A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.207A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.549A pdb=" N VAL F 79 " --> pdb=" O CYS F 22 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 11 through 13 removed outlier: 6.587A pdb=" N MET F 12 " --> pdb=" O SER F 126 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ARG F 38 " --> pdb=" O PHE F 47 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N PHE F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 11 through 13 removed outlier: 6.587A pdb=" N MET F 12 " --> pdb=" O SER F 126 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.563A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.420A pdb=" N GLY D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N SER D 126 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N MET D 12 " --> pdb=" O SER D 126 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N MET D 34 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.420A pdb=" N GLY D 10 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N SER D 126 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N MET D 12 " --> pdb=" O SER D 126 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 3 through 8 removed outlier: 3.950A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.141A pdb=" N GLY E 10 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N SER E 126 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N MET E 12 " --> pdb=" O SER E 126 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL E 93 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ARG E 38 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N PHE E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.141A pdb=" N GLY E 10 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N SER E 126 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N MET E 12 " --> pdb=" O SER E 126 " (cutoff:3.500A) 1140 hydrogen bonds defined for protein. 3061 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: 7.72 Time building geometry restraints manager: 3.51 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: 8491 1.34 - 1.47: 7115 1.47 - 1.59: 11732 1.59 - 1.71: 0 1.71 - 1.84: 159 Bond restraints: 27497 Sorted by residual: bond pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " ideal model delta sigma weight residual 1.808 1.719 0.089 3.30e-02 9.18e+02 7.34e+00 bond pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " ideal model delta sigma weight residual 1.808 1.736 0.072 3.30e-02 9.18e+02 4.78e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.94e+00 bond pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " ideal model delta sigma weight residual 1.808 1.742 0.066 3.30e-02 9.18e+02 3.94e+00 bond pdb=" CB CYS C 301 " pdb=" SG CYS C 301 " ideal model delta sigma weight residual 1.808 1.745 0.063 3.30e-02 9.18e+02 3.64e+00 ... (remaining 27492 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 36783 2.29 - 4.58: 587 4.58 - 6.86: 30 6.86 - 9.15: 6 9.15 - 11.44: 3 Bond angle restraints: 37409 Sorted by residual: angle pdb=" CA CYS A 760 " pdb=" CB CYS A 760 " pdb=" SG CYS A 760 " ideal model delta sigma weight residual 114.40 102.96 11.44 2.30e+00 1.89e-01 2.47e+01 angle pdb=" N VAL C 130 " pdb=" CA VAL C 130 " pdb=" C VAL C 130 " ideal model delta sigma weight residual 111.88 107.47 4.41 1.06e+00 8.90e-01 1.73e+01 angle pdb=" CA CYS C 760 " pdb=" CB CYS C 760 " pdb=" SG CYS C 760 " ideal model delta sigma weight residual 114.40 105.40 9.00 2.30e+00 1.89e-01 1.53e+01 angle pdb=" N THR A 124 " pdb=" CA THR A 124 " pdb=" C THR A 124 " ideal model delta sigma weight residual 114.62 110.37 4.25 1.14e+00 7.69e-01 1.39e+01 angle pdb=" N ASN B 122 " pdb=" CA ASN B 122 " pdb=" C ASN B 122 " ideal model delta sigma weight residual 113.20 108.78 4.42 1.21e+00 6.83e-01 1.34e+01 ... (remaining 37404 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 14558 17.97 - 35.95: 990 35.95 - 53.92: 199 53.92 - 71.89: 45 71.89 - 89.87: 30 Dihedral angle restraints: 15822 sinusoidal: 6059 harmonic: 9763 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -172.92 86.92 1 1.00e+01 1.00e-02 9.08e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual -86.00 -169.72 83.72 1 1.00e+01 1.00e-02 8.55e+01 dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual -86.00 -168.69 82.69 1 1.00e+01 1.00e-02 8.38e+01 ... (remaining 15819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3768 0.067 - 0.135: 645 0.135 - 0.202: 18 0.202 - 0.269: 9 0.269 - 0.337: 3 Chirality restraints: 4443 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.68 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 4440 not shown) Planarity restraints: 4774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS B 336 " -0.063 5.00e-02 4.00e+02 9.66e-02 1.49e+01 pdb=" N PRO B 337 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO B 337 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 337 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 616 " 0.004 2.00e-02 2.50e+03 3.38e-02 1.43e+01 pdb=" CG ASN A 616 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN A 616 " 0.040 2.00e-02 2.50e+03 pdb=" ND2 ASN A 616 " -0.035 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 36 " 0.023 2.00e-02 2.50e+03 2.25e-02 1.27e+01 pdb=" CG TRP E 36 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP E 36 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP E 36 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 36 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP E 36 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 36 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 36 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 36 " 0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP E 36 " -0.008 2.00e-02 2.50e+03 ... (remaining 4771 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 811 2.70 - 3.25: 25915 3.25 - 3.80: 42795 3.80 - 4.35: 55365 4.35 - 4.90: 94354 Nonbonded interactions: 219240 Sorted by model distance: nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.149 3.040 nonbonded pdb=" O GLU C 309 " pdb=" OH TYR C 313 " model vdw 2.196 3.040 nonbonded pdb=" O GLU B 309 " pdb=" OH TYR B 313 " model vdw 2.216 3.040 nonbonded pdb=" O TYR E 109 " pdb=" OH TYR E 114 " model vdw 2.219 3.040 nonbonded pdb=" OG1 THR B 912 " pdb=" OD1 ASN B 914 " model vdw 2.219 3.040 ... (remaining 219235 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 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 66 or resid 82 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (re \ sid 99 and (name N or name CA or name C or name O or name CB )) or resid 100 thr \ ough 110 or (resid 111 through 113 and (name N or name CA or name C or name O or \ name CB )) or resid 116 through 128 or (resid 129 and (name N or name CA or nam \ e C or name O or name CB )) or resid 130 through 134 or (resid 135 through 138 a \ nd (name N or name CA or name C or name O or name CB )) or resid 139 through 140 \ or resid 166 through 168 or (resid 169 and (name N or name CA or name C or name \ O or name CB )) or resid 170 through 172 or resid 187 or (resid 188 and (name N \ or name CA or name C or name O or name CB )) or resid 189 through 210 or (resid \ 211 through 215 and (name N or name CA or name C or name O or name CB )) or res \ id 216 through 241 or (resid 242 through 263 and (name N or name CA or name C or \ name O or name CB )) or resid 265 through 280 or (resid 281 and (name N or name \ CA or name C or name O or name CB )) or resid 282 through 567 or (resid 568 and \ (name N or name CA or name C or name O or name CB )) or resid 569 through 570 o \ r (resid 571 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 72 through 581 or (resid 582 through 583 and (name N or name CA or name C or nam \ e O or name CB )) or resid 584 through 585 or (resid 586 and (name N or name CA \ or name C or name O or name CB )) or resid 587 through 660 or (resid 661 and (na \ me N or name CA or name C or name O or name CB )) or resid 662 through 676 or re \ sid 690 through 747 or (resid 748 and (name N or name CA or name C or name O or \ name CB )) or resid 749 through 810 or (resid 811 and (name N or name CA or name \ C or name O or name CB )) or resid 812 through 827 or resid 856 through 939 or \ (resid 940 and (name N or name CA or name C or name O or name CB )) or resid 941 \ through 984 or (resid 985 and (name N or name CA or name C or name O or name CB \ )) or resid 986 through 1143 or (resid 1144 through 1146 and (name N or name CA \ or name C or name O or name CB )) or resid 1147 through 1308)) selection = (chain 'B' and (resid 27 through 45 or (resid 46 and (name N or name CA or name \ C or name O or name CB )) or resid 47 through 52 or (resid 53 and (name N or nam \ e CA or name C or name O or name CB )) or resid 54 through 66 or resid 82 throug \ h 95 or (resid 96 through 97 and (name N or name CA or name C or name O or name \ CB )) or resid 98 through 111 or (resid 112 through 113 and (name N or name CA o \ r name C or name O or name CB )) or resid 116 through 124 or (resid 125 and (nam \ e N or name CA or name C or name O or name CB )) or resid 126 through 131 or (re \ sid 132 and (name N or name CA or name C or name O or name CB )) or resid 133 or \ (resid 134 through 138 and (name N or name CA or name C or name O or name CB )) \ or resid 139 through 140 or resid 166 through 168 or (resid 169 and (name N or \ name CA or name C or name O or name CB )) or resid 170 through 171 or (resid 172 \ and (name N or name CA or name C or name O or name CB )) or resid 187 through 1 \ 96 or resid 200 through 210 or (resid 211 and (name N or name CA or name C or na \ me O or name CB )) or (resid 215 and (name N or name CA or name C or name O or n \ ame CB )) or resid 216 through 263 or resid 265 through 528 or (resid 529 and (n \ ame N or name CA or name C or name O or name CB )) or resid 530 through 660 or ( \ resid 661 and (name N or name CA or name C or name O or name CB )) or resid 662 \ through 747 or (resid 748 and (name N or name CA or name C or name O or name CB \ )) or resid 749 through 810 or (resid 811 and (name N or name CA or name C or na \ me O or name CB )) or resid 812 through 827 or resid 856 through 939 or (resid 9 \ 40 and (name N or name CA or name C or name O or name CB )) or resid 941 through \ 984 or (resid 985 and (name N or name CA or name C or name O or name CB )) or r \ esid 986 through 1141 or (resid 1142 and (name N or name CA or name C or name O \ or name CB )) or resid 1143 through 1144 or (resid 1145 through 1146 and (name N \ or name CA or name C or name O or name CB )) or resid 1147 through 1308)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 110 or (resid 111 through 113 and (name N or name CA or name C o \ r name O or name CB )) or resid 116 through 124 or (resid 125 and (name N or nam \ e CA or name C or name O or name CB )) or resid 126 through 128 or (resid 129 an \ d (name N or name CA or name C or name O or name CB )) or resid 130 through 133 \ or (resid 134 through 138 and (name N or name CA or name C or name O or name CB \ )) or resid 139 through 140 or resid 166 through 187 or (resid 188 and (name N o \ r name CA or name C or name O or name CB )) or resid 189 through 196 or resid 20 \ 0 through 211 or (resid 215 and (name N or name CA or name C or name O or name C \ B )) or resid 216 through 528 or (resid 529 and (name N or name CA or name C or \ name O or name CB )) or resid 530 through 567 or (resid 568 and (name N or name \ CA or name C or name O or name CB )) or resid 569 through 570 or (resid 571 and \ (name N or name CA or name C or name O or name CB )) or resid 572 through 581 or \ (resid 582 through 583 and (name N or name CA or name C or name O or name CB )) \ or resid 584 through 585 or (resid 586 and (name N or name CA or name C or name \ O or name CB )) or resid 587 through 1141 or (resid 1142 and (name N or name CA \ or name C or name O or name CB )) or resid 1143 or (resid 1144 through 1146 and \ (name N or name CA or name C or name O or name CB )) or resid 1147 through 1408 \ )) } ncs_group { reference = (chain 'D' and (resid 1 through 33 or resid 35 through 95 or resid 97 through 10 \ 3 or resid 105 through 128)) selection = (chain 'E' and (resid 1 through 33 or resid 35 through 95 or resid 97 through 10 \ 3 or resid 105 through 128)) selection = (chain 'F' and (resid 1 through 33 or resid 35 through 95 or resid 97 through 10 \ 3 or resid 105 through 128)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.480 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: 0.030 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 29.930 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 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 : 0.006 0.089 27608 Z= 0.289 Angle : 0.745 11.439 37697 Z= 0.404 Chirality : 0.049 0.337 4443 Planarity : 0.004 0.097 4728 Dihedral : 13.336 89.865 9421 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.25 % Favored : 95.72 % Rotamer: Outliers : 0.11 % Allowed : 0.49 % Favored : 99.40 % 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: -0.13 (0.14), residues: 3302 helix: 1.46 (0.21), residues: 659 sheet: -0.16 (0.17), residues: 837 loop : -0.60 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 237 TYR 0.043 0.002 TYR B 453 PHE 0.028 0.002 PHE A 275 TRP 0.057 0.002 TRP E 36 HIS 0.007 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00649 / 0.29 (27497) covalent geometry : angle 0.71952 / 0.40 (37409) SS BOND : bond 0.00479 / 0.31 ( 45) SS BOND : angle 2.35957 / 1.40 ( 90) hydrogen bonds : bond 0.18393 / 12.21 ( 1128) hydrogen bonds : angle 8.13308 / 5.68 ( 3061) link_BETA1-4 : bond 0.00405 / 0.20 ( 20) link_BETA1-4 : angle 1.74189 / 1.11 ( 60) link_NAG-ASN : bond 0.00416 / 0.25 ( 46) link_NAG-ASN : angle 2.49088 / 1.56 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 242 time to evaluate : 1.218 Fit side-chains REVERT: B 453 TYR cc_start: 0.6675 (p90) cc_final: 0.6244 (p90) REVERT: B 1145 LEU cc_start: 0.6272 (pp) cc_final: 0.5808 (pp) REVERT: C 355 ARG cc_start: 0.7671 (tpt-90) cc_final: 0.7423 (tpp80) REVERT: C 360 ASN cc_start: 0.6932 (m-40) cc_final: 0.5680 (t0) REVERT: C 400 PHE cc_start: 0.7627 (p90) cc_final: 0.7373 (p90) REVERT: C 424 LYS cc_start: 0.7069 (tptt) cc_final: 0.6808 (tptp) REVERT: C 427 ASP cc_start: 0.5725 (p0) cc_final: 0.4893 (t70) REVERT: E 114 TYR cc_start: 0.6258 (m-80) cc_final: 0.5359 (m-80) outliers start: 1 outliers final: 0 residues processed: 242 average time/residue: 0.1790 time to fit residues: 70.8141 Evaluate side-chains 189 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.0170 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 20.0000 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 901 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 388 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 804 GLN C 960 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.172555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.117011 restraints weight = 99061.568| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 5.36 r_work: 0.2898 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2889 r_free = 0.2889 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27608 Z= 0.131 Angle : 0.580 14.843 37697 Z= 0.296 Chirality : 0.045 0.516 4443 Planarity : 0.004 0.070 4728 Dihedral : 4.501 30.784 3616 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.55 % Favored : 97.42 % Rotamer: Outliers : 0.56 % Allowed : 4.43 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.12 (0.14), residues: 3302 helix: 1.79 (0.21), residues: 667 sheet: -0.05 (0.17), residues: 817 loop : -0.46 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 237 TYR 0.021 0.001 TYR A 369 PHE 0.014 0.001 PHE A 275 TRP 0.029 0.001 TRP E 36 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (27497) covalent geometry : angle 0.55617 / 0.29 (37409) SS BOND : bond 0.00433 / 0.31 ( 45) SS BOND : angle 1.60390 / 0.95 ( 90) hydrogen bonds : bond 0.04683 / 3.08 ( 1128) hydrogen bonds : angle 6.26334 / 4.35 ( 3061) link_BETA1-4 : bond 0.00625 / 0.35 ( 20) link_BETA1-4 : angle 1.19861 / 0.81 ( 60) link_NAG-ASN : bond 0.00491 / 0.34 ( 46) link_NAG-ASN : angle 2.36797 / 1.44 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 215 time to evaluate : 1.056 Fit side-chains revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7992 (m-30) cc_final: 0.7757 (m-30) REVERT: A 129 LYS cc_start: 0.8067 (ptpp) cc_final: 0.7662 (ptpp) REVERT: A 140 PHE cc_start: 0.6796 (p90) cc_final: 0.6577 (p90) REVERT: A 168 PHE cc_start: 0.7990 (t80) cc_final: 0.7561 (t80) REVERT: A 218 GLN cc_start: 0.8404 (tt0) cc_final: 0.8158 (tt0) REVERT: A 389 ASP cc_start: 0.7423 (m-30) cc_final: 0.7025 (p0) REVERT: A 1107 ARG cc_start: 0.8880 (ptp-170) cc_final: 0.8654 (mtt180) REVERT: B 453 TYR cc_start: 0.7122 (p90) cc_final: 0.6702 (p90) REVERT: B 541 PHE cc_start: 0.8709 (p90) cc_final: 0.8462 (p90) REVERT: C 316 SER cc_start: 0.8868 (t) cc_final: 0.8518 (p) REVERT: C 360 ASN cc_start: 0.7070 (m-40) cc_final: 0.5956 (t0) REVERT: C 400 PHE cc_start: 0.7648 (p90) cc_final: 0.7376 (p90) REVERT: C 424 LYS cc_start: 0.7095 (tptt) cc_final: 0.6843 (tptp) REVERT: C 427 ASP cc_start: 0.5966 (p0) cc_final: 0.5080 (t70) REVERT: E 103 ARG cc_start: 0.6459 (mmm160) cc_final: 0.5727 (tpp-160) REVERT: E 114 TYR cc_start: 0.6126 (m-80) cc_final: 0.5167 (m-80) outliers start: 13 outliers final: 10 residues processed: 220 average time/residue: 0.1669 time to fit residues: 60.4840 Evaluate side-chains 196 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 186 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 868 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 230 optimal weight: 3.9990 chunk 234 optimal weight: 20.0000 chunk 217 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 174 optimal weight: 0.9990 chunk 257 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 242 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 294 optimal weight: 0.6980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 450 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 935 GLN C1005 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.171859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.114498 restraints weight = 84730.404| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 4.64 r_work: 0.2922 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 27608 Z= 0.161 Angle : 0.554 9.557 37697 Z= 0.281 Chirality : 0.044 0.235 4443 Planarity : 0.004 0.057 4728 Dihedral : 4.374 30.516 3616 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.04 % Favored : 96.93 % Rotamer: Outliers : 0.98 % Allowed : 6.25 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.15 (0.14), residues: 3302 helix: 1.88 (0.21), residues: 667 sheet: -0.13 (0.17), residues: 857 loop : -0.42 (0.15), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 355 TYR 0.022 0.001 TYR A 369 PHE 0.012 0.001 PHE A 275 TRP 0.027 0.001 TRP E 36 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (27497) covalent geometry : angle 0.53817 / 0.28 (37409) SS BOND : bond 0.00459 / 0.32 ( 45) SS BOND : angle 1.48905 / 0.89 ( 90) hydrogen bonds : bond 0.04303 / 2.82 ( 1128) hydrogen bonds : angle 5.87454 / 4.06 ( 3061) link_BETA1-4 : bond 0.00368 / 0.19 ( 20) link_BETA1-4 : angle 1.19288 / 0.78 ( 60) link_NAG-ASN : bond 0.00303 / 0.18 ( 46) link_NAG-ASN : angle 1.81160 / 1.17 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7925 (m-30) cc_final: 0.7687 (m-30) REVERT: A 140 PHE cc_start: 0.6761 (p90) cc_final: 0.6525 (p90) REVERT: A 168 PHE cc_start: 0.7962 (t80) cc_final: 0.7753 (t80) REVERT: A 218 GLN cc_start: 0.8543 (tt0) cc_final: 0.8294 (tt0) REVERT: A 314 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8352 (tm130) REVERT: A 389 ASP cc_start: 0.7387 (m-30) cc_final: 0.7008 (p0) REVERT: A 796 ASP cc_start: 0.8170 (t0) cc_final: 0.7913 (t0) REVERT: B 453 TYR cc_start: 0.7298 (p90) cc_final: 0.6832 (p90) REVERT: B 461 LEU cc_start: 0.7765 (mt) cc_final: 0.7208 (mm) REVERT: B 508 TYR cc_start: 0.6616 (m-80) cc_final: 0.6403 (m-80) REVERT: B 541 PHE cc_start: 0.8628 (p90) cc_final: 0.8255 (p90) REVERT: B 900 MET cc_start: 0.9211 (mtp) cc_final: 0.8961 (mtm) REVERT: C 316 SER cc_start: 0.8827 (t) cc_final: 0.8405 (p) REVERT: C 360 ASN cc_start: 0.6940 (m-40) cc_final: 0.5895 (t0) REVERT: C 400 PHE cc_start: 0.7710 (p90) cc_final: 0.7486 (p90) REVERT: C 427 ASP cc_start: 0.5982 (p0) cc_final: 0.5072 (t70) REVERT: E 103 ARG cc_start: 0.6590 (mmm160) cc_final: 0.5800 (tpp-160) REVERT: E 114 TYR cc_start: 0.6132 (m-80) cc_final: 0.5281 (m-80) outliers start: 25 outliers final: 15 residues processed: 213 average time/residue: 0.1719 time to fit residues: 60.2867 Evaluate side-chains 203 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 747 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 262 optimal weight: 2.9990 chunk 277 optimal weight: 1.9990 chunk 234 optimal weight: 20.0000 chunk 93 optimal weight: 5.9990 chunk 255 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 195 optimal weight: 0.4980 chunk 247 optimal weight: 1.9990 chunk 278 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A1106 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 935 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.172921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.113593 restraints weight = 80695.152| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 4.68 r_work: 0.2954 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 27608 Z= 0.128 Angle : 0.519 9.581 37697 Z= 0.265 Chirality : 0.043 0.238 4443 Planarity : 0.004 0.049 4728 Dihedral : 4.196 29.992 3616 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.49 % Favored : 97.48 % Rotamer: Outliers : 1.16 % Allowed : 7.13 % Favored : 91.71 % 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: 0.27 (0.15), residues: 3302 helix: 2.12 (0.21), residues: 661 sheet: -0.13 (0.17), residues: 870 loop : -0.36 (0.15), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 355 TYR 0.020 0.001 TYR A 369 PHE 0.012 0.001 PHE C 392 TRP 0.024 0.001 TRP E 36 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (27497) covalent geometry : angle 0.50637 / 0.26 (37409) SS BOND : bond 0.00317 / 0.21 ( 45) SS BOND : angle 1.38990 / 0.83 ( 90) hydrogen bonds : bond 0.03887 / 2.54 ( 1128) hydrogen bonds : angle 5.59280 / 3.86 ( 3061) link_BETA1-4 : bond 0.00379 / 0.20 ( 20) link_BETA1-4 : angle 1.10250 / 0.73 ( 60) link_NAG-ASN : bond 0.00263 / 0.15 ( 46) link_NAG-ASN : angle 1.54869 / 1.01 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7914 (m-30) cc_final: 0.7694 (m-30) REVERT: A 129 LYS cc_start: 0.7831 (ptpp) cc_final: 0.7556 (ptpp) REVERT: A 140 PHE cc_start: 0.6724 (p90) cc_final: 0.6504 (p90) REVERT: A 218 GLN cc_start: 0.8501 (tt0) cc_final: 0.8274 (tt0) REVERT: A 242 LEU cc_start: 0.7601 (mp) cc_final: 0.7219 (mm) REVERT: A 314 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8366 (tm130) REVERT: A 389 ASP cc_start: 0.7382 (m-30) cc_final: 0.6761 (t0) REVERT: A 796 ASP cc_start: 0.8115 (t0) cc_final: 0.7840 (t0) REVERT: B 394 ASN cc_start: 0.7577 (t0) cc_final: 0.7242 (m-40) REVERT: B 453 TYR cc_start: 0.7386 (p90) cc_final: 0.6816 (p90) REVERT: B 461 LEU cc_start: 0.7750 (mt) cc_final: 0.7198 (mm) REVERT: B 508 TYR cc_start: 0.6672 (m-80) cc_final: 0.6408 (m-80) REVERT: B 541 PHE cc_start: 0.8609 (p90) cc_final: 0.8133 (p90) REVERT: B 900 MET cc_start: 0.9071 (mtp) cc_final: 0.8791 (mtm) REVERT: C 316 SER cc_start: 0.8781 (t) cc_final: 0.8355 (p) REVERT: C 360 ASN cc_start: 0.6950 (m-40) cc_final: 0.5897 (t0) REVERT: C 427 ASP cc_start: 0.5904 (p0) cc_final: 0.4978 (t70) REVERT: E 103 ARG cc_start: 0.6678 (mmm160) cc_final: 0.5848 (tpp-160) REVERT: E 114 TYR cc_start: 0.6140 (m-80) cc_final: 0.5267 (m-80) outliers start: 30 outliers final: 20 residues processed: 231 average time/residue: 0.1649 time to fit residues: 61.8797 Evaluate side-chains 214 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 936 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 185 optimal weight: 1.9990 chunk 328 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 236 optimal weight: 20.0000 chunk 64 optimal weight: 2.9990 chunk 308 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 292 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS B 207 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 907 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.170412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.107255 restraints weight = 72556.423| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 4.09 r_work: 0.2936 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 27608 Z= 0.241 Angle : 0.608 9.667 37697 Z= 0.305 Chirality : 0.045 0.234 4443 Planarity : 0.004 0.046 4728 Dihedral : 4.509 30.310 3616 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.89 % Favored : 96.08 % Rotamer: Outliers : 1.41 % Allowed : 8.33 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.04 (0.15), residues: 3302 helix: 1.91 (0.21), residues: 657 sheet: -0.20 (0.17), residues: 856 loop : -0.54 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 355 TYR 0.019 0.002 TYR C1067 PHE 0.016 0.002 PHE C 92 TRP 0.026 0.001 TRP E 36 HIS 0.006 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.24 (27497) covalent geometry : angle 0.59200 / 0.30 (37409) SS BOND : bond 0.00506 / 0.35 ( 45) SS BOND : angle 1.82785 / 1.09 ( 90) hydrogen bonds : bond 0.04558 / 2.99 ( 1128) hydrogen bonds : angle 5.69083 / 3.92 ( 3061) link_BETA1-4 : bond 0.00338 / 0.16 ( 20) link_BETA1-4 : angle 1.32066 / 0.85 ( 60) link_NAG-ASN : bond 0.00384 / 0.23 ( 46) link_NAG-ASN : angle 1.76495 / 1.15 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 205 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7984 (m-30) cc_final: 0.7769 (m-30) REVERT: A 129 LYS cc_start: 0.7886 (ptpp) cc_final: 0.7456 (ptpp) REVERT: A 140 PHE cc_start: 0.6691 (p90) cc_final: 0.6449 (p90) REVERT: A 168 PHE cc_start: 0.7850 (t80) cc_final: 0.7444 (t80) REVERT: A 314 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8381 (tm130) REVERT: A 389 ASP cc_start: 0.7421 (m-30) cc_final: 0.6763 (t0) REVERT: A 796 ASP cc_start: 0.8191 (t0) cc_final: 0.7957 (t0) REVERT: B 453 TYR cc_start: 0.7485 (p90) cc_final: 0.7128 (p90) REVERT: B 461 LEU cc_start: 0.7773 (mt) cc_final: 0.7302 (mm) REVERT: B 508 TYR cc_start: 0.6698 (m-80) cc_final: 0.6268 (m-80) REVERT: B 528 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7484 (mmmm) REVERT: B 541 PHE cc_start: 0.8615 (p90) cc_final: 0.8137 (p90) REVERT: B 867 ASP cc_start: 0.7860 (m-30) cc_final: 0.7649 (m-30) REVERT: B 990 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7476 (mm-30) REVERT: C 360 ASN cc_start: 0.6983 (m-40) cc_final: 0.5914 (t0) REVERT: C 427 ASP cc_start: 0.5912 (p0) cc_final: 0.4950 (t70) REVERT: E 103 ARG cc_start: 0.6690 (mmm160) cc_final: 0.5845 (tpp-160) REVERT: E 114 TYR cc_start: 0.6201 (m-80) cc_final: 0.5239 (m-80) outliers start: 37 outliers final: 27 residues processed: 229 average time/residue: 0.1727 time to fit residues: 64.3899 Evaluate side-chains 224 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 916 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 170 optimal weight: 0.9980 chunk 113 optimal weight: 0.0970 chunk 123 optimal weight: 7.9990 chunk 179 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 194 optimal weight: 0.9990 chunk 208 optimal weight: 6.9990 chunk 329 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS A 779 GLN B 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.172762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.117559 restraints weight = 100266.342| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 5.27 r_work: 0.2893 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 27608 Z= 0.114 Angle : 0.515 9.569 37697 Z= 0.262 Chirality : 0.043 0.236 4443 Planarity : 0.004 0.044 4728 Dihedral : 4.175 29.672 3616 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.46 % Favored : 97.51 % Rotamer: Outliers : 1.23 % Allowed : 9.14 % Favored : 89.63 % 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: 0.26 (0.15), residues: 3302 helix: 2.18 (0.21), residues: 659 sheet: -0.16 (0.17), residues: 859 loop : -0.37 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 355 TYR 0.021 0.001 TYR B 449 PHE 0.015 0.001 PHE C 400 TRP 0.022 0.001 TRP E 36 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (27497) covalent geometry : angle 0.50208 / 0.26 (37409) SS BOND : bond 0.00330 / 0.23 ( 45) SS BOND : angle 1.46751 / 0.87 ( 90) hydrogen bonds : bond 0.03759 / 2.46 ( 1128) hydrogen bonds : angle 5.41588 / 3.73 ( 3061) link_BETA1-4 : bond 0.00374 / 0.20 ( 20) link_BETA1-4 : angle 1.08646 / 0.71 ( 60) link_NAG-ASN : bond 0.00262 / 0.16 ( 46) link_NAG-ASN : angle 1.45439 / 0.96 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 208 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8074 (m-30) cc_final: 0.7856 (m-30) REVERT: A 140 PHE cc_start: 0.6774 (p90) cc_final: 0.6556 (p90) REVERT: A 168 PHE cc_start: 0.8002 (t80) cc_final: 0.7672 (t80) REVERT: A 314 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8461 (tm130) REVERT: A 389 ASP cc_start: 0.7527 (m-30) cc_final: 0.6826 (t0) REVERT: A 796 ASP cc_start: 0.8300 (t0) cc_final: 0.8019 (t0) REVERT: B 394 ASN cc_start: 0.7741 (OUTLIER) cc_final: 0.7382 (t0) REVERT: B 453 TYR cc_start: 0.7615 (p90) cc_final: 0.7322 (p90) REVERT: B 461 LEU cc_start: 0.7866 (mt) cc_final: 0.7385 (mm) REVERT: B 541 PHE cc_start: 0.8573 (p90) cc_final: 0.7902 (p90) REVERT: B 646 ARG cc_start: 0.8343 (tpt170) cc_final: 0.7971 (tpt90) REVERT: B 900 MET cc_start: 0.9169 (mtp) cc_final: 0.8945 (mtm) REVERT: B 990 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7438 (mm-30) REVERT: C 229 LEU cc_start: 0.7071 (mp) cc_final: 0.6605 (mp) REVERT: C 316 SER cc_start: 0.8828 (t) cc_final: 0.8444 (p) REVERT: C 360 ASN cc_start: 0.6796 (m-40) cc_final: 0.5786 (t0) REVERT: C 427 ASP cc_start: 0.5854 (p0) cc_final: 0.4900 (t70) REVERT: C 577 ARG cc_start: 0.7074 (ttm170) cc_final: 0.6199 (ttm170) REVERT: E 103 ARG cc_start: 0.6682 (mmm160) cc_final: 0.5833 (tpp-160) REVERT: E 114 TYR cc_start: 0.6116 (m-80) cc_final: 0.5197 (m-80) outliers start: 32 outliers final: 24 residues processed: 228 average time/residue: 0.1728 time to fit residues: 64.6833 Evaluate side-chains 224 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain E residue 101 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 46 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 chunk 232 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 221 optimal weight: 0.2980 chunk 90 optimal weight: 0.0370 chunk 4 optimal weight: 4.9990 chunk 320 optimal weight: 20.0000 chunk 282 optimal weight: 0.8980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 207 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.173735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.114580 restraints weight = 82774.949| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 4.86 r_work: 0.2965 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 27608 Z= 0.101 Angle : 0.499 9.551 37697 Z= 0.254 Chirality : 0.042 0.238 4443 Planarity : 0.003 0.043 4728 Dihedral : 4.042 29.522 3616 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.52 % Favored : 97.45 % Rotamer: Outliers : 1.16 % Allowed : 9.52 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.15), residues: 3302 helix: 2.27 (0.21), residues: 661 sheet: -0.11 (0.17), residues: 837 loop : -0.28 (0.15), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 355 TYR 0.020 0.001 TYR B 453 PHE 0.015 0.001 PHE C 400 TRP 0.021 0.001 TRP E 36 HIS 0.021 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (27497) covalent geometry : angle 0.48802 / 0.25 (37409) SS BOND : bond 0.00413 / 0.29 ( 45) SS BOND : angle 1.33292 / 0.79 ( 90) hydrogen bonds : bond 0.03588 / 2.34 ( 1128) hydrogen bonds : angle 5.28803 / 3.65 ( 3061) link_BETA1-4 : bond 0.00359 / 0.20 ( 20) link_BETA1-4 : angle 1.06971 / 0.71 ( 60) link_NAG-ASN : bond 0.00232 / 0.14 ( 46) link_NAG-ASN : angle 1.38619 / 0.92 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 217 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7954 (m-30) cc_final: 0.7706 (m-30) REVERT: A 140 PHE cc_start: 0.6660 (p90) cc_final: 0.6458 (p90) REVERT: A 168 PHE cc_start: 0.8042 (t80) cc_final: 0.7806 (t80) REVERT: A 220 PHE cc_start: 0.7339 (t80) cc_final: 0.6353 (t80) REVERT: A 314 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8366 (tm130) REVERT: A 389 ASP cc_start: 0.7450 (m-30) cc_final: 0.6786 (t0) REVERT: A 796 ASP cc_start: 0.8150 (t0) cc_final: 0.7915 (t0) REVERT: B 453 TYR cc_start: 0.7487 (p90) cc_final: 0.7277 (p90) REVERT: B 461 LEU cc_start: 0.7760 (mt) cc_final: 0.7277 (mm) REVERT: B 541 PHE cc_start: 0.8495 (p90) cc_final: 0.7907 (p90) REVERT: B 646 ARG cc_start: 0.8239 (tpt170) cc_final: 0.7859 (tpt90) REVERT: B 900 MET cc_start: 0.9085 (mtp) cc_final: 0.8852 (mtm) REVERT: C 229 LEU cc_start: 0.7008 (mp) cc_final: 0.6568 (mp) REVERT: C 316 SER cc_start: 0.8776 (t) cc_final: 0.8386 (p) REVERT: C 360 ASN cc_start: 0.6869 (m-40) cc_final: 0.5858 (t0) REVERT: C 427 ASP cc_start: 0.5686 (p0) cc_final: 0.4739 (t70) REVERT: E 103 ARG cc_start: 0.6478 (mmm160) cc_final: 0.5885 (tpp-160) REVERT: E 114 TYR cc_start: 0.6278 (m-80) cc_final: 0.5293 (m-80) outliers start: 30 outliers final: 23 residues processed: 234 average time/residue: 0.1567 time to fit residues: 60.4830 Evaluate side-chains 229 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 916 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 286 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 317 optimal weight: 30.0000 chunk 48 optimal weight: 5.9990 chunk 73 optimal weight: 0.1980 chunk 95 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 249 optimal weight: 0.0170 chunk 175 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 302 optimal weight: 0.9980 overall best weight: 0.5620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS B 207 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.174192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.118213 restraints weight = 94974.473| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 5.59 r_work: 0.2935 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 27608 Z= 0.099 Angle : 0.489 9.546 37697 Z= 0.249 Chirality : 0.042 0.241 4443 Planarity : 0.003 0.043 4728 Dihedral : 3.927 29.495 3616 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.34 % Favored : 97.63 % Rotamer: Outliers : 1.16 % Allowed : 10.01 % Favored : 88.83 % 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 (0.15), residues: 3302 helix: 2.33 (0.21), residues: 662 sheet: -0.09 (0.17), residues: 851 loop : -0.24 (0.15), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 355 TYR 0.018 0.001 TYR A 369 PHE 0.033 0.001 PHE C 643 TRP 0.023 0.001 TRP E 36 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (27497) covalent geometry : angle 0.47929 / 0.25 (37409) SS BOND : bond 0.00310 / 0.22 ( 45) SS BOND : angle 1.22860 / 0.73 ( 90) hydrogen bonds : bond 0.03473 / 2.27 ( 1128) hydrogen bonds : angle 5.15525 / 3.55 ( 3061) link_BETA1-4 : bond 0.00359 / 0.20 ( 20) link_BETA1-4 : angle 1.06366 / 0.70 ( 60) link_NAG-ASN : bond 0.00224 / 0.14 ( 46) link_NAG-ASN : angle 1.30564 / 0.87 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 225 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7979 (m-30) cc_final: 0.7765 (m-30) REVERT: A 314 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8437 (tm130) REVERT: A 389 ASP cc_start: 0.7452 (m-30) cc_final: 0.6797 (t0) REVERT: A 796 ASP cc_start: 0.8252 (t0) cc_final: 0.7974 (t0) REVERT: B 102 ARG cc_start: 0.6016 (tpp-160) cc_final: 0.5661 (tpp-160) REVERT: B 461 LEU cc_start: 0.7797 (mt) cc_final: 0.7299 (mm) REVERT: B 541 PHE cc_start: 0.8489 (p90) cc_final: 0.7858 (p90) REVERT: B 907 ASN cc_start: 0.8916 (t0) cc_final: 0.8635 (t0) REVERT: C 316 SER cc_start: 0.8799 (t) cc_final: 0.8429 (p) REVERT: C 360 ASN cc_start: 0.6970 (m-40) cc_final: 0.5951 (t0) REVERT: C 427 ASP cc_start: 0.5684 (p0) cc_final: 0.4719 (t70) REVERT: C 564 GLN cc_start: 0.7267 (mm110) cc_final: 0.6818 (mm110) REVERT: C 577 ARG cc_start: 0.7027 (ttm170) cc_final: 0.6136 (ttm170) REVERT: E 114 TYR cc_start: 0.6288 (m-80) cc_final: 0.5293 (m-80) outliers start: 30 outliers final: 26 residues processed: 240 average time/residue: 0.1598 time to fit residues: 62.8894 Evaluate side-chains 238 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 211 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 916 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 325 optimal weight: 6.9990 chunk 261 optimal weight: 0.5980 chunk 157 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 204 optimal weight: 7.9990 chunk 215 optimal weight: 0.9990 chunk 286 optimal weight: 2.9990 chunk 270 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 254 optimal weight: 0.5980 chunk 34 optimal weight: 7.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN A 207 HIS B 207 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 957 GLN C1119 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.173240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.117356 restraints weight = 80901.902| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 4.82 r_work: 0.2961 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27608 Z= 0.177 Angle : 0.541 9.584 37697 Z= 0.272 Chirality : 0.044 0.237 4443 Planarity : 0.004 0.043 4728 Dihedral : 4.117 30.072 3616 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.61 % Favored : 96.36 % Rotamer: Outliers : 1.19 % Allowed : 10.47 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.33 (0.15), residues: 3302 helix: 2.20 (0.21), residues: 660 sheet: -0.09 (0.17), residues: 857 loop : -0.33 (0.15), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 355 TYR 0.027 0.001 TYR B 495 PHE 0.019 0.001 PHE C 643 TRP 0.025 0.001 TRP E 36 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (27497) covalent geometry : angle 0.52813 / 0.27 (37409) SS BOND : bond 0.00365 / 0.25 ( 45) SS BOND : angle 1.55732 / 0.94 ( 90) hydrogen bonds : bond 0.03953 / 2.59 ( 1128) hydrogen bonds : angle 5.27521 / 3.63 ( 3061) link_BETA1-4 : bond 0.00332 / 0.17 ( 20) link_BETA1-4 : angle 1.18200 / 0.77 ( 60) link_NAG-ASN : bond 0.00258 / 0.15 ( 46) link_NAG-ASN : angle 1.42831 / 0.94 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 215 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8378 (tm130) REVERT: A 389 ASP cc_start: 0.7459 (m-30) cc_final: 0.6703 (t0) REVERT: A 796 ASP cc_start: 0.8198 (t0) cc_final: 0.7991 (t0) REVERT: B 102 ARG cc_start: 0.6152 (tpp-160) cc_final: 0.5832 (tpp-160) REVERT: B 461 LEU cc_start: 0.7824 (mt) cc_final: 0.7318 (mm) REVERT: B 495 TYR cc_start: 0.7766 (m-80) cc_final: 0.6210 (m-80) REVERT: B 541 PHE cc_start: 0.8603 (p90) cc_final: 0.7986 (p90) REVERT: B 990 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7392 (mm-30) REVERT: C 360 ASN cc_start: 0.6991 (m-40) cc_final: 0.5956 (t0) REVERT: C 427 ASP cc_start: 0.5733 (p0) cc_final: 0.4772 (t70) REVERT: E 47 PHE cc_start: 0.5217 (t80) cc_final: 0.4998 (t80) REVERT: E 114 TYR cc_start: 0.6209 (m-80) cc_final: 0.5251 (m-80) outliers start: 31 outliers final: 29 residues processed: 229 average time/residue: 0.1724 time to fit residues: 64.2974 Evaluate side-chains 239 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 916 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 288 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 256 optimal weight: 0.7980 chunk 184 optimal weight: 0.5980 chunk 169 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS B 207 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.174725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.120659 restraints weight = 89430.052| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 5.77 r_work: 0.2975 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27608 Z= 0.112 Angle : 0.499 9.553 37697 Z= 0.254 Chirality : 0.043 0.240 4443 Planarity : 0.003 0.043 4728 Dihedral : 3.965 29.800 3616 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.49 % Favored : 97.48 % Rotamer: Outliers : 1.12 % Allowed : 10.51 % Favored : 88.37 % 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: 0.42 (0.15), residues: 3302 helix: 2.30 (0.21), residues: 660 sheet: -0.05 (0.17), residues: 850 loop : -0.28 (0.15), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 103 TYR 0.018 0.001 TYR A 369 PHE 0.021 0.001 PHE C 643 TRP 0.025 0.001 TRP E 36 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (27497) covalent geometry : angle 0.48874 / 0.25 (37409) SS BOND : bond 0.00317 / 0.23 ( 45) SS BOND : angle 1.32197 / 0.79 ( 90) hydrogen bonds : bond 0.03567 / 2.34 ( 1128) hydrogen bonds : angle 5.16147 / 3.55 ( 3061) link_BETA1-4 : bond 0.00360 / 0.20 ( 20) link_BETA1-4 : angle 1.07027 / 0.70 ( 60) link_NAG-ASN : bond 0.00224 / 0.13 ( 46) link_NAG-ASN : angle 1.30659 / 0.87 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6604 Ramachandran restraints generated. 3302 Oldfield, 0 Emsley, 3302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 206 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8398 (tm130) REVERT: A 389 ASP cc_start: 0.7471 (m-30) cc_final: 0.6701 (t0) REVERT: A 796 ASP cc_start: 0.8211 (t0) cc_final: 0.7998 (t0) REVERT: B 102 ARG cc_start: 0.6047 (tpp-160) cc_final: 0.5727 (tpp-160) REVERT: B 461 LEU cc_start: 0.7811 (mt) cc_final: 0.7335 (mm) REVERT: B 495 TYR cc_start: 0.7679 (m-80) cc_final: 0.6414 (m-80) REVERT: B 541 PHE cc_start: 0.8625 (p90) cc_final: 0.8000 (p90) REVERT: C 316 SER cc_start: 0.8815 (t) cc_final: 0.8503 (p) REVERT: C 427 ASP cc_start: 0.5724 (p0) cc_final: 0.4779 (t70) REVERT: C 564 GLN cc_start: 0.7115 (mm110) cc_final: 0.6655 (mm110) REVERT: C 577 ARG cc_start: 0.7024 (ttm170) cc_final: 0.6157 (ttm170) REVERT: E 47 PHE cc_start: 0.5334 (t80) cc_final: 0.5121 (t80) REVERT: E 114 TYR cc_start: 0.6204 (m-80) cc_final: 0.5309 (m-80) outliers start: 29 outliers final: 26 residues processed: 219 average time/residue: 0.1669 time to fit residues: 59.6822 Evaluate side-chains 229 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 868 GLU Chi-restraints excluded: chain C residue 916 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 245 optimal weight: 4.9990 chunk 289 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 166 optimal weight: 0.5980 chunk 6 optimal weight: 4.9990 chunk 306 optimal weight: 5.9990 chunk 195 optimal weight: 0.6980 chunk 313 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 312 optimal weight: 5.9990 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS B 207 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 957 GLN C1119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.173090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.117516 restraints weight = 83400.961| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 5.09 r_work: 0.2956 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27608 Z= 0.175 Angle : 0.544 9.582 37697 Z= 0.274 Chirality : 0.044 0.237 4443 Planarity : 0.004 0.042 4728 Dihedral : 4.146 30.247 3616 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.77 % Favored : 96.20 % Rotamer: Outliers : 1.16 % Allowed : 10.75 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.30 (0.15), residues: 3302 helix: 2.21 (0.21), residues: 653 sheet: -0.09 (0.17), residues: 844 loop : -0.36 (0.15), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 103 TYR 0.021 0.001 TYR B 495 PHE 0.017 0.001 PHE C 643 TRP 0.028 0.001 TRP E 36 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (27497) covalent geometry : angle 0.53132 / 0.27 (37409) SS BOND : bond 0.00359 / 0.24 ( 45) SS BOND : angle 1.56223 / 0.94 ( 90) hydrogen bonds : bond 0.03999 / 2.62 ( 1128) hydrogen bonds : angle 5.27100 / 3.62 ( 3061) link_BETA1-4 : bond 0.00333 / 0.17 ( 20) link_BETA1-4 : angle 1.19504 / 0.78 ( 60) link_NAG-ASN : bond 0.00263 / 0.16 ( 46) link_NAG-ASN : angle 1.43181 / 0.95 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7301.22 seconds wall clock time: 140 minutes 52.58 seconds (8452.58 seconds total)