Starting phenix.real_space_refine on Fri Mar 6 01:24:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z7x_14539/03_2026/7z7x_14539.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z7x_14539/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7z7x_14539/03_2026/7z7x_14539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z7x_14539/03_2026/7z7x_14539.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z7x_14539/03_2026/7z7x_14539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z7x_14539/03_2026/7z7x_14539.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 24 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 dihedrals: 30 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.04, per 1000 atoms: 0.22 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: 1.89 Conformation dependent library (CDL) restraints added in 1.1 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: 0.91 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: 6.53 Time building geometry restraints manager: 2.61 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: 15796 17.97 - 35.95: 1066 35.95 - 53.92: 258 53.92 - 71.89: 58 71.89 - 89.87: 30 Dihedral angle restraints: 17208 sinusoidal: 7445 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 17205 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 24.350 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.070 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 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 : 13.275 89.865 10807 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 covalent geometry : bond 0.00649 (27497) covalent geometry : angle 0.71952 (37409) SS BOND : bond 0.00479 ( 45) SS BOND : angle 2.35957 ( 90) hydrogen bonds : bond 0.18393 ( 1128) hydrogen bonds : angle 8.13308 ( 3061) link_BETA1-4 : bond 0.00405 ( 20) link_BETA1-4 : angle 1.74189 ( 60) link_NAG-ASN : bond 0.00416 ( 46) link_NAG-ASN : angle 2.49088 ( 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 : 0.789 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: 0.1624 time to fit residues: 64.1793 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 : 0.743 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 901 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 804 GLN C 314 GLN C 388 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 613 GLN C 804 GLN C 960 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.172613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.118588 restraints weight = 98997.036| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 4.87 r_work: 0.2903 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 27608 Z= 0.129 Angle : 0.578 17.454 37697 Z= 0.295 Chirality : 0.044 0.396 4443 Planarity : 0.004 0.070 4728 Dihedral : 6.889 59.644 5002 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.49 % Favored : 97.48 % Rotamer: Outliers : 0.56 % Allowed : 4.57 % Favored : 94.87 % 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: -0.06 (0.17), residues: 816 loop : -0.46 (0.14), residues: 1819 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 0.028 0.001 TRP E 36 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00284 (27497) covalent geometry : angle 0.55322 (37409) SS BOND : bond 0.00440 ( 45) SS BOND : angle 1.60279 ( 90) hydrogen bonds : bond 0.04637 ( 1128) hydrogen bonds : angle 6.24534 ( 3061) link_BETA1-4 : bond 0.00428 ( 20) link_BETA1-4 : angle 1.25336 ( 60) link_NAG-ASN : bond 0.00390 ( 46) link_NAG-ASN : angle 2.46060 ( 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 227 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 214 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8000 (m-30) cc_final: 0.7768 (m-30) REVERT: A 129 LYS cc_start: 0.8126 (ptpp) cc_final: 0.7722 (ptpp) REVERT: A 140 PHE cc_start: 0.6833 (p90) cc_final: 0.6612 (p90) REVERT: A 168 PHE cc_start: 0.8017 (t80) cc_final: 0.7622 (t80) REVERT: A 218 GLN cc_start: 0.8392 (tt0) cc_final: 0.8158 (tt0) REVERT: A 389 ASP cc_start: 0.7425 (m-30) cc_final: 0.7041 (p0) REVERT: B 453 TYR cc_start: 0.7181 (p90) cc_final: 0.6772 (p90) REVERT: B 541 PHE cc_start: 0.8731 (p90) cc_final: 0.8474 (p90) REVERT: C 360 ASN cc_start: 0.7064 (m-40) cc_final: 0.5951 (t0) REVERT: C 400 PHE cc_start: 0.7699 (p90) cc_final: 0.7427 (p90) REVERT: C 424 LYS cc_start: 0.7179 (tptt) cc_final: 0.6918 (tptp) REVERT: C 427 ASP cc_start: 0.5936 (p0) cc_final: 0.5058 (t70) REVERT: E 103 ARG cc_start: 0.6505 (mmm160) cc_final: 0.5742 (tpp-160) REVERT: E 114 TYR cc_start: 0.6040 (m-80) cc_final: 0.5178 (m-80) outliers start: 13 outliers final: 10 residues processed: 219 average time/residue: 0.1742 time to fit residues: 62.3516 Evaluate side-chains 194 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 184 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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: 0.0870 chunk 234 optimal weight: 20.0000 chunk 217 optimal weight: 2.9990 chunk 87 optimal weight: 0.3980 chunk 145 optimal weight: 0.3980 chunk 174 optimal weight: 0.8980 chunk 257 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 242 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 294 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 450 ASN C 30 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 907 ASN C 935 GLN C1005 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.174271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.117449 restraints weight = 85001.008| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 4.90 r_work: 0.2965 rms_B_bonded: 3.86 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: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 27608 Z= 0.107 Angle : 0.517 9.559 37697 Z= 0.264 Chirality : 0.043 0.246 4443 Planarity : 0.004 0.056 4728 Dihedral : 5.819 54.857 5002 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.43 % Favored : 97.54 % Rotamer: Outliers : 0.91 % Allowed : 6.15 % Favored : 92.94 % 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: 2.04 (0.21), residues: 666 sheet: -0.08 (0.17), residues: 852 loop : -0.32 (0.15), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 567 TYR 0.022 0.001 TYR A 369 PHE 0.012 0.001 PHE C 515 TRP 0.026 0.001 TRP E 36 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00234 (27497) covalent geometry : angle 0.50120 (37409) SS BOND : bond 0.00335 ( 45) SS BOND : angle 1.30579 ( 90) hydrogen bonds : bond 0.03899 ( 1128) hydrogen bonds : angle 5.73091 ( 3061) link_BETA1-4 : bond 0.00345 ( 20) link_BETA1-4 : angle 1.18997 ( 60) link_NAG-ASN : bond 0.00268 ( 46) link_NAG-ASN : angle 1.75478 ( 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 237 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 214 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8056 (ptpp) cc_final: 0.7609 (ptpp) REVERT: A 218 GLN cc_start: 0.8434 (tt0) cc_final: 0.8208 (tt0) REVERT: A 314 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8334 (tm130) REVERT: A 389 ASP cc_start: 0.7356 (m-30) cc_final: 0.6989 (p0) REVERT: A 537 LYS cc_start: 0.9035 (tttp) cc_final: 0.8664 (ttpt) REVERT: A 796 ASP cc_start: 0.8137 (t0) cc_final: 0.7866 (t0) REVERT: A 855 PHE cc_start: 0.7086 (m-80) cc_final: 0.6812 (m-80) REVERT: B 453 TYR cc_start: 0.7244 (p90) cc_final: 0.6755 (p90) REVERT: B 508 TYR cc_start: 0.6415 (m-80) cc_final: 0.6192 (m-80) REVERT: B 541 PHE cc_start: 0.8605 (p90) cc_final: 0.8226 (p90) REVERT: B 614 ASP cc_start: 0.7276 (p0) cc_final: 0.6954 (p0) REVERT: B 867 ASP cc_start: 0.7963 (m-30) cc_final: 0.7748 (m-30) REVERT: B 900 MET cc_start: 0.9079 (mtp) cc_final: 0.8796 (mtm) REVERT: C 122 ASN cc_start: 0.4499 (p0) cc_final: 0.4287 (p0) REVERT: C 316 SER cc_start: 0.8788 (t) cc_final: 0.8399 (p) REVERT: C 360 ASN cc_start: 0.6890 (m-40) cc_final: 0.5862 (t0) REVERT: C 400 PHE cc_start: 0.7668 (p90) cc_final: 0.7416 (p90) REVERT: C 427 ASP cc_start: 0.5943 (p0) cc_final: 0.5061 (t70) REVERT: C 577 ARG cc_start: 0.7024 (ttm170) cc_final: 0.5976 (ttm170) REVERT: E 114 TYR cc_start: 0.5980 (m-80) cc_final: 0.5130 (m-80) outliers start: 23 outliers final: 13 residues processed: 226 average time/residue: 0.1738 time to fit residues: 64.2372 Evaluate side-chains 200 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS 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 1045 LYS 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 747 THR Chi-restraints excluded: chain C residue 936 ASP 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: 0.9980 chunk 234 optimal weight: 20.0000 chunk 93 optimal weight: 0.8980 chunk 255 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 209 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 195 optimal weight: 0.4980 chunk 247 optimal weight: 2.9990 chunk 278 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 207 HIS A1106 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 935 GLN ** C 422 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.173919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.114685 restraints weight = 81101.847| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 4.60 r_work: 0.2980 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27608 Z= 0.112 Angle : 0.503 9.609 37697 Z= 0.257 Chirality : 0.043 0.233 4443 Planarity : 0.004 0.047 4728 Dihedral : 5.137 54.779 5002 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.25 % Favored : 97.72 % Rotamer: Outliers : 1.02 % Allowed : 7.17 % Favored : 91.81 % 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: 0.40 (0.15), residues: 3302 helix: 2.21 (0.21), residues: 660 sheet: -0.01 (0.17), residues: 845 loop : -0.28 (0.15), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 355 TYR 0.020 0.001 TYR A 369 PHE 0.026 0.001 PHE A 168 TRP 0.023 0.001 TRP E 36 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00252 (27497) covalent geometry : angle 0.48892 (37409) SS BOND : bond 0.00284 ( 45) SS BOND : angle 1.33728 ( 90) hydrogen bonds : bond 0.03717 ( 1128) hydrogen bonds : angle 5.49750 ( 3061) link_BETA1-4 : bond 0.00344 ( 20) link_BETA1-4 : angle 1.18068 ( 60) link_NAG-ASN : bond 0.00242 ( 46) link_NAG-ASN : angle 1.58232 ( 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 236 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.8121 (ptpp) cc_final: 0.7792 (ptpp) REVERT: A 218 GLN cc_start: 0.8501 (tt0) cc_final: 0.8269 (tt0) REVERT: A 314 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8344 (tm130) REVERT: A 389 ASP cc_start: 0.7359 (m-30) cc_final: 0.6744 (t0) REVERT: A 796 ASP cc_start: 0.8088 (t0) cc_final: 0.7810 (t0) REVERT: A 855 PHE cc_start: 0.7061 (m-80) cc_final: 0.6788 (m-80) REVERT: B 394 ASN cc_start: 0.7578 (t0) cc_final: 0.7290 (m-40) REVERT: B 453 TYR cc_start: 0.7334 (p90) cc_final: 0.6952 (p90) REVERT: B 455 LEU cc_start: 0.7326 (mm) cc_final: 0.6966 (mt) REVERT: B 461 LEU cc_start: 0.7691 (mt) cc_final: 0.7143 (mm) REVERT: B 508 TYR cc_start: 0.6605 (m-80) cc_final: 0.6307 (m-80) REVERT: B 541 PHE cc_start: 0.8614 (p90) cc_final: 0.8173 (p90) REVERT: B 646 ARG cc_start: 0.8252 (tpt170) cc_final: 0.7884 (tpt90) REVERT: B 900 MET cc_start: 0.9042 (mtp) cc_final: 0.8800 (mtm) REVERT: C 122 ASN cc_start: 0.4505 (p0) cc_final: 0.4152 (p0) REVERT: C 316 SER cc_start: 0.8761 (t) cc_final: 0.8348 (p) REVERT: C 360 ASN cc_start: 0.7005 (m-40) cc_final: 0.5919 (t0) REVERT: C 427 ASP cc_start: 0.5870 (p0) cc_final: 0.4990 (t70) REVERT: E 114 TYR cc_start: 0.6000 (m-80) cc_final: 0.5120 (m-80) outliers start: 26 outliers final: 16 residues processed: 225 average time/residue: 0.1764 time to fit residues: 63.8810 Evaluate side-chains 204 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 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 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 916 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 185 optimal weight: 0.7980 chunk 328 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 236 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 308 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 292 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 613 GLN ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.169035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.106017 restraints weight = 72529.293| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 4.21 r_work: 0.2907 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 27608 Z= 0.331 Angle : 0.687 10.228 37697 Z= 0.344 Chirality : 0.048 0.222 4443 Planarity : 0.004 0.044 4728 Dihedral : 5.992 53.234 5002 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.13 % Favored : 95.84 % Rotamer: Outliers : 1.41 % Allowed : 8.36 % Favored : 90.23 % 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: -0.11 (0.14), residues: 3302 helix: 1.72 (0.21), residues: 656 sheet: -0.25 (0.17), residues: 864 loop : -0.63 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1014 TYR 0.024 0.002 TYR B 279 PHE 0.023 0.002 PHE B 456 TRP 0.027 0.002 TRP E 36 HIS 0.007 0.002 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00789 (27497) covalent geometry : angle 0.66862 (37409) SS BOND : bond 0.00565 ( 45) SS BOND : angle 1.97539 ( 90) hydrogen bonds : bond 0.05098 ( 1128) hydrogen bonds : angle 5.83425 ( 3061) link_BETA1-4 : bond 0.00402 ( 20) link_BETA1-4 : angle 1.54846 ( 60) link_NAG-ASN : bond 0.00500 ( 46) link_NAG-ASN : angle 2.03353 ( 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 241 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 204 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8129 (m-30) cc_final: 0.7823 (m-30) REVERT: A 129 LYS cc_start: 0.7978 (ptpp) cc_final: 0.7596 (ptpp) REVERT: A 314 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8440 (tm130) REVERT: A 389 ASP cc_start: 0.7359 (m-30) cc_final: 0.6710 (t0) REVERT: A 796 ASP cc_start: 0.8269 (t0) cc_final: 0.8023 (t0) REVERT: A 855 PHE cc_start: 0.7155 (m-80) cc_final: 0.6934 (m-80) REVERT: B 461 LEU cc_start: 0.7735 (mt) cc_final: 0.7214 (mm) REVERT: B 508 TYR cc_start: 0.6809 (m-80) cc_final: 0.6366 (m-80) REVERT: B 541 PHE cc_start: 0.8652 (p90) cc_final: 0.8217 (p90) REVERT: B 867 ASP cc_start: 0.7880 (m-30) cc_final: 0.7672 (m-30) REVERT: B 990 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7515 (mm-30) REVERT: B 1142 GLN cc_start: 0.8289 (tp40) cc_final: 0.8087 (tp40) REVERT: C 122 ASN cc_start: 0.4507 (p0) cc_final: 0.4219 (p0) REVERT: C 360 ASN cc_start: 0.6998 (m-40) cc_final: 0.5893 (t0) REVERT: C 427 ASP cc_start: 0.5885 (p0) cc_final: 0.4908 (t70) REVERT: C 787 GLN cc_start: 0.8400 (mt0) cc_final: 0.8200 (mt0) REVERT: E 114 TYR cc_start: 0.6231 (m-80) cc_final: 0.5241 (m-80) outliers start: 37 outliers final: 31 residues processed: 227 average time/residue: 0.1642 time to fit residues: 61.5411 Evaluate side-chains 223 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 191 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 207 HIS 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 900 MET 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 170 optimal weight: 0.7980 chunk 113 optimal weight: 0.5980 chunk 123 optimal weight: 7.9990 chunk 179 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 chunk 194 optimal weight: 1.9990 chunk 208 optimal weight: 7.9990 chunk 329 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 779 GLN B 207 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.172802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.117675 restraints weight = 100096.433| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 5.28 r_work: 0.2879 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27608 Z= 0.114 Angle : 0.522 9.616 37697 Z= 0.266 Chirality : 0.043 0.226 4443 Planarity : 0.004 0.043 4728 Dihedral : 5.169 55.177 5002 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.49 % Favored : 97.48 % Rotamer: Outliers : 1.09 % Allowed : 9.28 % 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: 0.20 (0.15), residues: 3302 helix: 2.13 (0.21), residues: 650 sheet: -0.17 (0.17), residues: 835 loop : -0.41 (0.14), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 355 TYR 0.024 0.001 TYR B 453 PHE 0.016 0.001 PHE B 456 TRP 0.021 0.001 TRP E 36 HIS 0.020 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00253 (27497) covalent geometry : angle 0.50761 (37409) SS BOND : bond 0.00333 ( 45) SS BOND : angle 1.50743 ( 90) hydrogen bonds : bond 0.03838 ( 1128) hydrogen bonds : angle 5.47320 ( 3061) link_BETA1-4 : bond 0.00387 ( 20) link_BETA1-4 : angle 1.18148 ( 60) link_NAG-ASN : bond 0.00276 ( 46) link_NAG-ASN : angle 1.60904 ( 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 238 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 0.993 Fit side-chains REVERT: A 88 ASP cc_start: 0.8216 (m-30) cc_final: 0.7878 (m-30) REVERT: A 129 LYS cc_start: 0.8128 (ptpp) cc_final: 0.7645 (ptpp) REVERT: A 314 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8506 (tm130) REVERT: A 389 ASP cc_start: 0.7519 (m-30) cc_final: 0.6809 (t0) REVERT: A 796 ASP cc_start: 0.8328 (t0) cc_final: 0.8025 (t0) REVERT: A 855 PHE cc_start: 0.7204 (m-80) cc_final: 0.6948 (m-80) REVERT: B 220 PHE cc_start: 0.7539 (t80) cc_final: 0.7013 (t80) REVERT: B 455 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7252 (mt) REVERT: B 461 LEU cc_start: 0.7852 (mt) cc_final: 0.7345 (mm) REVERT: B 495 TYR cc_start: 0.7860 (m-80) cc_final: 0.6330 (m-80) REVERT: B 541 PHE cc_start: 0.8603 (p90) cc_final: 0.7978 (p90) REVERT: B 646 ARG cc_start: 0.8360 (tpt170) cc_final: 0.7985 (tpt90) REVERT: B 900 MET cc_start: 0.9167 (mtp) cc_final: 0.8942 (mtm) REVERT: B 990 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7485 (mm-30) REVERT: C 316 SER cc_start: 0.8845 (t) cc_final: 0.8474 (p) REVERT: C 360 ASN cc_start: 0.6894 (m-40) cc_final: 0.5873 (t0) REVERT: C 427 ASP cc_start: 0.5680 (p0) cc_final: 0.4740 (t70) REVERT: C 577 ARG cc_start: 0.6934 (ttm170) cc_final: 0.6024 (ttm170) REVERT: E 114 TYR cc_start: 0.6127 (m-80) cc_final: 0.5219 (m-80) outliers start: 28 outliers final: 18 residues processed: 223 average time/residue: 0.1683 time to fit residues: 61.4057 Evaluate side-chains 213 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 193 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 314 GLN Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 455 LEU 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 731 MET Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 936 ASP 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: 0.9980 chunk 60 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 232 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 221 optimal weight: 0.3980 chunk 90 optimal weight: 0.0170 chunk 4 optimal weight: 0.6980 chunk 320 optimal weight: 8.9990 chunk 282 optimal weight: 0.9980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4089 r_free = 0.4089 target = 0.173707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.113838 restraints weight = 82873.987| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 4.71 r_work: 0.2974 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 27608 Z= 0.105 Angle : 0.497 9.622 37697 Z= 0.253 Chirality : 0.043 0.233 4443 Planarity : 0.003 0.041 4728 Dihedral : 4.637 55.226 5002 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.95 % Favored : 97.02 % Rotamer: Outliers : 1.02 % Allowed : 9.77 % Favored : 89.21 % 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: 0.35 (0.15), residues: 3302 helix: 2.19 (0.21), residues: 667 sheet: -0.14 (0.17), residues: 840 loop : -0.27 (0.15), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 567 TYR 0.018 0.001 TYR A 369 PHE 0.016 0.001 PHE C 400 TRP 0.023 0.001 TRP E 36 HIS 0.007 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00235 (27497) covalent geometry : angle 0.48349 (37409) SS BOND : bond 0.00344 ( 45) SS BOND : angle 1.32754 ( 90) hydrogen bonds : bond 0.03560 ( 1128) hydrogen bonds : angle 5.25403 ( 3061) link_BETA1-4 : bond 0.00329 ( 20) link_BETA1-4 : angle 1.19278 ( 60) link_NAG-ASN : bond 0.00237 ( 46) link_NAG-ASN : angle 1.50089 ( 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 235 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8080 (m-30) cc_final: 0.7733 (m-30) REVERT: A 129 LYS cc_start: 0.8073 (ptpp) cc_final: 0.7574 (ptpp) REVERT: A 314 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8366 (tm130) REVERT: A 389 ASP cc_start: 0.7488 (m-30) cc_final: 0.6806 (t0) REVERT: A 796 ASP cc_start: 0.8231 (t0) cc_final: 0.7970 (t0) REVERT: A 855 PHE cc_start: 0.7102 (m-80) cc_final: 0.6858 (m-80) REVERT: B 461 LEU cc_start: 0.7759 (mt) cc_final: 0.7291 (mm) REVERT: B 495 TYR cc_start: 0.7694 (m-80) cc_final: 0.6332 (m-80) REVERT: B 541 PHE cc_start: 0.8486 (p90) cc_final: 0.7898 (p90) REVERT: B 646 ARG cc_start: 0.8237 (tpt170) cc_final: 0.7868 (tpt90) REVERT: B 900 MET cc_start: 0.9067 (mtp) cc_final: 0.8839 (mtm) REVERT: C 122 ASN cc_start: 0.4433 (p0) cc_final: 0.4090 (p0) REVERT: C 316 SER cc_start: 0.8775 (t) cc_final: 0.8393 (p) REVERT: C 360 ASN cc_start: 0.6897 (m-40) cc_final: 0.5827 (t0) REVERT: C 427 ASP cc_start: 0.5706 (p0) cc_final: 0.4741 (t70) REVERT: C 564 GLN cc_start: 0.7189 (mm110) cc_final: 0.6703 (mm110) REVERT: C 577 ARG cc_start: 0.6903 (ttm170) cc_final: 0.6019 (ttm170) REVERT: E 114 TYR cc_start: 0.6223 (m-80) cc_final: 0.5250 (m-80) outliers start: 26 outliers final: 18 residues processed: 221 average time/residue: 0.1773 time to fit residues: 63.9784 Evaluate side-chains 217 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 198 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 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 900 MET Chi-restraints excluded: chain B residue 453 TYR 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 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 531 THR Chi-restraints excluded: chain C residue 731 MET 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: 0.9980 chunk 317 optimal weight: 30.0000 chunk 48 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 249 optimal weight: 1.9990 chunk 175 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 302 optimal weight: 9.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4077 r_free = 0.4077 target = 0.172624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.116327 restraints weight = 92180.415| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 5.18 r_work: 0.2914 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2907 r_free = 0.2907 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.2907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27608 Z= 0.136 Angle : 0.510 9.626 37697 Z= 0.259 Chirality : 0.043 0.230 4443 Planarity : 0.004 0.046 4728 Dihedral : 4.644 55.354 5002 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.73 % Favored : 97.24 % Rotamer: Outliers : 1.23 % Allowed : 9.94 % 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: 0.35 (0.15), residues: 3302 helix: 2.26 (0.21), residues: 659 sheet: -0.08 (0.17), residues: 844 loop : -0.32 (0.15), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 52 TYR 0.026 0.001 TYR B 449 PHE 0.015 0.001 PHE C 515 TRP 0.024 0.001 TRP E 36 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00317 (27497) covalent geometry : angle 0.49659 (37409) SS BOND : bond 0.00331 ( 45) SS BOND : angle 1.43487 ( 90) hydrogen bonds : bond 0.03734 ( 1128) hydrogen bonds : angle 5.24474 ( 3061) link_BETA1-4 : bond 0.00327 ( 20) link_BETA1-4 : angle 1.21300 ( 60) link_NAG-ASN : bond 0.00245 ( 46) link_NAG-ASN : angle 1.51227 ( 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 233 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8155 (m-30) cc_final: 0.7817 (m-30) REVERT: A 129 LYS cc_start: 0.8085 (ptpp) cc_final: 0.7556 (ptpp) REVERT: A 314 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8456 (tm130) REVERT: A 389 ASP cc_start: 0.7429 (m-30) cc_final: 0.6740 (t0) REVERT: A 796 ASP cc_start: 0.8322 (t0) cc_final: 0.8036 (t0) REVERT: A 855 PHE cc_start: 0.7202 (m-80) cc_final: 0.6955 (m-80) REVERT: B 360 ASN cc_start: 0.8719 (m-40) cc_final: 0.8316 (m-40) REVERT: B 455 LEU cc_start: 0.7655 (mm) cc_final: 0.7422 (mt) REVERT: B 461 LEU cc_start: 0.7805 (mt) cc_final: 0.7336 (mm) REVERT: B 495 TYR cc_start: 0.7666 (m-80) cc_final: 0.6467 (m-80) REVERT: B 541 PHE cc_start: 0.8561 (p90) cc_final: 0.7955 (p90) REVERT: B 646 ARG cc_start: 0.8277 (tpt170) cc_final: 0.7931 (tpt90) REVERT: C 122 ASN cc_start: 0.4482 (p0) cc_final: 0.4151 (p0) REVERT: C 360 ASN cc_start: 0.6917 (m-40) cc_final: 0.5879 (t0) REVERT: C 427 ASP cc_start: 0.5646 (p0) cc_final: 0.4673 (t70) REVERT: C 577 ARG cc_start: 0.6949 (ttm170) cc_final: 0.6289 (ttm170) REVERT: E 47 PHE cc_start: 0.5225 (t80) cc_final: 0.4988 (t80) REVERT: E 114 TYR cc_start: 0.6222 (m-80) cc_final: 0.5259 (m-80) outliers start: 32 outliers final: 28 residues processed: 216 average time/residue: 0.1666 time to fit residues: 58.7423 Evaluate side-chains 227 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 198 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 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 900 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 453 TYR 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 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 Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 325 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 204 optimal weight: 9.9990 chunk 215 optimal weight: 0.9990 chunk 286 optimal weight: 1.9990 chunk 270 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 254 optimal weight: 4.9990 chunk 34 optimal weight: 30.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4089 r_free = 0.4089 target = 0.173018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.117117 restraints weight = 80839.000| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 5.01 r_work: 0.2955 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- 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 = 0.02 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1889 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= 0.167 Angle : 0.536 9.640 37697 Z= 0.271 Chirality : 0.044 0.229 4443 Planarity : 0.004 0.049 4728 Dihedral : 4.818 55.229 5002 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.64 % Favored : 96.33 % Rotamer: Outliers : 1.19 % Allowed : 10.12 % Favored : 88.69 % 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: 0.29 (0.15), residues: 3302 helix: 2.22 (0.21), residues: 654 sheet: -0.11 (0.17), residues: 841 loop : -0.37 (0.15), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 457 TYR 0.021 0.001 TYR B 449 PHE 0.017 0.001 PHE B 643 TRP 0.027 0.001 TRP E 36 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00395 (27497) covalent geometry : angle 0.52107 (37409) SS BOND : bond 0.00360 ( 45) SS BOND : angle 1.59781 ( 90) hydrogen bonds : bond 0.03990 ( 1128) hydrogen bonds : angle 5.30773 ( 3061) link_BETA1-4 : bond 0.00330 ( 20) link_BETA1-4 : angle 1.28902 ( 60) link_NAG-ASN : bond 0.00278 ( 46) link_NAG-ASN : angle 1.58460 ( 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 231 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8187 (m-30) cc_final: 0.7861 (m-30) REVERT: A 129 LYS cc_start: 0.8092 (ptpp) cc_final: 0.7577 (ptpp) REVERT: A 168 PHE cc_start: 0.8003 (t80) cc_final: 0.7610 (t80) REVERT: A 314 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8423 (tm130) REVERT: A 389 ASP cc_start: 0.7403 (m-30) cc_final: 0.6726 (t0) REVERT: A 796 ASP cc_start: 0.8258 (t0) cc_final: 0.8043 (t0) REVERT: A 855 PHE cc_start: 0.7174 (m-80) cc_final: 0.6962 (m-80) REVERT: B 360 ASN cc_start: 0.8713 (m-40) cc_final: 0.8310 (m-40) REVERT: B 461 LEU cc_start: 0.7848 (mt) cc_final: 0.7415 (mm) REVERT: B 541 PHE cc_start: 0.8658 (p90) cc_final: 0.8055 (p90) REVERT: B 646 ARG cc_start: 0.8286 (tpt170) cc_final: 0.7947 (tpt90) REVERT: B 990 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7397 (mm-30) REVERT: C 360 ASN cc_start: 0.6930 (m-40) cc_final: 0.5899 (t0) REVERT: C 427 ASP cc_start: 0.5676 (p0) cc_final: 0.4699 (t70) REVERT: E 47 PHE cc_start: 0.5250 (t80) cc_final: 0.4999 (t80) REVERT: E 114 TYR cc_start: 0.6209 (m-80) cc_final: 0.5272 (m-80) outliers start: 31 outliers final: 27 residues processed: 215 average time/residue: 0.1729 time to fit residues: 60.6401 Evaluate side-chains 224 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 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 900 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 453 TYR 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 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 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 Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 288 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 256 optimal weight: 0.8980 chunk 184 optimal weight: 0.5980 chunk 169 optimal weight: 0.6980 chunk 98 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4104 r_free = 0.4104 target = 0.174282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.119182 restraints weight = 88661.189| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 5.16 r_work: 0.2973 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- 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 = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 27608 Z= 0.110 Angle : 0.496 9.602 37697 Z= 0.252 Chirality : 0.042 0.231 4443 Planarity : 0.003 0.051 4728 Dihedral : 4.533 55.399 5002 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.73 % Favored : 97.24 % Rotamer: Outliers : 1.16 % Allowed : 10.33 % Favored : 88.51 % 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: 2.30 (0.21), residues: 658 sheet: -0.09 (0.17), residues: 843 loop : -0.29 (0.15), residues: 1801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 567 TYR 0.029 0.001 TYR B 495 PHE 0.014 0.001 PHE B 643 TRP 0.025 0.001 TRP E 36 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00248 (27497) covalent geometry : angle 0.48332 (37409) SS BOND : bond 0.00341 ( 45) SS BOND : angle 1.35619 ( 90) hydrogen bonds : bond 0.03577 ( 1128) hydrogen bonds : angle 5.17569 ( 3061) link_BETA1-4 : bond 0.00359 ( 20) link_BETA1-4 : angle 1.17061 ( 60) link_NAG-ASN : bond 0.00239 ( 46) link_NAG-ASN : angle 1.43567 ( 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 236 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8184 (m-30) cc_final: 0.7884 (m-30) REVERT: A 314 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8424 (tm130) REVERT: A 389 ASP cc_start: 0.7435 (m-30) cc_final: 0.6742 (t0) REVERT: A 796 ASP cc_start: 0.8224 (t0) cc_final: 0.7997 (t0) REVERT: A 855 PHE cc_start: 0.7135 (m-80) cc_final: 0.6924 (m-80) REVERT: B 29 THR cc_start: 0.6531 (m) cc_final: 0.6179 (m) REVERT: B 102 ARG cc_start: 0.5996 (tpp-160) cc_final: 0.5660 (tpp-160) REVERT: B 360 ASN cc_start: 0.8714 (m-40) cc_final: 0.8305 (m-40) REVERT: B 455 LEU cc_start: 0.7507 (mm) cc_final: 0.7009 (mp) REVERT: B 461 LEU cc_start: 0.7718 (mt) cc_final: 0.7266 (mm) REVERT: B 493 GLN cc_start: 0.6648 (tt0) cc_final: 0.6083 (mt0) REVERT: B 541 PHE cc_start: 0.8641 (p90) cc_final: 0.8055 (p90) REVERT: B 646 ARG cc_start: 0.8274 (tpt170) cc_final: 0.7951 (tpt90) REVERT: C 427 ASP cc_start: 0.5656 (p0) cc_final: 0.4675 (t70) REVERT: C 577 ARG cc_start: 0.6936 (ttm170) cc_final: 0.5975 (ttm170) REVERT: E 47 PHE cc_start: 0.5232 (t80) cc_final: 0.4984 (t80) REVERT: E 114 TYR cc_start: 0.6289 (m-80) cc_final: 0.5285 (m-80) outliers start: 30 outliers final: 27 residues processed: 219 average time/residue: 0.1688 time to fit residues: 60.3259 Evaluate side-chains 229 residues out of total 2893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 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 900 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 453 TYR 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 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 Chi-restraints excluded: chain C residue 1032 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 332 random chunks: chunk 245 optimal weight: 0.0570 chunk 289 optimal weight: 0.2980 chunk 121 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 chunk 306 optimal weight: 0.3980 chunk 195 optimal weight: 0.9990 chunk 313 optimal weight: 0.0270 chunk 128 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 312 optimal weight: 6.9990 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 613 GLN B 207 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 613 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.174995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.117169 restraints weight = 83247.750| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 4.68 r_work: 0.3002 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27608 Z= 0.088 Angle : 0.475 9.577 37697 Z= 0.242 Chirality : 0.042 0.235 4443 Planarity : 0.003 0.045 4728 Dihedral : 4.146 55.546 5002 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.73 % Favored : 97.24 % Rotamer: Outliers : 0.95 % Allowed : 10.61 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.15), residues: 3302 helix: 2.35 (0.21), residues: 668 sheet: -0.04 (0.17), residues: 866 loop : -0.19 (0.15), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 567 TYR 0.027 0.001 TYR B 495 PHE 0.022 0.001 PHE C 515 TRP 0.025 0.001 TRP E 36 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00191 (27497) covalent geometry : angle 0.46506 (37409) SS BOND : bond 0.00285 ( 45) SS BOND : angle 1.04529 ( 90) hydrogen bonds : bond 0.03258 ( 1128) hydrogen bonds : angle 4.98948 ( 3061) link_BETA1-4 : bond 0.00363 ( 20) link_BETA1-4 : angle 1.13061 ( 60) link_NAG-ASN : bond 0.00228 ( 46) link_NAG-ASN : angle 1.30649 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7770.99 seconds wall clock time: 133 minutes 29.87 seconds (8009.87 seconds total)