Starting phenix.real_space_refine on Fri Mar 6 12:08:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7epx_31249/03_2026/7epx_31249.cif Found real_map, /net/cci-nas-00/data/ceres_data/7epx_31249/03_2026/7epx_31249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7epx_31249/03_2026/7epx_31249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7epx_31249/03_2026/7epx_31249.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7epx_31249/03_2026/7epx_31249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7epx_31249/03_2026/7epx_31249.map" } resolution = 3.0 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= 0.004 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 128 5.16 5 C 19542 2.51 5 N 5052 2.21 5 O 6124 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.03s 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: 30846 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 7872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7872 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 53, 'TRANS': 953} Chain breaks: 8 Chain: "B" Number of atoms: 7866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7866 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 53, 'TRANS': 952} Chain breaks: 8 Chain: "C" Number of atoms: 7584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7584 Classifications: {'peptide': 971} Link IDs: {'PTRANS': 51, 'TRANS': 919} Chain breaks: 9 Chain: "H" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1701 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 13, 'TRANS': 214} Chain: "L" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1564 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 16, 'TRANS': 194} Chain: "I" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1701 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 13, 'TRANS': 214} Chain: "M" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1564 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 16, 'TRANS': 194} Chain: "D" 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: 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: "b" 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: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" 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: "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: 7.07, per 1000 atoms: 0.23 Number of scatterers: 30846 At special positions: 0 Unit cell: (189.138, 173.92, 194.573, 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 128 16.00 O 6124 8.00 N 5052 7.00 C 19542 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 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=2.05 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=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.08 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 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=2.05 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=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.15 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.12 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=1.96 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 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=1.98 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 137 " - pdb=" SG CYS L 196 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 154 " - pdb=" SG CYS I 210 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 137 " - pdb=" SG CYS M 196 " distance=2.04 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 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 a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1074 " " NAG K 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 331 " " NAG P 1 " - " ASN B 343 " " NAG Q 1 " - " ASN B 709 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 331 " " NAG W 1 " - " ASN C 343 " " NAG X 1 " - " ASN C 709 " " NAG Y 1 " - " ASN C 717 " " NAG Z 1 " - " ASN C 801 " " NAG a 1 " - " ASN C1074 " " NAG b 1 " - " ASN C1098 " " NAG c 1 " - " ASN C1134 " " NAG d 1 " - " ASN B1074 " Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.3 seconds 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7192 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 63 sheets defined 19.9% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 341 removed outlier: 4.064A pdb=" N GLU A 340 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.567A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 417 through 421 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 removed outlier: 3.630A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) 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 removed outlier: 3.773A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.634A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.773A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.573A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.993A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.625A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.577A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA A 956 " --> pdb=" O VAL A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 982 through 984 No H-bonds generated for 'chain 'A' and resid 982 through 984' Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.864A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.647A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 341 removed outlier: 4.064A pdb=" N GLU B 340 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.568A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.694A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.963A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.545A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.603A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.565A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.246A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 370 Processing helix chain 'C' and resid 384 through 390 removed outlier: 3.568A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 417 through 421 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 754 removed outlier: 3.716A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.560A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.699A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.634A 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 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.590A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.623A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA C 956 " --> pdb=" O VAL C 952 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C 958 " --> pdb=" O GLN C 954 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (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 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.221A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 201 through 203 No H-bonds generated for 'chain 'H' and resid 201 through 203' Processing helix chain 'L' and resid 124 through 130 Processing helix chain 'L' and resid 184 through 191 Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 201 through 203 No H-bonds generated for 'chain 'I' and resid 201 through 203' Processing helix chain 'M' and resid 124 through 130 Processing helix chain 'M' and resid 184 through 191 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.081A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A 593 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.871A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 539 through 543 removed outlier: 5.338A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.720A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 9.060A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.504A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.714A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.061A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 309 through 319 removed outlier: 6.369A pdb=" N LYS B 310 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY B 601 " --> pdb=" O LYS B 310 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 327 through 328 removed outlier: 5.339A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.871A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.292A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.579A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD7, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 309 through 319 removed outlier: 6.141A pdb=" N LYS C 310 " --> pdb=" O GLY C 601 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLY C 601 " --> pdb=" O LYS C 310 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 4.620A 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 327 removed outlier: 4.026A pdb=" N ASN C 542 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR C 573 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASP C 568 " --> pdb=" O THR C 573 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.871A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.608A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.569A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.197A pdb=" N GLY H 10 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 134 through 138 removed outlier: 5.008A pdb=" N ALA H 151 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL H 198 " --> pdb=" O ALA H 151 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 153 " --> pdb=" O VAL H 196 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL H 196 " --> pdb=" O GLY H 153 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU H 155 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 194 " --> pdb=" O LEU H 155 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LYS H 157 " --> pdb=" O LEU H 192 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU H 192 " --> pdb=" O LYS H 157 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 134 through 138 removed outlier: 5.008A pdb=" N ALA H 151 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL H 198 " --> pdb=" O ALA H 151 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 153 " --> pdb=" O VAL H 196 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL H 196 " --> pdb=" O GLY H 153 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU H 155 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 194 " --> pdb=" O LEU H 155 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LYS H 157 " --> pdb=" O LEU H 192 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU H 192 " --> pdb=" O LYS H 157 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 164 through 168 Processing sheet with id=AF4, first strand: chain 'L' and resid 17 through 23 Processing sheet with id=AF5, first strand: chain 'L' and resid 46 through 49 removed outlier: 6.370A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN L 35 " --> pdb=" O ALA L 90 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 117 through 121 Processing sheet with id=AF7, first strand: chain 'L' and resid 117 through 121 Processing sheet with id=AF8, first strand: chain 'L' and resid 157 through 158 removed outlier: 4.439A pdb=" N TRP L 151 " --> pdb=" O VAL L 158 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AG1, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.197A pdb=" N GLY I 10 " --> pdb=" O THR I 124 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 134 through 138 removed outlier: 5.007A pdb=" N ALA I 151 " --> pdb=" O VAL I 198 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL I 198 " --> pdb=" O ALA I 151 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY I 153 " --> pdb=" O VAL I 196 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL I 196 " --> pdb=" O GLY I 153 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU I 155 " --> pdb=" O SER I 194 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER I 194 " --> pdb=" O LEU I 155 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS I 157 " --> pdb=" O LEU I 192 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU I 192 " --> pdb=" O LYS I 157 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 134 through 138 removed outlier: 5.007A pdb=" N ALA I 151 " --> pdb=" O VAL I 198 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL I 198 " --> pdb=" O ALA I 151 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY I 153 " --> pdb=" O VAL I 196 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL I 196 " --> pdb=" O GLY I 153 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU I 155 " --> pdb=" O SER I 194 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER I 194 " --> pdb=" O LEU I 155 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS I 157 " --> pdb=" O LEU I 192 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU I 192 " --> pdb=" O LYS I 157 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 164 through 168 Processing sheet with id=AG5, first strand: chain 'M' and resid 17 through 23 Processing sheet with id=AG6, first strand: chain 'M' and resid 46 through 49 removed outlier: 6.370A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN M 35 " --> pdb=" O ALA M 90 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 117 through 121 Processing sheet with id=AG8, first strand: chain 'M' and resid 117 through 121 Processing sheet with id=AG9, first strand: chain 'M' and resid 157 through 158 removed outlier: 4.440A pdb=" N TRP M 151 " --> pdb=" O VAL M 158 " (cutoff:3.500A) 1176 hydrogen bonds defined for protein. 3108 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.31 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8179 1.33 - 1.46: 8454 1.46 - 1.58: 14739 1.58 - 1.71: 0 1.71 - 1.84: 161 Bond restraints: 31533 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.444 0.078 1.20e-02 6.94e+03 4.25e+01 bond pdb=" C ASP A 985 " pdb=" N PRO A 986 " ideal model delta sigma weight residual 1.329 1.389 -0.060 1.18e-02 7.18e+03 2.57e+01 bond pdb=" C GLN C 321 " pdb=" N PRO C 322 " ideal model delta sigma weight residual 1.331 1.390 -0.060 1.31e-02 5.83e+03 2.08e+01 bond pdb=" C PRO A 986 " pdb=" N PRO A 987 " ideal model delta sigma weight residual 1.336 1.389 -0.053 1.23e-02 6.61e+03 1.89e+01 bond pdb=" N PRO A 986 " pdb=" CD PRO A 986 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.84e+01 ... (remaining 31528 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 41817 2.74 - 5.48: 1024 5.48 - 8.22: 72 8.22 - 10.96: 6 10.96 - 13.70: 8 Bond angle restraints: 42927 Sorted by residual: angle pdb=" C ASP A 985 " pdb=" N PRO A 986 " pdb=" CA PRO A 986 " ideal model delta sigma weight residual 120.38 114.09 6.29 1.03e+00 9.43e-01 3.72e+01 angle pdb=" C PHE C 86 " pdb=" N ASN C 87 " pdb=" CA ASN C 87 " ideal model delta sigma weight residual 121.54 132.78 -11.24 1.91e+00 2.74e-01 3.47e+01 angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.78 -11.24 1.91e+00 2.74e-01 3.46e+01 angle pdb=" C PHE B 86 " pdb=" N ASN B 87 " pdb=" CA ASN B 87 " ideal model delta sigma weight residual 121.54 132.77 -11.23 1.91e+00 2.74e-01 3.45e+01 angle pdb=" C GLN C 321 " pdb=" N PRO C 322 " pdb=" CA PRO C 322 " ideal model delta sigma weight residual 119.85 114.08 5.77 1.01e+00 9.80e-01 3.27e+01 ... (remaining 42922 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 16971 17.93 - 35.86: 1951 35.86 - 53.79: 608 53.79 - 71.72: 160 71.72 - 89.65: 48 Dihedral angle restraints: 19738 sinusoidal: 8548 harmonic: 11190 Sorted by residual: dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.08 71.92 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.09 71.91 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.11 71.89 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 19735 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 5067 0.329 - 0.659: 4 0.659 - 0.988: 5 0.988 - 1.317: 0 1.317 - 1.647: 1 Chirality restraints: 5077 Sorted by residual: chirality pdb=" C1 NAG d 2 " pdb=" O4 NAG d 1 " pdb=" C2 NAG d 2 " pdb=" O5 NAG d 2 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.16e+03 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-02 2.50e+03 1.02e+03 chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-01 2.50e+01 6.78e+01 ... (remaining 5074 not shown) Planarity restraints: 5509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " -0.104 2.00e-02 2.50e+03 1.98e-01 4.90e+02 pdb=" CG ASN C 331 " 0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.089 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " 0.355 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " -0.218 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.141 2.00e-02 2.50e+03 1.67e-01 3.49e+02 pdb=" CG ASN B 331 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.278 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " 0.198 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.131 2.00e-02 2.50e+03 1.61e-01 3.23e+02 pdb=" CG ASN A 331 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.270 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.192 2.00e-02 2.50e+03 ... (remaining 5506 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 315 2.53 - 3.12: 23040 3.12 - 3.71: 45182 3.71 - 4.31: 66002 4.31 - 4.90: 109745 Nonbonded interactions: 244284 Sorted by model distance: nonbonded pdb=" O VAL H 125 " pdb=" OG SER H 126 " model vdw 1.934 3.040 nonbonded pdb=" O VAL I 125 " pdb=" OG SER I 126 " model vdw 1.934 3.040 nonbonded pdb=" OD1 ASN C 532 " pdb=" N LEU C 533 " model vdw 1.966 3.120 nonbonded pdb=" N GLU B 748 " pdb=" OE1 GLU B 748 " model vdw 2.140 3.120 nonbonded pdb=" O GLY A 700 " pdb=" O ALA A 701 " model vdw 2.167 3.040 ... (remaining 244279 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 455 or resid 491 through 939 or resid 944 throu \ gh 1408)) selection = (chain 'B' and (resid 27 through 455 or resid 491 through 1408)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'K' 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' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.630 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: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 28.620 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 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 : 0.011 0.194 31650 Z= 0.482 Angle : 1.199 48.921 43232 Z= 0.636 Chirality : 0.072 1.647 5077 Planarity : 0.007 0.090 5461 Dihedral : 17.351 89.648 12408 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 2.40 % Allowed : 10.93 % Favored : 86.68 % Rotamer: Outliers : 10.46 % Allowed : 18.18 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.96 (0.11), residues: 3798 helix: -2.43 (0.15), residues: 712 sheet: -1.64 (0.14), residues: 1053 loop : -3.36 (0.11), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1039 TYR 0.028 0.003 TYR B1067 PHE 0.033 0.003 PHE H 29 TRP 0.025 0.003 TRP C 104 HIS 0.010 0.002 HIS H 32 Details of bonding type rmsd covalent geometry : bond 0.01059 (31533) covalent geometry : angle 1.03004 (42927) SS BOND : bond 0.02830 ( 46) SS BOND : angle 8.05020 ( 92) hydrogen bonds : bond 0.18409 ( 1096) hydrogen bonds : angle 7.94373 ( 3108) link_BETA1-4 : bond 0.04239 ( 23) link_BETA1-4 : angle 6.09256 ( 69) link_NAG-ASN : bond 0.02245 ( 48) link_NAG-ASN : angle 7.49448 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 351 poor density : 359 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 THR cc_start: 0.5565 (OUTLIER) cc_final: 0.5314 (m) REVERT: A 143 VAL cc_start: 0.7014 (OUTLIER) cc_final: 0.6406 (t) REVERT: A 335 LEU cc_start: 0.5196 (OUTLIER) cc_final: 0.4920 (mp) REVERT: A 983 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7424 (mtm110) REVERT: A 1039 ARG cc_start: 0.9213 (OUTLIER) cc_final: 0.8890 (mtp180) REVERT: B 109 THR cc_start: 0.6101 (OUTLIER) cc_final: 0.5703 (m) REVERT: B 153 MET cc_start: 0.4251 (mpp) cc_final: 0.2476 (ptt) REVERT: B 164 ASN cc_start: 0.4183 (OUTLIER) cc_final: 0.3169 (m-40) REVERT: B 422 ASN cc_start: 0.0201 (OUTLIER) cc_final: -0.0138 (t0) REVERT: B 950 ASP cc_start: 0.7990 (m-30) cc_final: 0.7786 (m-30) REVERT: C 153 MET cc_start: 0.3196 (mpp) cc_final: 0.1184 (ptp) REVERT: C 158 ARG cc_start: 0.6004 (OUTLIER) cc_final: 0.4532 (ttp-170) REVERT: C 218 GLN cc_start: 0.7063 (tt0) cc_final: 0.6668 (tm130) REVERT: C 314 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: C 528 LYS cc_start: 0.6981 (OUTLIER) cc_final: 0.6511 (mmmm) REVERT: C 529 LYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6757 (ptmm) REVERT: C 535 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7757 (ttmt) REVERT: H 83 MET cc_start: -0.0818 (mtp) cc_final: -0.1317 (mmm) REVERT: H 114 MET cc_start: 0.0113 (mtm) cc_final: -0.0127 (mtp) REVERT: H 178 HIS cc_start: 0.0303 (OUTLIER) cc_final: -0.0230 (m-70) REVERT: I 102 TYR cc_start: 0.2377 (OUTLIER) cc_final: 0.2136 (p90) REVERT: I 211 ASN cc_start: 0.0918 (OUTLIER) cc_final: 0.0579 (m110) REVERT: M 183 LEU cc_start: 0.0426 (OUTLIER) cc_final: -0.0507 (tp) outliers start: 351 outliers final: 74 residues processed: 654 average time/residue: 0.5223 time to fit residues: 417.5641 Evaluate side-chains 263 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 172 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 983 ARG Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 379 CYS Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1037 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 178 HIS Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 131 ASN Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 168 SER Chi-restraints excluded: chain M residue 183 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 137 ASN A 239 GLN A 450 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 658 ASN A 804 GLN A 856 ASN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 955 ASN A 960 ASN A 969 ASN A 992 GLN A1011 GLN A1101 HIS B 134 GLN B 137 ASN B 317 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN B 498 GLN B 644 GLN B 804 GLN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 992 GLN B1005 GLN B1054 GLN C 134 GLN C 137 ASN C 188 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 613 GLN C 644 GLN C 703 ASN C 751 ASN C 755 GLN C 784 GLN C 804 GLN C 901 GLN C 914 ASN C 926 GLN C 969 ASN C 992 GLN C1071 GLN C1101 HIS L 6 GLN L 38 GLN ** L 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 GLN M 6 GLN M 191 HIS ** M 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.207233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.166077 restraints weight = 50655.428| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.95 r_work: 0.3290 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 31650 Z= 0.229 Angle : 0.863 17.496 43232 Z= 0.417 Chirality : 0.053 0.567 5077 Planarity : 0.006 0.061 5461 Dihedral : 10.000 94.078 5755 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.61 % Favored : 91.18 % Rotamer: Outliers : 5.69 % Allowed : 21.49 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.12), residues: 3798 helix: -0.44 (0.19), residues: 703 sheet: -1.02 (0.15), residues: 1083 loop : -2.74 (0.12), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 237 TYR 0.034 0.002 TYR A 453 PHE 0.017 0.002 PHE C 338 TRP 0.016 0.002 TRP A 104 HIS 0.007 0.002 HIS M 191 Details of bonding type rmsd covalent geometry : bond 0.00544 (31533) covalent geometry : angle 0.82121 (42927) SS BOND : bond 0.00465 ( 46) SS BOND : angle 1.96119 ( 92) hydrogen bonds : bond 0.05421 ( 1096) hydrogen bonds : angle 5.97845 ( 3108) link_BETA1-4 : bond 0.00759 ( 23) link_BETA1-4 : angle 2.58817 ( 69) link_NAG-ASN : bond 0.00629 ( 48) link_NAG-ASN : angle 4.10379 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 182 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.3363 (p0) cc_final: 0.3042 (p0) REVERT: A 153 MET cc_start: 0.2641 (OUTLIER) cc_final: 0.2398 (mtp) REVERT: A 164 ASN cc_start: 0.4728 (OUTLIER) cc_final: 0.4218 (p0) REVERT: A 237 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6949 (mmm-85) REVERT: A 335 LEU cc_start: 0.5219 (OUTLIER) cc_final: 0.4864 (mp) REVERT: A 546 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.6916 (mm) REVERT: A 1094 VAL cc_start: 0.9221 (OUTLIER) cc_final: 0.9006 (t) REVERT: B 153 MET cc_start: 0.4057 (mpp) cc_final: 0.2141 (ptt) REVERT: B 554 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6998 (tp30) REVERT: C 153 MET cc_start: 0.2912 (mpp) cc_final: 0.0073 (ttp) REVERT: C 158 ARG cc_start: 0.6330 (OUTLIER) cc_final: 0.4423 (ttt180) REVERT: C 190 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8269 (mtm180) REVERT: C 529 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7561 (tppt) REVERT: C 814 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.7270 (mmtt) REVERT: C 1029 MET cc_start: 0.9103 (tpp) cc_final: 0.8859 (tpp) REVERT: H 34 MET cc_start: 0.5268 (mpm) cc_final: 0.4538 (mpm) REVERT: H 83 MET cc_start: -0.1348 (mtp) cc_final: -0.1765 (mmm) REVERT: H 114 MET cc_start: -0.0680 (mtm) cc_final: -0.0960 (mtp) REVERT: H 178 HIS cc_start: 0.0628 (OUTLIER) cc_final: -0.0101 (m-70) REVERT: I 83 MET cc_start: 0.2900 (mmp) cc_final: 0.1612 (mtp) REVERT: I 106 ASP cc_start: 0.4164 (OUTLIER) cc_final: 0.3582 (m-30) REVERT: I 184 LEU cc_start: 0.2319 (OUTLIER) cc_final: 0.2007 (pt) REVERT: I 211 ASN cc_start: 0.1611 (OUTLIER) cc_final: 0.0687 (m110) outliers start: 191 outliers final: 71 residues processed: 345 average time/residue: 0.4562 time to fit residues: 197.5461 Evaluate side-chains 231 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 145 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 178 HIS Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 190 SER Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 193 SER Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 156 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 80 optimal weight: 0.6980 chunk 246 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 366 optimal weight: 5.9990 chunk 242 optimal weight: 10.0000 chunk 361 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 121 optimal weight: 0.0010 chunk 222 optimal weight: 2.9990 chunk 202 optimal weight: 9.9990 overall best weight: 2.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 207 HIS ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN B1010 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 969 ASN L 191 HIS ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.208120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.158951 restraints weight = 49618.303| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 3.65 r_work: 0.3051 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31650 Z= 0.172 Angle : 0.761 14.051 43232 Z= 0.364 Chirality : 0.050 0.653 5077 Planarity : 0.005 0.050 5461 Dihedral : 8.684 94.489 5666 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.79 % Favored : 92.02 % Rotamer: Outliers : 5.16 % Allowed : 21.07 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.13), residues: 3798 helix: 0.24 (0.20), residues: 706 sheet: -0.59 (0.15), residues: 1078 loop : -2.42 (0.12), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 72 TYR 0.020 0.001 TYR B1067 PHE 0.022 0.002 PHE A 238 TRP 0.014 0.001 TRP M 98 HIS 0.006 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00404 (31533) covalent geometry : angle 0.72685 (42927) SS BOND : bond 0.00376 ( 46) SS BOND : angle 1.72160 ( 92) hydrogen bonds : bond 0.04658 ( 1096) hydrogen bonds : angle 5.54898 ( 3108) link_BETA1-4 : bond 0.00768 ( 23) link_BETA1-4 : angle 2.34416 ( 69) link_NAG-ASN : bond 0.00714 ( 48) link_NAG-ASN : angle 3.46911 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 161 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.7209 (p90) cc_final: 0.6861 (p90) REVERT: A 190 ARG cc_start: 0.8573 (mtt90) cc_final: 0.8139 (mpp80) REVERT: A 237 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6563 (mmm-85) REVERT: A 335 LEU cc_start: 0.4999 (OUTLIER) cc_final: 0.4791 (mp) REVERT: A 379 CYS cc_start: 0.2358 (OUTLIER) cc_final: 0.1670 (p) REVERT: A 546 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.6940 (mm) REVERT: A 855 PHE cc_start: 0.6451 (OUTLIER) cc_final: 0.5713 (t80) REVERT: A 869 MET cc_start: 0.9271 (mtt) cc_final: 0.8979 (mtt) REVERT: A 1094 VAL cc_start: 0.9385 (OUTLIER) cc_final: 0.9156 (t) REVERT: B 153 MET cc_start: 0.3764 (mpp) cc_final: 0.1995 (ptt) REVERT: B 544 ASN cc_start: 0.7812 (OUTLIER) cc_final: 0.7399 (m-40) REVERT: B 554 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7143 (tp30) REVERT: C 140 PHE cc_start: 0.8110 (p90) cc_final: 0.7678 (p90) REVERT: C 153 MET cc_start: 0.2961 (mpp) cc_final: 0.0198 (ttp) REVERT: C 158 ARG cc_start: 0.6256 (OUTLIER) cc_final: 0.3932 (ttt180) REVERT: C 190 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8109 (mtm180) REVERT: C 314 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8663 (tm-30) REVERT: C 529 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7532 (tppt) REVERT: C 814 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7542 (mmtt) REVERT: C 1129 VAL cc_start: 0.9495 (OUTLIER) cc_final: 0.9226 (t) REVERT: H 114 MET cc_start: -0.1144 (mtm) cc_final: -0.1724 (mtp) REVERT: H 178 HIS cc_start: 0.0551 (OUTLIER) cc_final: -0.0078 (m-70) REVERT: L 152 LYS cc_start: 0.1526 (OUTLIER) cc_final: 0.1300 (ptpt) REVERT: I 106 ASP cc_start: 0.3875 (OUTLIER) cc_final: 0.3333 (m-30) REVERT: I 184 LEU cc_start: 0.2907 (OUTLIER) cc_final: 0.2323 (pt) REVERT: I 211 ASN cc_start: 0.1562 (OUTLIER) cc_final: 0.0494 (m110) REVERT: M 183 LEU cc_start: -0.0134 (OUTLIER) cc_final: -0.1101 (tp) outliers start: 173 outliers final: 78 residues processed: 314 average time/residue: 0.4532 time to fit residues: 178.8355 Evaluate side-chains 229 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 131 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 178 HIS Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 152 LYS Chi-restraints excluded: chain L residue 171 SER Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 156 SER Chi-restraints excluded: chain M residue 174 LYS Chi-restraints excluded: chain M residue 183 LEU Chi-restraints excluded: chain M residue 190 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 29 optimal weight: 30.0000 chunk 265 optimal weight: 3.9990 chunk 260 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 135 optimal weight: 30.0000 chunk 337 optimal weight: 10.0000 chunk 329 optimal weight: 20.0000 chunk 360 optimal weight: 30.0000 chunk 335 optimal weight: 7.9990 chunk 192 optimal weight: 2.9990 chunk 34 optimal weight: 0.0000 overall best weight: 3.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 239 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C1005 GLN ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.204642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.155839 restraints weight = 49322.799| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 3.71 r_work: 0.3014 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 31650 Z= 0.261 Angle : 0.819 14.867 43232 Z= 0.390 Chirality : 0.053 0.859 5077 Planarity : 0.005 0.054 5461 Dihedral : 8.471 94.089 5648 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.08 % Favored : 91.73 % Rotamer: Outliers : 6.20 % Allowed : 20.24 % Favored : 73.56 % 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: -1.88 (0.13), residues: 3798 helix: 0.29 (0.20), residues: 705 sheet: -0.50 (0.15), residues: 1093 loop : -2.34 (0.12), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 765 TYR 0.022 0.002 TYR B1067 PHE 0.027 0.002 PHE A 140 TRP 0.012 0.002 TRP M 36 HIS 0.011 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00637 (31533) covalent geometry : angle 0.78226 (42927) SS BOND : bond 0.00546 ( 46) SS BOND : angle 2.09876 ( 92) hydrogen bonds : bond 0.05351 ( 1096) hydrogen bonds : angle 5.62432 ( 3108) link_BETA1-4 : bond 0.00691 ( 23) link_BETA1-4 : angle 2.42450 ( 69) link_NAG-ASN : bond 0.00655 ( 48) link_NAG-ASN : angle 3.63306 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 140 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.7033 (p90) cc_final: 0.6730 (p90) REVERT: A 237 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6392 (mtp85) REVERT: A 333 THR cc_start: 0.4995 (OUTLIER) cc_final: 0.4666 (t) REVERT: A 379 CYS cc_start: 0.2202 (OUTLIER) cc_final: 0.1571 (p) REVERT: A 546 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.6970 (mm) REVERT: A 869 MET cc_start: 0.9296 (mtt) cc_final: 0.9051 (mtt) REVERT: A 1094 VAL cc_start: 0.9401 (OUTLIER) cc_final: 0.9177 (t) REVERT: B 153 MET cc_start: 0.3780 (OUTLIER) cc_final: 0.1984 (ppp) REVERT: B 237 ARG cc_start: 0.7517 (mtp85) cc_final: 0.7307 (mtm180) REVERT: B 544 ASN cc_start: 0.7732 (OUTLIER) cc_final: 0.7510 (m110) REVERT: B 554 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7185 (tp30) REVERT: B 861 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9326 (mt) REVERT: B 957 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8628 (tp-100) REVERT: B 994 ASP cc_start: 0.8499 (t70) cc_final: 0.8238 (t0) REVERT: C 153 MET cc_start: 0.1864 (mpp) cc_final: -0.0629 (ttm) REVERT: C 190 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8188 (mtm180) REVERT: C 518 LEU cc_start: -0.0713 (OUTLIER) cc_final: -0.0965 (tp) REVERT: C 529 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7644 (tppt) REVERT: C 535 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.7698 (ttmt) REVERT: C 558 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.6357 (pmmt) REVERT: C 814 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7908 (mmtt) REVERT: H 34 MET cc_start: 0.4792 (mpm) cc_final: 0.4317 (mpm) REVERT: H 60 TYR cc_start: 0.2721 (OUTLIER) cc_final: 0.2008 (m-10) REVERT: H 114 MET cc_start: -0.1410 (mtm) cc_final: -0.1999 (mtp) REVERT: H 178 HIS cc_start: 0.0771 (OUTLIER) cc_final: 0.0166 (m-70) REVERT: L 190 SER cc_start: 0.0393 (OUTLIER) cc_final: 0.0030 (m) REVERT: I 34 MET cc_start: 0.3823 (OUTLIER) cc_final: 0.2660 (mpt) REVERT: I 83 MET cc_start: 0.2951 (mmp) cc_final: 0.1815 (mtp) REVERT: I 106 ASP cc_start: 0.4195 (OUTLIER) cc_final: 0.3516 (m-30) REVERT: I 184 LEU cc_start: 0.2899 (OUTLIER) cc_final: 0.2243 (pt) REVERT: I 211 ASN cc_start: 0.1518 (OUTLIER) cc_final: 0.0485 (m110) REVERT: M 183 LEU cc_start: -0.0265 (OUTLIER) cc_final: -0.1212 (tp) outliers start: 208 outliers final: 103 residues processed: 318 average time/residue: 0.4495 time to fit residues: 180.1776 Evaluate side-chains 253 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 127 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 178 HIS Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 171 SER Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 190 SER Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 156 SER Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 174 LYS Chi-restraints excluded: chain M residue 183 LEU Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain M residue 190 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 374 optimal weight: 9.9990 chunk 258 optimal weight: 0.3980 chunk 103 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 chunk 267 optimal weight: 3.9990 chunk 348 optimal weight: 30.0000 chunk 244 optimal weight: 7.9990 chunk 278 optimal weight: 0.8980 chunk 142 optimal weight: 0.2980 chunk 203 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN B 99 ASN B 125 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 935 GLN ** H 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.207333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.159367 restraints weight = 49664.261| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 3.52 r_work: 0.3075 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31650 Z= 0.124 Angle : 0.713 12.840 43232 Z= 0.337 Chirality : 0.048 0.691 5077 Planarity : 0.004 0.055 5461 Dihedral : 7.923 98.830 5639 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.90 % Favored : 92.92 % Rotamer: Outliers : 4.77 % Allowed : 22.35 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.13), residues: 3798 helix: 0.81 (0.20), residues: 704 sheet: -0.24 (0.15), residues: 1087 loop : -2.13 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 190 TYR 0.016 0.001 TYR B1067 PHE 0.027 0.001 PHE A 140 TRP 0.011 0.001 TRP M 98 HIS 0.004 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00274 (31533) covalent geometry : angle 0.68142 (42927) SS BOND : bond 0.00388 ( 46) SS BOND : angle 1.74674 ( 92) hydrogen bonds : bond 0.03900 ( 1096) hydrogen bonds : angle 5.26121 ( 3108) link_BETA1-4 : bond 0.00565 ( 23) link_BETA1-4 : angle 2.04852 ( 69) link_NAG-ASN : bond 0.00788 ( 48) link_NAG-ASN : angle 3.23202 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 145 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.7020 (p90) cc_final: 0.6754 (p90) REVERT: A 190 ARG cc_start: 0.8573 (mtt90) cc_final: 0.8051 (mpp80) REVERT: A 333 THR cc_start: 0.5171 (OUTLIER) cc_final: 0.4761 (t) REVERT: A 546 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.6970 (mm) REVERT: A 855 PHE cc_start: 0.6454 (OUTLIER) cc_final: 0.5772 (t80) REVERT: A 1094 VAL cc_start: 0.9383 (OUTLIER) cc_final: 0.9159 (t) REVERT: A 1113 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8822 (mt0) REVERT: B 122 ASN cc_start: 0.4870 (OUTLIER) cc_final: 0.4400 (m-40) REVERT: B 153 MET cc_start: 0.3737 (mpp) cc_final: 0.1980 (ppp) REVERT: B 190 ARG cc_start: 0.7449 (mpt-90) cc_final: 0.7185 (mpt-90) REVERT: B 554 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7004 (tp30) REVERT: B 957 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8489 (tm-30) REVERT: B 994 ASP cc_start: 0.8323 (t70) cc_final: 0.8093 (t0) REVERT: C 96 GLU cc_start: 0.5875 (OUTLIER) cc_final: 0.5390 (pm20) REVERT: C 153 MET cc_start: 0.1866 (mpp) cc_final: -0.0528 (ttt) REVERT: C 518 LEU cc_start: -0.0722 (OUTLIER) cc_final: -0.0967 (mt) REVERT: C 529 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7556 (tppt) REVERT: C 535 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7680 (ttmt) REVERT: H 34 MET cc_start: 0.4827 (mpm) cc_final: 0.4541 (mpm) REVERT: H 114 MET cc_start: -0.1843 (mtm) cc_final: -0.2160 (mtp) REVERT: H 178 HIS cc_start: 0.0802 (OUTLIER) cc_final: 0.0180 (m-70) REVERT: I 34 MET cc_start: 0.3746 (OUTLIER) cc_final: 0.2680 (mpt) REVERT: I 83 MET cc_start: 0.2851 (mmp) cc_final: 0.1809 (mtp) REVERT: I 106 ASP cc_start: 0.4196 (OUTLIER) cc_final: 0.3651 (m-30) REVERT: I 184 LEU cc_start: 0.2831 (OUTLIER) cc_final: 0.2172 (pt) REVERT: I 211 ASN cc_start: 0.1485 (OUTLIER) cc_final: 0.0325 (m110) REVERT: M 136 VAL cc_start: 0.1112 (OUTLIER) cc_final: 0.0818 (m) REVERT: M 183 LEU cc_start: -0.0423 (OUTLIER) cc_final: -0.1316 (tp) REVERT: M 195 SER cc_start: 0.1471 (OUTLIER) cc_final: 0.1199 (p) outliers start: 160 outliers final: 68 residues processed: 284 average time/residue: 0.4634 time to fit residues: 165.5536 Evaluate side-chains 210 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 123 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 178 HIS Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 171 SER Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 144 SER Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 136 VAL Chi-restraints excluded: chain M residue 156 SER Chi-restraints excluded: chain M residue 174 LYS Chi-restraints excluded: chain M residue 178 SER Chi-restraints excluded: chain M residue 183 LEU Chi-restraints excluded: chain M residue 190 SER Chi-restraints excluded: chain M residue 195 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 284 optimal weight: 5.9990 chunk 326 optimal weight: 50.0000 chunk 241 optimal weight: 20.0000 chunk 305 optimal weight: 40.0000 chunk 261 optimal weight: 6.9990 chunk 336 optimal weight: 6.9990 chunk 213 optimal weight: 3.9990 chunk 28 optimal weight: 20.0000 chunk 125 optimal weight: 0.0980 chunk 36 optimal weight: 10.0000 chunk 325 optimal weight: 8.9990 overall best weight: 4.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN B 81 ASN B 99 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** H 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.206701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.158262 restraints weight = 49227.490| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 3.64 r_work: 0.3004 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 31650 Z= 0.309 Angle : 0.836 14.733 43232 Z= 0.399 Chirality : 0.054 0.644 5077 Planarity : 0.005 0.056 5461 Dihedral : 8.218 101.046 5634 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.56 % Favored : 91.26 % Rotamer: Outliers : 5.31 % Allowed : 22.15 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.13), residues: 3798 helix: 0.43 (0.20), residues: 705 sheet: -0.32 (0.15), residues: 1084 loop : -2.17 (0.12), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1107 TYR 0.022 0.002 TYR A1067 PHE 0.023 0.002 PHE A 86 TRP 0.016 0.002 TRP C 436 HIS 0.009 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00759 (31533) covalent geometry : angle 0.79911 (42927) SS BOND : bond 0.00671 ( 46) SS BOND : angle 2.05342 ( 92) hydrogen bonds : bond 0.05653 ( 1096) hydrogen bonds : angle 5.61961 ( 3108) link_BETA1-4 : bond 0.00620 ( 23) link_BETA1-4 : angle 2.33487 ( 69) link_NAG-ASN : bond 0.01040 ( 48) link_NAG-ASN : angle 3.78198 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 131 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.6964 (p90) cc_final: 0.6700 (p90) REVERT: A 333 THR cc_start: 0.5145 (OUTLIER) cc_final: 0.4688 (t) REVERT: A 379 CYS cc_start: 0.2125 (OUTLIER) cc_final: 0.1588 (p) REVERT: A 546 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7034 (mm) REVERT: A 1094 VAL cc_start: 0.9394 (OUTLIER) cc_final: 0.9168 (t) REVERT: A 1113 GLN cc_start: 0.9299 (OUTLIER) cc_final: 0.8817 (mt0) REVERT: B 153 MET cc_start: 0.3714 (mpp) cc_final: 0.1842 (pp-130) REVERT: B 554 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7192 (tp30) REVERT: B 861 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9309 (mt) REVERT: B 957 GLN cc_start: 0.8909 (tm-30) cc_final: 0.8594 (tm-30) REVERT: B 994 ASP cc_start: 0.8564 (t70) cc_final: 0.8314 (t0) REVERT: C 96 GLU cc_start: 0.6148 (OUTLIER) cc_final: 0.5649 (pm20) REVERT: C 153 MET cc_start: 0.1702 (mpp) cc_final: -0.0197 (ttt) REVERT: C 529 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7642 (tppt) REVERT: C 535 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7575 (ttmt) REVERT: C 537 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8352 (mtmm) REVERT: H 34 MET cc_start: 0.4835 (mpm) cc_final: 0.4560 (mpm) REVERT: H 60 TYR cc_start: 0.2653 (OUTLIER) cc_final: 0.1985 (m-10) REVERT: H 114 MET cc_start: -0.1675 (mtm) cc_final: -0.2183 (mtp) REVERT: H 178 HIS cc_start: 0.0629 (OUTLIER) cc_final: 0.0020 (m-70) REVERT: I 34 MET cc_start: 0.4173 (OUTLIER) cc_final: 0.2978 (mpt) REVERT: I 83 MET cc_start: 0.2792 (mmp) cc_final: 0.1888 (mtp) REVERT: I 106 ASP cc_start: 0.4322 (OUTLIER) cc_final: 0.3648 (m-30) REVERT: I 114 MET cc_start: -0.0595 (OUTLIER) cc_final: -0.0916 (pp-130) REVERT: I 184 LEU cc_start: 0.2884 (OUTLIER) cc_final: 0.2185 (pt) REVERT: I 211 ASN cc_start: 0.0879 (OUTLIER) cc_final: -0.0111 (m110) REVERT: M 134 THR cc_start: -0.0415 (m) cc_final: -0.0807 (t) REVERT: M 195 SER cc_start: 0.1330 (OUTLIER) cc_final: 0.1035 (m) outliers start: 178 outliers final: 92 residues processed: 286 average time/residue: 0.4243 time to fit residues: 155.6354 Evaluate side-chains 233 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 122 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 178 HIS Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 171 SER Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 114 MET Chi-restraints excluded: chain I residue 144 SER Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain M residue 119 THR Chi-restraints excluded: chain M residue 136 VAL Chi-restraints excluded: chain M residue 156 SER Chi-restraints excluded: chain M residue 174 LYS Chi-restraints excluded: chain M residue 178 SER Chi-restraints excluded: chain M residue 190 SER Chi-restraints excluded: chain M residue 195 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 99 optimal weight: 0.9980 chunk 237 optimal weight: 20.0000 chunk 366 optimal weight: 3.9990 chunk 346 optimal weight: 20.0000 chunk 337 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 148 optimal weight: 1.9990 chunk 265 optimal weight: 0.8980 chunk 296 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C1005 GLN ** H 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 211 ASN ** L 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 ASN ** M 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.206927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.158929 restraints weight = 49478.907| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 3.60 r_work: 0.3061 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31650 Z= 0.133 Angle : 0.700 12.896 43232 Z= 0.331 Chirality : 0.048 0.640 5077 Planarity : 0.004 0.056 5461 Dihedral : 7.707 101.924 5633 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.77 % Favored : 93.08 % Rotamer: Outliers : 3.93 % Allowed : 23.37 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.13), residues: 3798 helix: 0.91 (0.20), residues: 700 sheet: -0.05 (0.15), residues: 1048 loop : -1.99 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 190 TYR 0.018 0.001 TYR B1067 PHE 0.029 0.001 PHE A 140 TRP 0.018 0.001 TRP L 151 HIS 0.003 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00303 (31533) covalent geometry : angle 0.66910 (42927) SS BOND : bond 0.00470 ( 46) SS BOND : angle 1.61074 ( 92) hydrogen bonds : bond 0.03941 ( 1096) hydrogen bonds : angle 5.26377 ( 3108) link_BETA1-4 : bond 0.00534 ( 23) link_BETA1-4 : angle 1.95832 ( 69) link_NAG-ASN : bond 0.00634 ( 48) link_NAG-ASN : angle 3.16916 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 144 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.6922 (p90) cc_final: 0.6577 (p90) REVERT: A 333 THR cc_start: 0.4628 (OUTLIER) cc_final: 0.4304 (t) REVERT: A 546 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7082 (mm) REVERT: A 855 PHE cc_start: 0.6720 (OUTLIER) cc_final: 0.5966 (t80) REVERT: A 1113 GLN cc_start: 0.9285 (OUTLIER) cc_final: 0.8886 (mt0) REVERT: B 153 MET cc_start: 0.3606 (OUTLIER) cc_final: 0.1862 (tmm) REVERT: B 233 ILE cc_start: 0.6270 (OUTLIER) cc_final: 0.5755 (tp) REVERT: B 237 ARG cc_start: 0.7394 (mtp85) cc_final: 0.7107 (ttm-80) REVERT: B 554 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7280 (tp30) REVERT: B 957 GLN cc_start: 0.8907 (tm-30) cc_final: 0.8580 (tm-30) REVERT: B 994 ASP cc_start: 0.8395 (t70) cc_final: 0.8148 (t0) REVERT: C 131 CYS cc_start: 0.3072 (m) cc_final: 0.2210 (m) REVERT: C 153 MET cc_start: 0.1640 (mpp) cc_final: -0.0269 (ttt) REVERT: C 529 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7582 (tppt) REVERT: H 34 MET cc_start: 0.4998 (mpm) cc_final: 0.4741 (mpm) REVERT: H 114 MET cc_start: -0.1861 (mtm) cc_final: -0.2293 (mtp) REVERT: H 178 HIS cc_start: 0.0755 (OUTLIER) cc_final: 0.0111 (m-70) REVERT: L 190 SER cc_start: 0.0439 (OUTLIER) cc_final: 0.0224 (m) REVERT: I 34 MET cc_start: 0.3951 (OUTLIER) cc_final: 0.2682 (mpt) REVERT: I 83 MET cc_start: 0.2640 (mmp) cc_final: 0.1660 (mtp) REVERT: I 106 ASP cc_start: 0.4319 (OUTLIER) cc_final: 0.3627 (m-30) REVERT: I 114 MET cc_start: -0.0401 (OUTLIER) cc_final: -0.0705 (pp-130) REVERT: I 184 LEU cc_start: 0.2880 (OUTLIER) cc_final: 0.2153 (pt) REVERT: I 211 ASN cc_start: 0.0794 (OUTLIER) cc_final: -0.0354 (m110) REVERT: M 134 THR cc_start: -0.0435 (m) cc_final: -0.0872 (t) REVERT: M 136 VAL cc_start: 0.1211 (OUTLIER) cc_final: 0.0895 (m) outliers start: 132 outliers final: 79 residues processed: 259 average time/residue: 0.3978 time to fit residues: 132.4770 Evaluate side-chains 223 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 128 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 935 GLN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 178 HIS Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 171 SER Chi-restraints excluded: chain L residue 190 SER Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 114 MET Chi-restraints excluded: chain I residue 131 LYS Chi-restraints excluded: chain I residue 144 SER Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 136 VAL Chi-restraints excluded: chain M residue 156 SER Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 174 LYS Chi-restraints excluded: chain M residue 190 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 343 optimal weight: 40.0000 chunk 80 optimal weight: 6.9990 chunk 87 optimal weight: 0.5980 chunk 42 optimal weight: 30.0000 chunk 277 optimal weight: 0.9980 chunk 204 optimal weight: 9.9990 chunk 309 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 170 optimal weight: 0.3980 chunk 96 optimal weight: 3.9990 chunk 259 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.205532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.156949 restraints weight = 49346.461| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 3.65 r_work: 0.3044 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31650 Z= 0.150 Angle : 0.703 12.798 43232 Z= 0.332 Chirality : 0.048 0.655 5077 Planarity : 0.005 0.056 5461 Dihedral : 7.538 102.790 5633 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.50 % Favored : 92.34 % Rotamer: Outliers : 3.90 % Allowed : 23.58 % Favored : 72.52 % 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: -1.15 (0.13), residues: 3798 helix: 1.03 (0.20), residues: 701 sheet: -0.02 (0.15), residues: 1055 loop : -1.90 (0.13), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 190 TYR 0.021 0.001 TYR B1067 PHE 0.018 0.001 PHE C 106 TRP 0.011 0.001 TRP C 436 HIS 0.006 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00355 (31533) covalent geometry : angle 0.67133 (42927) SS BOND : bond 0.00421 ( 46) SS BOND : angle 1.73230 ( 92) hydrogen bonds : bond 0.04164 ( 1096) hydrogen bonds : angle 5.22967 ( 3108) link_BETA1-4 : bond 0.00570 ( 23) link_BETA1-4 : angle 1.95931 ( 69) link_NAG-ASN : bond 0.00617 ( 48) link_NAG-ASN : angle 3.19273 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 135 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ASN cc_start: 0.3430 (p0) cc_final: 0.3095 (p0) REVERT: A 333 THR cc_start: 0.4641 (OUTLIER) cc_final: 0.4342 (t) REVERT: A 379 CYS cc_start: 0.1995 (OUTLIER) cc_final: 0.1413 (p) REVERT: A 546 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7027 (mm) REVERT: A 855 PHE cc_start: 0.6732 (m-80) cc_final: 0.5989 (t80) REVERT: A 1113 GLN cc_start: 0.9310 (OUTLIER) cc_final: 0.8903 (mt0) REVERT: B 153 MET cc_start: 0.3588 (OUTLIER) cc_final: 0.1854 (tmm) REVERT: B 233 ILE cc_start: 0.6244 (OUTLIER) cc_final: 0.5728 (tp) REVERT: B 237 ARG cc_start: 0.7405 (mtp85) cc_final: 0.7141 (ttm-80) REVERT: B 554 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7363 (tp30) REVERT: B 957 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8541 (tm-30) REVERT: C 153 MET cc_start: 0.1811 (mpp) cc_final: -0.0481 (ttt) REVERT: C 529 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7621 (tppt) REVERT: H 34 MET cc_start: 0.4967 (mpm) cc_final: 0.4699 (mpm) REVERT: H 114 MET cc_start: -0.2145 (mtm) cc_final: -0.2573 (mtp) REVERT: H 178 HIS cc_start: 0.0632 (OUTLIER) cc_final: 0.0050 (m-70) REVERT: L 190 SER cc_start: 0.0455 (OUTLIER) cc_final: 0.0252 (m) REVERT: I 34 MET cc_start: 0.3788 (OUTLIER) cc_final: 0.2725 (mpt) REVERT: I 83 MET cc_start: 0.2286 (mmp) cc_final: 0.1493 (mtp) REVERT: I 114 MET cc_start: -0.0507 (OUTLIER) cc_final: -0.0745 (pp-130) REVERT: I 184 LEU cc_start: 0.2912 (OUTLIER) cc_final: 0.2173 (pt) REVERT: I 211 ASN cc_start: 0.0757 (OUTLIER) cc_final: -0.0363 (m110) REVERT: M 134 THR cc_start: -0.0464 (m) cc_final: -0.0898 (t) REVERT: M 136 VAL cc_start: 0.1160 (OUTLIER) cc_final: 0.0852 (m) outliers start: 131 outliers final: 86 residues processed: 248 average time/residue: 0.4143 time to fit residues: 132.8599 Evaluate side-chains 222 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 121 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 144 SER Chi-restraints excluded: chain H residue 178 HIS Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 171 SER Chi-restraints excluded: chain L residue 190 SER Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 114 MET Chi-restraints excluded: chain I residue 131 LYS Chi-restraints excluded: chain I residue 144 SER Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 136 VAL Chi-restraints excluded: chain M residue 156 SER Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 174 LYS Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain M residue 190 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 381 optimal weight: 30.0000 chunk 105 optimal weight: 7.9990 chunk 239 optimal weight: 0.4980 chunk 288 optimal weight: 0.7980 chunk 108 optimal weight: 0.0970 chunk 303 optimal weight: 8.9990 chunk 207 optimal weight: 8.9990 chunk 222 optimal weight: 0.6980 chunk 283 optimal weight: 1.9990 chunk 269 optimal weight: 0.3980 chunk 214 optimal weight: 9.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 703 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.206841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.158320 restraints weight = 49634.651| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 3.58 r_work: 0.3101 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 31650 Z= 0.107 Angle : 0.671 12.812 43232 Z= 0.315 Chirality : 0.047 0.549 5077 Planarity : 0.004 0.057 5461 Dihedral : 7.242 102.772 5633 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.16 % Favored : 93.68 % Rotamer: Outliers : 3.31 % Allowed : 24.29 % Favored : 72.40 % 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: -0.89 (0.13), residues: 3798 helix: 1.31 (0.20), residues: 708 sheet: 0.13 (0.15), residues: 1074 loop : -1.78 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 190 TYR 0.017 0.001 TYR A1067 PHE 0.029 0.001 PHE A 140 TRP 0.011 0.001 TRP A 436 HIS 0.006 0.000 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00229 (31533) covalent geometry : angle 0.64359 (42927) SS BOND : bond 0.00349 ( 46) SS BOND : angle 1.37658 ( 92) hydrogen bonds : bond 0.03333 ( 1096) hydrogen bonds : angle 4.98049 ( 3108) link_BETA1-4 : bond 0.00528 ( 23) link_BETA1-4 : angle 1.87342 ( 69) link_NAG-ASN : bond 0.00648 ( 48) link_NAG-ASN : angle 2.94540 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 137 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8627 (mtt90) cc_final: 0.7783 (mtt180) REVERT: A 546 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7043 (mm) REVERT: A 855 PHE cc_start: 0.6747 (OUTLIER) cc_final: 0.5994 (t80) REVERT: B 95 THR cc_start: 0.6621 (OUTLIER) cc_final: 0.6324 (t) REVERT: B 153 MET cc_start: 0.3617 (OUTLIER) cc_final: 0.1881 (tmm) REVERT: B 233 ILE cc_start: 0.6158 (OUTLIER) cc_final: 0.5694 (tp) REVERT: B 237 ARG cc_start: 0.7308 (mtp85) cc_final: 0.7097 (ttm-80) REVERT: B 703 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7846 (p0) REVERT: B 957 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8512 (tm-30) REVERT: B 994 ASP cc_start: 0.8299 (t70) cc_final: 0.8080 (t0) REVERT: C 153 MET cc_start: 0.1827 (mpp) cc_final: -0.0482 (ttt) REVERT: C 529 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7578 (tppt) REVERT: H 34 MET cc_start: 0.5023 (mpm) cc_final: 0.4663 (mpm) REVERT: H 114 MET cc_start: -0.2025 (mtm) cc_final: -0.2273 (mtp) REVERT: H 178 HIS cc_start: 0.0739 (OUTLIER) cc_final: 0.0171 (m-70) REVERT: I 34 MET cc_start: 0.3801 (OUTLIER) cc_final: 0.2645 (mpt) REVERT: I 83 MET cc_start: 0.2439 (mmp) cc_final: 0.1646 (mtp) REVERT: I 114 MET cc_start: -0.0679 (OUTLIER) cc_final: -0.0911 (pp-130) REVERT: I 184 LEU cc_start: 0.2922 (OUTLIER) cc_final: 0.2238 (pt) REVERT: I 211 ASN cc_start: 0.0839 (OUTLIER) cc_final: -0.0137 (m110) REVERT: M 134 THR cc_start: -0.0442 (m) cc_final: -0.0929 (t) REVERT: M 136 VAL cc_start: 0.1038 (OUTLIER) cc_final: 0.0731 (m) outliers start: 111 outliers final: 71 residues processed: 234 average time/residue: 0.4301 time to fit residues: 129.8455 Evaluate side-chains 211 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 127 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 178 HIS Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 171 SER Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 114 MET Chi-restraints excluded: chain I residue 144 SER Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 136 VAL Chi-restraints excluded: chain M residue 156 SER Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 174 LYS Chi-restraints excluded: chain M residue 190 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 182 optimal weight: 0.9990 chunk 379 optimal weight: 0.7980 chunk 102 optimal weight: 0.2980 chunk 234 optimal weight: 0.0870 chunk 377 optimal weight: 6.9990 chunk 209 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 230 optimal weight: 1.9990 chunk 279 optimal weight: 3.9990 chunk 295 optimal weight: 0.9980 chunk 369 optimal weight: 50.0000 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN B 703 ASN B1002 GLN C 115 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** H 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.206796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.158899 restraints weight = 49498.517| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 3.61 r_work: 0.3101 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.364 31650 Z= 0.161 Angle : 0.788 59.199 43232 Z= 0.397 Chirality : 0.047 0.550 5077 Planarity : 0.004 0.053 5461 Dihedral : 7.183 102.782 5630 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.11 % Favored : 93.73 % Rotamer: Outliers : 2.68 % Allowed : 24.92 % Favored : 72.40 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.13), residues: 3798 helix: 1.35 (0.20), residues: 708 sheet: 0.15 (0.15), residues: 1074 loop : -1.77 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 190 TYR 0.017 0.001 TYR A1067 PHE 0.017 0.001 PHE A 140 TRP 0.014 0.001 TRP L 36 HIS 0.005 0.000 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00378 (31533) covalent geometry : angle 0.74838 (42927) SS BOND : bond 0.01626 ( 46) SS BOND : angle 3.76957 ( 92) hydrogen bonds : bond 0.03366 ( 1096) hydrogen bonds : angle 4.98208 ( 3108) link_BETA1-4 : bond 0.00486 ( 23) link_BETA1-4 : angle 1.87787 ( 69) link_NAG-ASN : bond 0.00603 ( 48) link_NAG-ASN : angle 2.95026 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7596 Ramachandran restraints generated. 3798 Oldfield, 0 Emsley, 3798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 126 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8564 (mtt90) cc_final: 0.7813 (mtt180) REVERT: A 546 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7011 (mm) REVERT: A 855 PHE cc_start: 0.6754 (OUTLIER) cc_final: 0.6006 (t80) REVERT: A 1142 GLN cc_start: 0.8179 (tp40) cc_final: 0.7894 (tp40) REVERT: B 153 MET cc_start: 0.3659 (OUTLIER) cc_final: 0.1893 (tmm) REVERT: B 233 ILE cc_start: 0.6241 (OUTLIER) cc_final: 0.5782 (tp) REVERT: B 237 ARG cc_start: 0.7377 (mtp85) cc_final: 0.7176 (ttm-80) REVERT: B 554 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7052 (tp30) REVERT: B 703 ASN cc_start: 0.8264 (OUTLIER) cc_final: 0.7978 (t0) REVERT: B 704 SER cc_start: 0.9274 (OUTLIER) cc_final: 0.8955 (t) REVERT: B 957 GLN cc_start: 0.8800 (tm-30) cc_final: 0.8513 (tm-30) REVERT: B 994 ASP cc_start: 0.8273 (t70) cc_final: 0.8050 (t0) REVERT: C 153 MET cc_start: 0.1857 (mpp) cc_final: -0.0451 (ttt) REVERT: C 529 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7609 (tppt) REVERT: H 34 MET cc_start: 0.5028 (mpm) cc_final: 0.4663 (mpm) REVERT: H 114 MET cc_start: -0.1977 (mtm) cc_final: -0.2220 (mtp) REVERT: H 178 HIS cc_start: 0.0727 (OUTLIER) cc_final: 0.0169 (m-70) REVERT: I 34 MET cc_start: 0.3813 (OUTLIER) cc_final: 0.2680 (mpt) REVERT: I 83 MET cc_start: 0.2472 (mmp) cc_final: 0.1662 (mtp) REVERT: I 114 MET cc_start: -0.0743 (OUTLIER) cc_final: -0.0969 (pp-130) REVERT: I 184 LEU cc_start: 0.2928 (OUTLIER) cc_final: 0.2255 (pt) REVERT: I 211 ASN cc_start: 0.0764 (OUTLIER) cc_final: -0.0295 (m110) REVERT: M 134 THR cc_start: -0.0415 (m) cc_final: -0.0902 (t) REVERT: M 136 VAL cc_start: 0.1079 (OUTLIER) cc_final: 0.0764 (m) outliers start: 90 outliers final: 70 residues processed: 204 average time/residue: 0.4469 time to fit residues: 116.8567 Evaluate side-chains 207 residues out of total 3355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 123 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 703 ASN Chi-restraints excluded: chain B residue 704 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 112 TYR Chi-restraints excluded: chain H residue 134 SER Chi-restraints excluded: chain H residue 178 HIS Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain L residue 171 SER Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain I residue 106 ASP Chi-restraints excluded: chain I residue 114 MET Chi-restraints excluded: chain I residue 144 SER Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 184 LEU Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 136 VAL Chi-restraints excluded: chain M residue 156 SER Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 174 LYS Chi-restraints excluded: chain M residue 190 SER Chi-restraints excluded: chain M residue 195 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 383 random chunks: chunk 277 optimal weight: 3.9990 chunk 342 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 355 optimal weight: 8.9990 chunk 242 optimal weight: 8.9990 chunk 203 optimal weight: 6.9990 chunk 325 optimal weight: 20.0000 chunk 185 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.206847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.158936 restraints weight = 49756.127| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 3.62 r_work: 0.3112 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.364 31650 Z= 0.164 Angle : 0.785 55.071 43232 Z= 0.399 Chirality : 0.047 0.550 5077 Planarity : 0.004 0.053 5461 Dihedral : 7.183 102.782 5630 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.11 % Favored : 93.73 % Rotamer: Outliers : 2.53 % Allowed : 25.10 % Favored : 72.37 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.13), residues: 3798 helix: 1.35 (0.20), residues: 708 sheet: 0.15 (0.15), residues: 1074 loop : -1.77 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 190 TYR 0.017 0.001 TYR A1067 PHE 0.017 0.001 PHE A 140 TRP 0.014 0.001 TRP L 36 HIS 0.005 0.000 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00381 (31533) covalent geometry : angle 0.74416 (42927) SS BOND : bond 0.01626 ( 46) SS BOND : angle 3.76956 ( 92) hydrogen bonds : bond 0.03366 ( 1096) hydrogen bonds : angle 4.98208 ( 3108) link_BETA1-4 : bond 0.00486 ( 23) link_BETA1-4 : angle 1.87787 ( 69) link_NAG-ASN : bond 0.01268 ( 48) link_NAG-ASN : angle 3.01690 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10299.69 seconds wall clock time: 176 minutes 20.34 seconds (10580.34 seconds total)