Starting phenix.real_space_refine on Mon Jul 6 13:59:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cwu_30488/07_2026/7cwu_30488.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cwu_30488/07_2026/7cwu_30488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7cwu_30488/07_2026/7cwu_30488.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cwu_30488/07_2026/7cwu_30488.cif" model { file = "/net/cci-nas-00/data/ceres_data/7cwu_30488/07_2026/7cwu_30488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cwu_30488/07_2026/7cwu_30488.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cwu_30488/07_2026/7cwu_30488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cwu_30488/07_2026/7cwu_30488.map" } resolution = 3.5 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= 0.001 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 162 5.16 5 C 22886 2.51 5 N 5998 2.21 5 O 7082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 76 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36128 Number of models: 1 Model: "" Number of chains: 33 Chain: "P" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 931 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "I" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 789 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "N" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 931 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "G" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 789 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "J" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 931 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "F" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 789 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "B" Number of atoms: 8392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8392 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 51, 'TRANS': 1024} Chain breaks: 6 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 8340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8340 Classifications: {'peptide': 1070} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 50, 'TRANS': 1018} Chain breaks: 6 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 8387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1075, 8387 Classifications: {'peptide': 1075} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 51, 'TRANS': 1023} Chain breaks: 6 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "H" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "M" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "O" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} 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 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 chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 chiralities: 2 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 7.74, per 1000 atoms: 0.21 Number of scatterers: 36128 At special positions: 0 Unit cell: (202.8, 216.32, 208, 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 162 16.00 O 7082 8.00 N 5998 7.00 C 22886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 97 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 89 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 97 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.00 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.00 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.05 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.09 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.04 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 88 " 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 K 1 " - " NAG K 2 " " NAG Q 1 " - " NAG Q 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 A1301 " - " ASN A 603 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A1074 " " NAG B1301 " - " ASN B 603 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG D 1 " - " ASN B 234 " " NAG E 1 " - " ASN C 234 " " NAG Q 1 " - " ASN A 801 " " NAG T 1 " - " ASN A1098 " " NAG U 1 " - " ASN A1134 " " NAG V 1 " - " ASN B 717 " " NAG W 1 " - " ASN B 801 " " NAG X 1 " - " ASN B1098 " " NAG Y 1 " - " ASN B1134 " " NAG Z 1 " - " ASN C 717 " " NAG a 1 " - " ASN C 801 " " NAG b 1 " - " ASN C1134 " " NAG c 1 " - " ASN C1098 " " NAG d 1 " - " ASN A 717 " Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.4 seconds 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8500 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 82 sheets defined 18.0% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'P' and resid 29 through 33 Processing helix chain 'N' and resid 29 through 33 Processing helix chain 'G' and resid 80 through 84 removed outlier: 4.334A pdb=" N GLU G 84 " --> pdb=" O THR G 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 33 Processing helix chain 'B' and resid 296 through 304 removed outlier: 3.725A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 364 through 372 removed outlier: 4.139A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.909A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 385 through 389' Processing helix chain 'B' and resid 405 through 409 removed outlier: 3.953A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.675A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.981A 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: 3.723A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.635A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 856 Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.705A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.882A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 3.518A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.540A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.618A pdb=" N ALA B 989 " --> pdb=" O ASP B 985 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.920A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 364 through 372 removed outlier: 4.141A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.910A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 385 through 389' Processing helix chain 'C' and resid 405 through 409 removed outlier: 3.953A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.674A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.505A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (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: 3.642A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.501A pdb=" N ASP C 820 " --> pdb=" O SER C 816 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 856 removed outlier: 4.024A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.548A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY C 885 " --> pdb=" O THR C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.545A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 940 removed outlier: 3.518A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS C 933 " --> pdb=" O SER C 929 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.612A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.542A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.039A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.749A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 364 through 372 removed outlier: 4.140A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.910A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 385 through 389' Processing helix chain 'A' and resid 405 through 409 removed outlier: 3.952A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.675A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.505A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.596A 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: 3.643A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.500A pdb=" N ASP A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 856 removed outlier: 4.024A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.548A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.544A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 940 removed outlier: 3.519A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.613A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.598A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.038A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'M' and resid 74 through 76 No H-bonds generated for 'chain 'M' and resid 74 through 76' Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'O' and resid 74 through 76 No H-bonds generated for 'chain 'O' and resid 74 through 76' Processing helix chain 'O' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'P' and resid 3 through 4 removed outlier: 3.835A pdb=" N GLN P 3 " --> pdb=" O SER P 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 22 through 23 removed outlier: 3.600A pdb=" N ALA P 80 " --> pdb=" O CYS P 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 46 through 49 Processing sheet with id=AA4, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.688A pdb=" N ASP I 86 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TYR I 50 " --> pdb=" O VAL I 34 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.734A pdb=" N THR I 91 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL I 100 " --> pdb=" O THR I 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 20 through 23 Processing sheet with id=AA7, first strand: chain 'N' and resid 3 through 4 removed outlier: 3.835A pdb=" N GLN N 3 " --> pdb=" O SER N 26 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 22 through 23 removed outlier: 3.601A pdb=" N ALA N 80 " --> pdb=" O CYS N 23 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 46 through 49 Processing sheet with id=AB1, first strand: chain 'G' and resid 9 through 12 removed outlier: 3.688A pdb=" N ASP G 86 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N TYR G 50 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 9 through 12 removed outlier: 3.733A pdb=" N THR G 91 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL G 100 " --> pdb=" O THR G 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 20 through 23 Processing sheet with id=AB4, first strand: chain 'J' and resid 3 through 4 removed outlier: 3.835A pdb=" N GLN J 3 " --> pdb=" O SER J 26 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 22 through 23 removed outlier: 3.601A pdb=" N ALA J 80 " --> pdb=" O CYS J 23 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 46 through 49 Processing sheet with id=AB7, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.688A pdb=" N ASP F 86 " --> pdb=" O GLN F 39 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR F 50 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.733A pdb=" N THR F 91 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL F 100 " --> pdb=" O THR F 91 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 20 through 23 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.510A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.274A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B 205 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA B 263 " --> pdb=" O ALA B 67 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.585A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 101 through 104 removed outlier: 6.015A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 116 through 120 removed outlier: 6.402A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 317 removed outlier: 3.933A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.804A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 removed outlier: 4.010A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 553 through 554 removed outlier: 3.840A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.349A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.502A pdb=" N ALA B 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.870A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.235A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AD9, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AE1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE2, first strand: chain 'C' and resid 28 through 31 removed outlier: 7.848A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER C 205 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 28 through 31 Processing sheet with id=AE4, first strand: chain 'C' and resid 48 through 55 Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE6, first strand: chain 'C' and resid 101 through 104 removed outlier: 6.016A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 116 through 118 removed outlier: 6.403A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.843A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.847A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AF2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF3, first strand: chain 'C' and resid 473 through 474 removed outlier: 4.010A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.388A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.844A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.166A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF8, first strand: chain 'C' and resid 787 through 789 removed outlier: 5.660A pdb=" N ILE C 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.768A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.095A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 205 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.192A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'A' and resid 69 through 70 Processing sheet with id=AG4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AG5, first strand: chain 'A' and resid 101 through 104 removed outlier: 6.015A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'A' and resid 116 through 120 removed outlier: 6.403A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.841A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.685A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AH1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AH2, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.009A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.389A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.848A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.169A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AH7, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.769A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AH9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.550A pdb=" N THR H 113 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'L' and resid 4 through 7 removed outlier: 11.870A pdb=" N CYS L 23 " --> pdb=" O THR L 74 " (cutoff:3.500A) removed outlier: 10.398A pdb=" N THR L 74 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 11.550A pdb=" N ALA L 25 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 11.278A pdb=" N THR L 72 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.345A pdb=" N GLN L 27 " --> pdb=" O ASP L 70 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ASP L 70 " --> pdb=" O GLN L 27 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.605A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AI4, first strand: chain 'M' and resid 10 through 12 removed outlier: 3.550A pdb=" N THR M 113 " --> pdb=" O TYR M 94 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'R' and resid 4 through 7 removed outlier: 11.871A pdb=" N CYS R 23 " --> pdb=" O THR R 74 " (cutoff:3.500A) removed outlier: 10.398A pdb=" N THR R 74 " --> pdb=" O CYS R 23 " (cutoff:3.500A) removed outlier: 11.551A pdb=" N ALA R 25 " --> pdb=" O THR R 72 " (cutoff:3.500A) removed outlier: 11.278A pdb=" N THR R 72 " --> pdb=" O ALA R 25 " (cutoff:3.500A) removed outlier: 10.345A pdb=" N GLN R 27 " --> pdb=" O ASP R 70 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASP R 70 " --> pdb=" O GLN R 27 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'R' and resid 10 through 13 removed outlier: 3.606A pdb=" N GLU R 105 " --> pdb=" O LEU R 11 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N TRP R 35 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'O' and resid 3 through 6 Processing sheet with id=AI8, first strand: chain 'O' and resid 10 through 12 removed outlier: 3.550A pdb=" N THR O 113 " --> pdb=" O TYR O 94 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET O 34 " --> pdb=" O VAL O 50 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'S' and resid 4 through 7 removed outlier: 11.870A pdb=" N CYS S 23 " --> pdb=" O THR S 74 " (cutoff:3.500A) removed outlier: 10.397A pdb=" N THR S 74 " --> pdb=" O CYS S 23 " (cutoff:3.500A) removed outlier: 11.551A pdb=" N ALA S 25 " --> pdb=" O THR S 72 " (cutoff:3.500A) removed outlier: 11.278A pdb=" N THR S 72 " --> pdb=" O ALA S 25 " (cutoff:3.500A) removed outlier: 10.345A pdb=" N GLN S 27 " --> pdb=" O ASP S 70 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASP S 70 " --> pdb=" O GLN S 27 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'S' and resid 10 through 13 removed outlier: 3.606A pdb=" N GLU S 105 " --> pdb=" O LEU S 11 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N TRP S 35 " --> pdb=" O LEU S 47 " (cutoff:3.500A) 1186 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: 11.00 Time building geometry restraints manager: 4.03 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: 8578 1.33 - 1.45: 9288 1.45 - 1.58: 18848 1.58 - 1.70: 0 1.70 - 1.83: 213 Bond restraints: 36927 Sorted by residual: bond pdb=" CA SER B 60 " pdb=" CB SER B 60 " ideal model delta sigma weight residual 1.533 1.476 0.058 1.51e-02 4.39e+03 1.45e+01 bond pdb=" N THR B 588 " pdb=" CA THR B 588 " ideal model delta sigma weight residual 1.456 1.493 -0.037 9.80e-03 1.04e+04 1.42e+01 bond pdb=" N LEU B 24 " pdb=" CA LEU B 24 " ideal model delta sigma weight residual 1.455 1.490 -0.035 9.60e-03 1.09e+04 1.35e+01 bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.337 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.337 0.069 2.00e-02 2.50e+03 1.18e+01 ... (remaining 36922 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 47657 2.25 - 4.50: 2275 4.50 - 6.75: 234 6.75 - 9.00: 42 9.00 - 11.25: 9 Bond angle restraints: 50217 Sorted by residual: angle pdb=" N ILE B 100 " pdb=" CA ILE B 100 " pdb=" C ILE B 100 " ideal model delta sigma weight residual 113.20 102.84 10.36 9.60e-01 1.09e+00 1.16e+02 angle pdb=" N ILE A 100 " pdb=" CA ILE A 100 " pdb=" C ILE A 100 " ideal model delta sigma weight residual 113.20 102.87 10.33 9.60e-01 1.09e+00 1.16e+02 angle pdb=" N CYS C 301 " pdb=" CA CYS C 301 " pdb=" C CYS C 301 " ideal model delta sigma weight residual 113.23 102.37 10.86 1.24e+00 6.50e-01 7.67e+01 angle pdb=" CA GLY A 283 " pdb=" C GLY A 283 " pdb=" O GLY A 283 " ideal model delta sigma weight residual 122.56 116.28 6.28 1.03e+00 9.43e-01 3.72e+01 angle pdb=" C ASP N 110 " pdb=" CA ASP N 110 " pdb=" CB ASP N 110 " ideal model delta sigma weight residual 110.17 121.42 -11.25 1.97e+00 2.58e-01 3.26e+01 ... (remaining 50212 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 20644 16.86 - 33.71: 718 33.71 - 50.57: 146 50.57 - 67.43: 33 67.43 - 84.28: 21 Dihedral angle restraints: 21562 sinusoidal: 8290 harmonic: 13272 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -158.99 72.99 1 1.00e+01 1.00e-02 6.79e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -158.92 72.92 1 1.00e+01 1.00e-02 6.78e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -158.28 72.28 1 1.00e+01 1.00e-02 6.68e+01 ... (remaining 21559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.315: 5783 0.315 - 0.631: 11 0.631 - 0.946: 0 0.946 - 1.261: 0 1.261 - 1.577: 2 Chirality restraints: 5796 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.82 -1.58 2.00e-01 2.50e+01 6.21e+01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.00 -1.40 2.00e-01 2.50e+01 4.89e+01 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 2.10e+01 ... (remaining 5793 not shown) Planarity restraints: 6449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 1 " -0.333 2.00e-02 2.50e+03 2.81e-01 9.88e+02 pdb=" C7 NAG T 1 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG T 1 " -0.188 2.00e-02 2.50e+03 pdb=" N2 NAG T 1 " 0.489 2.00e-02 2.50e+03 pdb=" O7 NAG T 1 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Y 1 " 0.262 2.00e-02 2.50e+03 2.23e-01 6.24e+02 pdb=" C7 NAG Y 1 " -0.056 2.00e-02 2.50e+03 pdb=" C8 NAG Y 1 " -0.027 2.00e-02 2.50e+03 pdb=" N2 NAG Y 1 " -0.373 2.00e-02 2.50e+03 pdb=" O7 NAG Y 1 " 0.195 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " 0.019 2.00e-02 2.50e+03 1.16e-01 1.67e+02 pdb=" CG ASN B 234 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " -0.119 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " 0.192 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.121 2.00e-02 2.50e+03 ... (remaining 6446 not shown) Histogram of nonbonded interaction distances: 1.09 - 1.85: 7 1.85 - 2.61: 617 2.61 - 3.38: 48580 3.38 - 4.14: 88172 4.14 - 4.90: 156749 Nonbonded interactions: 294125 Sorted by model distance: nonbonded pdb=" O PRO B 527 " pdb=" CG LYS B 529 " model vdw 1.089 3.440 nonbonded pdb=" CD2 LEU A 48 " pdb=" CE2 PHE A 306 " model vdw 1.462 3.760 nonbonded pdb=" CB PRO B 527 " pdb=" CD LYS B 529 " model vdw 1.635 3.840 nonbonded pdb=" O PRO A 527 " pdb=" CG LYS A 529 " model vdw 1.741 3.440 nonbonded pdb=" OD1 ASP P 110 " pdb=" CD PRO P 111 " model vdw 1.753 3.440 ... (remaining 294120 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 14 through 20 or (resid 21 and (name N or name CA or name \ C or name O or name CB )) or resid 22 through 328 or resid 334 through 527 or re \ sid 531 through 698 or (resid 699 and (name N or name CA or name C or name O or \ name CB )) or resid 700 through 1305)) selection = (chain 'B' and (resid 14 through 20 or (resid 21 and (name N or name CA or name \ C or name O or name CB )) or resid 22 through 328 or resid 334 through 527 or re \ sid 531 through 1305)) selection = (chain 'C' and (resid 14 through 698 or (resid 699 and (name N or name CA or nam \ e C or name O or name CB )) or resid 700 through 1305)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'K' selection = chain 'Q' 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 'F' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'J' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'R' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.740 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 36.570 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5589 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 : 0.008 0.393 37023 Z= 0.460 Angle : 1.077 25.668 50454 Z= 0.649 Chirality : 0.069 1.577 5796 Planarity : 0.008 0.281 6419 Dihedral : 9.808 84.285 12909 Min Nonbonded Distance : 1.089 Molprobity Statistics. All-atom Clashscore : 21.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.49 % Favored : 92.44 % Rotamer: Outliers : 0.25 % Allowed : 1.58 % Favored : 98.17 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -3.61 (0.10), residues: 4526 helix: -3.25 (0.15), residues: 598 sheet: -2.11 (0.14), residues: 1047 loop : -2.41 (0.09), residues: 2881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG S 61 TYR 0.030 0.003 TYR M 94 PHE 0.035 0.003 PHE C 392 TRP 0.026 0.003 TRP H 47 HIS 0.011 0.002 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00797 / 0.44 (36927) covalent geometry : angle 1.05204 / 0.64 (50217) SS BOND : bond 0.01210 / 0.84 ( 51) SS BOND : angle 1.53182 / 0.98 ( 102) hydrogen bonds : bond 0.25836 / 17.08 ( 1167) hydrogen bonds : angle 11.69153 / 8.12 ( 3108) link_BETA1-4 : bond 0.00738 / 0.51 ( 15) link_BETA1-4 : angle 3.22162 / 2.03 ( 45) link_NAG-ASN : bond 0.10121 / 6.40 ( 30) link_NAG-ASN : angle 4.93100 / 3.20 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 379 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 THR cc_start: 0.7795 (p) cc_final: 0.7187 (p) REVERT: B 287 ASP cc_start: 0.6680 (t0) cc_final: 0.6130 (m-30) REVERT: C 52 GLN cc_start: 0.7811 (pt0) cc_final: 0.7458 (pp30) REVERT: A 66 HIS cc_start: 0.4870 (m-70) cc_final: 0.4425 (m-70) outliers start: 10 outliers final: 3 residues processed: 389 average time/residue: 0.2411 time to fit residues: 148.8102 Evaluate side-chains 164 residues out of total 3953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 161 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 524 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 0.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 50.0000 chunk 424 optimal weight: 20.0000 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 GLN I 6 GLN ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN ** N 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 GLN F 6 GLN B 61 ASN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 282 ASN B 317 ASN B 354 ASN B 498 GLN B 501 ASN B 556 ASN B 655 HIS ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN B 935 GLN B1010 GLN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN C 498 GLN C 501 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C1101 HIS ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN A 234 ASN A 239 GLN A 498 GLN A 501 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A1002 GLN H 84 ASN H 104 ASN L 38 GLN L 55 GLN M 84 ASN M 104 ASN R 38 GLN R 55 GLN O 84 ASN O 104 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.131220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.097031 restraints weight = 159598.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.098478 restraints weight = 88331.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.098943 restraints weight = 52276.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.099314 restraints weight = 38329.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.099585 restraints weight = 32480.221| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 37023 Z= 0.171 Angle : 0.725 16.356 50454 Z= 0.371 Chirality : 0.048 0.613 5796 Planarity : 0.005 0.052 6419 Dihedral : 6.369 31.390 4933 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.02 % Favored : 94.92 % Rotamer: Outliers : 1.55 % Allowed : 5.50 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.62 (0.11), residues: 4526 helix: -0.96 (0.18), residues: 647 sheet: -1.65 (0.14), residues: 1108 loop : -2.02 (0.10), residues: 2771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 328 TYR 0.028 0.002 TYR B 421 PHE 0.030 0.002 PHE B 643 TRP 0.025 0.002 TRP B 64 HIS 0.007 0.002 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 (36927) covalent geometry : angle 0.70889 / 0.37 (50217) SS BOND : bond 0.00376 / 0.21 ( 51) SS BOND : angle 1.00646 / 0.66 ( 102) hydrogen bonds : bond 0.05205 / 3.40 ( 1167) hydrogen bonds : angle 8.00354 / 5.51 ( 3108) link_BETA1-4 : bond 0.00536 / 0.39 ( 15) link_BETA1-4 : angle 2.22791 / 1.44 ( 45) link_NAG-ASN : bond 0.00495 / 0.33 ( 30) link_NAG-ASN : angle 3.23067 / 2.14 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 209 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 20 ARG cc_start: 0.7716 (mtm-85) cc_final: 0.7083 (tmm160) REVERT: P 60 MET cc_start: 0.7646 (ttm) cc_final: 0.7392 (ptm) REVERT: N 20 ARG cc_start: 0.7563 (mtm-85) cc_final: 0.6834 (tmm160) REVERT: N 49 MET cc_start: 0.5713 (tpp) cc_final: 0.5345 (ptt) REVERT: J 20 ARG cc_start: 0.7859 (mtm-85) cc_final: 0.7084 (tmm160) REVERT: J 49 MET cc_start: 0.5814 (tpp) cc_final: 0.5039 (ptt) REVERT: B 53 ASP cc_start: 0.6963 (OUTLIER) cc_final: 0.6664 (m-30) REVERT: B 221 SER cc_start: 0.7119 (m) cc_final: 0.6754 (p) REVERT: B 237 ARG cc_start: 0.7043 (ptt180) cc_final: 0.6063 (ptm-80) REVERT: C 51 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8064 (p) REVERT: C 64 TRP cc_start: 0.7932 (t60) cc_final: 0.7512 (t60) REVERT: C 221 SER cc_start: 0.7054 (m) cc_final: 0.6574 (p) REVERT: C 237 ARG cc_start: 0.6845 (ttp-110) cc_final: 0.6528 (ptt180) REVERT: C 1089 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.7431 (m-10) REVERT: A 52 GLN cc_start: 0.7983 (pm20) cc_final: 0.7749 (pp30) REVERT: A 53 ASP cc_start: 0.6819 (OUTLIER) cc_final: 0.6618 (m-30) REVERT: A 64 TRP cc_start: 0.8004 (t60) cc_final: 0.7689 (t60) REVERT: H 103 MET cc_start: 0.3707 (OUTLIER) cc_final: 0.3218 (tpp) outliers start: 61 outliers final: 32 residues processed: 257 average time/residue: 0.2220 time to fit residues: 94.2871 Evaluate side-chains 176 residues out of total 3953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain S residue 63 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 210 optimal weight: 8.9990 chunk 203 optimal weight: 8.9990 chunk 349 optimal weight: 1.9990 chunk 384 optimal weight: 5.9990 chunk 291 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 165 optimal weight: 4.9990 chunk 397 optimal weight: 30.0000 chunk 407 optimal weight: 0.5980 chunk 164 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 354 ASN B 901 GLN B 935 GLN B1002 GLN C 87 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 ASN C 354 ASN C 655 HIS ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN S 55 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.129499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.094094 restraints weight = 157710.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.094768 restraints weight = 86256.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.095286 restraints weight = 50615.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.095827 restraints weight = 37325.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.096669 restraints weight = 29866.737| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 37023 Z= 0.175 Angle : 0.669 15.407 50454 Z= 0.338 Chirality : 0.046 0.545 5796 Planarity : 0.004 0.062 6419 Dihedral : 5.659 25.030 4932 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.88 % Favored : 95.05 % Rotamer: Outliers : 1.55 % Allowed : 7.23 % Favored : 91.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.02 % 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: -2.08 (0.12), residues: 4526 helix: 0.10 (0.20), residues: 669 sheet: -1.36 (0.14), residues: 1220 loop : -1.82 (0.11), residues: 2637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1107 TYR 0.023 0.002 TYR B 421 PHE 0.024 0.002 PHE B 86 TRP 0.028 0.002 TRP B 64 HIS 0.010 0.002 HIS C 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 (36927) covalent geometry : angle 0.65250 / 0.33 (50217) SS BOND : bond 0.00260 / 0.15 ( 51) SS BOND : angle 0.90873 / 0.61 ( 102) hydrogen bonds : bond 0.04367 / 2.86 ( 1167) hydrogen bonds : angle 7.11195 / 4.91 ( 3108) link_BETA1-4 : bond 0.00620 / 0.49 ( 15) link_BETA1-4 : angle 2.35116 / 1.56 ( 45) link_NAG-ASN : bond 0.00631 / 0.40 ( 30) link_NAG-ASN : angle 3.09331 / 2.05 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 163 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 60 MET cc_start: 0.7671 (ttm) cc_final: 0.7283 (ptm) REVERT: J 49 MET cc_start: 0.5806 (OUTLIER) cc_final: 0.5221 (ptt) REVERT: J 112 TRP cc_start: 0.7891 (p90) cc_final: 0.7547 (p90) REVERT: B 52 GLN cc_start: 0.7592 (pp30) cc_final: 0.7371 (pp30) REVERT: B 221 SER cc_start: 0.7471 (m) cc_final: 0.6833 (p) REVERT: C 64 TRP cc_start: 0.8044 (t60) cc_final: 0.7505 (t60) REVERT: C 221 SER cc_start: 0.7475 (m) cc_final: 0.6876 (p) REVERT: C 237 ARG cc_start: 0.6886 (ttp-110) cc_final: 0.6627 (ptp-110) REVERT: A 64 TRP cc_start: 0.7912 (t60) cc_final: 0.7583 (t60) REVERT: A 170 TYR cc_start: 0.7141 (t80) cc_final: 0.6895 (t80) REVERT: A 900 MET cc_start: 0.7389 (mtp) cc_final: 0.7180 (mtp) REVERT: H 103 MET cc_start: 0.3683 (OUTLIER) cc_final: 0.3185 (tpp) outliers start: 61 outliers final: 30 residues processed: 213 average time/residue: 0.2128 time to fit residues: 76.5160 Evaluate side-chains 167 residues out of total 3953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain S residue 63 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 60 optimal weight: 0.0000 chunk 364 optimal weight: 2.9990 chunk 199 optimal weight: 0.5980 chunk 198 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 250 optimal weight: 0.0980 chunk 111 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 chunk 49 optimal weight: 0.3980 chunk 196 optimal weight: 2.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 7 GLN ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.130024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.094291 restraints weight = 156968.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.096864 restraints weight = 85065.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.096783 restraints weight = 48044.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.096838 restraints weight = 44315.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.096997 restraints weight = 43781.558| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 37023 Z= 0.116 Angle : 0.604 14.465 50454 Z= 0.302 Chirality : 0.044 0.504 5796 Planarity : 0.004 0.064 6419 Dihedral : 5.196 26.059 4932 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.02 % Favored : 94.90 % Rotamer: Outliers : 1.45 % Allowed : 7.76 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.02 % 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: -1.78 (0.12), residues: 4526 helix: 0.50 (0.20), residues: 668 sheet: -1.13 (0.14), residues: 1245 loop : -1.69 (0.11), residues: 2613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 646 TYR 0.014 0.001 TYR B 421 PHE 0.021 0.001 PHE A 86 TRP 0.013 0.001 TRP B 64 HIS 0.008 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (36927) covalent geometry : angle 0.58802 / 0.30 (50217) SS BOND : bond 0.00316 / 0.16 ( 51) SS BOND : angle 1.10162 / 0.75 ( 102) hydrogen bonds : bond 0.03717 / 2.44 ( 1167) hydrogen bonds : angle 6.53139 / 4.52 ( 3108) link_BETA1-4 : bond 0.00572 / 0.45 ( 15) link_BETA1-4 : angle 2.17179 / 1.45 ( 45) link_NAG-ASN : bond 0.00449 / 0.29 ( 30) link_NAG-ASN : angle 2.79829 / 1.88 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 3953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 153 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 35 MET cc_start: 0.1983 (ttm) cc_final: 0.1639 (mmm) REVERT: N 112 TRP cc_start: 0.8301 (p90) cc_final: 0.7987 (p90) REVERT: J 49 MET cc_start: 0.5610 (OUTLIER) cc_final: 0.5069 (ptt) REVERT: J 71 MET cc_start: 0.2353 (mtt) cc_final: 0.1986 (mtt) REVERT: J 112 TRP cc_start: 0.8108 (p90) cc_final: 0.7734 (p90) REVERT: B 221 SER cc_start: 0.7517 (m) cc_final: 0.6994 (p) REVERT: B 237 ARG cc_start: 0.7172 (ptt180) cc_final: 0.6425 (ptt90) REVERT: B 239 GLN cc_start: 0.6216 (tt0) cc_final: 0.5347 (tp40) REVERT: C 64 TRP cc_start: 0.8027 (t60) cc_final: 0.7516 (t60) REVERT: C 221 SER cc_start: 0.7375 (m) cc_final: 0.6839 (p) REVERT: C 237 ARG cc_start: 0.6948 (ttp-110) cc_final: 0.6384 (ptp-110) REVERT: C 239 GLN cc_start: 0.6433 (tt0) cc_final: 0.5485 (tp40) REVERT: C 1089 PHE cc_start: 0.7778 (OUTLIER) cc_final: 0.7430 (m-80) REVERT: A 170 TYR cc_start: 0.7197 (t80) cc_final: 0.6841 (t80) REVERT: A 239 GLN cc_start: 0.6311 (tt0) cc_final: 0.5603 (tp40) REVERT: A 855 PHE cc_start: 0.7509 (m-80) cc_final: 0.7243 (m-10) REVERT: H 103 MET cc_start: 0.3156 (OUTLIER) cc_final: 0.2786 (tpp) outliers start: 57 outliers final: 31 residues processed: 202 average time/residue: 0.2035 time to fit residues: 69.8466 Evaluate side-chains 162 residues out of total 3953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 299 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain S residue 63 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 200 optimal weight: 1.9990 chunk 202 optimal weight: 0.8980 chunk 227 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 228 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 52 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 762 GLN C 901 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN A 655 HIS A 762 GLN ** A 913 GLN ** 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 = 0.4523 r_free = 0.4523 target = 0.132099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.100636 restraints weight = 153932.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.102732 restraints weight = 78979.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.103197 restraints weight = 47936.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.103598 restraints weight = 50839.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.103666 restraints weight = 40754.558| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 37023 Z= 0.211 Angle : 0.674 14.395 50454 Z= 0.338 Chirality : 0.046 0.398 5796 Planarity : 0.004 0.072 6419 Dihedral : 5.241 24.557 4931 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.15 % Favored : 94.76 % Rotamer: Outliers : 2.01 % Allowed : 7.99 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.02 % 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: -1.75 (0.12), residues: 4526 helix: 0.53 (0.20), residues: 687 sheet: -1.22 (0.14), residues: 1300 loop : -1.61 (0.11), residues: 2539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 328 TYR 0.029 0.002 TYR C 144 PHE 0.020 0.002 PHE B 201 TRP 0.055 0.002 TRP C 152 HIS 0.008 0.002 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.21 (36927) covalent geometry : angle 0.65785 / 0.33 (50217) SS BOND : bond 0.00281 / 0.15 ( 51) SS BOND : angle 1.20896 / 0.72 ( 102) hydrogen bonds : bond 0.04031 / 2.65 ( 1167) hydrogen bonds : angle 6.46235 / 4.47 ( 3108) link_BETA1-4 : bond 0.00527 / 0.36 ( 15) link_BETA1-4 : angle 2.26405 / 1.51 ( 45) link_NAG-ASN : bond 0.00707 / 0.45 ( 30) link_NAG-ASN : angle 2.95585 / 1.96 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 142 time to evaluate : 1.138 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: P 49 MET cc_start: 0.5628 (tpp) cc_final: 0.5392 (ptt) REVERT: P 110 ASP cc_start: 0.1201 (OUTLIER) cc_final: 0.0923 (t0) REVERT: N 35 MET cc_start: 0.1824 (ttm) cc_final: 0.1582 (mmm) REVERT: N 112 TRP cc_start: 0.7594 (p90) cc_final: 0.7223 (p90) REVERT: J 49 MET cc_start: 0.5570 (OUTLIER) cc_final: 0.5281 (ptt) REVERT: J 71 MET cc_start: 0.0906 (mtt) cc_final: 0.0663 (mtt) REVERT: F 28 ASN cc_start: 0.4724 (OUTLIER) cc_final: 0.4435 (t0) REVERT: B 86 PHE cc_start: 0.6558 (t80) cc_final: 0.6167 (t80) REVERT: B 153 MET cc_start: 0.6022 (ptp) cc_final: 0.5772 (ptp) REVERT: B 221 SER cc_start: 0.7524 (m) cc_final: 0.7016 (p) REVERT: B 237 ARG cc_start: 0.7518 (ptt180) cc_final: 0.6866 (ptt90) REVERT: B 906 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7324 (m-10) REVERT: C 86 PHE cc_start: 0.6345 (t80) cc_final: 0.5958 (t80) REVERT: C 221 SER cc_start: 0.7437 (m) cc_final: 0.6963 (p) REVERT: C 237 ARG cc_start: 0.7089 (ttp-110) cc_final: 0.6762 (ptp-110) REVERT: C 1089 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7868 (m-10) REVERT: A 64 TRP cc_start: 0.8000 (t60) cc_final: 0.7743 (t60) REVERT: A 66 HIS cc_start: 0.7610 (OUTLIER) cc_final: 0.7224 (m-70) REVERT: A 152 TRP cc_start: 0.6479 (m100) cc_final: 0.6131 (t-100) REVERT: H 103 MET cc_start: 0.3758 (OUTLIER) cc_final: 0.3047 (tpp) outliers start: 79 outliers final: 47 residues processed: 214 average time/residue: 0.2026 time to fit residues: 73.5630 Evaluate side-chains 173 residues out of total 3953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 119 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 82 MET Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain S residue 63 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 159 optimal weight: 5.9990 chunk 116 optimal weight: 0.4980 chunk 259 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 312 optimal weight: 2.9990 chunk 3 optimal weight: 50.0000 chunk 68 optimal weight: 2.9990 chunk 326 optimal weight: 20.0000 chunk 387 optimal weight: 50.0000 chunk 361 optimal weight: 3.9990 chunk 347 optimal weight: 3.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 28 ASN ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 7 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS A 239 GLN A 641 ASN ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.129681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.093202 restraints weight = 133555.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.093370 restraints weight = 77870.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.093659 restraints weight = 51653.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.093952 restraints weight = 46805.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.093889 restraints weight = 40682.806| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 37023 Z= 0.189 Angle : 0.617 12.798 50454 Z= 0.312 Chirality : 0.045 0.363 5796 Planarity : 0.004 0.066 6419 Dihedral : 5.083 24.675 4931 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.35 % Favored : 94.56 % Rotamer: Outliers : 1.88 % Allowed : 8.32 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.02 % 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: -1.65 (0.12), residues: 4526 helix: 0.57 (0.20), residues: 684 sheet: -1.18 (0.14), residues: 1219 loop : -1.53 (0.11), residues: 2623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 78 TYR 0.031 0.001 TYR A 170 PHE 0.020 0.002 PHE B 855 TRP 0.044 0.002 TRP C 152 HIS 0.009 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 (36927) covalent geometry : angle 0.60211 / 0.31 (50217) SS BOND : bond 0.00323 / 0.21 ( 51) SS BOND : angle 1.46321 / 1.00 ( 102) hydrogen bonds : bond 0.03784 / 2.50 ( 1167) hydrogen bonds : angle 6.28337 / 4.37 ( 3108) link_BETA1-4 : bond 0.00521 / 0.40 ( 15) link_BETA1-4 : angle 2.08142 / 1.40 ( 45) link_NAG-ASN : bond 0.00528 / 0.34 ( 30) link_NAG-ASN : angle 2.59812 / 1.74 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 3953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 125 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 49 MET cc_start: 0.5783 (tpp) cc_final: 0.5427 (ptt) REVERT: P 110 ASP cc_start: 0.1360 (OUTLIER) cc_final: 0.1069 (t0) REVERT: N 112 TRP cc_start: 0.7815 (p90) cc_final: 0.7204 (p90) REVERT: G 76 ILE cc_start: -0.1802 (OUTLIER) cc_final: -0.2035 (mt) REVERT: J 49 MET cc_start: 0.5787 (OUTLIER) cc_final: 0.5363 (ptt) REVERT: J 71 MET cc_start: 0.0742 (mtt) cc_final: 0.0485 (mtt) REVERT: F 28 ASN cc_start: 0.4686 (OUTLIER) cc_final: 0.4406 (t0) REVERT: B 221 SER cc_start: 0.7273 (m) cc_final: 0.6911 (p) REVERT: B 531 THR cc_start: 0.8385 (OUTLIER) cc_final: 0.8097 (p) REVERT: C 221 SER cc_start: 0.7303 (m) cc_final: 0.6994 (p) REVERT: C 237 ARG cc_start: 0.7088 (ttp-110) cc_final: 0.6716 (ptp-110) REVERT: C 546 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7560 (pp) REVERT: C 794 ILE cc_start: 0.8206 (mp) cc_final: 0.7866 (tp) REVERT: C 1089 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7641 (m-80) REVERT: A 1002 GLN cc_start: 0.7544 (pt0) cc_final: 0.7244 (pt0) REVERT: A 1050 MET cc_start: 0.8005 (ptm) cc_final: 0.7687 (ptm) REVERT: H 103 MET cc_start: 0.3183 (OUTLIER) cc_final: 0.2509 (tmm) outliers start: 74 outliers final: 50 residues processed: 187 average time/residue: 0.1929 time to fit residues: 63.0149 Evaluate side-chains 166 residues out of total 3953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 108 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 82 MET Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain N residue 82 MET Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 28 ASN Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 152 TRP Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain S residue 63 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 319 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 chunk 113 optimal weight: 0.0270 chunk 327 optimal weight: 30.0000 chunk 103 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 292 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 274 optimal weight: 0.5980 chunk 262 optimal weight: 0.6980 chunk 433 optimal weight: 50.0000 overall best weight: 1.2642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B 955 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.132013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.100627 restraints weight = 154485.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.103143 restraints weight = 77552.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.103221 restraints weight = 45050.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.103454 restraints weight = 44824.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.103595 restraints weight = 40253.276| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 37023 Z= 0.120 Angle : 0.569 10.941 50454 Z= 0.287 Chirality : 0.044 0.354 5796 Planarity : 0.004 0.064 6419 Dihedral : 4.798 22.546 4931 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.77 % Favored : 95.14 % Rotamer: Outliers : 1.76 % Allowed : 8.60 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.02 % 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: -1.44 (0.12), residues: 4526 helix: 0.79 (0.20), residues: 689 sheet: -1.01 (0.14), residues: 1246 loop : -1.42 (0.11), residues: 2591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 78 TYR 0.023 0.001 TYR A 170 PHE 0.020 0.001 PHE N 109 TRP 0.046 0.001 TRP B 152 HIS 0.006 0.001 HIS B 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (36927) covalent geometry : angle 0.55428 / 0.28 (50217) SS BOND : bond 0.00388 / 0.18 ( 51) SS BOND : angle 1.44776 / 1.01 ( 102) hydrogen bonds : bond 0.03479 / 2.28 ( 1167) hydrogen bonds : angle 6.03584 / 4.19 ( 3108) link_BETA1-4 : bond 0.00537 / 0.41 ( 15) link_BETA1-4 : angle 2.04697 / 1.38 ( 45) link_NAG-ASN : bond 0.00468 / 0.30 ( 30) link_NAG-ASN : angle 2.39218 / 1.62 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 120 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 49 MET cc_start: 0.5787 (tpp) cc_final: 0.5451 (ptt) REVERT: P 110 ASP cc_start: 0.1503 (OUTLIER) cc_final: 0.1202 (t0) REVERT: N 49 MET cc_start: 0.5784 (tpp) cc_final: 0.5561 (ptm) REVERT: N 112 TRP cc_start: 0.7545 (p90) cc_final: 0.6951 (p90) REVERT: G 76 ILE cc_start: -0.1827 (OUTLIER) cc_final: -0.2090 (mt) REVERT: J 49 MET cc_start: 0.5939 (OUTLIER) cc_final: 0.5581 (ptt) REVERT: B 221 SER cc_start: 0.7252 (m) cc_final: 0.6905 (p) REVERT: B 239 GLN cc_start: 0.6468 (tt0) cc_final: 0.5882 (tt0) REVERT: B 531 THR cc_start: 0.8394 (OUTLIER) cc_final: 0.8059 (p) REVERT: B 906 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.7296 (m-10) REVERT: C 221 SER cc_start: 0.7417 (m) cc_final: 0.7071 (p) REVERT: C 237 ARG cc_start: 0.7067 (ttp-110) cc_final: 0.6662 (ptp-110) REVERT: C 794 ILE cc_start: 0.8267 (mp) cc_final: 0.7930 (tp) REVERT: C 985 ASP cc_start: 0.7571 (t70) cc_final: 0.7034 (m-30) REVERT: C 1050 MET cc_start: 0.8070 (ptp) cc_final: 0.7810 (ptp) REVERT: C 1089 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7472 (m-80) REVERT: A 985 ASP cc_start: 0.7427 (t70) cc_final: 0.7016 (p0) REVERT: A 1002 GLN cc_start: 0.7685 (pt0) cc_final: 0.7338 (pt0) REVERT: H 103 MET cc_start: 0.3476 (OUTLIER) cc_final: 0.2827 (tmm) outliers start: 69 outliers final: 46 residues processed: 178 average time/residue: 0.1862 time to fit residues: 57.1423 Evaluate side-chains 165 residues out of total 3953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 112 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 82 MET Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain N residue 82 MET Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain S residue 63 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 157 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 222 optimal weight: 40.0000 chunk 117 optimal weight: 9.9990 chunk 211 optimal weight: 0.4980 chunk 10 optimal weight: 7.9990 chunk 283 optimal weight: 2.9990 chunk 29 optimal weight: 40.0000 chunk 53 optimal weight: 40.0000 chunk 49 optimal weight: 0.5980 chunk 36 optimal weight: 30.0000 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 52 ASN ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN A 234 ASN A 317 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.128037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.090142 restraints weight = 132954.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.090806 restraints weight = 79775.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.091063 restraints weight = 52292.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.091389 restraints weight = 48284.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.091305 restraints weight = 43072.152| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.5780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 37023 Z= 0.233 Angle : 0.650 12.601 50454 Z= 0.328 Chirality : 0.046 0.310 5796 Planarity : 0.004 0.072 6419 Dihedral : 5.098 23.304 4931 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.12 % Favored : 93.79 % Rotamer: Outliers : 2.04 % Allowed : 8.60 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.02 % 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: -1.50 (0.12), residues: 4526 helix: 0.74 (0.20), residues: 674 sheet: -1.05 (0.14), residues: 1266 loop : -1.44 (0.11), residues: 2586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 815 TYR 0.024 0.002 TYR B 269 PHE 0.048 0.002 PHE B 855 TRP 0.037 0.002 TRP C 152 HIS 0.009 0.002 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.23 (36927) covalent geometry : angle 0.63424 / 0.32 (50217) SS BOND : bond 0.00253 / 0.14 ( 51) SS BOND : angle 1.44008 / 0.95 ( 102) hydrogen bonds : bond 0.03968 / 2.62 ( 1167) hydrogen bonds : angle 6.25555 / 4.33 ( 3108) link_BETA1-4 : bond 0.00572 / 0.41 ( 15) link_BETA1-4 : angle 2.13274 / 1.45 ( 45) link_NAG-ASN : bond 0.00759 / 0.48 ( 30) link_NAG-ASN : angle 2.73039 / 1.82 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 123 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 49 MET cc_start: 0.5868 (tpp) cc_final: 0.5522 (ptt) REVERT: P 60 MET cc_start: 0.6286 (ptm) cc_final: 0.5963 (ptm) REVERT: P 110 ASP cc_start: 0.1797 (OUTLIER) cc_final: 0.1494 (t0) REVERT: N 49 MET cc_start: 0.5821 (tpp) cc_final: 0.5435 (ptm) REVERT: G 76 ILE cc_start: -0.1773 (OUTLIER) cc_final: -0.1991 (mt) REVERT: J 49 MET cc_start: 0.6045 (OUTLIER) cc_final: 0.5577 (ptt) REVERT: B 133 PHE cc_start: 0.6751 (m-80) cc_final: 0.6385 (m-80) REVERT: B 221 SER cc_start: 0.7346 (m) cc_final: 0.6938 (p) REVERT: B 239 GLN cc_start: 0.6711 (tt0) cc_final: 0.6346 (tt0) REVERT: B 531 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8151 (p) REVERT: C 78 ARG cc_start: 0.7176 (mmp-170) cc_final: 0.6770 (mmm160) REVERT: C 221 SER cc_start: 0.7678 (m) cc_final: 0.7295 (p) REVERT: C 237 ARG cc_start: 0.7332 (ttp-110) cc_final: 0.6828 (ptp-110) REVERT: C 239 GLN cc_start: 0.6892 (tt0) cc_final: 0.6510 (tt0) REVERT: C 276 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8723 (pp) REVERT: C 546 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7546 (pp) REVERT: C 1089 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.7942 (m-10) REVERT: A 86 PHE cc_start: 0.6578 (t80) cc_final: 0.6105 (t80) REVERT: A 307 THR cc_start: 0.8379 (m) cc_final: 0.8084 (t) REVERT: A 985 ASP cc_start: 0.7523 (t70) cc_final: 0.7070 (p0) REVERT: H 103 MET cc_start: 0.3049 (OUTLIER) cc_final: 0.2426 (tmm) outliers start: 80 outliers final: 54 residues processed: 190 average time/residue: 0.1854 time to fit residues: 61.0589 Evaluate side-chains 172 residues out of total 3953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 110 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 92 THR Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain N residue 82 MET Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain S residue 63 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 6 optimal weight: 0.0970 chunk 400 optimal weight: 7.9990 chunk 395 optimal weight: 8.9990 chunk 359 optimal weight: 4.9990 chunk 401 optimal weight: 6.9990 chunk 291 optimal weight: 7.9990 chunk 403 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 381 optimal weight: 1.9990 chunk 338 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 ASN M 105 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.128665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.090317 restraints weight = 128790.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.090971 restraints weight = 77456.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.091226 restraints weight = 54469.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.093342 restraints weight = 43278.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.092066 restraints weight = 39037.491| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.6108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.143 37023 Z= 0.232 Angle : 0.648 15.708 50454 Z= 0.327 Chirality : 0.045 0.302 5796 Planarity : 0.004 0.072 6419 Dihedral : 5.103 23.163 4931 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.63 % Favored : 94.26 % Rotamer: Outliers : 1.81 % Allowed : 8.93 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.02 % 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: -1.52 (0.12), residues: 4526 helix: 0.68 (0.20), residues: 679 sheet: -1.07 (0.14), residues: 1261 loop : -1.45 (0.11), residues: 2586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 328 TYR 0.023 0.002 TYR B 269 PHE 0.023 0.002 PHE B 855 TRP 0.045 0.002 TRP B 64 HIS 0.008 0.002 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.23 (36927) covalent geometry : angle 0.63028 / 0.32 (50217) SS BOND : bond 0.00280 / 0.15 ( 51) SS BOND : angle 2.11569 / 1.26 ( 102) hydrogen bonds : bond 0.03845 / 2.56 ( 1167) hydrogen bonds : angle 6.26427 / 4.35 ( 3108) link_BETA1-4 : bond 0.00528 / 0.38 ( 15) link_BETA1-4 : angle 2.06200 / 1.39 ( 45) link_NAG-ASN : bond 0.00673 / 0.43 ( 30) link_NAG-ASN : angle 2.57164 / 1.71 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 114 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 49 MET cc_start: 0.5905 (tpp) cc_final: 0.5593 (ptt) REVERT: P 60 MET cc_start: 0.6396 (ptm) cc_final: 0.6066 (ptm) REVERT: P 110 ASP cc_start: 0.1867 (OUTLIER) cc_final: 0.1560 (t0) REVERT: N 49 MET cc_start: 0.5802 (tpp) cc_final: 0.5488 (ptm) REVERT: G 76 ILE cc_start: -0.1799 (OUTLIER) cc_final: -0.2037 (mt) REVERT: J 49 MET cc_start: 0.6009 (OUTLIER) cc_final: 0.5620 (ptt) REVERT: B 221 SER cc_start: 0.7388 (m) cc_final: 0.6982 (p) REVERT: B 239 GLN cc_start: 0.6712 (tt0) cc_final: 0.6328 (tt0) REVERT: B 531 THR cc_start: 0.8426 (OUTLIER) cc_final: 0.8183 (p) REVERT: B 902 MET cc_start: 0.8698 (mmm) cc_final: 0.8485 (tpp) REVERT: B 906 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7552 (m-10) REVERT: C 221 SER cc_start: 0.7713 (m) cc_final: 0.7306 (p) REVERT: C 237 ARG cc_start: 0.7228 (ttp-110) cc_final: 0.6842 (ptp-110) REVERT: C 869 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7771 (mtm) REVERT: C 985 ASP cc_start: 0.7462 (t70) cc_final: 0.7181 (m-30) REVERT: C 1089 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7912 (m-10) REVERT: A 86 PHE cc_start: 0.6468 (t80) cc_final: 0.6071 (t80) REVERT: A 239 GLN cc_start: 0.6822 (tt0) cc_final: 0.6441 (tt0) REVERT: A 307 THR cc_start: 0.8420 (m) cc_final: 0.8146 (t) REVERT: A 985 ASP cc_start: 0.7491 (t70) cc_final: 0.7155 (p0) REVERT: H 103 MET cc_start: 0.2843 (OUTLIER) cc_final: 0.2221 (tmm) REVERT: M 34 MET cc_start: -0.0515 (ppp) cc_final: -0.1046 (ppp) outliers start: 71 outliers final: 57 residues processed: 173 average time/residue: 0.1870 time to fit residues: 56.3721 Evaluate side-chains 173 residues out of total 3953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 108 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain N residue 82 MET Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain J residue 49 MET Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 577 ARG Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain S residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 271 optimal weight: 0.7980 chunk 336 optimal weight: 2.9990 chunk 53 optimal weight: 40.0000 chunk 91 optimal weight: 0.9990 chunk 441 optimal weight: 7.9990 chunk 123 optimal weight: 0.0000 chunk 318 optimal weight: 7.9990 chunk 414 optimal weight: 30.0000 chunk 212 optimal weight: 30.0000 chunk 378 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 804 GLN B 935 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** 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 = 0.4502 r_free = 0.4502 target = 0.127086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.096152 restraints weight = 149592.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.097434 restraints weight = 82187.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.097654 restraints weight = 49787.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.098264 restraints weight = 49617.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.098338 restraints weight = 40476.845| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.6214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 37023 Z= 0.124 Angle : 0.575 11.958 50454 Z= 0.290 Chirality : 0.043 0.332 5796 Planarity : 0.004 0.094 6419 Dihedral : 4.810 22.201 4931 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.19 % Favored : 94.72 % Rotamer: Outliers : 1.40 % Allowed : 9.52 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.02 % 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: -1.30 (0.12), residues: 4526 helix: 0.97 (0.20), residues: 671 sheet: -0.93 (0.15), residues: 1242 loop : -1.33 (0.12), residues: 2613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 78 TYR 0.022 0.001 TYR A 170 PHE 0.044 0.002 PHE B 855 TRP 0.034 0.001 TRP B 64 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (36927) covalent geometry : angle 0.55883 / 0.29 (50217) SS BOND : bond 0.00195 / 0.12 ( 51) SS BOND : angle 1.78782 / 1.07 ( 102) hydrogen bonds : bond 0.03400 / 2.25 ( 1167) hydrogen bonds : angle 6.00237 / 4.16 ( 3108) link_BETA1-4 : bond 0.00511 / 0.39 ( 15) link_BETA1-4 : angle 1.97687 / 1.34 ( 45) link_NAG-ASN : bond 0.00482 / 0.31 ( 30) link_NAG-ASN : angle 2.33019 / 1.57 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9052 Ramachandran restraints generated. 4526 Oldfield, 0 Emsley, 4526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 3953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 118 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 49 MET cc_start: 0.5856 (tpp) cc_final: 0.5649 (ptt) REVERT: P 60 MET cc_start: 0.6635 (ptm) cc_final: 0.6252 (ptm) REVERT: P 110 ASP cc_start: 0.1520 (OUTLIER) cc_final: 0.1253 (t0) REVERT: N 112 TRP cc_start: 0.7487 (p90) cc_final: 0.7144 (p90) REVERT: G 76 ILE cc_start: -0.1853 (OUTLIER) cc_final: -0.2149 (mm) REVERT: F 76 ILE cc_start: -0.1750 (OUTLIER) cc_final: -0.2000 (mt) REVERT: B 64 TRP cc_start: 0.7993 (t60) cc_final: 0.7193 (t60) REVERT: B 221 SER cc_start: 0.7023 (m) cc_final: 0.6711 (p) REVERT: B 239 GLN cc_start: 0.6761 (tt0) cc_final: 0.6228 (tt0) REVERT: B 531 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8170 (p) REVERT: B 906 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7332 (m-10) REVERT: C 78 ARG cc_start: 0.7386 (mmp-170) cc_final: 0.6993 (tpp-160) REVERT: C 221 SER cc_start: 0.7542 (m) cc_final: 0.7190 (p) REVERT: C 237 ARG cc_start: 0.7146 (ttp-110) cc_final: 0.6683 (ptp-110) REVERT: C 239 GLN cc_start: 0.6661 (tt0) cc_final: 0.6155 (tt0) REVERT: C 985 ASP cc_start: 0.7656 (t70) cc_final: 0.7342 (m-30) REVERT: C 1089 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: A 86 PHE cc_start: 0.6168 (t80) cc_final: 0.5819 (t80) REVERT: A 239 GLN cc_start: 0.6956 (tt0) cc_final: 0.6542 (tt0) REVERT: A 307 THR cc_start: 0.8345 (m) cc_final: 0.8069 (t) REVERT: A 985 ASP cc_start: 0.7599 (t70) cc_final: 0.7108 (p0) REVERT: H 103 MET cc_start: 0.3608 (OUTLIER) cc_final: 0.2830 (tpp) REVERT: M 34 MET cc_start: -0.0096 (ppp) cc_final: -0.0807 (ppp) outliers start: 55 outliers final: 43 residues processed: 165 average time/residue: 0.1854 time to fit residues: 53.4688 Evaluate side-chains 160 residues out of total 3953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 110 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain N residue 60 MET Chi-restraints excluded: chain N residue 82 MET Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 816 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain H residue 103 MET Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain S residue 63 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 229 optimal weight: 5.9990 chunk 343 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 268 optimal weight: 0.7980 chunk 310 optimal weight: 3.9990 chunk 407 optimal weight: 0.5980 chunk 52 optimal weight: 30.0000 chunk 281 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 438 optimal weight: 30.0000 chunk 313 optimal weight: 40.0000 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.124576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.091697 restraints weight = 144815.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.092003 restraints weight = 84020.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.092188 restraints weight = 53112.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.092669 restraints weight = 50829.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.092709 restraints weight = 42907.719| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.6368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 37023 Z= 0.171 Angle : 0.597 9.908 50454 Z= 0.302 Chirality : 0.044 0.298 5796 Planarity : 0.004 0.097 6419 Dihedral : 4.827 27.516 4930 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.66 % Favored : 94.26 % Rotamer: Outliers : 1.42 % Allowed : 9.67 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.02 % 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: -1.33 (0.12), residues: 4526 helix: 0.95 (0.21), residues: 672 sheet: -0.89 (0.14), residues: 1253 loop : -1.39 (0.11), residues: 2601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 78 TYR 0.019 0.001 TYR A 145 PHE 0.021 0.002 PHE B 201 TRP 0.066 0.002 TRP B 64 HIS 0.008 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (36927) covalent geometry : angle 0.58178 / 0.30 (50217) SS BOND : bond 0.00225 / 0.13 ( 51) SS BOND : angle 1.58321 / 0.97 ( 102) hydrogen bonds : bond 0.03579 / 2.38 ( 1167) hydrogen bonds : angle 5.97848 / 4.15 ( 3108) link_BETA1-4 : bond 0.00552 / 0.42 ( 15) link_BETA1-4 : angle 2.01586 / 1.36 ( 45) link_NAG-ASN : bond 0.00563 / 0.36 ( 30) link_NAG-ASN : angle 2.44323 / 1.63 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7557.12 seconds wall clock time: 130 minutes 59.35 seconds (7859.35 seconds total)