Starting phenix.real_space_refine on Sat Feb 7 17:19:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v88_31793/02_2026/7v88_31793.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v88_31793/02_2026/7v88_31793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v88_31793/02_2026/7v88_31793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v88_31793/02_2026/7v88_31793.map" model { file = "/net/cci-nas-00/data/ceres_data/7v88_31793/02_2026/7v88_31793.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v88_31793/02_2026/7v88_31793.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.047 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 166 5.16 5 C 22330 2.51 5 N 5732 2.21 5 O 6870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35098 Number of models: 1 Model: "" Number of chains: 47 Chain: "A" Number of atoms: 8016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8016 Classifications: {'peptide': 1027} Link IDs: {'PTRANS': 53, 'TRANS': 973} Chain breaks: 7 Chain: "B" Number of atoms: 8077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8077 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 53, 'TRANS': 979} Chain breaks: 7 Chain: "C" Number of atoms: 8035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 8035 Classifications: {'peptide': 1029} Link IDs: {'PTRANS': 53, 'TRANS': 975} Chain breaks: 7 Chain: "F" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "G" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 9.54, per 1000 atoms: 0.27 Number of scatterers: 35098 At special positions: 0 Unit cell: (139.7, 155.1, 245.3, 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 166 16.00 O 6870 8.00 N 5732 7.00 C 22330 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 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 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.03 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " 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 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.04 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 523 " distance=2.03 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.03 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.02 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.02 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.03 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 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.03 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 536 " - pdb=" SG CYS C 588 " distance=2.03 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=2.03 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " distance=2.04 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " distance=2.03 Simple disulfide: pdb=" SG CYS G 133 " - pdb=" SG CYS G 141 " distance=2.03 Simple disulfide: pdb=" SG CYS G 344 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 530 " - pdb=" SG CYS G 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 601 " " NAG A2003 " - " ASN A 655 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 232 " " NAG B2003 " - " ASN B 329 " " NAG B2004 " - " ASN B 601 " " NAG B2005 " - " ASN B 655 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 601 " " NAG C2003 " - " ASN C 655 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 163 " " NAG F 901 " - " ASN F 103 " " NAG F 902 " - " ASN F 322 " " NAG G 901 " - " ASN G 90 " " NAG G 902 " - " ASN G 322 " " NAG H 1 " - " ASN A 232 " " NAG I 1 " - " ASN A 280 " " NAG J 1 " - " ASN A 329 " " NAG K 1 " - " ASN A 341 " " NAG L 1 " - " ASN A 614 " " NAG M 1 " - " ASN A 707 " " NAG N 1 " - " ASN A 715 " " NAG O 1 " - " ASN A 799 " " NAG P 1 " - " ASN A1072 " " NAG Q 1 " - " ASN A1096 " " NAG R 1 " - " ASN A1132 " " NAG S 1 " - " ASN B 122 " " NAG T 1 " - " ASN B 163 " " NAG U 1 " - " ASN B 280 " " NAG V 1 " - " ASN B 341 " " NAG W 1 " - " ASN B 614 " " NAG X 1 " - " ASN B 707 " " NAG Y 1 " - " ASN B 715 " " NAG Z 1 " - " ASN B 799 " " NAG a 1 " - " ASN B1072 " " NAG b 1 " - " ASN B1096 " " NAG c 1 " - " ASN B1132 " " NAG d 1 " - " ASN C 122 " " NAG e 1 " - " ASN C 163 " " NAG f 1 " - " ASN C 232 " " NAG g 1 " - " ASN C 280 " " NAG h 1 " - " ASN C 329 " " NAG i 1 " - " ASN C 341 " " NAG j 1 " - " ASN C 614 " " NAG k 1 " - " ASN C 707 " " NAG l 1 " - " ASN C 715 " " NAG m 1 " - " ASN C 799 " " NAG n 1 " - " ASN C1072 " " NAG o 1 " - " ASN C1096 " " NAG p 1 " - " ASN C1132 " Time building additional restraints: 3.91 Conformation dependent library (CDL) restraints added in 2.0 seconds 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8044 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 48 sheets defined 36.5% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 336 through 341 removed outlier: 3.520A pdb=" N PHE A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 362 through 368 removed outlier: 4.197A pdb=" N LEU A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 removed outlier: 3.993A pdb=" N ASN A 386 " --> pdb=" O PRO A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 removed outlier: 4.670A pdb=" N ARG A 406 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 408 " --> pdb=" O VAL A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 735 through 742 Processing helix chain 'A' and resid 744 through 752 Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 757 through 781 removed outlier: 3.917A pdb=" N LEU A 761 " --> pdb=" O PHE A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 824 removed outlier: 3.622A pdb=" N VAL A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 883 Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 895 through 908 removed outlier: 3.506A pdb=" N ILE A 907 " --> pdb=" O ARG A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 917 removed outlier: 3.505A pdb=" N TYR A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 939 Processing helix chain 'A' and resid 943 through 963 removed outlier: 3.500A pdb=" N GLN A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 980 removed outlier: 3.525A pdb=" N ILE A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1031 removed outlier: 4.889A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN A 990 " --> pdb=" O GLU A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1143 Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 347 through 351 removed outlier: 3.707A pdb=" N TRP B 351 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 369 removed outlier: 4.190A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 403 through 408 removed outlier: 4.363A pdb=" N ARG B 406 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B 408 " --> pdb=" O VAL B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 436 through 441 Processing helix chain 'B' and resid 566 through 570 removed outlier: 3.692A pdb=" N THR B 570 " --> pdb=" O ILE B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 741 Processing helix chain 'B' and resid 744 through 752 Processing helix chain 'B' and resid 756 through 781 removed outlier: 3.782A pdb=" N GLN B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.672A pdb=" N VAL B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.723A pdb=" N GLY B 883 " --> pdb=" O THR B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 895 through 906 Processing helix chain 'B' and resid 911 through 917 removed outlier: 3.724A pdb=" N TYR B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 916 " --> pdb=" O ASN B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 938 removed outlier: 3.541A pdb=" N ASP B 934 " --> pdb=" O GLY B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 963 Processing helix chain 'B' and resid 964 through 966 No H-bonds generated for 'chain 'B' and resid 964 through 966' Processing helix chain 'B' and resid 974 through 982 removed outlier: 3.531A pdb=" N ILE B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 982 " --> pdb=" O ILE B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1031 removed outlier: 4.650A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG B 993 " --> pdb=" O VAL B 989 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU B 994 " --> pdb=" O GLN B 990 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1116 No H-bonds generated for 'chain 'B' and resid 1114 through 1116' Processing helix chain 'B' and resid 1138 through 1144 removed outlier: 3.986A pdb=" N ASP B1144 " --> pdb=" O GLN B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 347 through 351 removed outlier: 3.615A pdb=" N TRP C 351 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 368 removed outlier: 4.403A pdb=" N LEU C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 386 removed outlier: 4.029A pdb=" N ASN C 386 " --> pdb=" O PRO C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.816A pdb=" N ARG C 406 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 436 through 441 Processing helix chain 'C' and resid 500 through 503 Processing helix chain 'C' and resid 735 through 741 Processing helix chain 'C' and resid 744 through 752 Processing helix chain 'C' and resid 753 through 755 No H-bonds generated for 'chain 'C' and resid 753 through 755' Processing helix chain 'C' and resid 758 through 781 removed outlier: 3.505A pdb=" N ASN C 762 " --> pdb=" O CYS C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 824 Processing helix chain 'C' and resid 864 through 883 removed outlier: 3.540A pdb=" N GLY C 883 " --> pdb=" O THR C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 Processing helix chain 'C' and resid 895 through 906 Processing helix chain 'C' and resid 910 through 939 removed outlier: 4.335A pdb=" N LEU C 914 " --> pdb=" O THR C 910 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS C 919 " --> pdb=" O TYR C 915 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU C 920 " --> pdb=" O GLU C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 963 Processing helix chain 'C' and resid 964 through 966 No H-bonds generated for 'chain 'C' and resid 964 through 966' Processing helix chain 'C' and resid 974 through 982 Processing helix chain 'C' and resid 983 through 1032 removed outlier: 5.426A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN C 990 " --> pdb=" O GLU C 986 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG C 993 " --> pdb=" O VAL C 989 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C 994 " --> pdb=" O GLN C 990 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C1032 " --> pdb=" O SER C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1144 removed outlier: 3.825A pdb=" N ASP C1144 " --> pdb=" O GLN C1140 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 53 removed outlier: 3.623A pdb=" N GLN F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU F 39 " --> pdb=" O GLU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 79 removed outlier: 3.519A pdb=" N VAL F 59 " --> pdb=" O THR F 55 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN F 76 " --> pdb=" O PHE F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 101 removed outlier: 3.536A pdb=" N ALA F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU F 100 " --> pdb=" O GLN F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 154 Processing helix chain 'F' and resid 158 through 172 removed outlier: 3.667A pdb=" N LEU F 162 " --> pdb=" O TYR F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 194 Processing helix chain 'F' and resid 198 through 205 removed outlier: 3.656A pdb=" N TYR F 202 " --> pdb=" O ASP F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 218 through 229 removed outlier: 3.963A pdb=" N LEU F 222 " --> pdb=" O SER F 218 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE F 223 " --> pdb=" O ARG F 219 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU F 227 " --> pdb=" O ILE F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 252 removed outlier: 3.656A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 300 Processing helix chain 'F' and resid 303 through 319 Processing helix chain 'F' and resid 326 through 331 Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.520A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.720A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 412 removed outlier: 4.120A pdb=" N HIS F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU F 402 " --> pdb=" O GLU F 398 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 473 through 484 removed outlier: 3.858A pdb=" N GLU F 483 " --> pdb=" O GLU F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 507 removed outlier: 3.738A pdb=" N SER F 507 " --> pdb=" O PHE F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 512 through 532 removed outlier: 3.813A pdb=" N TYR F 516 " --> pdb=" O PHE F 512 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.506A pdb=" N GLY F 551 " --> pdb=" O SER F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 564 removed outlier: 3.532A pdb=" N SER F 563 " --> pdb=" O LEU F 560 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU F 564 " --> pdb=" O GLY F 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 560 through 564' Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 581 through 588 removed outlier: 3.669A pdb=" N PHE F 588 " --> pdb=" O LEU F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 599 removed outlier: 3.786A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 53 removed outlier: 4.018A pdb=" N HIS G 34 " --> pdb=" O ASP G 30 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU G 35 " --> pdb=" O LYS G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 80 removed outlier: 3.519A pdb=" N VAL G 59 " --> pdb=" O THR G 55 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN G 60 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU G 75 " --> pdb=" O ALA G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 101 Processing helix chain 'G' and resid 109 through 129 Processing helix chain 'G' and resid 147 through 154 Processing helix chain 'G' and resid 158 through 194 removed outlier: 3.793A pdb=" N LYS G 174 " --> pdb=" O SER G 170 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN G 175 " --> pdb=" O GLU G 171 " (cutoff:3.500A) Proline residue: G 178 - end of helix Processing helix chain 'G' and resid 198 through 204 Processing helix chain 'G' and resid 218 through 231 removed outlier: 3.567A pdb=" N LEU G 222 " --> pdb=" O SER G 218 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE G 223 " --> pdb=" O ARG G 219 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU G 227 " --> pdb=" O ILE G 223 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS G 228 " --> pdb=" O GLU G 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 252 Processing helix chain 'G' and resid 275 through 279 Processing helix chain 'G' and resid 293 through 300 Processing helix chain 'G' and resid 303 through 319 Processing helix chain 'G' and resid 326 through 331 Processing helix chain 'G' and resid 365 through 386 Processing helix chain 'G' and resid 387 through 388 No H-bonds generated for 'chain 'G' and resid 387 through 388' Processing helix chain 'G' and resid 389 through 393 Processing helix chain 'G' and resid 399 through 412 removed outlier: 3.798A pdb=" N MET G 408 " --> pdb=" O VAL G 404 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER G 409 " --> pdb=" O GLY G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 421 removed outlier: 3.784A pdb=" N ILE G 421 " --> pdb=" O HIS G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 431 through 447 removed outlier: 4.237A pdb=" N THR G 445 " --> pdb=" O LYS G 441 " (cutoff:3.500A) Processing helix chain 'G' and resid 449 through 465 Processing helix chain 'G' and resid 473 through 485 removed outlier: 3.885A pdb=" N GLU G 483 " --> pdb=" O GLU G 479 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 502 removed outlier: 3.508A pdb=" N SER G 502 " --> pdb=" O ASP G 499 " (cutoff:3.500A) Processing helix chain 'G' and resid 503 through 507 removed outlier: 3.526A pdb=" N VAL G 506 " --> pdb=" O LEU G 503 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER G 507 " --> pdb=" O PHE G 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 503 through 507' Processing helix chain 'G' and resid 513 through 532 removed outlier: 3.680A pdb=" N THR G 517 " --> pdb=" O ILE G 513 " (cutoff:3.500A) Processing helix chain 'G' and resid 538 through 542 Processing helix chain 'G' and resid 547 through 559 removed outlier: 3.680A pdb=" N GLY G 551 " --> pdb=" O SER G 547 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N MET G 557 " --> pdb=" O LYS G 553 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG G 559 " --> pdb=" O PHE G 555 " (cutoff:3.500A) Processing helix chain 'G' and resid 560 through 564 removed outlier: 3.721A pdb=" N GLU G 564 " --> pdb=" O GLY G 561 " (cutoff:3.500A) Processing helix chain 'G' and resid 565 through 570 Processing helix chain 'G' and resid 581 through 588 Processing helix chain 'G' and resid 588 through 599 removed outlier: 3.585A pdb=" N PHE G 592 " --> pdb=" O PHE G 588 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP G 597 " --> pdb=" O THR G 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.993A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 9.677A pdb=" N HIS A 205 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 9.357A pdb=" N LEU A 221 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL A 36 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.619A pdb=" N GLY C 564 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ASP C 572 " --> pdb=" O ILE C 585 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL C 574 " --> pdb=" O LEU C 583 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.018A pdb=" N ASP A 285 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.573A pdb=" N LEU A 84 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.573A pdb=" N LEU A 84 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU A 239 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 317 removed outlier: 6.970A pdb=" N VAL A 593 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ASN A 315 " --> pdb=" O GLY A 591 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY A 591 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 323 through 324 Processing sheet with id=AA8, first strand: chain 'A' and resid 352 through 356 Processing sheet with id=AA9, first strand: chain 'A' and resid 450 through 452 Processing sheet with id=AB1, first strand: chain 'A' and resid 571 through 574 removed outlier: 6.529A pdb=" N GLY A 564 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N PHE A 563 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 652 through 658 removed outlier: 5.873A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N VAL A 654 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA A 670 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 709 through 711 removed outlier: 3.670A pdb=" N THR A1074 " --> pdb=" O SER A1095 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 715 through 726 removed outlier: 3.586A pdb=" N MET A1048 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 731 through 734 removed outlier: 4.474A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1118 through 1120 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.391A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 9.430A pdb=" N HIS B 205 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N LEU B 221 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 36 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.099A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.518A pdb=" N LEU B 239 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL B 126 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE B 128 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 130 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU B 132 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ASN B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N GLN B 134 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ALA B 161 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 309 through 317 removed outlier: 5.256A pdb=" N ILE B 310 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N THR B 597 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N GLN B 312 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL B 595 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER B 314 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 323 through 326 Processing sheet with id=AC3, first strand: chain 'B' and resid 352 through 356 Processing sheet with id=AC4, first strand: chain 'B' and resid 450 through 451 Processing sheet with id=AC5, first strand: chain 'B' and resid 471 through 472 Processing sheet with id=AC6, first strand: chain 'B' and resid 563 through 564 removed outlier: 6.931A pdb=" N PHE B 563 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 652 through 653 removed outlier: 6.287A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 699 through 701 removed outlier: 7.007A pdb=" N ALA B 699 " --> pdb=" O ILE C 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 715 through 726 removed outlier: 6.026A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 731 through 734 removed outlier: 4.492A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1118 through 1123 removed outlier: 5.155A pdb=" N ALA B1085 " --> pdb=" O SER B1121 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1092 through 1095 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.496A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N HIS C 205 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N LEU C 221 " --> pdb=" O HIS C 205 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL C 36 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.078A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.407A pdb=" N ARG C 235 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N PHE C 106 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLN C 237 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N TRP C 104 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU C 239 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL C 126 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE C 128 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLU C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL C 130 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU C 132 " --> pdb=" O ASN C 163 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASN C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N GLN C 134 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA C 161 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 309 through 317 removed outlier: 6.963A pdb=" N VAL C 593 " --> pdb=" O THR C 313 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ASN C 315 " --> pdb=" O GLY C 591 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLY C 591 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AD9, first strand: chain 'C' and resid 359 through 360 removed outlier: 6.871A pdb=" N CYS C 359 " --> pdb=" O CYS C 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 450 through 452 Processing sheet with id=AE2, first strand: chain 'C' and resid 471 through 472 Processing sheet with id=AE3, first strand: chain 'C' and resid 652 through 653 removed outlier: 6.201A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ALA C 670 " --> pdb=" O PRO C 663 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 709 through 711 Processing sheet with id=AE5, first strand: chain 'C' and resid 715 through 726 removed outlier: 3.547A pdb=" N MET C1048 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 731 through 734 removed outlier: 4.606A pdb=" N LYS C 731 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1118 through 1120 Processing sheet with id=AE8, first strand: chain 'C' and resid 1092 through 1095 removed outlier: 4.837A pdb=" N GLN C1104 " --> pdb=" O GLU C1109 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N GLU C1109 " --> pdb=" O GLN C1104 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 262 through 263 removed outlier: 6.892A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'F' and resid 347 through 352 removed outlier: 6.247A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 131 through 133 Processing sheet with id=AF3, first strand: chain 'G' and resid 347 through 350 1491 hydrogen bonds defined for protein. 4158 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: 9.88 Time building geometry restraints manager: 5.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11134 1.34 - 1.46: 8944 1.46 - 1.58: 15609 1.58 - 1.70: 0 1.70 - 1.82: 232 Bond restraints: 35919 Sorted by residual: bond pdb=" C1 NAG a 1 " pdb=" O5 NAG a 1 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.78e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.72e+00 bond pdb=" C1 NAG n 1 " pdb=" O5 NAG n 1 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.30e+00 bond pdb=" C1 NAG d 1 " pdb=" O5 NAG d 1 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.14e+00 bond pdb=" C1 NAG Z 2 " pdb=" O5 NAG Z 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.53e+00 ... (remaining 35914 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 47732 1.89 - 3.79: 1009 3.79 - 5.68: 89 5.68 - 7.57: 18 7.57 - 9.47: 7 Bond angle restraints: 48855 Sorted by residual: angle pdb=" N VAL G 506 " pdb=" CA VAL G 506 " pdb=" C VAL G 506 " ideal model delta sigma weight residual 113.71 108.12 5.59 9.50e-01 1.11e+00 3.46e+01 angle pdb=" N VAL F 172 " pdb=" CA VAL F 172 " pdb=" C VAL F 172 " ideal model delta sigma weight residual 112.96 108.33 4.63 1.00e+00 1.00e+00 2.15e+01 angle pdb=" CB ARG F 192 " pdb=" CG ARG F 192 " pdb=" CD ARG F 192 " ideal model delta sigma weight residual 111.30 120.23 -8.93 2.30e+00 1.89e-01 1.51e+01 angle pdb=" C GLN C 23 " pdb=" N LEU C 24 " pdb=" CA LEU C 24 " ideal model delta sigma weight residual 121.80 131.27 -9.47 2.44e+00 1.68e-01 1.51e+01 angle pdb=" C TRP G 461 " pdb=" N MET G 462 " pdb=" CA MET G 462 " ideal model delta sigma weight residual 122.38 115.51 6.87 1.81e+00 3.05e-01 1.44e+01 ... (remaining 48850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 20181 17.94 - 35.89: 1842 35.89 - 53.83: 380 53.83 - 71.77: 76 71.77 - 89.72: 43 Dihedral angle restraints: 22522 sinusoidal: 10030 harmonic: 12492 Sorted by residual: dihedral pdb=" CB CYS C 660 " pdb=" SG CYS C 660 " pdb=" SG CYS C 669 " pdb=" CB CYS C 669 " ideal model delta sinusoidal sigma weight residual -86.00 -171.39 85.39 1 1.00e+01 1.00e-02 8.83e+01 dihedral pdb=" CB CYS A 660 " pdb=" SG CYS A 660 " pdb=" SG CYS A 669 " pdb=" CB CYS A 669 " ideal model delta sinusoidal sigma weight residual -86.00 -170.06 84.06 1 1.00e+01 1.00e-02 8.61e+01 dihedral pdb=" CB CYS A 289 " pdb=" SG CYS A 289 " pdb=" SG CYS A 299 " pdb=" CB CYS A 299 " ideal model delta sinusoidal sigma weight residual -86.00 -169.15 83.15 1 1.00e+01 1.00e-02 8.45e+01 ... (remaining 22519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 5104 0.080 - 0.160: 562 0.160 - 0.240: 16 0.240 - 0.320: 1 0.320 - 0.400: 1 Chirality restraints: 5684 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 232 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A 329 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 5681 not shown) Planarity restraints: 6261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B1072 " 0.032 2.00e-02 2.50e+03 2.96e-02 1.10e+01 pdb=" CG ASN B1072 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN B1072 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B1072 " -0.033 2.00e-02 2.50e+03 pdb=" C1 NAG a 1 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 232 " -0.024 2.00e-02 2.50e+03 2.23e-02 6.19e+00 pdb=" CG ASN A 232 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN A 232 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 232 " 0.025 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 234 " 0.034 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO F 235 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO F 235 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 235 " 0.029 5.00e-02 4.00e+02 ... (remaining 6258 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 742 2.66 - 3.22: 34513 3.22 - 3.78: 54832 3.78 - 4.34: 70687 4.34 - 4.90: 116840 Nonbonded interactions: 277614 Sorted by model distance: nonbonded pdb=" OG SER C 814 " pdb=" OE1 GLU C 817 " model vdw 2.106 3.040 nonbonded pdb=" OG1 THR A 124 " pdb=" OD1 ASN A 125 " model vdw 2.147 3.040 nonbonded pdb=" OG SER C 347 " pdb=" O ARG C 450 " model vdw 2.151 3.040 nonbonded pdb=" OH TYR G 237 " pdb=" O VAL G 485 " model vdw 2.154 3.040 nonbonded pdb=" O PHE A 345 " pdb=" OH TYR A 449 " model vdw 2.154 3.040 ... (remaining 277609 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' selection = (chain 'B' and (resid 14 through 619 or resid 635 through 825 or resid 853 throu \ gh 2003)) selection = (chain 'C' and (resid 14 through 619 or resid 635 through 2003)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.720 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 39.480 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.220 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:1.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 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 : 0.005 0.048 36054 Z= 0.213 Angle : 0.650 9.469 49214 Z= 0.325 Chirality : 0.046 0.400 5684 Planarity : 0.004 0.056 6209 Dihedral : 14.134 89.719 14340 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.68 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.13), residues: 4229 helix: 1.52 (0.14), residues: 1357 sheet: 0.09 (0.18), residues: 775 loop : -1.52 (0.13), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 192 TYR 0.020 0.001 TYR G 385 PHE 0.031 0.001 PHE B 904 TRP 0.019 0.001 TRP A 884 HIS 0.004 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00463 (35919) covalent geometry : angle 0.63209 (48855) SS BOND : bond 0.00296 ( 46) SS BOND : angle 1.41460 ( 92) hydrogen bonds : bond 0.12763 ( 1488) hydrogen bonds : angle 5.98769 ( 4158) link_BETA1-4 : bond 0.00357 ( 37) link_BETA1-4 : angle 1.91260 ( 111) link_NAG-ASN : bond 0.00264 ( 52) link_NAG-ASN : angle 2.10295 ( 156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 513 PHE cc_start: 0.8614 (m-10) cc_final: 0.8138 (m-80) REVERT: C 363 TYR cc_start: 0.9291 (m-80) cc_final: 0.8982 (m-80) REVERT: F 82 MET cc_start: 0.6586 (pmm) cc_final: 0.6168 (pmm) REVERT: F 462 MET cc_start: 0.3424 (mmt) cc_final: 0.3064 (ptt) REVERT: F 557 MET cc_start: 0.7578 (tpt) cc_final: 0.6929 (ttm) REVERT: F 579 MET cc_start: -0.0641 (mmt) cc_final: -0.3153 (tpt) REVERT: F 600 LYS cc_start: 0.3925 (tttt) cc_final: 0.3704 (tptp) REVERT: G 190 MET cc_start: 0.7884 (mpp) cc_final: 0.7665 (mpp) REVERT: G 249 MET cc_start: 0.3159 (mmt) cc_final: 0.1310 (ttp) REVERT: G 360 MET cc_start: 0.6524 (ppp) cc_final: 0.6233 (ppp) REVERT: G 455 MET cc_start: 0.8141 (tmm) cc_final: 0.7903 (tmm) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.2219 time to fit residues: 53.3001 Evaluate side-chains 113 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 40.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 30.0000 chunk 424 optimal weight: 40.0000 chunk 155 optimal weight: 4.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 GLN A 802 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 ASN B 899 GLN B 905 ASN B 917 ASN ** B1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN C 924 GLN C 955 GLN ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 531 GLN G 524 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.109324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.062143 restraints weight = 118984.645| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 4.74 r_work: 0.2846 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.0753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 36054 Z= 0.213 Angle : 0.624 9.318 49214 Z= 0.314 Chirality : 0.045 0.254 5684 Planarity : 0.004 0.063 6209 Dihedral : 7.438 59.907 6462 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.05 % Favored : 93.88 % Rotamer: Outliers : 0.11 % Allowed : 6.61 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.13), residues: 4229 helix: 1.60 (0.14), residues: 1381 sheet: 0.07 (0.18), residues: 738 loop : -1.50 (0.13), residues: 2110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 192 TYR 0.028 0.001 TYR C1065 PHE 0.028 0.002 PHE B 904 TRP 0.013 0.001 TRP G 203 HIS 0.006 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00500 (35919) covalent geometry : angle 0.61037 (48855) SS BOND : bond 0.00361 ( 46) SS BOND : angle 1.44688 ( 92) hydrogen bonds : bond 0.05582 ( 1488) hydrogen bonds : angle 5.09733 ( 4158) link_BETA1-4 : bond 0.00319 ( 37) link_BETA1-4 : angle 1.57011 ( 111) link_NAG-ASN : bond 0.00234 ( 52) link_NAG-ASN : angle 1.79818 ( 156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 time to evaluate : 1.487 Fit side-chains revert: symmetry clash REVERT: A 449 TYR cc_start: 0.8338 (m-80) cc_final: 0.7800 (m-80) REVERT: A 777 GLN cc_start: 0.9366 (tm-30) cc_final: 0.9125 (tm-30) REVERT: C 363 TYR cc_start: 0.9441 (m-80) cc_final: 0.9029 (m-80) REVERT: C 738 MET cc_start: 0.9069 (mmm) cc_final: 0.8818 (tmm) REVERT: F 82 MET cc_start: 0.6815 (pmm) cc_final: 0.6534 (pmm) REVERT: F 557 MET cc_start: 0.8241 (tpt) cc_final: 0.7426 (ptm) REVERT: G 249 MET cc_start: 0.3706 (mmt) cc_final: 0.2380 (ttp) REVERT: G 557 MET cc_start: 0.8599 (mpp) cc_final: 0.8389 (mpp) outliers start: 4 outliers final: 1 residues processed: 118 average time/residue: 0.2135 time to fit residues: 43.7861 Evaluate side-chains 108 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 618 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 413 optimal weight: 0.9980 chunk 424 optimal weight: 50.0000 chunk 93 optimal weight: 0.4980 chunk 305 optimal weight: 4.9990 chunk 373 optimal weight: 8.9990 chunk 159 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 206 optimal weight: 8.9990 chunk 129 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 ASN B 899 GLN B 905 ASN ** B1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 277 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.110700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.064077 restraints weight = 117955.970| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 4.74 r_work: 0.2887 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 36054 Z= 0.113 Angle : 0.550 9.614 49214 Z= 0.274 Chirality : 0.043 0.237 5684 Planarity : 0.004 0.059 6209 Dihedral : 6.471 58.173 6462 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.54 % Favored : 95.41 % Rotamer: Outliers : 0.67 % Allowed : 8.79 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.13), residues: 4229 helix: 1.76 (0.14), residues: 1370 sheet: 0.31 (0.19), residues: 743 loop : -1.45 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 317 TYR 0.021 0.001 TYR G 385 PHE 0.018 0.001 PHE A 375 TRP 0.017 0.001 TRP G 477 HIS 0.004 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00248 (35919) covalent geometry : angle 0.53658 (48855) SS BOND : bond 0.00260 ( 46) SS BOND : angle 1.18527 ( 92) hydrogen bonds : bond 0.04570 ( 1488) hydrogen bonds : angle 4.75267 ( 4158) link_BETA1-4 : bond 0.00402 ( 37) link_BETA1-4 : angle 1.53940 ( 111) link_NAG-ASN : bond 0.00187 ( 52) link_NAG-ASN : angle 1.60978 ( 156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 1.428 Fit side-chains revert: symmetry clash REVERT: A 447 TYR cc_start: 0.8963 (m-80) cc_final: 0.8641 (m-10) REVERT: A 449 TYR cc_start: 0.8311 (m-80) cc_final: 0.6594 (m-80) REVERT: A 955 GLN cc_start: 0.9038 (tm-30) cc_final: 0.8746 (tm-30) REVERT: B 513 PHE cc_start: 0.7959 (m-80) cc_final: 0.7519 (m-80) REVERT: C 363 TYR cc_start: 0.9459 (m-80) cc_final: 0.9041 (m-80) REVERT: C 738 MET cc_start: 0.9014 (mmm) cc_final: 0.8743 (tmm) REVERT: C 898 MET cc_start: 0.9128 (mtt) cc_final: 0.8836 (mtt) REVERT: F 557 MET cc_start: 0.8120 (tpt) cc_final: 0.7302 (ptm) REVERT: G 190 MET cc_start: 0.7355 (mpp) cc_final: 0.7132 (mpp) REVERT: G 249 MET cc_start: 0.3760 (mmt) cc_final: 0.2420 (ttp) REVERT: G 332 MET cc_start: 0.5308 (ppp) cc_final: 0.5066 (ppp) REVERT: G 366 MET cc_start: 0.6907 (tpp) cc_final: 0.6632 (mmm) outliers start: 25 outliers final: 8 residues processed: 141 average time/residue: 0.2047 time to fit residues: 50.3283 Evaluate side-chains 118 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 905 ASN Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 703 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 155 optimal weight: 0.8980 chunk 309 optimal weight: 20.0000 chunk 154 optimal weight: 8.9990 chunk 288 optimal weight: 3.9990 chunk 424 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 193 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 376 optimal weight: 0.1980 chunk 227 optimal weight: 9.9990 chunk 282 optimal weight: 0.5980 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 990 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 GLN C 762 ASN ** C1003 GLN ** 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 = 0.4161 r_free = 0.4161 target = 0.109705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.064538 restraints weight = 118661.013| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 5.67 r_work: 0.2830 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 36054 Z= 0.177 Angle : 0.573 9.476 49214 Z= 0.287 Chirality : 0.043 0.240 5684 Planarity : 0.004 0.056 6209 Dihedral : 6.221 59.829 6462 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.63 % Favored : 94.32 % Rotamer: Outliers : 0.83 % Allowed : 10.60 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.13), residues: 4229 helix: 1.76 (0.14), residues: 1377 sheet: 0.24 (0.19), residues: 716 loop : -1.47 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 344 TYR 0.023 0.001 TYR C1065 PHE 0.021 0.001 PHE A1119 TRP 0.014 0.001 TRP G 477 HIS 0.005 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00417 (35919) covalent geometry : angle 0.55950 (48855) SS BOND : bond 0.00299 ( 46) SS BOND : angle 1.28872 ( 92) hydrogen bonds : bond 0.04938 ( 1488) hydrogen bonds : angle 4.76372 ( 4158) link_BETA1-4 : bond 0.00324 ( 37) link_BETA1-4 : angle 1.57707 ( 111) link_NAG-ASN : bond 0.00194 ( 52) link_NAG-ASN : angle 1.66582 ( 156) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 1.401 Fit side-chains revert: symmetry clash REVERT: A 729 MET cc_start: 0.9380 (ptt) cc_final: 0.9138 (ptt) REVERT: A 955 GLN cc_start: 0.9044 (tm-30) cc_final: 0.8736 (tm-30) REVERT: B 513 PHE cc_start: 0.7864 (m-80) cc_final: 0.7482 (m-80) REVERT: C 363 TYR cc_start: 0.9465 (m-80) cc_final: 0.9052 (m-80) REVERT: F 557 MET cc_start: 0.8216 (tpt) cc_final: 0.7375 (ptm) REVERT: G 249 MET cc_start: 0.3741 (mmt) cc_final: 0.2406 (ttp) REVERT: G 332 MET cc_start: 0.5743 (ppp) cc_final: 0.5475 (ppp) REVERT: G 366 MET cc_start: 0.6858 (tpp) cc_final: 0.6343 (mmm) REVERT: G 579 MET cc_start: 0.4239 (OUTLIER) cc_final: 0.3262 (tmm) outliers start: 31 outliers final: 15 residues processed: 141 average time/residue: 0.1989 time to fit residues: 49.3960 Evaluate side-chains 124 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain F residue 159 ASN Chi-restraints excluded: chain F residue 600 LYS Chi-restraints excluded: chain G residue 579 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 313 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 235 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 chunk 380 optimal weight: 20.0000 chunk 367 optimal weight: 20.0000 chunk 389 optimal weight: 20.0000 chunk 100 optimal weight: 4.9990 chunk 411 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN ** B1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 GLN ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.109496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.064476 restraints weight = 118180.801| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 5.15 r_work: 0.2836 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 36054 Z= 0.186 Angle : 0.586 12.370 49214 Z= 0.291 Chirality : 0.044 0.242 5684 Planarity : 0.004 0.057 6209 Dihedral : 6.046 59.587 6462 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.60 % Favored : 94.35 % Rotamer: Outliers : 1.23 % Allowed : 12.12 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.13), residues: 4229 helix: 1.78 (0.14), residues: 1370 sheet: 0.18 (0.19), residues: 685 loop : -1.48 (0.13), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 317 TYR 0.024 0.001 TYR C1065 PHE 0.023 0.001 PHE B 390 TRP 0.014 0.001 TRP G 477 HIS 0.005 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00440 (35919) covalent geometry : angle 0.57274 (48855) SS BOND : bond 0.00306 ( 46) SS BOND : angle 1.29661 ( 92) hydrogen bonds : bond 0.05026 ( 1488) hydrogen bonds : angle 4.74998 ( 4158) link_BETA1-4 : bond 0.00342 ( 37) link_BETA1-4 : angle 1.60130 ( 111) link_NAG-ASN : bond 0.00197 ( 52) link_NAG-ASN : angle 1.65932 ( 156) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 109 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 CYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8627 (m) REVERT: A 449 TYR cc_start: 0.7821 (m-80) cc_final: 0.7522 (m-80) REVERT: A 506 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.7983 (m-80) REVERT: A 729 MET cc_start: 0.9387 (ptt) cc_final: 0.9143 (ptt) REVERT: A 955 GLN cc_start: 0.9040 (tm-30) cc_final: 0.8721 (tm-30) REVERT: B 513 PHE cc_start: 0.7932 (m-80) cc_final: 0.7586 (m-80) REVERT: B 1000 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8278 (tm-30) REVERT: B 1037 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8087 (ptm160) REVERT: C 114 THR cc_start: 0.8229 (OUTLIER) cc_final: 0.7997 (p) REVERT: C 363 TYR cc_start: 0.9467 (m-80) cc_final: 0.9042 (m-80) REVERT: F 557 MET cc_start: 0.8212 (tpt) cc_final: 0.7365 (ptm) REVERT: G 190 MET cc_start: 0.7349 (mpp) cc_final: 0.7122 (mpp) REVERT: G 249 MET cc_start: 0.3901 (mmt) cc_final: 0.2433 (ttp) REVERT: G 332 MET cc_start: 0.5836 (ppp) cc_final: 0.5541 (ppp) REVERT: G 366 MET cc_start: 0.6922 (tpp) cc_final: 0.6645 (mmm) REVERT: G 579 MET cc_start: 0.4261 (OUTLIER) cc_final: 0.3264 (tmm) outliers start: 46 outliers final: 25 residues processed: 152 average time/residue: 0.2047 time to fit residues: 54.6405 Evaluate side-chains 135 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 506 TYR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 1131 VAL Chi-restraints excluded: chain F residue 600 LYS Chi-restraints excluded: chain G residue 579 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 168 optimal weight: 3.9990 chunk 218 optimal weight: 9.9990 chunk 370 optimal weight: 9.9990 chunk 363 optimal weight: 7.9990 chunk 188 optimal weight: 0.9990 chunk 49 optimal weight: 0.0050 chunk 235 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 418 optimal weight: 30.0000 chunk 388 optimal weight: 30.0000 chunk 275 optimal weight: 8.9990 overall best weight: 3.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN ** B1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 572 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.108425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.064596 restraints weight = 118230.552| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 5.23 r_work: 0.2812 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 36054 Z= 0.268 Angle : 0.655 9.886 49214 Z= 0.326 Chirality : 0.046 0.245 5684 Planarity : 0.004 0.059 6209 Dihedral : 6.192 59.384 6462 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.29 % Favored : 93.66 % Rotamer: Outliers : 1.39 % Allowed : 13.48 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.13), residues: 4229 helix: 1.66 (0.14), residues: 1375 sheet: -0.03 (0.19), residues: 704 loop : -1.58 (0.13), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 317 TYR 0.028 0.001 TYR C1065 PHE 0.028 0.002 PHE C1119 TRP 0.012 0.001 TRP F 477 HIS 0.007 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00635 (35919) covalent geometry : angle 0.64079 (48855) SS BOND : bond 0.00391 ( 46) SS BOND : angle 1.47014 ( 92) hydrogen bonds : bond 0.05758 ( 1488) hydrogen bonds : angle 4.91259 ( 4158) link_BETA1-4 : bond 0.00302 ( 37) link_BETA1-4 : angle 1.72029 ( 111) link_NAG-ASN : bond 0.00323 ( 52) link_NAG-ASN : angle 1.82602 ( 156) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 105 time to evaluate : 1.412 Fit side-chains revert: symmetry clash REVERT: A 449 TYR cc_start: 0.7952 (m-80) cc_final: 0.7643 (m-80) REVERT: A 506 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.7854 (m-80) REVERT: A 729 MET cc_start: 0.9358 (ptt) cc_final: 0.9136 (ptt) REVERT: A 986 GLU cc_start: 0.9049 (mp0) cc_final: 0.8780 (tp30) REVERT: B 513 PHE cc_start: 0.8004 (m-80) cc_final: 0.7675 (m-80) REVERT: B 894 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8959 (tp) REVERT: B 1000 GLN cc_start: 0.8604 (tm-30) cc_final: 0.8363 (tm-30) REVERT: B 1037 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.8258 (ptm160) REVERT: C 114 THR cc_start: 0.8170 (OUTLIER) cc_final: 0.7953 (p) REVERT: C 363 TYR cc_start: 0.9467 (m-80) cc_final: 0.9030 (m-80) REVERT: F 360 MET cc_start: 0.3976 (mpp) cc_final: 0.3769 (mpp) REVERT: F 557 MET cc_start: 0.8266 (tpt) cc_final: 0.7449 (ptm) REVERT: F 579 MET cc_start: 0.0538 (mmt) cc_final: -0.2622 (tpt) REVERT: G 249 MET cc_start: 0.3914 (mmt) cc_final: 0.2397 (ttp) REVERT: G 332 MET cc_start: 0.5996 (ppp) cc_final: 0.5753 (ppp) REVERT: G 366 MET cc_start: 0.6892 (tpp) cc_final: 0.6635 (mmm) REVERT: G 579 MET cc_start: 0.4303 (OUTLIER) cc_final: 0.3356 (tmm) outliers start: 52 outliers final: 32 residues processed: 154 average time/residue: 0.2083 time to fit residues: 56.0338 Evaluate side-chains 142 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 105 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 506 TYR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 894 ILE Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 1131 VAL Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 600 LYS Chi-restraints excluded: chain G residue 579 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 29 optimal weight: 30.0000 chunk 273 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 chunk 286 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 226 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 133 optimal weight: 7.9990 chunk 407 optimal weight: 20.0000 chunk 135 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN ** B1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.110465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.065984 restraints weight = 117440.549| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 5.04 r_work: 0.2880 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 36054 Z= 0.110 Angle : 0.562 14.424 49214 Z= 0.277 Chirality : 0.043 0.239 5684 Planarity : 0.004 0.060 6209 Dihedral : 5.610 58.128 6462 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.80 % Favored : 95.15 % Rotamer: Outliers : 0.99 % Allowed : 14.28 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.13), residues: 4229 helix: 1.86 (0.14), residues: 1367 sheet: 0.26 (0.19), residues: 703 loop : -1.45 (0.13), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 317 TYR 0.022 0.001 TYR G 385 PHE 0.020 0.001 PHE A 375 TRP 0.013 0.001 TRP G 163 HIS 0.004 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00240 (35919) covalent geometry : angle 0.54942 (48855) SS BOND : bond 0.00269 ( 46) SS BOND : angle 1.12237 ( 92) hydrogen bonds : bond 0.04437 ( 1488) hydrogen bonds : angle 4.61736 ( 4158) link_BETA1-4 : bond 0.00380 ( 37) link_BETA1-4 : angle 1.58257 ( 111) link_NAG-ASN : bond 0.00206 ( 52) link_NAG-ASN : angle 1.55870 ( 156) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.7952 (m-80) cc_final: 0.7573 (m-80) REVERT: A 506 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.7875 (m-80) REVERT: A 729 MET cc_start: 0.9378 (ptt) cc_final: 0.9134 (ptt) REVERT: A 955 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8678 (tm-30) REVERT: A 983 ASP cc_start: 0.7896 (p0) cc_final: 0.6195 (p0) REVERT: A 986 GLU cc_start: 0.9065 (mp0) cc_final: 0.8839 (mp0) REVERT: B 513 PHE cc_start: 0.8002 (m-80) cc_final: 0.7680 (m-80) REVERT: B 964 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9257 (mm) REVERT: B 1000 GLN cc_start: 0.8543 (tm-30) cc_final: 0.8299 (tm-30) REVERT: B 1037 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8186 (ptm160) REVERT: C 114 THR cc_start: 0.8208 (OUTLIER) cc_final: 0.7979 (p) REVERT: C 142 ASP cc_start: 0.5078 (OUTLIER) cc_final: 0.4706 (m-30) REVERT: C 363 TYR cc_start: 0.9455 (m-80) cc_final: 0.9020 (m-80) REVERT: F 557 MET cc_start: 0.8150 (tpt) cc_final: 0.7330 (ptm) REVERT: G 249 MET cc_start: 0.3702 (mmt) cc_final: 0.2400 (ttp) REVERT: G 332 MET cc_start: 0.5935 (ppp) cc_final: 0.5684 (ppp) REVERT: G 579 MET cc_start: 0.4152 (OUTLIER) cc_final: 0.3104 (tmm) outliers start: 37 outliers final: 21 residues processed: 147 average time/residue: 0.2044 time to fit residues: 52.6063 Evaluate side-chains 136 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 506 TYR Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 905 ASN Chi-restraints excluded: chain B residue 964 LEU Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 600 LYS Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 141 CYS Chi-restraints excluded: chain G residue 579 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 98 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 40 optimal weight: 20.0000 chunk 326 optimal weight: 0.0020 chunk 159 optimal weight: 2.9990 chunk 355 optimal weight: 0.0870 chunk 387 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 overall best weight: 0.9970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 417 HIS G 540 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.110530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.064600 restraints weight = 118034.472| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 4.72 r_work: 0.2875 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36054 Z= 0.114 Angle : 0.564 12.825 49214 Z= 0.276 Chirality : 0.043 0.245 5684 Planarity : 0.004 0.061 6209 Dihedral : 5.428 57.909 6462 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.15 % Favored : 94.80 % Rotamer: Outliers : 0.99 % Allowed : 14.49 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.13), residues: 4229 helix: 1.89 (0.14), residues: 1370 sheet: 0.33 (0.19), residues: 717 loop : -1.41 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 317 TYR 0.021 0.001 TYR G 385 PHE 0.020 0.001 PHE A 375 TRP 0.012 0.001 TRP G 477 HIS 0.004 0.001 HIS G 374 Details of bonding type rmsd covalent geometry : bond 0.00254 (35919) covalent geometry : angle 0.55184 (48855) SS BOND : bond 0.00267 ( 46) SS BOND : angle 1.13458 ( 92) hydrogen bonds : bond 0.04296 ( 1488) hydrogen bonds : angle 4.54557 ( 4158) link_BETA1-4 : bond 0.00344 ( 37) link_BETA1-4 : angle 1.56495 ( 111) link_NAG-ASN : bond 0.00167 ( 52) link_NAG-ASN : angle 1.57566 ( 156) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 116 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.7919 (m-80) cc_final: 0.7565 (m-80) REVERT: A 506 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.7906 (m-80) REVERT: A 729 MET cc_start: 0.9418 (ptt) cc_final: 0.9156 (ptt) REVERT: A 955 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8674 (tm-30) REVERT: A 986 GLU cc_start: 0.9090 (mp0) cc_final: 0.8706 (tp30) REVERT: B 513 PHE cc_start: 0.7978 (m-80) cc_final: 0.7728 (m-80) REVERT: B 1037 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8077 (ptm160) REVERT: C 114 THR cc_start: 0.8155 (OUTLIER) cc_final: 0.7931 (p) REVERT: C 142 ASP cc_start: 0.5086 (OUTLIER) cc_final: 0.4737 (m-30) REVERT: C 363 TYR cc_start: 0.9472 (m-80) cc_final: 0.9028 (m-80) REVERT: F 557 MET cc_start: 0.8192 (tpt) cc_final: 0.7301 (ptm) REVERT: G 249 MET cc_start: 0.3707 (mmt) cc_final: 0.2379 (ttp) REVERT: G 332 MET cc_start: 0.5869 (ppp) cc_final: 0.5662 (ppp) REVERT: G 408 MET cc_start: 0.8251 (mpp) cc_final: 0.8045 (pmm) REVERT: G 462 MET cc_start: 0.7275 (pmm) cc_final: 0.7050 (pmm) REVERT: G 579 MET cc_start: 0.4142 (OUTLIER) cc_final: 0.2991 (tmm) outliers start: 37 outliers final: 23 residues processed: 151 average time/residue: 0.2037 time to fit residues: 52.9553 Evaluate side-chains 138 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 506 TYR Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 600 LYS Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 141 CYS Chi-restraints excluded: chain G residue 579 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 69 optimal weight: 2.9990 chunk 336 optimal weight: 20.0000 chunk 55 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 263 optimal weight: 0.8980 chunk 338 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 148 optimal weight: 9.9990 chunk 325 optimal weight: 20.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.109574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.065521 restraints weight = 117216.373| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 5.29 r_work: 0.2844 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 36054 Z= 0.177 Angle : 0.603 12.527 49214 Z= 0.297 Chirality : 0.044 0.241 5684 Planarity : 0.004 0.058 6209 Dihedral : 5.554 59.905 6462 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.44 % Favored : 94.51 % Rotamer: Outliers : 1.12 % Allowed : 14.57 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.13), residues: 4229 helix: 1.84 (0.14), residues: 1371 sheet: 0.27 (0.20), residues: 679 loop : -1.42 (0.13), residues: 2179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 317 TYR 0.025 0.001 TYR C1065 PHE 0.044 0.001 PHE B 390 TRP 0.011 0.001 TRP G 163 HIS 0.005 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00417 (35919) covalent geometry : angle 0.59024 (48855) SS BOND : bond 0.00316 ( 46) SS BOND : angle 1.28657 ( 92) hydrogen bonds : bond 0.04861 ( 1488) hydrogen bonds : angle 4.64277 ( 4158) link_BETA1-4 : bond 0.00310 ( 37) link_BETA1-4 : angle 1.61312 ( 111) link_NAG-ASN : bond 0.00194 ( 52) link_NAG-ASN : angle 1.64534 ( 156) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 109 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.7945 (m-80) cc_final: 0.7614 (m-80) REVERT: A 506 TYR cc_start: 0.8448 (OUTLIER) cc_final: 0.7835 (m-80) REVERT: A 729 MET cc_start: 0.9379 (ptt) cc_final: 0.9136 (ptt) REVERT: A 955 GLN cc_start: 0.9039 (tm-30) cc_final: 0.8717 (tm-30) REVERT: B 1037 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8185 (ptm160) REVERT: C 114 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7927 (p) REVERT: C 142 ASP cc_start: 0.4754 (OUTLIER) cc_final: 0.4413 (m-30) REVERT: C 363 TYR cc_start: 0.9460 (m-80) cc_final: 0.9020 (m-80) REVERT: F 557 MET cc_start: 0.8216 (tpt) cc_final: 0.7350 (ptm) REVERT: G 249 MET cc_start: 0.3802 (mmt) cc_final: 0.2299 (ttp) REVERT: G 332 MET cc_start: 0.6073 (ppp) cc_final: 0.5862 (ppp) REVERT: G 462 MET cc_start: 0.7254 (pmm) cc_final: 0.7008 (pmm) REVERT: G 579 MET cc_start: 0.4447 (OUTLIER) cc_final: 0.3369 (tmm) outliers start: 42 outliers final: 28 residues processed: 147 average time/residue: 0.1979 time to fit residues: 50.4273 Evaluate side-chains 141 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 506 TYR Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 600 LYS Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 141 CYS Chi-restraints excluded: chain G residue 579 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 277 optimal weight: 0.0270 chunk 297 optimal weight: 2.9990 chunk 198 optimal weight: 0.0770 chunk 14 optimal weight: 6.9990 chunk 416 optimal weight: 20.0000 chunk 270 optimal weight: 6.9990 chunk 254 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 312 optimal weight: 20.0000 chunk 117 optimal weight: 3.9990 chunk 182 optimal weight: 0.7980 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.110118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.066016 restraints weight = 118178.066| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 5.63 r_work: 0.2855 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36054 Z= 0.136 Angle : 0.592 12.857 49214 Z= 0.291 Chirality : 0.043 0.241 5684 Planarity : 0.004 0.061 6209 Dihedral : 5.455 58.585 6462 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.06 % Favored : 94.89 % Rotamer: Outliers : 0.88 % Allowed : 14.97 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.13), residues: 4229 helix: 1.83 (0.14), residues: 1370 sheet: 0.32 (0.20), residues: 682 loop : -1.40 (0.13), residues: 2177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 981 TYR 0.021 0.001 TYR G 385 PHE 0.030 0.001 PHE B 390 TRP 0.012 0.001 TRP G 477 HIS 0.005 0.001 HIS B 517 Details of bonding type rmsd covalent geometry : bond 0.00315 (35919) covalent geometry : angle 0.58060 (48855) SS BOND : bond 0.00279 ( 46) SS BOND : angle 1.21288 ( 92) hydrogen bonds : bond 0.04565 ( 1488) hydrogen bonds : angle 4.60019 ( 4158) link_BETA1-4 : bond 0.00340 ( 37) link_BETA1-4 : angle 1.58004 ( 111) link_NAG-ASN : bond 0.00156 ( 52) link_NAG-ASN : angle 1.57953 ( 156) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.7957 (m-80) cc_final: 0.7627 (m-80) REVERT: A 506 TYR cc_start: 0.8462 (OUTLIER) cc_final: 0.7797 (m-80) REVERT: A 729 MET cc_start: 0.9376 (ptt) cc_final: 0.9129 (ptt) REVERT: A 955 GLN cc_start: 0.9013 (tm-30) cc_final: 0.8682 (tm-30) REVERT: B 1037 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8205 (ptm160) REVERT: C 114 THR cc_start: 0.8089 (OUTLIER) cc_final: 0.7869 (p) REVERT: C 142 ASP cc_start: 0.4528 (OUTLIER) cc_final: 0.4195 (m-30) REVERT: C 363 TYR cc_start: 0.9487 (m-80) cc_final: 0.9024 (m-80) REVERT: F 557 MET cc_start: 0.8147 (tpt) cc_final: 0.7316 (ptm) REVERT: F 579 MET cc_start: -0.0397 (mmt) cc_final: -0.3131 (tpt) REVERT: G 249 MET cc_start: 0.3587 (mmt) cc_final: 0.2173 (ttp) REVERT: G 332 MET cc_start: 0.6035 (ppp) cc_final: 0.5817 (ppp) REVERT: G 366 MET cc_start: 0.5765 (mmm) cc_final: 0.5493 (mmm) REVERT: G 462 MET cc_start: 0.7238 (pmm) cc_final: 0.7001 (pmm) REVERT: G 579 MET cc_start: 0.4390 (OUTLIER) cc_final: 0.3297 (tmm) outliers start: 33 outliers final: 24 residues processed: 141 average time/residue: 0.2058 time to fit residues: 50.1897 Evaluate side-chains 137 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 506 TYR Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 600 LYS Chi-restraints excluded: chain G residue 141 CYS Chi-restraints excluded: chain G residue 579 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 94 optimal weight: 0.9990 chunk 380 optimal weight: 20.0000 chunk 236 optimal weight: 2.9990 chunk 208 optimal weight: 6.9990 chunk 222 optimal weight: 10.0000 chunk 420 optimal weight: 20.0000 chunk 7 optimal weight: 0.6980 chunk 387 optimal weight: 9.9990 chunk 151 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 304 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.109268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.063725 restraints weight = 117893.045| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 5.14 r_work: 0.2819 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 36054 Z= 0.198 Angle : 0.625 12.746 49214 Z= 0.308 Chirality : 0.044 0.241 5684 Planarity : 0.004 0.060 6209 Dihedral : 5.622 59.854 6462 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.84 % Favored : 94.11 % Rotamer: Outliers : 0.99 % Allowed : 14.97 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.13), residues: 4229 helix: 1.83 (0.14), residues: 1362 sheet: 0.21 (0.19), residues: 690 loop : -1.44 (0.13), residues: 2177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 981 TYR 0.025 0.001 TYR C1065 PHE 0.022 0.001 PHE C1119 TRP 0.011 0.001 TRP G 163 HIS 0.005 0.001 HIS B 517 Details of bonding type rmsd covalent geometry : bond 0.00466 (35919) covalent geometry : angle 0.61198 (48855) SS BOND : bond 0.00330 ( 46) SS BOND : angle 1.33708 ( 92) hydrogen bonds : bond 0.05082 ( 1488) hydrogen bonds : angle 4.70172 ( 4158) link_BETA1-4 : bond 0.00316 ( 37) link_BETA1-4 : angle 1.63654 ( 111) link_NAG-ASN : bond 0.00220 ( 52) link_NAG-ASN : angle 1.67670 ( 156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12536.96 seconds wall clock time: 214 minutes 30.85 seconds (12870.85 seconds total)