Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 18 05:01:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8a_31795/07_2023/7v8a_31795.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8a_31795/07_2023/7v8a_31795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8a_31795/07_2023/7v8a_31795.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8a_31795/07_2023/7v8a_31795.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8a_31795/07_2023/7v8a_31795.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v8a_31795/07_2023/7v8a_31795.pdb" } resolution = 2.7 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 ------------------------------------------------------------------------------- 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= 0.067 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 195 5.16 5 C 25408 2.51 5 N 6527 2.21 5 O 7792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 853": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 39922 Number of models: 1 Model: "" Number of chains: 50 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: 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: "C" 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: "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: "H" 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 chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 17.28, per 1000 atoms: 0.43 Number of scatterers: 39922 At special positions: 0 Unit cell: (165, 174.9, 239.8, 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 195 16.00 O 7792 8.00 N 6527 7.00 C 25408 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, 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=2.04 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=2.03 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=2.04 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 660 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.04 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=2.04 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 Simple disulfide: pdb=" SG CYS H 133 " - pdb=" SG CYS H 141 " distance=2.02 Simple disulfide: pdb=" SG CYS H 344 " - pdb=" SG CYS H 361 " distance=2.03 Simple disulfide: pdb=" SG CYS H 530 " - pdb=" SG CYS H 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 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 q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 341 " " NAG A2003 " - " ASN A 601 " " NAG A2004 " - " ASN A 655 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 341 " " NAG B2003 " - " ASN B 601 " " NAG B2004 " - " ASN B 655 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 341 " " NAG C2003 " - " ASN C 601 " " NAG C2004 " - " ASN C 655 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 163 " " NAG F2001 " - " ASN F 53 " " NAG G2001 " - " ASN G 53 " " NAG G2002 " - " ASN G 322 " " NAG H 901 " - " ASN H 322 " " NAG I 1 " - " ASN A 232 " " NAG J 1 " - " ASN A 280 " " NAG K 1 " - " ASN A 329 " " 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 232 " " NAG V 1 " - " ASN B 280 " " NAG W 1 " - " ASN B 329 " " NAG X 1 " - " ASN B 614 " " NAG Y 1 " - " ASN B 707 " " NAG Z 1 " - " ASN B 715 " " NAG a 1 " - " ASN B 799 " " NAG b 1 " - " ASN B1072 " " NAG c 1 " - " ASN B1096 " " NAG d 1 " - " ASN B1132 " " NAG e 1 " - " ASN C 122 " " NAG f 1 " - " ASN C 163 " " NAG g 1 " - " ASN C 232 " " NAG h 1 " - " ASN C 280 " " NAG i 1 " - " ASN C 329 " " 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 " " NAG q 1 " - " ASN F 322 " Time building additional restraints: 16.47 Conformation dependent library (CDL) restraints added in 5.3 seconds 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9156 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 52 sheets defined 39.1% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.44 Creating SS restraints... Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 381 through 386 removed outlier: 4.250A pdb=" N ASN A 386 " --> pdb=" O PRO A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 removed outlier: 4.191A pdb=" N ARG A 406 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 500 through 503 Processing helix chain 'A' and resid 735 through 741 Processing helix chain 'A' and resid 744 through 753 removed outlier: 3.954A pdb=" N GLN A 753 " --> pdb=" O ASN A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 781 removed outlier: 3.576A pdb=" N ALA A 764 " --> pdb=" O GLN A 760 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU A 765 " --> pdb=" O LEU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 824 Processing helix chain 'A' and resid 864 through 883 removed outlier: 3.635A pdb=" N GLY A 883 " --> pdb=" O THR A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 895 through 906 Processing helix chain 'A' and resid 910 through 916 removed outlier: 4.078A pdb=" N LEU A 914 " --> pdb=" O THR A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 939 Processing helix chain 'A' and resid 943 through 963 Processing helix chain 'A' and resid 974 through 981 removed outlier: 3.667A pdb=" N ILE A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1031 removed outlier: 4.262A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG A 993 " --> pdb=" O VAL A 989 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 994 " --> pdb=" O GLN A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1144 removed outlier: 3.793A pdb=" N ASP A1144 " --> pdb=" O GLN A1140 " (cutoff:3.500A) 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: 3.555A pdb=" N TRP B 351 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 368 removed outlier: 4.048A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 386 removed outlier: 3.961A pdb=" N ASN B 386 " --> pdb=" O PRO B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 4.395A pdb=" N ARG B 406 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'B' and resid 735 through 741 Processing helix chain 'B' and resid 744 through 753 removed outlier: 4.025A pdb=" N GLN B 753 " --> pdb=" O ASN B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 781 Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.530A pdb=" N VAL B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.656A 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 910 through 916 removed outlier: 4.022A pdb=" N LEU B 914 " --> pdb=" O THR B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 939 removed outlier: 3.756A pdb=" N GLN B 933 " --> pdb=" O ILE B 929 " (cutoff:3.500A) removed outlier: 3.563A 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 980 Processing helix chain 'B' and resid 983 through 1031 removed outlier: 4.768A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN B 990 " --> pdb=" O GLU B 986 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY B 997 " --> pdb=" O ARG B 993 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL B1031 " --> pdb=" O MET B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1143 Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 362 through 368 removed outlier: 4.146A pdb=" N LEU C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 386 Processing helix chain 'C' and resid 403 through 408 removed outlier: 4.456A 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 735 through 742 Processing helix chain 'C' and resid 744 through 753 removed outlier: 4.180A pdb=" N GLN C 753 " --> pdb=" O ASN C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 781 Processing helix chain 'C' and resid 814 through 824 Processing helix chain 'C' and resid 864 through 883 removed outlier: 3.588A 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 916 removed outlier: 3.993A pdb=" N LEU C 914 " --> pdb=" O THR C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 939 removed outlier: 3.744A pdb=" N GLN C 933 " --> pdb=" O ILE C 929 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP C 934 " --> pdb=" O GLY C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 963 Processing helix chain 'C' and resid 974 through 981 removed outlier: 4.077A pdb=" N ILE C 978 " --> pdb=" O VAL C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 1031 removed outlier: 3.860A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG C 993 " --> pdb=" O VAL C 989 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C 994 " --> pdb=" O GLN C 990 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1143 Processing helix chain 'F' and resid 20 through 53 removed outlier: 3.970A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 79 removed outlier: 3.514A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN F 61 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET F 62 " --> pdb=" O ASN F 58 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN F 63 " --> pdb=" O VAL F 59 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LYS F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLU F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 101 removed outlier: 3.710A pdb=" N ALA F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU F 100 " --> pdb=" O GLN F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 108 removed outlier: 3.649A pdb=" N SER F 106 " --> pdb=" O ASN F 103 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL F 107 " --> pdb=" O GLY F 104 " (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 174 Processing helix chain 'F' and resid 176 through 194 Processing helix chain 'F' and resid 198 through 205 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: 3.534A pdb=" N LEU F 222 " --> pdb=" O SER F 218 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE F 223 " --> pdb=" O ARG F 219 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU F 227 " --> pdb=" O ILE F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 232 No H-bonds generated for 'chain 'F' and resid 230 through 232' Processing helix chain 'F' and resid 233 through 252 Processing helix chain 'F' and resid 265 through 268 removed outlier: 4.092A pdb=" N GLY F 268 " --> pdb=" O HIS F 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 265 through 268' Processing helix chain 'F' and resid 293 through 301 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 Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.792A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 412 removed outlier: 4.400A pdb=" N HIS F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU F 402 " --> pdb=" O GLU F 398 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.807A 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 447 removed outlier: 3.989A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 473 through 485 removed outlier: 3.726A pdb=" N TRP F 477 " --> pdb=" O TRP F 473 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG F 482 " --> pdb=" O TRP F 478 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU F 483 " --> pdb=" O GLU F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 508 removed outlier: 3.638A pdb=" N SER F 507 " --> pdb=" O LEU F 503 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN F 508 " --> pdb=" O PHE F 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 503 through 508' Processing helix chain 'F' and resid 512 through 532 removed outlier: 4.069A pdb=" N TYR F 516 " --> pdb=" O PHE F 512 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.598A pdb=" N GLY F 551 " --> pdb=" O SER F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 581 through 588 Processing helix chain 'F' and resid 588 through 597 removed outlier: 3.875A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 53 removed outlier: 3.526A pdb=" N GLN G 24 " --> pdb=" O THR G 20 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU G 35 " --> pdb=" O LYS G 31 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP G 38 " --> pdb=" O HIS G 34 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 79 removed outlier: 4.152A pdb=" N ASN G 61 " --> pdb=" O GLU G 57 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N MET G 62 " --> pdb=" O ASN G 58 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN G 63 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS G 68 " --> pdb=" O ASN G 64 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLU G 75 " --> pdb=" O ALA G 71 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN G 76 " --> pdb=" O PHE G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 101 Processing helix chain 'G' and resid 103 through 108 removed outlier: 3.565A pdb=" N VAL G 107 " --> pdb=" O GLY G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 129 removed outlier: 3.817A pdb=" N ARG G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 154 Processing helix chain 'G' and resid 158 through 173 removed outlier: 3.798A pdb=" N LEU G 162 " --> pdb=" O TYR G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 194 Processing helix chain 'G' and resid 198 through 205 Processing helix chain 'G' and resid 206 through 208 No H-bonds generated for 'chain 'G' and resid 206 through 208' Processing helix chain 'G' and resid 218 through 229 removed outlier: 3.818A pdb=" N LEU G 222 " --> pdb=" O SER G 218 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE G 223 " --> pdb=" O ARG G 219 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU G 224 " --> pdb=" O GLY G 220 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU G 227 " --> pdb=" O ILE G 223 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR G 229 " --> pdb=" O ASP G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 250 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 385 Processing helix chain 'G' and resid 389 through 393 removed outlier: 3.909A pdb=" N ARG G 393 " --> pdb=" O PHE G 390 " (cutoff:3.500A) Processing helix chain 'G' and resid 397 through 412 removed outlier: 4.154A pdb=" N HIS G 401 " --> pdb=" O ASN G 397 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU G 402 " --> pdb=" O GLU G 398 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N MET G 408 " --> pdb=" O VAL G 404 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER G 409 " --> pdb=" O GLY G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 421 Processing helix chain 'G' and resid 431 through 446 removed outlier: 3.830A pdb=" N THR G 445 " --> pdb=" O LYS G 441 " (cutoff:3.500A) Processing helix chain 'G' and resid 449 through 466 Processing helix chain 'G' and resid 473 through 485 removed outlier: 3.548A pdb=" N ARG G 482 " --> pdb=" O TRP G 478 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU G 483 " --> pdb=" O GLU G 479 " (cutoff:3.500A) Processing helix chain 'G' and resid 503 through 508 removed outlier: 4.219A pdb=" N SER G 507 " --> pdb=" O LEU G 503 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN G 508 " --> pdb=" O PHE G 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 503 through 508' Processing helix chain 'G' and resid 512 through 532 removed outlier: 4.078A pdb=" N TYR G 516 " --> pdb=" O PHE G 512 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR G 519 " --> pdb=" O TYR G 515 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU G 520 " --> pdb=" O TYR G 516 " (cutoff:3.500A) Processing helix chain 'G' and resid 547 through 559 removed outlier: 4.038A pdb=" N MET G 557 " --> pdb=" O LYS G 553 " (cutoff:3.500A) Processing helix chain 'G' and resid 560 through 564 removed outlier: 4.207A 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 removed outlier: 3.599A pdb=" N PHE G 588 " --> pdb=" O LEU G 584 " (cutoff:3.500A) Processing helix chain 'G' and resid 588 through 599 removed outlier: 3.595A pdb=" N ASP G 597 " --> pdb=" O THR G 593 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 53 removed outlier: 3.519A pdb=" N GLN H 24 " --> pdb=" O THR H 20 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS H 34 " --> pdb=" O ASP H 30 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU H 35 " --> pdb=" O LYS H 31 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP H 38 " --> pdb=" O HIS H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 80 removed outlier: 3.742A pdb=" N MET H 62 " --> pdb=" O ASN H 58 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN H 63 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU H 75 " --> pdb=" O ALA H 71 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN H 76 " --> pdb=" O PHE H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 101 Processing helix chain 'H' and resid 103 through 108 removed outlier: 4.085A pdb=" N SER H 106 " --> pdb=" O ASN H 103 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL H 107 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU H 108 " --> pdb=" O SER H 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 103 through 108' Processing helix chain 'H' and resid 109 through 129 Processing helix chain 'H' and resid 147 through 154 Processing helix chain 'H' and resid 159 through 172 removed outlier: 3.560A pdb=" N VAL H 172 " --> pdb=" O TRP H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 194 removed outlier: 4.353A pdb=" N LEU H 179 " --> pdb=" O GLN H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 205 removed outlier: 3.607A pdb=" N TYR H 202 " --> pdb=" O ASP H 198 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 208 No H-bonds generated for 'chain 'H' and resid 206 through 208' Processing helix chain 'H' and resid 218 through 229 removed outlier: 3.638A pdb=" N ILE H 223 " --> pdb=" O ARG H 219 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU H 224 " --> pdb=" O GLY H 220 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU H 227 " --> pdb=" O ILE H 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 232 No H-bonds generated for 'chain 'H' and resid 230 through 232' Processing helix chain 'H' and resid 233 through 252 removed outlier: 3.547A pdb=" N MET H 249 " --> pdb=" O ARG H 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 275 through 280 removed outlier: 4.193A pdb=" N SER H 280 " --> pdb=" O THR H 276 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 301 Processing helix chain 'H' and resid 303 through 319 Processing helix chain 'H' and resid 326 through 331 Processing helix chain 'H' and resid 365 through 385 Processing helix chain 'H' and resid 389 through 393 removed outlier: 3.773A pdb=" N ARG H 393 " --> pdb=" O PHE H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 397 through 412 removed outlier: 4.109A pdb=" N HIS H 401 " --> pdb=" O ASN H 397 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU H 402 " --> pdb=" O GLU H 398 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N MET H 408 " --> pdb=" O VAL H 404 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER H 409 " --> pdb=" O GLY H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 421 Processing helix chain 'H' and resid 431 through 447 removed outlier: 3.789A pdb=" N THR H 445 " --> pdb=" O LYS H 441 " (cutoff:3.500A) Processing helix chain 'H' and resid 449 through 466 Processing helix chain 'H' and resid 473 through 484 removed outlier: 3.509A pdb=" N TRP H 477 " --> pdb=" O TRP H 473 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARG H 482 " --> pdb=" O TRP H 478 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU H 483 " --> pdb=" O GLU H 479 " (cutoff:3.500A) Processing helix chain 'H' and resid 503 through 508 removed outlier: 3.911A pdb=" N SER H 507 " --> pdb=" O LEU H 503 " (cutoff:3.500A) Processing helix chain 'H' and resid 512 through 532 removed outlier: 4.304A pdb=" N TYR H 516 " --> pdb=" O PHE H 512 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR H 519 " --> pdb=" O TYR H 515 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU H 520 " --> pdb=" O TYR H 516 " (cutoff:3.500A) Processing helix chain 'H' and resid 547 through 559 removed outlier: 3.586A pdb=" N GLY H 551 " --> pdb=" O SER H 547 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET H 557 " --> pdb=" O LYS H 553 " (cutoff:3.500A) Processing helix chain 'H' and resid 560 through 564 removed outlier: 3.978A pdb=" N SER H 563 " --> pdb=" O LEU H 560 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU H 564 " --> pdb=" O GLY H 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 560 through 564' Processing helix chain 'H' and resid 565 through 570 Processing helix chain 'H' and resid 581 through 588 Processing helix chain 'H' and resid 588 through 599 removed outlier: 3.980A pdb=" N ASP H 597 " --> pdb=" O THR H 593 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASN H 599 " --> pdb=" O LEU H 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.958A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N HIS A 205 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 9.053A pdb=" N LEU A 221 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 6.912A 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: 5.951A pdb=" N PHE A 43 " --> pdb=" O ARG C 565 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLY C 564 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASP C 572 " --> pdb=" O ILE C 585 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.056A 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: 7.196A pdb=" N ARG A 235 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N PHE A 106 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLN A 237 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N TRP A 104 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU A 239 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 309 through 317 removed outlier: 5.554A pdb=" N ILE A 310 " --> pdb=" O THR A 597 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR A 597 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N GLN A 312 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL A 595 " --> pdb=" O GLN A 312 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER A 314 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 323 through 324 removed outlier: 5.865A pdb=" N ASP A 572 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLY A 564 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N PHE A 563 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 352 through 356 Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 360 removed outlier: 6.808A pdb=" N CYS A 359 " --> pdb=" O CYS A 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 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 471 through 472 Processing sheet with id=AB2, first strand: chain 'A' and resid 652 through 653 removed outlier: 6.359A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ALA A 670 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 699 through 701 removed outlier: 6.716A pdb=" N ALA A 699 " --> pdb=" O ILE B 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 709 through 711 removed outlier: 3.722A pdb=" N THR A1074 " --> pdb=" O SER A1095 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA A1076 " --> pdb=" O PHE A1093 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N PHE A1093 " --> pdb=" O ALA A1076 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 715 through 726 removed outlier: 6.038A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 731 through 734 removed outlier: 4.531A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 785 through 787 removed outlier: 3.503A pdb=" N ASN C 701 " --> pdb=" O ILE A 786 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1118 through 1120 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.006A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N HIS B 205 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N LEU B 221 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL B 36 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.045A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.167A pdb=" N ARG B 235 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N PHE B 106 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLN B 237 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N TRP B 104 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU B 239 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 11.451A pdb=" N VAL B 126 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 10.189A pdb=" N GLU B 167 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.271A pdb=" N ILE B 128 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N THR B 165 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL B 130 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ASN B 163 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU B 132 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA B 161 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N GLN B 134 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 309 through 317 removed outlier: 5.566A pdb=" N ILE B 310 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N THR B 597 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLN B 312 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL B 595 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER B 314 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 323 through 324 removed outlier: 5.740A pdb=" N ASP B 572 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR B 570 " --> pdb=" O ASP B 566 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLY B 564 " --> pdb=" O ASP B 572 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 352 through 356 Processing sheet with id=AC6, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.711A pdb=" N CYS B 359 " --> pdb=" O CYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 450 through 452 Processing sheet with id=AC8, first strand: chain 'B' and resid 471 through 472 Processing sheet with id=AC9, first strand: chain 'B' and resid 652 through 658 removed outlier: 6.007A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N VAL B 654 " --> pdb=" O THR B 694 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 699 through 700 removed outlier: 6.927A pdb=" N ALA B 699 " --> pdb=" O ILE C 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 709 through 711 removed outlier: 3.684A pdb=" N THR B1074 " --> pdb=" O SER B1095 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA B1076 " --> pdb=" O PHE B1093 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N PHE B1093 " --> pdb=" O ALA B1076 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 715 through 726 removed outlier: 3.541A pdb=" N MET B1048 " --> pdb=" O VAL B1063 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 731 through 734 removed outlier: 4.496A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1118 through 1120 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.879A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) removed outlier: 9.592A pdb=" N HIS C 205 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 9.373A pdb=" N LEU C 221 " --> pdb=" O HIS C 205 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL C 36 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.063A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.191A pdb=" N ARG C 235 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N PHE C 106 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLN C 237 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N TRP C 104 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU C 239 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 11.381A pdb=" N VAL C 126 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 10.081A pdb=" N GLU C 167 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.049A pdb=" N ILE C 128 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N THR C 165 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL C 130 " --> pdb=" O ASN C 163 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASN C 163 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLU C 132 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA C 161 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N GLN C 134 " --> pdb=" O SER C 159 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 309 through 317 removed outlier: 7.047A pdb=" N VAL C 593 " --> pdb=" O THR C 313 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ASN C 315 " --> pdb=" O GLY C 591 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY C 591 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AE2, first strand: chain 'C' and resid 359 through 360 removed outlier: 6.632A pdb=" N CYS C 359 " --> pdb=" O CYS C 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 451 through 452 Processing sheet with id=AE4, first strand: chain 'C' and resid 471 through 472 Processing sheet with id=AE5, first strand: chain 'C' and resid 652 through 653 removed outlier: 6.032A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA C 670 " --> pdb=" O PRO C 663 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 709 through 711 removed outlier: 3.602A pdb=" N THR C1074 " --> pdb=" O SER C1095 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA C1076 " --> pdb=" O PHE C1093 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE C1093 " --> pdb=" O ALA C1076 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 715 through 726 removed outlier: 3.531A pdb=" N MET C1048 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 731 through 734 removed outlier: 4.413A pdb=" N LYS C 731 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1118 through 1120 Processing sheet with id=AF1, first strand: chain 'F' and resid 132 through 133 Processing sheet with id=AF2, first strand: chain 'F' and resid 262 through 263 removed outlier: 6.745A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'F' and resid 347 through 350 Processing sheet with id=AF4, first strand: chain 'G' and resid 132 through 134 removed outlier: 4.097A pdb=" N ASN G 134 " --> pdb=" O GLU G 140 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N GLU G 140 " --> pdb=" O ASN G 134 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 347 through 350 Processing sheet with id=AF6, first strand: chain 'H' and resid 132 through 134 removed outlier: 4.303A pdb=" N ASN H 134 " --> pdb=" O GLU H 140 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU H 140 " --> pdb=" O ASN H 134 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 347 through 350 1709 hydrogen bonds defined for protein. 4830 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: 17.39 Time building geometry restraints manager: 17.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12682 1.34 - 1.46: 9956 1.46 - 1.58: 17956 1.58 - 1.70: 0 1.70 - 1.82: 282 Bond restraints: 40876 Sorted by residual: bond pdb=" C1 NAG n 1 " pdb=" O5 NAG n 1 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.11e+00 bond pdb=" C1 NAG b 1 " pdb=" O5 NAG b 1 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.87e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.53e+00 bond pdb=" C1 NAG q 1 " pdb=" O5 NAG q 1 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.76e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.04e+00 ... (remaining 40871 not shown) Histogram of bond angle deviations from ideal: 97.77 - 105.03: 745 105.03 - 112.30: 20793 112.30 - 119.56: 13143 119.56 - 126.83: 20334 126.83 - 134.09: 574 Bond angle restraints: 55589 Sorted by residual: angle pdb=" N VAL H 506 " pdb=" CA VAL H 506 " pdb=" C VAL H 506 " ideal model delta sigma weight residual 113.71 107.87 5.84 9.50e-01 1.11e+00 3.78e+01 angle pdb=" N VAL H 172 " pdb=" CA VAL H 172 " pdb=" C VAL H 172 " ideal model delta sigma weight residual 113.53 108.42 5.11 9.80e-01 1.04e+00 2.71e+01 angle pdb=" N VAL B 157 " pdb=" CA VAL B 157 " pdb=" C VAL B 157 " ideal model delta sigma weight residual 113.42 108.42 5.00 1.17e+00 7.31e-01 1.82e+01 angle pdb=" N ILE A 803 " pdb=" CA ILE A 803 " pdb=" C ILE A 803 " ideal model delta sigma weight residual 113.53 110.00 3.53 9.80e-01 1.04e+00 1.30e+01 angle pdb=" CB ARG G 192 " pdb=" CG ARG G 192 " pdb=" CD ARG G 192 " ideal model delta sigma weight residual 111.30 118.15 -6.85 2.30e+00 1.89e-01 8.87e+00 ... (remaining 55584 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 21145 17.90 - 35.79: 1940 35.79 - 53.69: 358 53.69 - 71.59: 66 71.59 - 89.48: 50 Dihedral angle restraints: 23559 sinusoidal: 9342 harmonic: 14217 Sorted by residual: dihedral pdb=" CB CYS C 289 " pdb=" SG CYS C 289 " pdb=" SG CYS C 299 " pdb=" CB CYS C 299 " ideal model delta sinusoidal sigma weight residual -86.00 -175.48 89.48 1 1.00e+01 1.00e-02 9.51e+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 93.00 178.89 -85.89 1 1.00e+01 1.00e-02 8.91e+01 dihedral pdb=" CB CYS B1080 " pdb=" SG CYS B1080 " pdb=" SG CYS B1124 " pdb=" CB CYS B1124 " ideal model delta sinusoidal sigma weight residual -86.00 -0.23 -85.77 1 1.00e+01 1.00e-02 8.89e+01 ... (remaining 23556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 5594 0.069 - 0.138: 767 0.138 - 0.207: 31 0.207 - 0.277: 3 0.277 - 0.346: 1 Chirality restraints: 6396 Sorted by residual: chirality pdb=" C1 NAG g 1 " pdb=" ND2 ASN C 232 " pdb=" C2 NAG g 1 " pdb=" O5 NAG g 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" C4 NAG n 1 " pdb=" C3 NAG n 1 " pdb=" C5 NAG n 1 " pdb=" O4 NAG n 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.29 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN A 707 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 6393 not shown) Planarity restraints: 7132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 232 " 0.024 2.00e-02 2.50e+03 2.18e-02 5.91e+00 pdb=" CG ASN C 232 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN C 232 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN C 232 " -0.024 2.00e-02 2.50e+03 pdb=" C1 NAG g 1 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 232 " -0.019 2.00e-02 2.50e+03 1.81e-02 4.10e+00 pdb=" CG ASN A 232 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN A 232 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 232 " 0.021 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 884 " 0.013 2.00e-02 2.50e+03 1.15e-02 3.30e+00 pdb=" CG TRP C 884 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP C 884 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP C 884 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 884 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 884 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 884 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 884 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 884 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 884 " 0.002 2.00e-02 2.50e+03 ... (remaining 7129 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 856 2.68 - 3.23: 39140 3.23 - 3.79: 63104 3.79 - 4.34: 81585 4.34 - 4.90: 135190 Nonbonded interactions: 319875 Sorted by model distance: nonbonded pdb=" OG SER C 347 " pdb=" O ARG C 450 " model vdw 2.123 2.440 nonbonded pdb=" OG1 THR A 124 " pdb=" OD1 ASN A 125 " model vdw 2.142 2.440 nonbonded pdb=" OG1 THR C 124 " pdb=" OD1 ASN C 125 " model vdw 2.157 2.440 nonbonded pdb=" OD1 ASP H 382 " pdb=" OH TYR H 385 " model vdw 2.163 2.440 nonbonded pdb=" OD1 ASP B 566 " pdb=" OG1 THR B 570 " model vdw 2.180 2.440 ... (remaining 319870 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' 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' selection = chain 'q' selection = chain 'r' } ncs_group { reference = chain 'F' selection = (chain 'G' and (resid 19 through 614 or resid 2001)) selection = chain 'H' } 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: 2.310 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: 0.050 Extract box with map and model: 15.680 Check model and map are aligned: 0.520 Set scattering table: 0.320 Process input model: 94.800 Find NCS groups from input model: 2.570 Set up NCS constraints: 0.790 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: 0.000 Load rotamer database and sin/cos tables:13.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 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 : 0.004 0.057 40876 Z= 0.280 Angle : 0.579 9.410 55589 Z= 0.287 Chirality : 0.045 0.346 6396 Planarity : 0.004 0.065 7079 Dihedral : 14.333 89.477 14259 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.92 % Favored : 95.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.12), residues: 4815 helix: 1.64 (0.13), residues: 1657 sheet: 0.30 (0.19), residues: 725 loop : -1.36 (0.12), residues: 2433 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 397 time to evaluate : 4.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 2 residues processed: 397 average time/residue: 1.4946 time to fit residues: 729.9726 Evaluate side-chains 187 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 185 time to evaluate : 4.312 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 1.3972 time to fit residues: 7.5817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 407 optimal weight: 40.0000 chunk 366 optimal weight: 30.0000 chunk 203 optimal weight: 0.1980 chunk 125 optimal weight: 0.9990 chunk 246 optimal weight: 20.0000 chunk 195 optimal weight: 1.9990 chunk 378 optimal weight: 10.0000 chunk 146 optimal weight: 40.0000 chunk 230 optimal weight: 3.9990 chunk 281 optimal weight: 1.9990 chunk 438 optimal weight: 50.0000 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 ASN ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 243 HIS ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 380 GLN ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 508 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 ASN ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 508 ASN ** H 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 40876 Z= 0.281 Angle : 0.589 9.665 55589 Z= 0.300 Chirality : 0.045 0.261 6396 Planarity : 0.004 0.048 7079 Dihedral : 4.285 24.490 5223 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.25 % Favored : 94.72 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.12), residues: 4815 helix: 1.59 (0.13), residues: 1717 sheet: 0.39 (0.19), residues: 722 loop : -1.37 (0.12), residues: 2376 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 206 time to evaluate : 4.623 Fit side-chains revert: symmetry clash outliers start: 58 outliers final: 17 residues processed: 242 average time/residue: 1.5361 time to fit residues: 459.2612 Evaluate side-chains 197 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 180 time to evaluate : 4.153 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 11 residues processed: 6 average time/residue: 0.6201 time to fit residues: 11.4284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 243 optimal weight: 40.0000 chunk 136 optimal weight: 7.9990 chunk 365 optimal weight: 20.0000 chunk 298 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 439 optimal weight: 40.0000 chunk 474 optimal weight: 7.9990 chunk 391 optimal weight: 20.0000 chunk 435 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 352 optimal weight: 7.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 762 ASN A 899 GLN A 912 ASN B 81 ASN C 749 ASN C 899 GLN C 912 ASN C1009 GLN ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 508 ASN H 117 ASN H 194 ASN H 239 HIS H 330 ASN H 531 GLN H 572 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.098 40876 Z= 0.582 Angle : 0.731 11.160 55589 Z= 0.372 Chirality : 0.053 0.403 6396 Planarity : 0.005 0.058 7079 Dihedral : 4.720 21.190 5223 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.06 % Favored : 93.91 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.12), residues: 4815 helix: 1.17 (0.12), residues: 1725 sheet: 0.02 (0.18), residues: 744 loop : -1.51 (0.12), residues: 2346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 183 time to evaluate : 4.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 54 residues processed: 264 average time/residue: 1.3623 time to fit residues: 455.9605 Evaluate side-chains 218 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 164 time to evaluate : 4.348 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 44 residues processed: 10 average time/residue: 0.6527 time to fit residues: 15.8767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 434 optimal weight: 20.0000 chunk 330 optimal weight: 5.9990 chunk 228 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 209 optimal weight: 2.9990 chunk 295 optimal weight: 0.8980 chunk 440 optimal weight: 20.0000 chunk 466 optimal weight: 50.0000 chunk 230 optimal weight: 5.9990 chunk 417 optimal weight: 50.0000 chunk 125 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 899 GLN A 912 ASN A 963 GLN C 802 GLN ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 239 HIS H 493 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.071 40876 Z= 0.282 Angle : 0.586 11.009 55589 Z= 0.296 Chirality : 0.045 0.312 6396 Planarity : 0.004 0.060 7079 Dihedral : 4.372 21.571 5223 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.09 % Favored : 94.89 % Rotamer Outliers : 2.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.12), residues: 4815 helix: 1.39 (0.13), residues: 1718 sheet: 0.32 (0.18), residues: 725 loop : -1.50 (0.12), residues: 2372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 183 time to evaluate : 4.560 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 122 outliers final: 64 residues processed: 283 average time/residue: 1.3185 time to fit residues: 479.0905 Evaluate side-chains 235 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 171 time to evaluate : 3.962 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 54 residues processed: 11 average time/residue: 0.6236 time to fit residues: 16.1686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 388 optimal weight: 30.0000 chunk 265 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 347 optimal weight: 1.9990 chunk 192 optimal weight: 0.7980 chunk 398 optimal weight: 20.0000 chunk 322 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 238 optimal weight: 10.0000 chunk 419 optimal weight: 40.0000 chunk 117 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 HIS ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 ASN C 963 GLN ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 ASN H 239 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 40876 Z= 0.289 Angle : 0.588 9.852 55589 Z= 0.296 Chirality : 0.045 0.317 6396 Planarity : 0.004 0.066 7079 Dihedral : 4.322 21.058 5223 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.38 % Favored : 94.60 % Rotamer Outliers : 2.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.12), residues: 4815 helix: 1.47 (0.13), residues: 1715 sheet: 0.29 (0.19), residues: 712 loop : -1.44 (0.12), residues: 2388 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 176 time to evaluate : 4.379 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 124 outliers final: 71 residues processed: 280 average time/residue: 1.3097 time to fit residues: 467.2042 Evaluate side-chains 234 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 163 time to evaluate : 4.396 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 62 residues processed: 10 average time/residue: 0.6058 time to fit residues: 16.0684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 157 optimal weight: 2.9990 chunk 420 optimal weight: 30.0000 chunk 92 optimal weight: 0.0970 chunk 274 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 467 optimal weight: 50.0000 chunk 387 optimal weight: 50.0000 chunk 216 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 245 optimal weight: 30.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 912 ASN ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 899 GLN C 912 ASN ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 ASN H 239 HIS ** H 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 40876 Z= 0.201 Angle : 0.558 18.316 55589 Z= 0.277 Chirality : 0.043 0.306 6396 Planarity : 0.004 0.062 7079 Dihedral : 4.160 21.100 5223 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.92 % Favored : 95.06 % Rotamer Outliers : 2.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.12), residues: 4815 helix: 1.62 (0.13), residues: 1706 sheet: 0.40 (0.19), residues: 717 loop : -1.40 (0.12), residues: 2392 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 172 time to evaluate : 4.727 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 113 outliers final: 73 residues processed: 269 average time/residue: 1.2818 time to fit residues: 444.2799 Evaluate side-chains 238 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 165 time to evaluate : 4.619 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 65 residues processed: 9 average time/residue: 0.7370 time to fit residues: 15.7031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 450 optimal weight: 40.0000 chunk 52 optimal weight: 0.9990 chunk 266 optimal weight: 0.8980 chunk 341 optimal weight: 30.0000 chunk 264 optimal weight: 0.4980 chunk 393 optimal weight: 30.0000 chunk 260 optimal weight: 1.9990 chunk 465 optimal weight: 9.9990 chunk 291 optimal weight: 1.9990 chunk 283 optimal weight: 1.9990 chunk 214 optimal weight: 9.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 912 ASN ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 912 ASN ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 ASN H 239 HIS ** H 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 40876 Z= 0.207 Angle : 0.550 12.681 55589 Z= 0.274 Chirality : 0.043 0.293 6396 Planarity : 0.004 0.057 7079 Dihedral : 4.079 20.679 5223 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.09 % Favored : 94.89 % Rotamer Outliers : 2.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.12), residues: 4815 helix: 1.65 (0.13), residues: 1718 sheet: 0.48 (0.19), residues: 703 loop : -1.35 (0.12), residues: 2394 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 184 time to evaluate : 4.873 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 123 outliers final: 81 residues processed: 282 average time/residue: 1.2507 time to fit residues: 453.6940 Evaluate side-chains 247 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 166 time to evaluate : 4.128 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 72 residues processed: 12 average time/residue: 0.5180 time to fit residues: 15.6948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 288 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 278 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 295 optimal weight: 0.9990 chunk 317 optimal weight: 10.0000 chunk 230 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 365 optimal weight: 30.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 912 ASN B 81 ASN ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 239 HIS H 524 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 40876 Z= 0.211 Angle : 0.555 13.832 55589 Z= 0.277 Chirality : 0.043 0.293 6396 Planarity : 0.004 0.096 7079 Dihedral : 4.056 21.061 5223 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.96 % Favored : 95.02 % Rotamer Outliers : 2.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.12), residues: 4815 helix: 1.67 (0.13), residues: 1721 sheet: 0.52 (0.19), residues: 698 loop : -1.34 (0.12), residues: 2396 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 171 time to evaluate : 4.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 108 outliers final: 73 residues processed: 263 average time/residue: 1.3199 time to fit residues: 447.7655 Evaluate side-chains 240 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 167 time to evaluate : 4.462 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 70 residues processed: 5 average time/residue: 0.7380 time to fit residues: 11.5595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 423 optimal weight: 30.0000 chunk 445 optimal weight: 3.9990 chunk 406 optimal weight: 8.9990 chunk 433 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 340 optimal weight: 20.0000 chunk 133 optimal weight: 6.9990 chunk 392 optimal weight: 0.0070 chunk 410 optimal weight: 30.0000 chunk 432 optimal weight: 0.9980 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 912 ASN ** B 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 912 ASN ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 394 ASN ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 239 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 40876 Z= 0.288 Angle : 0.598 11.741 55589 Z= 0.298 Chirality : 0.045 0.327 6396 Planarity : 0.004 0.087 7079 Dihedral : 4.189 20.960 5223 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.32 % Favored : 94.66 % Rotamer Outliers : 2.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.12), residues: 4815 helix: 1.60 (0.13), residues: 1719 sheet: 0.39 (0.19), residues: 700 loop : -1.38 (0.12), residues: 2396 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 174 time to evaluate : 4.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 73 residues processed: 258 average time/residue: 1.2843 time to fit residues: 423.8750 Evaluate side-chains 238 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 165 time to evaluate : 4.537 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 68 residues processed: 7 average time/residue: 0.5020 time to fit residues: 12.1889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 284 optimal weight: 1.9990 chunk 458 optimal weight: 40.0000 chunk 279 optimal weight: 0.8980 chunk 217 optimal weight: 2.9990 chunk 318 optimal weight: 9.9990 chunk 481 optimal weight: 20.0000 chunk 442 optimal weight: 50.0000 chunk 383 optimal weight: 8.9990 chunk 39 optimal weight: 30.0000 chunk 295 optimal weight: 1.9990 chunk 234 optimal weight: 8.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 899 GLN A 912 ASN ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 899 GLN F 63 ASN ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 305 GLN ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN H 194 ASN H 239 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.080 40876 Z= 0.459 Angle : 0.679 11.652 55589 Z= 0.341 Chirality : 0.049 0.383 6396 Planarity : 0.005 0.090 7079 Dihedral : 4.469 20.491 5223 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.84 % Favored : 94.14 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.12), residues: 4815 helix: 1.44 (0.13), residues: 1710 sheet: 0.14 (0.20), residues: 645 loop : -1.46 (0.12), residues: 2460 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9630 Ramachandran restraints generated. 4815 Oldfield, 0 Emsley, 4815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 168 time to evaluate : 4.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 68 residues processed: 252 average time/residue: 1.3057 time to fit residues: 424.9204 Evaluate side-chains 231 residues out of total 4272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 163 time to evaluate : 4.380 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 64 residues processed: 5 average time/residue: 0.7061 time to fit residues: 11.1959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 483 random chunks: chunk 304 optimal weight: 0.7980 chunk 408 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 353 optimal weight: 5.9990 chunk 56 optimal weight: 0.1980 chunk 106 optimal weight: 1.9990 chunk 383 optimal weight: 40.0000 chunk 160 optimal weight: 1.9990 chunk 394 optimal weight: 40.0000 chunk 48 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 899 GLN ** A 955 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN C 81 ASN C 899 GLN ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 239 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.225157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.169610 restraints weight = 63813.037| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 5.21 r_work: 0.3153 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 40876 Z= 0.199 Angle : 0.570 11.293 55589 Z= 0.283 Chirality : 0.043 0.307 6396 Planarity : 0.004 0.078 7079 Dihedral : 4.154 23.741 5223 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.76 % Favored : 95.22 % Rotamer Outliers : 1.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.12), residues: 4815 helix: 1.60 (0.13), residues: 1723 sheet: 0.39 (0.19), residues: 705 loop : -1.37 (0.12), residues: 2387 =============================================================================== Job complete usr+sys time: 10364.44 seconds wall clock time: 187 minutes 34.68 seconds (11254.68 seconds total)