Starting phenix.real_space_refine on Wed Apr 10 17:34:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dfh_7876/04_2024/6dfh_7876.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dfh_7876/04_2024/6dfh_7876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dfh_7876/04_2024/6dfh_7876.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dfh_7876/04_2024/6dfh_7876.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dfh_7876/04_2024/6dfh_7876.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dfh_7876/04_2024/6dfh_7876.pdb" } resolution = 3.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 120 5.16 5 C 12618 2.51 5 N 3288 2.21 5 O 4020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 20046 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3487 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 23, 'TRANS': 416} Chain breaks: 3 Chain: "B" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1025 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "H" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 977 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "L" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 797 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "C" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3487 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 23, 'TRANS': 416} Chain breaks: 3 Chain: "E" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1025 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "G" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 977 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "J" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 797 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "D" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3487 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 23, 'TRANS': 416} Chain breaks: 3 Chain: "F" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1025 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "I" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 977 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "K" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 797 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "a" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "i" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.33, per 1000 atoms: 0.52 Number of scatterers: 20046 At special positions: 0 Unit cell: (152.44, 156.56, 143.17, 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 120 16.00 O 4020 8.00 N 3288 7.00 C 12618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.02 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.01 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.02 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.01 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.08 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.02 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.02 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.01 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=1.99 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 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 ALPHA1-2 " MAN R 4 " - " MAN R 5 " " MAN S 4 " - " MAN S 5 " " MAN S 5 " - " MAN S 6 " " MAN Z 4 " - " MAN Z 5 " " MAN a 4 " - " MAN a 5 " " MAN a 5 " - " MAN a 6 " " MAN h 4 " - " MAN h 5 " " MAN i 4 " - " MAN i 5 " " MAN i 5 " - " MAN i 6 " ALPHA1-3 " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 4 " " BMA Z 3 " - " MAN Z 4 " " BMA a 3 " - " MAN a 4 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 4 " ALPHA1-6 " BMA S 3 " - " MAN S 7 " " BMA a 3 " - " MAN a 7 " " BMA i 3 " - " MAN i 7 " BETA1-4 " 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 R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " 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 Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " 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 h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A 603 " - " ASN A 160 " " NAG A 608 " - " ASN A 301 " " NAG A 611 " - " ASN A 197 " " NAG A 626 " - " ASN A 339 " " NAG A 627 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG C 603 " - " ASN C 160 " " NAG C 608 " - " ASN C 301 " " NAG C 611 " - " ASN C 197 " " NAG C 626 " - " ASN C 339 " " NAG C 627 " - " ASN C 392 " " NAG D 603 " - " ASN D 160 " " NAG D 608 " - " ASN D 301 " " NAG D 611 " - " ASN D 197 " " NAG D 626 " - " ASN D 339 " " NAG D 627 " - " ASN D 392 " " NAG E 701 " - " ASN E 611 " " NAG F 701 " - " ASN F 611 " " NAG M 1 " - " ASN A 156 " " NAG N 1 " - " ASN A 276 " " NAG O 1 " - " ASN A 295 " " NAG P 1 " - " ASN A 386 " " NAG Q 1 " - " ASN A 234 " " NAG R 1 " - " ASN A 262 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 448 " " NAG U 1 " - " ASN C 156 " " NAG V 1 " - " ASN C 276 " " NAG W 1 " - " ASN C 295 " " NAG X 1 " - " ASN C 386 " " NAG Y 1 " - " ASN C 234 " " NAG Z 1 " - " ASN C 262 " " NAG a 1 " - " ASN C 332 " " NAG b 1 " - " ASN C 448 " " NAG c 1 " - " ASN D 156 " " NAG d 1 " - " ASN D 276 " " NAG e 1 " - " ASN D 295 " " NAG f 1 " - " ASN D 386 " " NAG g 1 " - " ASN D 234 " " NAG h 1 " - " ASN D 262 " " NAG i 1 " - " ASN D 332 " " NAG j 1 " - " ASN D 448 " Time building additional restraints: 8.79 Conformation dependent library (CDL) restraints added in 3.3 seconds 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4458 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 54 sheets defined 19.2% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.55 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.950A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.603A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 350 removed outlier: 3.543A pdb=" N VAL A 345 " --> pdb=" O THR A 341 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 removed outlier: 3.726A pdb=" N PHE A 391 " --> pdb=" O SER A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.763A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 429' Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.924A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 535 removed outlier: 3.592A pdb=" N MET B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 532 through 535' Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.763A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 removed outlier: 3.589A pdb=" N LYS B 574 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU B 584 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ASP B 589 " --> pdb=" O HIS B 585 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN B 590 " --> pdb=" O TYR B 586 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY B 594 " --> pdb=" O GLN B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 625 Processing helix chain 'B' and resid 628 through 636 removed outlier: 3.714A pdb=" N LYS B 633 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU B 634 " --> pdb=" O GLN B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 650 removed outlier: 3.702A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 645 " --> pdb=" O ILE B 641 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 648 " --> pdb=" O GLY B 644 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 661 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.736A pdb=" N ASP H 86 " --> pdb=" O THR H 83 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 83 through 87' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.628A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.951A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.603A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 334 through 350 removed outlier: 3.543A pdb=" N VAL C 345 " --> pdb=" O THR C 341 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 removed outlier: 3.727A pdb=" N PHE C 391 " --> pdb=" O SER C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.762A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 425 through 429' Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.925A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 535 removed outlier: 3.593A pdb=" N MET E 535 " --> pdb=" O ALA E 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 532 through 535' Processing helix chain 'E' and resid 536 through 543 removed outlier: 3.763A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 596 removed outlier: 3.589A pdb=" N LYS E 574 " --> pdb=" O VAL E 570 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA E 582 " --> pdb=" O ALA E 578 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL E 583 " --> pdb=" O ARG E 579 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU E 584 " --> pdb=" O VAL E 580 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ASP E 589 " --> pdb=" O HIS E 585 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN E 590 " --> pdb=" O TYR E 586 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY E 594 " --> pdb=" O GLN E 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 621 through 625 Processing helix chain 'E' and resid 628 through 636 removed outlier: 3.714A pdb=" N LYS E 633 " --> pdb=" O LEU E 629 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU E 634 " --> pdb=" O GLN E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 650 removed outlier: 3.702A pdb=" N GLY E 644 " --> pdb=" O GLN E 640 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU E 645 " --> pdb=" O ILE E 641 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU E 648 " --> pdb=" O GLY E 644 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLN E 650 " --> pdb=" O LEU E 646 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 661 Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.735A pdb=" N ASP G 86 " --> pdb=" O THR G 83 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR G 87 " --> pdb=" O ALA G 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 83 through 87' Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.628A pdb=" N GLU J 83 " --> pdb=" O ALA J 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 117 removed outlier: 3.951A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE D 109 " --> pdb=" O HIS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 removed outlier: 3.603A pdb=" N CYS D 126 " --> pdb=" O THR D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 334 through 350 removed outlier: 3.543A pdb=" N VAL D 345 " --> pdb=" O THR D 341 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS D 347 " --> pdb=" O GLY D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 391 removed outlier: 3.727A pdb=" N PHE D 391 " --> pdb=" O SER D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 removed outlier: 3.763A pdb=" N GLN D 428 " --> pdb=" O ASN D 425 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG D 429 " --> pdb=" O MET D 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 425 through 429' Processing helix chain 'D' and resid 475 through 484 removed outlier: 3.925A pdb=" N TRP D 479 " --> pdb=" O MET D 475 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER D 481 " --> pdb=" O ASP D 477 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 535 removed outlier: 3.593A pdb=" N MET F 535 " --> pdb=" O ALA F 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 532 through 535' Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.764A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.589A pdb=" N LYS F 574 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA F 582 " --> pdb=" O ALA F 578 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL F 583 " --> pdb=" O ARG F 579 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU F 584 " --> pdb=" O VAL F 580 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ASP F 589 " --> pdb=" O HIS F 585 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN F 590 " --> pdb=" O TYR F 586 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY F 594 " --> pdb=" O GLN F 590 " (cutoff:3.500A) Processing helix chain 'F' and resid 621 through 625 Processing helix chain 'F' and resid 628 through 636 removed outlier: 3.714A pdb=" N LYS F 633 " --> pdb=" O LEU F 629 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 650 removed outlier: 3.702A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU F 645 " --> pdb=" O ILE F 641 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU F 648 " --> pdb=" O GLY F 644 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLN F 650 " --> pdb=" O LEU F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 656 through 661 Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.736A pdb=" N ASP I 86 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR I 87 " --> pdb=" O ALA I 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 83 through 87' Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.628A pdb=" N GLU K 83 " --> pdb=" O ALA K 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.559A pdb=" N LYS A 487 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 11.230A pdb=" N LYS A 487 " --> pdb=" O ASP A 47 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N ASP A 47 " --> pdb=" O LYS A 487 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N VAL A 489 " --> pdb=" O TRP A 45 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N TRP A 45 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 9.325A pdb=" N ILE A 491 " --> pdb=" O PRO A 43 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 92 removed outlier: 3.562A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 161 through 162 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 5.620A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 260 removed outlier: 3.595A pdb=" N LEU A 260 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 260 removed outlier: 3.595A pdb=" N LEU A 260 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 374 through 377 removed outlier: 4.332A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN A 295 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 301 through 308 removed outlier: 3.908A pdb=" N ASN A 301 " --> pdb=" O LEU A 323A" (cutoff:3.500A) removed outlier: 6.430A pdb=" N LYS A 305 " --> pdb=" O PHE A 320 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N PHE A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.185A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP H 36 " --> pdb=" O GLY H 49 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.185A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP H 36 " --> pdb=" O GLY H 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 67 through 72 Processing sheet with id=AB6, first strand: chain 'H' and resid 98 through 99 Processing sheet with id=AB7, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AB8, first strand: chain 'L' and resid 18 through 24 removed outlier: 3.762A pdb=" N CYS L 23 " --> pdb=" O VAL L 71 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.376A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.558A pdb=" N LYS C 487 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 11.229A pdb=" N LYS C 487 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N ASP C 47 " --> pdb=" O LYS C 487 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N VAL C 489 " --> pdb=" O TRP C 45 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N TRP C 45 " --> pdb=" O VAL C 489 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N ILE C 491 " --> pdb=" O PRO C 43 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N VAL C 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AC3, first strand: chain 'C' and resid 91 through 92 removed outlier: 3.560A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 173 through 177 Processing sheet with id=AC5, first strand: chain 'C' and resid 161 through 162 Processing sheet with id=AC6, first strand: chain 'C' and resid 200 through 203 removed outlier: 5.620A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 259 through 260 removed outlier: 3.595A pdb=" N LEU C 260 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 259 through 260 removed outlier: 3.595A pdb=" N LEU C 260 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 374 through 377 removed outlier: 4.331A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN C 295 " --> pdb=" O ASN C 332 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 301 through 308 removed outlier: 3.909A pdb=" N ASN C 301 " --> pdb=" O LEU C 323A" (cutoff:3.500A) removed outlier: 6.430A pdb=" N LYS C 305 " --> pdb=" O PHE C 320 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N PHE C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.185A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP G 36 " --> pdb=" O GLY G 49 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N CYS G 92 " --> pdb=" O TRP G 103 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TRP G 103 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARG G 94 " --> pdb=" O ASP G 101 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.185A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP G 36 " --> pdb=" O GLY G 49 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 67 through 72 Processing sheet with id=AD6, first strand: chain 'G' and resid 98 through 99 Processing sheet with id=AD7, first strand: chain 'J' and resid 9 through 12 Processing sheet with id=AD8, first strand: chain 'J' and resid 18 through 24 removed outlier: 3.762A pdb=" N CYS J 23 " --> pdb=" O VAL J 71 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 45 through 48 removed outlier: 6.375A pdb=" N TRP J 35 " --> pdb=" O VAL J 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 84 through 85 removed outlier: 3.559A pdb=" N LYS D 487 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 11.229A pdb=" N LYS D 487 " --> pdb=" O ASP D 47 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N ASP D 47 " --> pdb=" O LYS D 487 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N VAL D 489 " --> pdb=" O TRP D 45 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N TRP D 45 " --> pdb=" O VAL D 489 " (cutoff:3.500A) removed outlier: 9.325A pdb=" N ILE D 491 " --> pdb=" O PRO D 43 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL D 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AE3, first strand: chain 'D' and resid 91 through 92 removed outlier: 3.561A pdb=" N GLU D 91 " --> pdb=" O CYS D 239 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 173 through 177 Processing sheet with id=AE5, first strand: chain 'D' and resid 161 through 162 Processing sheet with id=AE6, first strand: chain 'D' and resid 200 through 203 removed outlier: 5.620A pdb=" N ALA D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TYR D 435 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 259 through 260 removed outlier: 3.595A pdb=" N LEU D 260 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 259 through 260 removed outlier: 3.595A pdb=" N LEU D 260 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 374 through 377 removed outlier: 4.331A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN D 295 " --> pdb=" O ASN D 332 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE D 443 " --> pdb=" O ARG D 298 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 301 through 308 removed outlier: 3.908A pdb=" N ASN D 301 " --> pdb=" O LEU D 323A" (cutoff:3.500A) removed outlier: 6.431A pdb=" N LYS D 305 " --> pdb=" O PHE D 320 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N PHE D 320 " --> pdb=" O LYS D 305 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ILE D 307 " --> pdb=" O TYR D 318 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N TYR D 318 " --> pdb=" O ILE D 307 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'I' and resid 57 through 59 removed outlier: 5.185A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP I 36 " --> pdb=" O GLY I 49 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N CYS I 92 " --> pdb=" O TRP I 103 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N TRP I 103 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG I 94 " --> pdb=" O ASP I 101 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 57 through 59 removed outlier: 5.185A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP I 36 " --> pdb=" O GLY I 49 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 67 through 72 Processing sheet with id=AF6, first strand: chain 'I' and resid 98 through 99 Processing sheet with id=AF7, first strand: chain 'K' and resid 9 through 12 Processing sheet with id=AF8, first strand: chain 'K' and resid 18 through 24 removed outlier: 3.763A pdb=" N CYS K 23 " --> pdb=" O VAL K 71 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 45 through 48 removed outlier: 6.375A pdb=" N TRP K 35 " --> pdb=" O VAL K 47 " (cutoff:3.500A) 603 hydrogen bonds defined for protein. 1539 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.44 Time building geometry restraints manager: 9.44 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: 6187 1.34 - 1.46: 4939 1.46 - 1.58: 9178 1.58 - 1.70: 0 1.70 - 1.82: 162 Bond restraints: 20466 Sorted by residual: bond pdb=" C5 MAN Z 4 " pdb=" O5 MAN Z 4 " ideal model delta sigma weight residual 1.418 1.466 -0.048 2.00e-02 2.50e+03 5.87e+00 bond pdb=" C5 MAN R 4 " pdb=" O5 MAN R 4 " ideal model delta sigma weight residual 1.418 1.465 -0.047 2.00e-02 2.50e+03 5.61e+00 bond pdb=" C5 MAN h 4 " pdb=" O5 MAN h 4 " ideal model delta sigma weight residual 1.418 1.465 -0.047 2.00e-02 2.50e+03 5.45e+00 bond pdb=" C1 NAG D 608 " pdb=" O5 NAG D 608 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.25e+00 bond pdb=" C5 MAN S 4 " pdb=" O5 MAN S 4 " ideal model delta sigma weight residual 1.418 1.462 -0.044 2.00e-02 2.50e+03 4.91e+00 ... (remaining 20461 not shown) Histogram of bond angle deviations from ideal: 98.72 - 105.81: 457 105.81 - 112.89: 11834 112.89 - 119.97: 6446 119.97 - 127.05: 8764 127.05 - 134.14: 315 Bond angle restraints: 27816 Sorted by residual: angle pdb=" C GLU A 64 " pdb=" N LYS A 65 " pdb=" CA LYS A 65 " ideal model delta sigma weight residual 121.54 132.51 -10.97 1.91e+00 2.74e-01 3.30e+01 angle pdb=" C GLU D 64 " pdb=" N LYS D 65 " pdb=" CA LYS D 65 " ideal model delta sigma weight residual 121.54 132.49 -10.95 1.91e+00 2.74e-01 3.28e+01 angle pdb=" C GLU C 64 " pdb=" N LYS C 65 " pdb=" CA LYS C 65 " ideal model delta sigma weight residual 121.54 132.42 -10.88 1.91e+00 2.74e-01 3.24e+01 angle pdb=" C GLU C 87 " pdb=" N ASN C 88 " pdb=" CA ASN C 88 " ideal model delta sigma weight residual 122.46 129.15 -6.69 1.41e+00 5.03e-01 2.25e+01 angle pdb=" C GLU D 87 " pdb=" N ASN D 88 " pdb=" CA ASN D 88 " ideal model delta sigma weight residual 122.46 129.15 -6.69 1.41e+00 5.03e-01 2.25e+01 ... (remaining 27811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.12: 12840 22.12 - 44.25: 435 44.25 - 66.37: 57 66.37 - 88.49: 48 88.49 - 110.61: 24 Dihedral angle restraints: 13404 sinusoidal: 6468 harmonic: 6936 Sorted by residual: dihedral pdb=" CB CYS C 501 " pdb=" SG CYS C 501 " pdb=" SG CYS E 605 " pdb=" CB CYS E 605 " ideal model delta sinusoidal sigma weight residual -86.00 -162.06 76.06 1 1.00e+01 1.00e-02 7.29e+01 dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS B 605 " pdb=" CB CYS B 605 " ideal model delta sinusoidal sigma weight residual -86.00 -161.94 75.94 1 1.00e+01 1.00e-02 7.27e+01 dihedral pdb=" CB CYS D 501 " pdb=" SG CYS D 501 " pdb=" SG CYS F 605 " pdb=" CB CYS F 605 " ideal model delta sinusoidal sigma weight residual -86.00 -161.71 75.71 1 1.00e+01 1.00e-02 7.23e+01 ... (remaining 13401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2579 0.068 - 0.135: 720 0.135 - 0.203: 78 0.203 - 0.270: 6 0.270 - 0.338: 10 Chirality restraints: 3393 Sorted by residual: chirality pdb=" C5 BMA S 3 " pdb=" C4 BMA S 3 " pdb=" C6 BMA S 3 " pdb=" O5 BMA S 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.61 0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" C5 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C6 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.61 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" C5 BMA i 3 " pdb=" C4 BMA i 3 " pdb=" C6 BMA i 3 " pdb=" O5 BMA i 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.61 0.33 2.00e-01 2.50e+01 2.79e+00 ... (remaining 3390 not shown) Planarity restraints: 3435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 65 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.93e+00 pdb=" C LYS D 65 " 0.052 2.00e-02 2.50e+03 pdb=" O LYS D 65 " -0.020 2.00e-02 2.50e+03 pdb=" N HIS D 66 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 65 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.85e+00 pdb=" C LYS A 65 " 0.051 2.00e-02 2.50e+03 pdb=" O LYS A 65 " -0.019 2.00e-02 2.50e+03 pdb=" N HIS A 66 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 65 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.78e+00 pdb=" C LYS C 65 " -0.051 2.00e-02 2.50e+03 pdb=" O LYS C 65 " 0.019 2.00e-02 2.50e+03 pdb=" N HIS C 66 " 0.017 2.00e-02 2.50e+03 ... (remaining 3432 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4696 2.78 - 3.31: 17698 3.31 - 3.84: 33530 3.84 - 4.37: 36996 4.37 - 4.90: 61133 Nonbonded interactions: 154053 Sorted by model distance: nonbonded pdb=" OE2 GLU D 64 " pdb=" O4 MAN h 4 " model vdw 2.252 2.440 nonbonded pdb=" O THR D 278 " pdb=" O6 NAG d 1 " model vdw 2.257 2.440 nonbonded pdb=" O ASN D 478 " pdb=" OG SER D 481 " model vdw 2.282 2.440 nonbonded pdb=" O ASN C 478 " pdb=" OG SER C 481 " model vdw 2.282 2.440 nonbonded pdb=" O ASN A 478 " pdb=" OG SER A 481 " model vdw 2.283 2.440 ... (remaining 154048 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 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'j' } ncs_group { reference = chain 'R' selection = chain 'Z' selection = chain 'h' } ncs_group { reference = chain 'S' selection = chain 'a' selection = chain 'i' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 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: 0.020 Extract box with map and model: 6.290 Check model and map are aligned: 0.290 Set scattering table: 0.200 Process input model: 54.280 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 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 : 0.009 0.103 20466 Z= 0.584 Angle : 1.049 10.967 27816 Z= 0.527 Chirality : 0.060 0.338 3393 Planarity : 0.007 0.067 3393 Dihedral : 12.651 110.613 8829 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 0.28 % Allowed : 1.85 % Favored : 97.86 % 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: -4.12 (0.15), residues: 2358 helix: -3.26 (0.18), residues: 354 sheet: -2.19 (0.19), residues: 657 loop : -2.94 (0.14), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP B 614 HIS 0.008 0.003 HIS D 66 PHE 0.023 0.004 PHE A 391 TYR 0.024 0.003 TYR C 217 ARG 0.004 0.001 ARG D 327 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 274 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 VAL cc_start: 0.9367 (t) cc_final: 0.8979 (t) REVERT: A 110 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8608 (tm-30) REVERT: A 116 LEU cc_start: 0.9669 (tp) cc_final: 0.9433 (tt) REVERT: A 150 MET cc_start: 0.9446 (mmm) cc_final: 0.8123 (mpp) REVERT: A 195 ASN cc_start: 0.8631 (p0) cc_final: 0.8346 (p0) REVERT: A 328 MET cc_start: 0.8724 (tpt) cc_final: 0.8222 (tpt) REVERT: B 539 VAL cc_start: 0.9350 (t) cc_final: 0.8864 (p) REVERT: B 589 ASP cc_start: 0.9395 (p0) cc_final: 0.8844 (p0) REVERT: B 612 SER cc_start: 0.9162 (p) cc_final: 0.8842 (m) REVERT: B 626 MET cc_start: 0.7987 (mtp) cc_final: 0.7216 (ttm) REVERT: B 648 GLU cc_start: 0.9674 (tt0) cc_final: 0.8986 (tp30) REVERT: B 654 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8772 (tm-30) REVERT: L 30 LYS cc_start: 0.9587 (mttt) cc_final: 0.9366 (mtpt) REVERT: C 36 VAL cc_start: 0.9412 (t) cc_final: 0.9119 (t) REVERT: C 150 MET cc_start: 0.9535 (mmm) cc_final: 0.9045 (mmm) REVERT: E 589 ASP cc_start: 0.9425 (p0) cc_final: 0.8687 (p0) REVERT: E 626 MET cc_start: 0.7859 (mtp) cc_final: 0.7124 (ttm) REVERT: E 638 TYR cc_start: 0.8947 (m-80) cc_final: 0.8702 (m-10) REVERT: E 648 GLU cc_start: 0.9617 (tt0) cc_final: 0.8965 (tp30) REVERT: E 654 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8770 (tm-30) REVERT: G 100 GLU cc_start: 0.8415 (tt0) cc_final: 0.8028 (tt0) REVERT: J 30 LYS cc_start: 0.9535 (mttt) cc_final: 0.9320 (mtpt) REVERT: D 36 VAL cc_start: 0.9272 (t) cc_final: 0.8875 (t) REVERT: D 150 MET cc_start: 0.9485 (mmm) cc_final: 0.8000 (mpp) REVERT: D 195 ASN cc_start: 0.8592 (p0) cc_final: 0.8371 (p0) REVERT: D 328 MET cc_start: 0.8851 (tpt) cc_final: 0.8289 (tpt) REVERT: F 589 ASP cc_start: 0.9400 (p0) cc_final: 0.8709 (p0) REVERT: F 612 SER cc_start: 0.9138 (p) cc_final: 0.8832 (m) REVERT: F 626 MET cc_start: 0.7765 (mtp) cc_final: 0.7256 (ttm) REVERT: F 638 TYR cc_start: 0.8984 (m-80) cc_final: 0.8768 (m-10) REVERT: F 648 GLU cc_start: 0.9647 (tt0) cc_final: 0.9140 (tp30) REVERT: F 654 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8819 (tm-30) REVERT: I 100 GLU cc_start: 0.8116 (tt0) cc_final: 0.7905 (tt0) REVERT: K 53 GLU cc_start: 0.9417 (mm-30) cc_final: 0.9098 (mp0) outliers start: 6 outliers final: 0 residues processed: 280 average time/residue: 0.4280 time to fit residues: 168.4881 Evaluate side-chains 153 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 2.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 7.9990 chunk 177 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 119 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 136 optimal weight: 30.0000 chunk 212 optimal weight: 9.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS B 543 ASN C 374 HIS D 374 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20466 Z= 0.250 Angle : 0.718 12.099 27816 Z= 0.369 Chirality : 0.046 0.200 3393 Planarity : 0.005 0.055 3393 Dihedral : 11.000 80.116 4407 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 1.38 % Allowed : 6.22 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.20 (0.16), residues: 2358 helix: -1.61 (0.23), residues: 396 sheet: -1.80 (0.18), residues: 717 loop : -2.51 (0.16), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 35 HIS 0.003 0.001 HIS C 105 PHE 0.018 0.002 PHE D 391 TYR 0.014 0.001 TYR F 586 ARG 0.009 0.001 ARG E 617 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 192 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8446 (tm-30) REVERT: A 150 MET cc_start: 0.9387 (mmm) cc_final: 0.8986 (mpp) REVERT: B 589 ASP cc_start: 0.9168 (p0) cc_final: 0.8662 (p0) REVERT: B 648 GLU cc_start: 0.9605 (tt0) cc_final: 0.8947 (tp30) REVERT: B 650 GLN cc_start: 0.7005 (pt0) cc_final: 0.6717 (mp10) REVERT: L 30 LYS cc_start: 0.9590 (mttt) cc_final: 0.9354 (mtpt) REVERT: C 110 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8296 (tm-30) REVERT: C 150 MET cc_start: 0.9347 (mmm) cc_final: 0.9104 (tpp) REVERT: C 328 MET cc_start: 0.8942 (tpt) cc_final: 0.8528 (tpt) REVERT: C 475 MET cc_start: 0.8663 (mmp) cc_final: 0.8348 (mmp) REVERT: E 530 MET cc_start: 0.7794 (mpp) cc_final: 0.7556 (mpp) REVERT: E 589 ASP cc_start: 0.9175 (p0) cc_final: 0.8587 (p0) REVERT: E 648 GLU cc_start: 0.9561 (tt0) cc_final: 0.8931 (tp30) REVERT: E 654 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8697 (tm-30) REVERT: G 18 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8508 (mm) REVERT: G 20 LEU cc_start: 0.9012 (mp) cc_final: 0.8378 (tt) REVERT: G 46 GLU cc_start: 0.8912 (tp30) cc_final: 0.8616 (tp30) REVERT: G 100 GLU cc_start: 0.8236 (tt0) cc_final: 0.7839 (tt0) REVERT: J 30 LYS cc_start: 0.9570 (mttt) cc_final: 0.9365 (mtpt) REVERT: D 65 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8261 (mmmt) REVERT: D 95 MET cc_start: 0.8935 (tmm) cc_final: 0.8696 (tmm) REVERT: D 116 LEU cc_start: 0.9673 (tp) cc_final: 0.9440 (tt) REVERT: D 150 MET cc_start: 0.9414 (mmm) cc_final: 0.8960 (mpp) REVERT: D 217 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.8310 (m-10) REVERT: F 530 MET cc_start: 0.7650 (mpp) cc_final: 0.7420 (mpp) REVERT: F 589 ASP cc_start: 0.9154 (p0) cc_final: 0.8543 (p0) REVERT: F 626 MET cc_start: 0.8362 (mtp) cc_final: 0.8143 (ptp) REVERT: F 648 GLU cc_start: 0.9542 (tt0) cc_final: 0.9048 (tp30) REVERT: I 20 LEU cc_start: 0.8910 (mp) cc_final: 0.8334 (tt) REVERT: I 77 GLN cc_start: 0.9403 (mt0) cc_final: 0.9086 (mm-40) REVERT: K 53 GLU cc_start: 0.9424 (mm-30) cc_final: 0.9047 (mp0) outliers start: 29 outliers final: 6 residues processed: 208 average time/residue: 0.3496 time to fit residues: 109.8028 Evaluate side-chains 160 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 151 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 616 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 0.0980 chunk 65 optimal weight: 4.9990 chunk 176 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 chunk 58 optimal weight: 0.3980 chunk 212 optimal weight: 20.0000 chunk 229 optimal weight: 10.0000 chunk 189 optimal weight: 2.9990 chunk 211 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 170 optimal weight: 8.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN B 563 GLN B 652 GLN C 478 ASN E 563 GLN E 652 GLN F 563 GLN F 652 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20466 Z= 0.187 Angle : 0.652 11.009 27816 Z= 0.328 Chirality : 0.044 0.188 3393 Planarity : 0.004 0.041 3393 Dihedral : 9.379 67.278 4407 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 1.09 % Allowed : 8.02 % Favored : 90.88 % 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: -2.60 (0.16), residues: 2358 helix: -0.84 (0.26), residues: 405 sheet: -1.40 (0.19), residues: 696 loop : -2.24 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 35 HIS 0.003 0.001 HIS I 53 PHE 0.014 0.001 PHE D 391 TYR 0.019 0.001 TYR B 638 ARG 0.005 0.000 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 179 time to evaluate : 2.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8339 (tm-30) REVERT: B 589 ASP cc_start: 0.9186 (p0) cc_final: 0.8575 (p0) REVERT: B 606 THR cc_start: 0.9180 (p) cc_final: 0.8719 (t) REVERT: B 626 MET cc_start: 0.7788 (ptp) cc_final: 0.7291 (ptp) REVERT: B 648 GLU cc_start: 0.9600 (tt0) cc_final: 0.8910 (tp30) REVERT: B 650 GLN cc_start: 0.7218 (pt0) cc_final: 0.6223 (mm-40) REVERT: H 100 GLU cc_start: 0.8042 (tt0) cc_final: 0.7746 (tt0) REVERT: H 100 MET cc_start: 0.6908 (ppp) cc_final: 0.5560 (ppp) REVERT: L 30 LYS cc_start: 0.9570 (mttt) cc_final: 0.9323 (mtpt) REVERT: C 110 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8318 (tm-30) REVERT: C 150 MET cc_start: 0.9331 (mmm) cc_final: 0.9112 (mmm) REVERT: C 328 MET cc_start: 0.8925 (tpt) cc_final: 0.8723 (tpt) REVERT: C 475 MET cc_start: 0.8648 (mmp) cc_final: 0.8400 (mmp) REVERT: C 494 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8710 (mm) REVERT: E 530 MET cc_start: 0.7897 (mpp) cc_final: 0.7688 (mpp) REVERT: E 589 ASP cc_start: 0.9122 (p0) cc_final: 0.8599 (p0) REVERT: E 626 MET cc_start: 0.7811 (ptp) cc_final: 0.7160 (ptm) REVERT: E 648 GLU cc_start: 0.9536 (tt0) cc_final: 0.8877 (tp30) REVERT: E 654 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8681 (tm-30) REVERT: G 20 LEU cc_start: 0.9036 (mp) cc_final: 0.8365 (tt) REVERT: G 46 GLU cc_start: 0.8886 (tp30) cc_final: 0.8600 (tp30) REVERT: G 100 GLU cc_start: 0.8143 (tt0) cc_final: 0.7738 (tt0) REVERT: G 100 TYR cc_start: 0.8126 (m-10) cc_final: 0.7846 (m-10) REVERT: D 65 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8259 (mmmt) REVERT: D 116 LEU cc_start: 0.9680 (tp) cc_final: 0.9241 (tt) REVERT: D 150 MET cc_start: 0.9391 (mmm) cc_final: 0.8146 (mmt) REVERT: D 217 TYR cc_start: 0.8618 (OUTLIER) cc_final: 0.8070 (m-10) REVERT: D 328 MET cc_start: 0.8856 (tpt) cc_final: 0.8455 (tpt) REVERT: F 530 MET cc_start: 0.7835 (mpp) cc_final: 0.7625 (mpp) REVERT: F 648 GLU cc_start: 0.9517 (tt0) cc_final: 0.9130 (pt0) REVERT: I 77 GLN cc_start: 0.9399 (mt0) cc_final: 0.9063 (mm-40) REVERT: I 100 TYR cc_start: 0.8433 (m-10) cc_final: 0.8161 (m-10) REVERT: K 53 GLU cc_start: 0.9380 (mm-30) cc_final: 0.9045 (mp0) outliers start: 23 outliers final: 14 residues processed: 193 average time/residue: 0.3495 time to fit residues: 102.9681 Evaluate side-chains 171 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 154 time to evaluate : 2.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 616 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 0.7980 chunk 160 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 142 optimal weight: 8.9990 chunk 213 optimal weight: 30.0000 chunk 226 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 202 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN C 82 GLN G 3 GLN D 82 GLN F 543 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20466 Z= 0.268 Angle : 0.654 9.762 27816 Z= 0.327 Chirality : 0.044 0.219 3393 Planarity : 0.004 0.037 3393 Dihedral : 8.232 57.854 4407 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 1.85 % Allowed : 8.88 % Favored : 89.27 % 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: -2.36 (0.17), residues: 2358 helix: -0.38 (0.27), residues: 405 sheet: -1.22 (0.19), residues: 690 loop : -2.21 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 623 HIS 0.003 0.001 HIS A 330 PHE 0.014 0.001 PHE D 391 TYR 0.017 0.001 TYR A 217 ARG 0.003 0.000 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 164 time to evaluate : 2.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8355 (tm-30) REVERT: B 589 ASP cc_start: 0.9155 (p0) cc_final: 0.8537 (p0) REVERT: B 648 GLU cc_start: 0.9595 (tt0) cc_final: 0.9010 (tp30) REVERT: B 650 GLN cc_start: 0.7401 (pt0) cc_final: 0.6788 (mt0) REVERT: H 100 GLU cc_start: 0.8019 (tt0) cc_final: 0.7764 (tt0) REVERT: H 100 TYR cc_start: 0.8618 (m-10) cc_final: 0.8357 (m-80) REVERT: L 30 LYS cc_start: 0.9525 (mttt) cc_final: 0.9302 (mtpt) REVERT: C 150 MET cc_start: 0.9343 (mmm) cc_final: 0.8925 (mmm) REVERT: C 328 MET cc_start: 0.8906 (tpt) cc_final: 0.8588 (tpp) REVERT: C 475 MET cc_start: 0.8787 (mmp) cc_final: 0.8575 (mmm) REVERT: C 494 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8869 (mm) REVERT: E 589 ASP cc_start: 0.9150 (p0) cc_final: 0.8569 (p0) REVERT: E 626 MET cc_start: 0.7800 (ptp) cc_final: 0.7098 (ptm) REVERT: E 648 GLU cc_start: 0.9567 (tt0) cc_final: 0.8945 (tp30) REVERT: E 654 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8667 (tm-30) REVERT: G 20 LEU cc_start: 0.9053 (mp) cc_final: 0.8379 (tt) REVERT: G 46 GLU cc_start: 0.8962 (tp30) cc_final: 0.8688 (tp30) REVERT: G 100 GLU cc_start: 0.8146 (tt0) cc_final: 0.7774 (tt0) REVERT: G 100 TYR cc_start: 0.8304 (m-10) cc_final: 0.7762 (m-10) REVERT: D 52 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8926 (tt) REVERT: D 65 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8198 (mmmt) REVERT: D 150 MET cc_start: 0.9378 (mmm) cc_final: 0.9019 (tpp) REVERT: D 217 TYR cc_start: 0.8657 (OUTLIER) cc_final: 0.8130 (m-10) REVERT: F 626 MET cc_start: 0.7669 (ptp) cc_final: 0.7010 (ptm) REVERT: F 648 GLU cc_start: 0.9535 (tt0) cc_final: 0.9145 (pt0) REVERT: I 100 TYR cc_start: 0.8513 (m-10) cc_final: 0.8165 (m-10) REVERT: I 100 MET cc_start: 0.7489 (ppp) cc_final: 0.7249 (ppp) REVERT: K 53 GLU cc_start: 0.9413 (mm-30) cc_final: 0.9018 (mp0) outliers start: 39 outliers final: 23 residues processed: 189 average time/residue: 0.3230 time to fit residues: 94.2791 Evaluate side-chains 180 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 153 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 606 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain I residue 86 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 0.6980 chunk 128 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 193 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 203 optimal weight: 6.9990 chunk 57 optimal weight: 30.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 33 ASN ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20466 Z= 0.310 Angle : 0.688 15.533 27816 Z= 0.341 Chirality : 0.045 0.235 3393 Planarity : 0.004 0.037 3393 Dihedral : 7.426 47.584 4407 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 2.47 % Allowed : 8.93 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.27 (0.17), residues: 2358 helix: -0.12 (0.28), residues: 396 sheet: -1.21 (0.19), residues: 735 loop : -2.19 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP I 36 HIS 0.004 0.001 HIS A 330 PHE 0.013 0.002 PHE A 391 TYR 0.016 0.001 TYR B 638 ARG 0.004 0.000 ARG I 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 162 time to evaluate : 2.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8348 (tm-30) REVERT: B 589 ASP cc_start: 0.9160 (OUTLIER) cc_final: 0.8528 (p0) REVERT: B 626 MET cc_start: 0.7520 (ptp) cc_final: 0.7154 (ptp) REVERT: B 648 GLU cc_start: 0.9511 (tt0) cc_final: 0.9048 (pt0) REVERT: H 100 GLU cc_start: 0.8027 (tt0) cc_final: 0.7642 (tt0) REVERT: H 100 TYR cc_start: 0.8649 (m-10) cc_final: 0.8362 (m-80) REVERT: H 100 MET cc_start: 0.7134 (ppp) cc_final: 0.6740 (ppp) REVERT: L 30 LYS cc_start: 0.9525 (mttt) cc_final: 0.9315 (mtpt) REVERT: C 150 MET cc_start: 0.9351 (mmm) cc_final: 0.9124 (mmm) REVERT: C 475 MET cc_start: 0.8911 (mmp) cc_final: 0.8686 (mmm) REVERT: E 589 ASP cc_start: 0.9150 (OUTLIER) cc_final: 0.8593 (p0) REVERT: E 626 MET cc_start: 0.7820 (ptp) cc_final: 0.7067 (ptm) REVERT: E 647 GLU cc_start: 0.9356 (pt0) cc_final: 0.9118 (pp20) REVERT: E 648 GLU cc_start: 0.9626 (tt0) cc_final: 0.9187 (pt0) REVERT: E 654 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8651 (tm-30) REVERT: G 46 GLU cc_start: 0.8975 (tp30) cc_final: 0.8705 (tp30) REVERT: G 100 GLU cc_start: 0.8042 (tt0) cc_final: 0.7627 (tt0) REVERT: G 100 TYR cc_start: 0.8359 (m-10) cc_final: 0.7764 (m-10) REVERT: D 52 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8909 (tt) REVERT: D 65 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8124 (mmmt) REVERT: D 150 MET cc_start: 0.9373 (mmm) cc_final: 0.8997 (tpp) REVERT: D 217 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.8167 (m-10) REVERT: F 589 ASP cc_start: 0.9192 (OUTLIER) cc_final: 0.8610 (p0) REVERT: F 648 GLU cc_start: 0.9518 (tt0) cc_final: 0.9172 (pt0) REVERT: I 100 GLU cc_start: 0.7925 (tt0) cc_final: 0.7568 (tt0) REVERT: I 100 TYR cc_start: 0.8511 (m-10) cc_final: 0.8038 (m-10) REVERT: I 100 MET cc_start: 0.7424 (ppp) cc_final: 0.7085 (ppp) REVERT: K 53 GLU cc_start: 0.9426 (mm-30) cc_final: 0.9094 (mp0) outliers start: 52 outliers final: 27 residues processed: 191 average time/residue: 0.3378 time to fit residues: 100.4577 Evaluate side-chains 181 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 148 time to evaluate : 2.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain E residue 535 MET Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 589 ASP Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 535 MET Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 589 ASP Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain I residue 81 LYS Chi-restraints excluded: chain I residue 86 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 20.0000 chunk 203 optimal weight: 0.4980 chunk 44 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 226 optimal weight: 9.9990 chunk 187 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 overall best weight: 6.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 607 ASN I 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 20466 Z= 0.418 Angle : 0.760 13.590 27816 Z= 0.376 Chirality : 0.046 0.229 3393 Planarity : 0.004 0.035 3393 Dihedral : 7.205 47.411 4407 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 2.52 % Allowed : 9.54 % Favored : 87.94 % 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: -2.34 (0.17), residues: 2358 helix: -0.27 (0.27), residues: 396 sheet: -1.13 (0.19), residues: 678 loop : -2.27 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 35 HIS 0.006 0.002 HIS C 66 PHE 0.014 0.002 PHE A 391 TYR 0.016 0.002 TYR B 638 ARG 0.004 0.001 ARG F 542 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 140 time to evaluate : 2.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8400 (tm-30) REVERT: A 150 MET cc_start: 0.9178 (mpp) cc_final: 0.8948 (mmt) REVERT: A 166 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7868 (tmm-80) REVERT: B 589 ASP cc_start: 0.9177 (OUTLIER) cc_final: 0.8572 (p0) REVERT: B 626 MET cc_start: 0.7549 (ptp) cc_final: 0.7055 (ptp) REVERT: B 648 GLU cc_start: 0.9553 (tt0) cc_final: 0.9145 (pt0) REVERT: H 100 GLU cc_start: 0.7979 (tt0) cc_final: 0.7614 (tt0) REVERT: H 100 TYR cc_start: 0.8754 (m-10) cc_final: 0.8466 (m-80) REVERT: H 100 MET cc_start: 0.7193 (ppp) cc_final: 0.6758 (ppp) REVERT: C 328 MET cc_start: 0.9020 (tpt) cc_final: 0.8810 (tpt) REVERT: E 589 ASP cc_start: 0.9193 (OUTLIER) cc_final: 0.8649 (p0) REVERT: E 626 MET cc_start: 0.7756 (ptp) cc_final: 0.6944 (ptp) REVERT: E 647 GLU cc_start: 0.9354 (pt0) cc_final: 0.9153 (pp20) REVERT: E 648 GLU cc_start: 0.9660 (tt0) cc_final: 0.9230 (pt0) REVERT: E 654 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8629 (tm-30) REVERT: G 46 GLU cc_start: 0.9035 (tp30) cc_final: 0.8782 (tp30) REVERT: G 100 GLU cc_start: 0.8107 (tt0) cc_final: 0.7643 (tt0) REVERT: G 100 TYR cc_start: 0.8486 (m-10) cc_final: 0.7929 (m-10) REVERT: D 52 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8930 (tt) REVERT: D 65 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.7940 (mmmt) REVERT: D 150 MET cc_start: 0.9433 (mmm) cc_final: 0.8227 (mmt) REVERT: D 201 ILE cc_start: 0.9562 (OUTLIER) cc_final: 0.9361 (mm) REVERT: D 217 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.8223 (m-10) REVERT: D 328 MET cc_start: 0.8908 (tpt) cc_final: 0.8453 (tpt) REVERT: F 648 GLU cc_start: 0.9527 (tt0) cc_final: 0.9182 (pt0) REVERT: I 100 TYR cc_start: 0.8590 (m-10) cc_final: 0.8197 (m-10) REVERT: K 53 GLU cc_start: 0.9451 (mm-30) cc_final: 0.9107 (mp0) outliers start: 53 outliers final: 30 residues processed: 180 average time/residue: 0.3216 time to fit residues: 89.5955 Evaluate side-chains 170 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 133 time to evaluate : 2.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 589 ASP Chi-restraints excluded: chain E residue 606 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 589 ASP Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain I residue 81 LYS Chi-restraints excluded: chain I residue 86 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 165 optimal weight: 0.9990 chunk 190 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 225 optimal weight: 9.9990 chunk 141 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 652 GLN G 1 GLN G 33 ASN D 478 ASN F 607 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20466 Z= 0.168 Angle : 0.648 15.514 27816 Z= 0.315 Chirality : 0.044 0.193 3393 Planarity : 0.004 0.038 3393 Dihedral : 6.464 50.834 4407 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 1.80 % Allowed : 10.73 % Favored : 87.46 % 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: -2.04 (0.17), residues: 2358 helix: 0.10 (0.28), residues: 396 sheet: -0.99 (0.19), residues: 735 loop : -2.10 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 623 HIS 0.002 0.001 HIS H 53 PHE 0.012 0.001 PHE A 391 TYR 0.010 0.001 TYR D 217 ARG 0.004 0.000 ARG D 500 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 162 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7760 (tmm-80) REVERT: B 589 ASP cc_start: 0.9160 (OUTLIER) cc_final: 0.8564 (p0) REVERT: B 626 MET cc_start: 0.7494 (ptp) cc_final: 0.7101 (ptp) REVERT: B 648 GLU cc_start: 0.9488 (tt0) cc_final: 0.9037 (pp20) REVERT: H 20 LEU cc_start: 0.9107 (mp) cc_final: 0.8450 (tt) REVERT: H 100 GLU cc_start: 0.7924 (tt0) cc_final: 0.7581 (tt0) REVERT: H 100 TYR cc_start: 0.8506 (m-10) cc_final: 0.8169 (m-80) REVERT: H 100 MET cc_start: 0.7060 (ppp) cc_final: 0.6618 (ppp) REVERT: C 475 MET cc_start: 0.8891 (mmp) cc_final: 0.8674 (mmm) REVERT: E 586 TYR cc_start: 0.9271 (t80) cc_final: 0.9060 (t80) REVERT: E 589 ASP cc_start: 0.9122 (OUTLIER) cc_final: 0.8504 (p0) REVERT: E 626 MET cc_start: 0.7737 (ptp) cc_final: 0.6806 (ptm) REVERT: E 648 GLU cc_start: 0.9592 (tt0) cc_final: 0.9123 (pp20) REVERT: E 654 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8640 (tm-30) REVERT: G 20 LEU cc_start: 0.9152 (mp) cc_final: 0.8913 (mt) REVERT: G 46 GLU cc_start: 0.8953 (tp30) cc_final: 0.8706 (tp30) REVERT: G 100 GLU cc_start: 0.7978 (tt0) cc_final: 0.7593 (tt0) REVERT: G 100 TYR cc_start: 0.8230 (m-10) cc_final: 0.7818 (m-10) REVERT: D 52 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8845 (tt) REVERT: D 65 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8189 (mmmt) REVERT: D 69 TRP cc_start: 0.9472 (OUTLIER) cc_final: 0.9252 (m100) REVERT: D 150 MET cc_start: 0.9350 (mmm) cc_final: 0.7917 (mmt) REVERT: D 201 ILE cc_start: 0.9454 (OUTLIER) cc_final: 0.9008 (mm) REVERT: D 217 TYR cc_start: 0.8633 (OUTLIER) cc_final: 0.8210 (m-10) REVERT: D 328 MET cc_start: 0.8874 (tpt) cc_final: 0.8479 (tpp) REVERT: F 589 ASP cc_start: 0.9148 (OUTLIER) cc_final: 0.8527 (p0) REVERT: F 626 MET cc_start: 0.7637 (ptm) cc_final: 0.7193 (ptm) REVERT: F 648 GLU cc_start: 0.9460 (tt0) cc_final: 0.8905 (tp30) REVERT: I 20 LEU cc_start: 0.8948 (mp) cc_final: 0.8288 (tt) REVERT: I 100 TYR cc_start: 0.8411 (m-10) cc_final: 0.8127 (m-80) REVERT: K 53 GLU cc_start: 0.9390 (mm-30) cc_final: 0.9040 (mp0) outliers start: 38 outliers final: 22 residues processed: 192 average time/residue: 0.3404 time to fit residues: 101.6682 Evaluate side-chains 178 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 147 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain E residue 589 ASP Chi-restraints excluded: chain E residue 606 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 589 ASP Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain I residue 86 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 10.0000 chunk 134 optimal weight: 30.0000 chunk 67 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 153 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 177 optimal weight: 9.9990 chunk 205 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 607 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 20466 Z= 0.472 Angle : 0.816 12.846 27816 Z= 0.399 Chirality : 0.047 0.243 3393 Planarity : 0.004 0.035 3393 Dihedral : 6.869 54.927 4407 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % Rotamer: Outliers : 2.52 % Allowed : 10.73 % Favored : 86.75 % 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: -2.26 (0.17), residues: 2358 helix: -0.09 (0.28), residues: 378 sheet: -1.03 (0.19), residues: 717 loop : -2.29 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 395 HIS 0.007 0.002 HIS C 66 PHE 0.013 0.002 PHE A 391 TYR 0.020 0.002 TYR A 217 ARG 0.005 0.001 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 139 time to evaluate : 1.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.9241 (mmt) cc_final: 0.8968 (mmt) REVERT: A 166 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7933 (tmm-80) REVERT: B 589 ASP cc_start: 0.9200 (OUTLIER) cc_final: 0.8608 (p0) REVERT: B 626 MET cc_start: 0.7605 (ptp) cc_final: 0.7231 (ptp) REVERT: B 648 GLU cc_start: 0.9549 (tt0) cc_final: 0.9087 (pp20) REVERT: H 100 GLU cc_start: 0.7982 (tt0) cc_final: 0.7638 (tt0) REVERT: H 100 TYR cc_start: 0.8790 (m-10) cc_final: 0.8471 (m-80) REVERT: H 100 MET cc_start: 0.7186 (ppp) cc_final: 0.6828 (ppp) REVERT: C 69 TRP cc_start: 0.9463 (OUTLIER) cc_final: 0.8739 (m100) REVERT: E 589 ASP cc_start: 0.9209 (OUTLIER) cc_final: 0.8670 (p0) REVERT: E 626 MET cc_start: 0.7794 (ptp) cc_final: 0.6907 (ptm) REVERT: E 648 GLU cc_start: 0.9603 (tt0) cc_final: 0.9233 (pp20) REVERT: E 654 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8581 (tm-30) REVERT: G 100 GLU cc_start: 0.8113 (tt0) cc_final: 0.7650 (tt0) REVERT: G 100 TYR cc_start: 0.8502 (m-10) cc_final: 0.7923 (m-10) REVERT: G 100 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.7624 (t80) REVERT: J 98 PHE cc_start: 0.9097 (OUTLIER) cc_final: 0.8559 (m-10) REVERT: D 52 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8965 (tt) REVERT: D 69 TRP cc_start: 0.9452 (OUTLIER) cc_final: 0.9144 (m100) REVERT: D 110 GLU cc_start: 0.9197 (tp30) cc_final: 0.8627 (tp30) REVERT: D 150 MET cc_start: 0.9424 (mmm) cc_final: 0.8241 (mmt) REVERT: D 217 TYR cc_start: 0.8782 (OUTLIER) cc_final: 0.8201 (m-10) REVERT: D 328 MET cc_start: 0.8935 (tpt) cc_final: 0.8415 (tpt) REVERT: F 589 ASP cc_start: 0.9285 (OUTLIER) cc_final: 0.8699 (p0) REVERT: F 648 GLU cc_start: 0.9514 (tt0) cc_final: 0.9130 (pp20) REVERT: I 20 LEU cc_start: 0.9052 (mp) cc_final: 0.8373 (tt) REVERT: I 100 TYR cc_start: 0.8575 (m-10) cc_final: 0.8255 (m-10) REVERT: I 100 TYR cc_start: 0.8804 (OUTLIER) cc_final: 0.7727 (t80) REVERT: I 100 MET cc_start: 0.7466 (ppp) cc_final: 0.6945 (ppp) REVERT: K 53 GLU cc_start: 0.9454 (mm-30) cc_final: 0.9100 (mp0) outliers start: 53 outliers final: 35 residues processed: 178 average time/residue: 0.3303 time to fit residues: 90.6335 Evaluate side-chains 178 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 132 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 589 ASP Chi-restraints excluded: chain E residue 606 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain J residue 98 PHE Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 589 ASP Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 608 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 81 LYS Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 100 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 8.9990 chunk 197 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 189 optimal weight: 0.8980 chunk 198 optimal weight: 4.9990 chunk 209 optimal weight: 2.9990 chunk 138 optimal weight: 20.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 607 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20466 Z= 0.207 Angle : 0.670 14.052 27816 Z= 0.327 Chirality : 0.045 0.206 3393 Planarity : 0.004 0.039 3393 Dihedral : 6.463 56.175 4407 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 1.90 % Allowed : 11.40 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.97 (0.17), residues: 2358 helix: 0.06 (0.28), residues: 396 sheet: -0.80 (0.19), residues: 735 loop : -2.14 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 479 HIS 0.003 0.001 HIS A 66 PHE 0.013 0.001 PHE A 391 TYR 0.013 0.001 TYR A 217 ARG 0.005 0.000 ARG F 617 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 149 time to evaluate : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.9467 (OUTLIER) cc_final: 0.9098 (m100) REVERT: A 150 MET cc_start: 0.9248 (mmt) cc_final: 0.8997 (mmt) REVERT: A 166 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7849 (tmm-80) REVERT: B 589 ASP cc_start: 0.9178 (OUTLIER) cc_final: 0.8599 (p0) REVERT: B 626 MET cc_start: 0.7514 (ptp) cc_final: 0.7140 (ptp) REVERT: B 648 GLU cc_start: 0.9475 (tt0) cc_final: 0.8893 (tp30) REVERT: H 100 GLU cc_start: 0.7967 (tt0) cc_final: 0.7576 (tt0) REVERT: H 100 TYR cc_start: 0.8622 (m-10) cc_final: 0.8289 (m-80) REVERT: H 100 TYR cc_start: 0.8486 (OUTLIER) cc_final: 0.6948 (t80) REVERT: H 100 MET cc_start: 0.7060 (ppp) cc_final: 0.6692 (ppp) REVERT: C 69 TRP cc_start: 0.9410 (OUTLIER) cc_final: 0.8732 (m100) REVERT: C 475 MET cc_start: 0.8959 (mmp) cc_final: 0.8726 (mmm) REVERT: E 589 ASP cc_start: 0.9151 (OUTLIER) cc_final: 0.8558 (p0) REVERT: E 626 MET cc_start: 0.7777 (ptp) cc_final: 0.6827 (ptm) REVERT: E 648 GLU cc_start: 0.9537 (tt0) cc_final: 0.9144 (pp20) REVERT: E 654 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8612 (tm-30) REVERT: E 655 LYS cc_start: 0.9451 (mttp) cc_final: 0.9211 (mmtm) REVERT: G 20 LEU cc_start: 0.9235 (mp) cc_final: 0.8990 (mt) REVERT: G 100 GLU cc_start: 0.8077 (tt0) cc_final: 0.7645 (tt0) REVERT: G 100 TYR cc_start: 0.8290 (m-10) cc_final: 0.7864 (m-10) REVERT: G 100 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.7584 (t80) REVERT: G 100 MET cc_start: 0.7206 (ppp) cc_final: 0.6915 (ppp) REVERT: D 52 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8868 (tt) REVERT: D 65 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8105 (mmmt) REVERT: D 69 TRP cc_start: 0.9442 (OUTLIER) cc_final: 0.9226 (m100) REVERT: D 150 MET cc_start: 0.9376 (mmm) cc_final: 0.8181 (mmt) REVERT: D 217 TYR cc_start: 0.8679 (OUTLIER) cc_final: 0.8207 (m-10) REVERT: D 328 MET cc_start: 0.8891 (tpt) cc_final: 0.8510 (tpt) REVERT: F 589 ASP cc_start: 0.9196 (OUTLIER) cc_final: 0.8552 (p0) REVERT: F 648 GLU cc_start: 0.9524 (tt0) cc_final: 0.9084 (pp20) REVERT: I 20 LEU cc_start: 0.8990 (mp) cc_final: 0.8322 (tt) REVERT: I 100 TYR cc_start: 0.8453 (m-10) cc_final: 0.8184 (m-10) REVERT: I 100 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.7562 (t80) REVERT: K 53 GLU cc_start: 0.9412 (mm-30) cc_final: 0.9042 (mp0) outliers start: 40 outliers final: 23 residues processed: 181 average time/residue: 0.3322 time to fit residues: 92.9491 Evaluate side-chains 180 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 144 time to evaluate : 2.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 589 ASP Chi-restraints excluded: chain E residue 606 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 217 TYR Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 478 ASN Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 589 ASP Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 100 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 7.9990 chunk 135 optimal weight: 20.0000 chunk 105 optimal weight: 9.9990 chunk 154 optimal weight: 20.0000 chunk 233 optimal weight: 5.9990 chunk 214 optimal weight: 5.9990 chunk 185 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 147 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 607 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 20466 Z= 0.437 Angle : 0.779 12.858 27816 Z= 0.381 Chirality : 0.046 0.221 3393 Planarity : 0.004 0.034 3393 Dihedral : 6.764 57.548 4407 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer: Outliers : 2.04 % Allowed : 11.25 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.12 (0.17), residues: 2358 helix: -0.16 (0.28), residues: 396 sheet: -0.83 (0.19), residues: 723 loop : -2.24 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 36 HIS 0.007 0.002 HIS C 66 PHE 0.012 0.002 PHE A 391 TYR 0.016 0.001 TYR A 217 ARG 0.007 0.000 ARG D 500 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4716 Ramachandran restraints generated. 2358 Oldfield, 0 Emsley, 2358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 133 time to evaluate : 2.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.9504 (OUTLIER) cc_final: 0.9070 (m100) REVERT: A 150 MET cc_start: 0.9237 (mmt) cc_final: 0.8946 (mmt) REVERT: A 166 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7947 (tmm-80) REVERT: B 589 ASP cc_start: 0.9214 (OUTLIER) cc_final: 0.8608 (p0) REVERT: B 626 MET cc_start: 0.7494 (ptp) cc_final: 0.7139 (ptp) REVERT: B 648 GLU cc_start: 0.9514 (tt0) cc_final: 0.9131 (pt0) REVERT: H 100 GLU cc_start: 0.8078 (tt0) cc_final: 0.7635 (tt0) REVERT: H 100 TYR cc_start: 0.8702 (m-10) cc_final: 0.8369 (m-80) REVERT: H 100 MET cc_start: 0.7042 (ppp) cc_final: 0.6724 (ppp) REVERT: C 69 TRP cc_start: 0.9454 (OUTLIER) cc_final: 0.8776 (m100) REVERT: E 589 ASP cc_start: 0.9201 (OUTLIER) cc_final: 0.8654 (p0) REVERT: E 626 MET cc_start: 0.7807 (ptp) cc_final: 0.6911 (ptp) REVERT: E 648 GLU cc_start: 0.9593 (tt0) cc_final: 0.9247 (pp20) REVERT: E 654 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8565 (tm-30) REVERT: G 100 GLU cc_start: 0.8132 (tt0) cc_final: 0.7637 (tt0) REVERT: G 100 TYR cc_start: 0.8445 (m-10) cc_final: 0.7937 (m-10) REVERT: G 100 TYR cc_start: 0.8729 (OUTLIER) cc_final: 0.7624 (t80) REVERT: D 69 TRP cc_start: 0.9460 (OUTLIER) cc_final: 0.9191 (m100) REVERT: D 150 MET cc_start: 0.9398 (mmm) cc_final: 0.8150 (mmt) REVERT: D 328 MET cc_start: 0.8923 (tpt) cc_final: 0.8396 (tpt) REVERT: F 589 ASP cc_start: 0.9252 (OUTLIER) cc_final: 0.8731 (p0) REVERT: F 648 GLU cc_start: 0.9514 (tt0) cc_final: 0.9138 (pp20) REVERT: I 20 LEU cc_start: 0.9091 (mp) cc_final: 0.8448 (tt) REVERT: I 100 TYR cc_start: 0.8550 (m-10) cc_final: 0.8240 (m-10) REVERT: I 100 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.7534 (t80) REVERT: K 53 GLU cc_start: 0.9440 (mm-30) cc_final: 0.9078 (mp0) outliers start: 43 outliers final: 31 residues processed: 167 average time/residue: 0.3446 time to fit residues: 89.6545 Evaluate side-chains 172 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 132 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 589 ASP Chi-restraints excluded: chain E residue 606 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain G residue 100 TYR Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 478 ASN Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 589 ASP Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 626 MET Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 81 LYS Chi-restraints excluded: chain I residue 86 ASP Chi-restraints excluded: chain I residue 100 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 185 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 190 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 34 optimal weight: 0.0980 chunk 163 optimal weight: 0.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 607 ASN F 625 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.040027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.030948 restraints weight = 148098.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.032011 restraints weight = 79366.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.032754 restraints weight = 52661.452| |-----------------------------------------------------------------------------| r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20466 Z= 0.189 Angle : 0.670 13.747 27816 Z= 0.324 Chirality : 0.044 0.193 3393 Planarity : 0.004 0.038 3393 Dihedral : 6.330 58.610 4407 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 1.80 % Allowed : 11.68 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.87 (0.17), residues: 2358 helix: 0.09 (0.28), residues: 396 sheet: -0.67 (0.19), residues: 735 loop : -2.10 (0.17), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 36 HIS 0.003 0.001 HIS C 66 PHE 0.013 0.001 PHE A 391 TYR 0.020 0.001 TYR D 217 ARG 0.006 0.000 ARG A 500 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3355.71 seconds wall clock time: 63 minutes 31.06 seconds (3811.06 seconds total)