Starting phenix.real_space_refine on Sat Sep 28 21:55:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ber_44482/09_2024/9ber_44482.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ber_44482/09_2024/9ber_44482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ber_44482/09_2024/9ber_44482.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ber_44482/09_2024/9ber_44482.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ber_44482/09_2024/9ber_44482.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ber_44482/09_2024/9ber_44482.cif" } resolution = 4.1 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= 0.004 sd= 0.020 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 115 5.16 5 C 12766 2.51 5 N 3371 2.21 5 O 4098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 20350 Number of models: 1 Model: "" Number of chains: 36 Chain: "G" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3504 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 2 Chain: "B" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "A" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3504 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 2 Chain: "C" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 966 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "F" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3504 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 22, 'TRANS': 422} Chain breaks: 3 Chain: "I" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 985 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "H" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "L" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "D" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "E" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "J" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain breaks: 1 Chain: "K" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 805 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 7, '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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "G" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 173 Unusual residues: {'NAG': 12, 'SO4': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 12.55, per 1000 atoms: 0.62 Number of scatterers: 20350 At special positions: 0 Unit cell: (152.409, 153.482, 152.409, 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 115 16.00 O 4098 8.00 N 3371 7.00 C 12766 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 113 " - pdb=" SG CYS G 431B" distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.04 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.04 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.03 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.03 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.04 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 431B" distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 431B" distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.05 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.04 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA O 3 " - " MAN O 4 " " BMA R 3 " - " MAN R 6 " " MAN R 4 " - " MAN R 5 " " BMA U 3 " - " MAN U 4 " " BMA X 3 " - " MAN X 6 " " MAN X 4 " - " MAN X 5 " " BMA a 3 " - " MAN a 4 " " BMA d 3 " - " MAN d 6 " " MAN d 4 " - " MAN d 5 " ALPHA1-6 " BMA R 3 " - " MAN R 4 " " BMA X 3 " - " MAN X 4 " " BMA d 3 " - " MAN d 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " 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 T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " 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 d 2 " - " BMA d 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 160 " " NAG A 603 " - " ASN A 276 " " NAG A 604 " - " ASN A 295 " " NAG A 605 " - " ASN A 301 " " NAG A 606 " - " ASN A 339 " " NAG A 607 " - " ASN A 362 " " NAG A 608 " - " ASN A 392 " " NAG A 609 " - " ASN A 197 " " NAG A 610 " - " ASN A 234 " " NAG A 611 " - " ASN A 355 " " NAG A 612 " - " ASN A 187 " " NAG B 701 " - " ASN B 625 " " NAG B 702 " - " ASN B 637 " " NAG B 703 " - " ASN B 611 " " NAG C 701 " - " ASN C 637 " " NAG C 702 " - " ASN C 611 " " NAG C 703 " - " ASN C 625 " " NAG C 704 " - " ASN C 616 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 160 " " NAG F 603 " - " ASN F 276 " " NAG F 604 " - " ASN F 295 " " NAG F 605 " - " ASN F 301 " " NAG F 606 " - " ASN F 339 " " NAG F 607 " - " ASN F 362 " " NAG F 608 " - " ASN F 392 " " NAG F 609 " - " ASN F 197 " " NAG F 610 " - " ASN F 234 " " NAG F 611 " - " ASN F 187 " " NAG G 601 " - " ASN G 88 " " NAG G 602 " - " ASN G 160 " " NAG G 603 " - " ASN G 276 " " NAG G 604 " - " ASN G 295 " " NAG G 605 " - " ASN G 301 " " NAG G 606 " - " ASN G 339 " " NAG G 607 " - " ASN G 362 " " NAG G 608 " - " ASN G 392 " " NAG G 609 " - " ASN G 197 " " NAG G 610 " - " ASN G 234 " " NAG G 611 " - " ASN G 355 " " NAG G 612 " - " ASN G 187 " " NAG I 702 " - " ASN I 637 " " NAG I 703 " - " ASN I 611 " " NAG M 1 " - " ASN G 156 " " NAG N 1 " - " ASN G 241 " " NAG O 1 " - " ASN G 262 " " NAG P 1 " - " ASN G 386 " " NAG Q 1 " - " ASN G 448 " " NAG R 1 " - " ASN G 332 " " NAG S 1 " - " ASN A 156 " " NAG T 1 " - " ASN A 241 " " NAG U 1 " - " ASN A 262 " " NAG V 1 " - " ASN A 386 " " NAG W 1 " - " ASN A 448 " " NAG X 1 " - " ASN A 332 " " NAG Y 1 " - " ASN F 156 " " NAG Z 1 " - " ASN F 241 " " NAG a 1 " - " ASN F 262 " " NAG b 1 " - " ASN F 386 " " NAG c 1 " - " ASN F 448 " " NAG d 1 " - " ASN F 332 " Time building additional restraints: 5.60 Conformation dependent library (CDL) restraints added in 2.3 seconds 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4474 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 52 sheets defined 18.5% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain 'G' and resid 98 through 116 removed outlier: 3.925A pdb=" N GLU G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE G 108 " --> pdb=" O MET G 104 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU G 116 " --> pdb=" O TRP G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 removed outlier: 4.024A pdb=" N CYS G 126 " --> pdb=" O THR G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 349 removed outlier: 3.816A pdb=" N LYS G 348 " --> pdb=" O GLN G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 373 removed outlier: 3.599A pdb=" N VAL G 372 " --> pdb=" O ASP G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 391 removed outlier: 3.586A pdb=" N LEU G 390 " --> pdb=" O SER G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 480 removed outlier: 4.383A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 482 through 484 No H-bonds generated for 'chain 'G' and resid 482 through 484' Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 545 removed outlier: 3.790A pdb=" N ARG B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 597 removed outlier: 4.149A pdb=" N LEU B 581 " --> pdb=" O GLN B 577 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP B 589 " --> pdb=" O ARG B 585 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 590 " --> pdb=" O TYR B 586 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU B 592 " --> pdb=" O GLY B 588 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY B 597 " --> pdb=" O LEU B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.570A pdb=" N ARG B 633 " --> pdb=" O MET B 629 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU B 634 " --> pdb=" O GLU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 645 removed outlier: 3.612A pdb=" N LEU B 645 " --> pdb=" O GLU B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 661 removed outlier: 3.783A pdb=" N LEU B 661 " --> pdb=" O GLU B 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.557A pdb=" N ILE A 109 " --> pdb=" O GLN A 105 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.966A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 348 removed outlier: 3.675A pdb=" N LYS A 348 " --> pdb=" O GLN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 4.036A pdb=" N VAL A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET A 373 " --> pdb=" O PRO A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 368 through 373' Processing helix chain 'A' and resid 388 through 392 removed outlier: 4.080A pdb=" N ASN A 392 " --> pdb=" O GLN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 431A Processing helix chain 'A' and resid 474 through 482 removed outlier: 3.650A pdb=" N ASN A 478 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP A 479 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG A 480 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER A 481 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU A 482 " --> pdb=" O TRP A 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 535 removed outlier: 3.933A pdb=" N SER C 534 " --> pdb=" O GLY C 531 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N MET C 535 " --> pdb=" O ALA C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 570 through 586 Processing helix chain 'C' and resid 589 through 594 Processing helix chain 'C' and resid 618 through 624 removed outlier: 3.692A pdb=" N ASN C 624 " --> pdb=" O ASP C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 635 removed outlier: 3.549A pdb=" N GLU C 634 " --> pdb=" O GLU C 630 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE C 635 " --> pdb=" O TRP C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 648 removed outlier: 3.999A pdb=" N THR C 644 " --> pdb=" O SER C 640 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 645 " --> pdb=" O GLU C 641 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU C 647 " --> pdb=" O TYR C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 661 removed outlier: 3.902A pdb=" N ASN C 656 " --> pdb=" O GLN C 652 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLU C 657 " --> pdb=" O GLN C 653 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN C 658 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 116 removed outlier: 3.558A pdb=" N GLN F 103 " --> pdb=" O ASN F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 removed outlier: 3.846A pdb=" N CYS F 126 " --> pdb=" O THR F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 350 removed outlier: 4.311A pdb=" N LYS F 348 " --> pdb=" O GLN F 344 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG F 350 " --> pdb=" O VAL F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 removed outlier: 3.673A pdb=" N VAL F 372 " --> pdb=" O ASP F 368 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET F 373 " --> pdb=" O PRO F 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 368 through 373' Processing helix chain 'F' and resid 427 through 431A Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 537 through 541 Processing helix chain 'I' and resid 570 through 589 removed outlier: 3.839A pdb=" N LEU I 581 " --> pdb=" O GLN I 577 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA I 582 " --> pdb=" O ALA I 578 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP I 589 " --> pdb=" O ARG I 585 " (cutoff:3.500A) Processing helix chain 'I' and resid 589 through 596 removed outlier: 3.784A pdb=" N LEU I 593 " --> pdb=" O ASP I 589 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP I 596 " --> pdb=" O LEU I 592 " (cutoff:3.500A) Processing helix chain 'I' and resid 618 through 623 Processing helix chain 'I' and resid 627 through 633 removed outlier: 3.623A pdb=" N ARG I 633 " --> pdb=" O MET I 629 " (cutoff:3.500A) Processing helix chain 'I' and resid 634 through 637 removed outlier: 6.079A pdb=" N ASN I 637 " --> pdb=" O GLU I 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 634 through 637' Processing helix chain 'I' and resid 638 through 647 removed outlier: 3.670A pdb=" N THR I 644 " --> pdb=" O SER I 640 " (cutoff:3.500A) Processing helix chain 'I' and resid 650 through 661 removed outlier: 4.081A pdb=" N ASN I 656 " --> pdb=" O GLN I 652 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU I 661 " --> pdb=" O GLU I 657 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.521A pdb=" N ASP H 31 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.744A pdb=" N LYS H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.651A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.542A pdb=" N ASP D 31 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN D 32 " --> pdb=" O VAL D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.806A pdb=" N GLU E 83 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.785A pdb=" N LYS J 64 " --> pdb=" O PRO J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.533A pdb=" N SER J 87 " --> pdb=" O ALA J 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.744A pdb=" N GLU K 83 " --> pdb=" O ALA K 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 494 through 499 removed outlier: 3.950A pdb=" N CYS B 604 " --> pdb=" O VAL G 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 84 through 85 removed outlier: 4.179A pdb=" N ILE G 225 " --> pdb=" O VAL G 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 91 through 93 removed outlier: 3.897A pdb=" N GLU G 91 " --> pdb=" O CYS G 239 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS G 239 " --> pdb=" O GLU G 91 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY G 237 " --> pdb=" O PHE G 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 129 through 130 Processing sheet with id=AA5, first strand: chain 'G' and resid 154 through 155 Processing sheet with id=AA6, first strand: chain 'G' and resid 158 through 162 removed outlier: 3.639A pdb=" N PHE G 159 " --> pdb=" O GLU G 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU G 172 " --> pdb=" O PHE G 159 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN G 170 " --> pdb=" O ILE G 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 202 through 203 removed outlier: 6.969A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 259 through 261 removed outlier: 3.692A pdb=" N VAL G 292 " --> pdb=" O ILE G 449 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N GLU G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N SER G 334 " --> pdb=" O GLU G 293 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASN G 295 " --> pdb=" O ASN G 332 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASN G 332 " --> pdb=" O ASN G 295 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR G 297 " --> pdb=" O HIS G 330 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N HIS G 330 " --> pdb=" O THR G 297 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA G 329 " --> pdb=" O CYS G 418 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 271 through 273 removed outlier: 3.717A pdb=" N VAL G 271 " --> pdb=" O GLN G 287 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU G 452 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE G 467 " --> pdb=" O ASP G 457 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 305 through 308 Processing sheet with id=AB2, first strand: chain 'A' and resid 494 through 499 removed outlier: 3.555A pdb=" N GLY A 495 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 37 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 36 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS C 604 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 83 through 85 removed outlier: 4.032A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 91 through 93 removed outlier: 4.051A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AB6, first strand: chain 'A' and resid 154 through 155 Processing sheet with id=AB7, first strand: chain 'A' and resid 158 through 160 Processing sheet with id=AB8, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.789A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 259 through 261 removed outlier: 7.400A pdb=" N VAL A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A 359 " --> pdb=" O TRP A 395 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP A 395 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 259 through 261 removed outlier: 4.559A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG A 298 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 292 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.763A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.976A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.029A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.859A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N GLU A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N SER A 334 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN A 295 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN A 332 " --> pdb=" O ASN A 295 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 304 through 305 Processing sheet with id=AC3, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.183A pdb=" N ARG A 419 " --> pdb=" O TYR A 384 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 496 through 499 removed outlier: 3.632A pdb=" N THR F 499 " --> pdb=" O TRP F 35 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL F 36 " --> pdb=" O THR I 606 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AC6, first strand: chain 'F' and resid 92 through 93 Processing sheet with id=AC7, first strand: chain 'F' and resid 129 through 130 Processing sheet with id=AC8, first strand: chain 'F' and resid 154 through 155 removed outlier: 3.654A pdb=" N PHE F 176 " --> pdb=" O LYS F 155 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 158 through 161 removed outlier: 3.542A pdb=" N GLU F 172 " --> pdb=" O PHE F 159 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 215 through 216 Processing sheet with id=AD2, first strand: chain 'F' and resid 223 through 227 Processing sheet with id=AD3, first strand: chain 'F' and resid 259 through 261 removed outlier: 3.574A pdb=" N GLY F 451 " --> pdb=" O LEU F 260 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE F 443 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS F 296 " --> pdb=" O CYS F 445 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER F 447 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 271 through 273 removed outlier: 3.525A pdb=" N VAL F 286 " --> pdb=" O LEU F 452 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU F 452 " --> pdb=" O VAL F 286 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 304 through 308 Processing sheet with id=AD6, first strand: chain 'F' and resid 329 through 334 removed outlier: 3.509A pdb=" N ALA F 329 " --> pdb=" O CYS F 418 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU F 381 " --> pdb=" O CYS F 378 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 360 through 361 removed outlier: 3.621A pdb=" N PHE F 361 " --> pdb=" O SER F 393 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER F 393 " --> pdb=" O PHE F 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'F' and resid 423 through 424 Processing sheet with id=AD9, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.695A pdb=" N LEU H 80 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.562A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR H 33 " --> pdb=" O THR H 95 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP H 36 " --> pdb=" O GLY H 49 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR H 50 " --> pdb=" O ASN H 58 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN H 58 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.562A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG H 100 " --> pdb=" O PHE H 100K" (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE H 100K" --> pdb=" O ARG H 100 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 6 through 13 removed outlier: 6.418A pdb=" N VAL L 11 " --> pdb=" O ILE L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'L' and resid 19 through 22 Processing sheet with id=AE5, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.279A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.898A pdb=" N VAL D 78 " --> pdb=" O CYS D 22 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER D 70 " --> pdb=" O SER D 79 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AE8, first strand: chain 'D' and resid 58 through 59 removed outlier: 3.524A pdb=" N TYR D 50 " --> pdb=" O ASN D 58 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE D 48 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TYR D 50 " --> pdb=" O TRP D 34 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TRP D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR D 33 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER D 35 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA D 93 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE D 37 " --> pdb=" O TYR D 91 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL D 102 " --> pdb=" O THR D 94 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LYS D 96 " --> pdb=" O MET D 100P" (cutoff:3.500A) removed outlier: 5.802A pdb=" N MET D 100P" --> pdb=" O LYS D 96 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N GLY D 98 " --> pdb=" O PHE D 100N" (cutoff:3.500A) removed outlier: 5.388A pdb=" N PHE D 100N" --> pdb=" O GLY D 98 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 58 through 59 removed outlier: 3.524A pdb=" N TYR D 50 " --> pdb=" O ASN D 58 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE D 48 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TYR D 50 " --> pdb=" O TRP D 34 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TRP D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR D 33 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER D 35 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA D 93 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE D 37 " --> pdb=" O TYR D 91 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 6 through 13 removed outlier: 3.531A pdb=" N THR E 102 " --> pdb=" O TYR E 86 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR E 86 " --> pdb=" O THR E 102 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP E 85 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TRP E 35 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE E 47 " --> pdb=" O TRP E 35 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 19 through 26 removed outlier: 3.845A pdb=" N ALA E 71 " --> pdb=" O CYS E 23 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AF4, first strand: chain 'J' and resid 11 through 12 Processing sheet with id=AF5, first strand: chain 'J' and resid 58 through 59 removed outlier: 7.058A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR J 50 " --> pdb=" O TRP J 34 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TRP J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR J 33 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER J 35 " --> pdb=" O ALA J 93 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA J 93 " --> pdb=" O SER J 35 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 6 through 13 removed outlier: 6.409A pdb=" N VAL K 11 " --> pdb=" O ILE K 105 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE K 48 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 19 through 21 489 hydrogen bonds defined for protein. 1233 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: 7.13 Time building geometry restraints manager: 6.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3503 1.33 - 1.46: 6547 1.46 - 1.59: 10573 1.59 - 1.72: 0 1.72 - 1.85: 150 Bond restraints: 20773 Sorted by residual: bond pdb=" N ILE A 161 " pdb=" CA ILE A 161 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.11e-02 8.12e+03 9.36e+00 bond pdb=" C PRO A 470 " pdb=" O PRO A 470 " ideal model delta sigma weight residual 1.235 1.196 0.039 1.30e-02 5.92e+03 9.18e+00 bond pdb=" N ILE A 165 " pdb=" CA ILE A 165 " ideal model delta sigma weight residual 1.460 1.491 -0.032 1.10e-02 8.26e+03 8.23e+00 bond pdb=" N ASP A 474 " pdb=" CA ASP A 474 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.21e-02 6.83e+03 7.80e+00 bond pdb=" N VAL A 169 " pdb=" CA VAL A 169 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 6.86e+00 ... (remaining 20768 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 27833 2.92 - 5.83: 346 5.83 - 8.75: 53 8.75 - 11.67: 4 11.67 - 14.58: 1 Bond angle restraints: 28237 Sorted by residual: angle pdb=" N MET A 475 " pdb=" CA MET A 475 " pdb=" C MET A 475 " ideal model delta sigma weight residual 112.87 105.25 7.62 1.20e+00 6.94e-01 4.04e+01 angle pdb=" C ASP A 167 " pdb=" CA ASP A 167 " pdb=" CB ASP A 167 " ideal model delta sigma weight residual 110.35 119.02 -8.67 1.91e+00 2.74e-01 2.06e+01 angle pdb=" C PRO A 470 " pdb=" CA PRO A 470 " pdb=" CB PRO A 470 " ideal model delta sigma weight residual 111.56 104.54 7.02 1.65e+00 3.67e-01 1.81e+01 angle pdb=" N SER A 164 " pdb=" CA SER A 164 " pdb=" C SER A 164 " ideal model delta sigma weight residual 111.28 106.70 4.58 1.09e+00 8.42e-01 1.77e+01 angle pdb=" CA LEU B 645 " pdb=" CB LEU B 645 " pdb=" CG LEU B 645 " ideal model delta sigma weight residual 116.30 130.88 -14.58 3.50e+00 8.16e-02 1.74e+01 ... (remaining 28232 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.05: 12513 22.05 - 44.10: 914 44.10 - 66.15: 130 66.15 - 88.20: 62 88.20 - 110.25: 40 Dihedral angle restraints: 13659 sinusoidal: 6711 harmonic: 6948 Sorted by residual: dihedral pdb=" CA VAL J 100D" pdb=" C VAL J 100D" pdb=" N VAL J 100E" pdb=" CA VAL J 100E" ideal model delta harmonic sigma weight residual 180.00 121.28 58.72 0 5.00e+00 4.00e-02 1.38e+02 dihedral pdb=" CB CYS A 113 " pdb=" SG CYS A 113 " pdb=" SG CYS A 431B" pdb=" CB CYS A 431B" ideal model delta sinusoidal sigma weight residual -86.00 -168.66 82.66 1 1.00e+01 1.00e-02 8.37e+01 dihedral pdb=" CB CYS G 119 " pdb=" SG CYS G 119 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual -86.00 -164.22 78.22 1 1.00e+01 1.00e-02 7.64e+01 ... (remaining 13656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 3351 0.122 - 0.243: 92 0.243 - 0.365: 9 0.365 - 0.486: 3 0.486 - 0.608: 3 Chirality restraints: 3458 Sorted by residual: chirality pdb=" C1 NAG d 1 " pdb=" ND2 ASN F 332 " pdb=" C2 NAG d 1 " pdb=" O5 NAG d 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.24e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN G 332 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.18e+00 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN A 332 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 6.90e+00 ... (remaining 3455 not shown) Planarity restraints: 3515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 386 " 0.007 2.00e-02 2.50e+03 4.13e-02 2.13e+01 pdb=" CG ASN F 386 " -0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN F 386 " 0.049 2.00e-02 2.50e+03 pdb=" ND2 ASN F 386 " -0.041 2.00e-02 2.50e+03 pdb=" C1 NAG b 1 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 596 " -0.024 2.00e-02 2.50e+03 2.45e-02 1.50e+01 pdb=" CG TRP C 596 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP C 596 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP C 596 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 596 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 596 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 596 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 596 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 596 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 596 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 197 " 0.034 2.00e-02 2.50e+03 3.11e-02 1.21e+01 pdb=" CG ASN G 197 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN G 197 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN G 197 " -0.032 2.00e-02 2.50e+03 pdb=" C1 NAG G 609 " 0.033 2.00e-02 2.50e+03 ... (remaining 3512 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 86 2.50 - 3.10: 13605 3.10 - 3.70: 28459 3.70 - 4.30: 39181 4.30 - 4.90: 64590 Nonbonded interactions: 145921 Sorted by model distance: nonbonded pdb=" NH1 ARG D 100 " pdb=" OD1 ASN E 50 " model vdw 1.899 3.120 nonbonded pdb=" OD1 ASN A 67 " pdb=" OG SER A 209 " model vdw 2.217 3.040 nonbonded pdb=" OG1 THR F 297 " pdb=" O ILE F 443 " model vdw 2.278 3.040 nonbonded pdb=" O ALA I 526 " pdb=" OG1 THR I 627 " model vdw 2.307 3.040 nonbonded pdb=" OD2 ASP G 107 " pdb=" OH TYR G 217 " model vdw 2.315 3.040 ... (remaining 145916 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 505 or resid 601 through 611)) selection = chain 'F' selection = (chain 'G' and (resid 32 through 505 or resid 601 through 611)) } ncs_group { reference = (chain 'B' and (resid 519 through 546 or resid 569 through 661 or resid 701 thro \ ugh 703)) selection = (chain 'C' and (resid 519 through 661 or resid 701 through 703)) selection = (chain 'I' and (resid 519 through 546 or resid 569 through 661 or resid 701 thro \ ugh 703)) } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' } ncs_group { reference = chain 'O' selection = chain 'U' selection = chain 'a' } ncs_group { reference = chain 'R' selection = chain 'X' selection = chain 'd' } 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: 4.490 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: 0.010 Extract box with map and model: 0.850 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 46.980 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.140 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 20773 Z= 0.303 Angle : 0.828 14.582 28237 Z= 0.408 Chirality : 0.057 0.608 3458 Planarity : 0.005 0.070 3453 Dihedral : 16.150 110.248 9068 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.38 % Favored : 92.53 % Rotamer: Outliers : 0.24 % Allowed : 0.38 % Favored : 99.39 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.06 (0.16), residues: 2370 helix: -2.73 (0.23), residues: 315 sheet: -0.19 (0.21), residues: 666 loop : -1.66 (0.15), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.001 TRP C 596 HIS 0.004 0.001 HIS A 330 PHE 0.018 0.001 PHE G 317 TYR 0.028 0.001 TYR J 100M ARG 0.013 0.000 ARG L 31 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 198 time to evaluate : 2.008 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: symmetry clash REVERT: G 95 MET cc_start: 0.9319 (ptm) cc_final: 0.8654 (ppp) REVERT: G 373 MET cc_start: 0.8561 (mmt) cc_final: 0.8043 (tpp) REVERT: B 626 MET cc_start: 0.8283 (ttt) cc_final: 0.7148 (tmm) REVERT: B 629 MET cc_start: 0.9071 (mmm) cc_final: 0.8844 (mmt) REVERT: B 630 GLU cc_start: 0.9115 (tp30) cc_final: 0.8904 (tm-30) REVERT: B 633 ARG cc_start: 0.9466 (mtt180) cc_final: 0.9251 (ptp-110) REVERT: A 163 THR cc_start: 0.6291 (OUTLIER) cc_final: 0.5983 (p) REVERT: A 373 MET cc_start: 0.8826 (mtm) cc_final: 0.8089 (pmm) REVERT: A 434 MET cc_start: 0.9241 (ttt) cc_final: 0.8854 (tmm) REVERT: C 626 MET cc_start: 0.8465 (ttm) cc_final: 0.7974 (tpp) REVERT: C 629 MET cc_start: 0.9266 (mmm) cc_final: 0.8662 (tpt) REVERT: C 630 GLU cc_start: 0.9531 (tp30) cc_final: 0.9034 (tp30) REVERT: C 647 GLU cc_start: 0.9200 (tt0) cc_final: 0.8985 (tp30) REVERT: F 61 TYR cc_start: 0.8515 (m-80) cc_final: 0.8264 (m-10) REVERT: F 167 ASP cc_start: 0.8888 (t0) cc_final: 0.8640 (t70) REVERT: I 577 GLN cc_start: 0.9060 (pt0) cc_final: 0.8227 (tm-30) REVERT: I 584 GLU cc_start: 0.9204 (pp20) cc_final: 0.8903 (pp20) REVERT: H 90 TYR cc_start: 0.8864 (m-80) cc_final: 0.8595 (m-10) REVERT: L 95 ASN cc_start: 0.9202 (m110) cc_final: 0.8951 (t0) REVERT: L 100 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8659 (pm20) REVERT: D 30 ARG cc_start: 0.9143 (ttp-170) cc_final: 0.8926 (ttp80) REVERT: D 101 ASP cc_start: 0.8966 (t0) cc_final: 0.8726 (m-30) REVERT: E 90 ILE cc_start: 0.9147 (mm) cc_final: 0.8880 (pt) REVERT: J 48 ILE cc_start: 0.8381 (mt) cc_final: 0.8077 (mm) REVERT: J 90 TYR cc_start: 0.8679 (m-80) cc_final: 0.8189 (m-10) outliers start: 5 outliers final: 1 residues processed: 203 average time/residue: 0.4110 time to fit residues: 118.6061 Evaluate side-chains 97 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 6.9990 chunk 179 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 121 optimal weight: 0.4980 chunk 95 optimal weight: 20.0000 chunk 185 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 chunk 215 optimal weight: 7.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 377 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN B 651 ASN A 287 GLN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 478 ASN I 575 GLN H 5 GLN ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 GLN ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 20773 Z= 0.299 Angle : 0.700 9.955 28237 Z= 0.355 Chirality : 0.050 0.459 3458 Planarity : 0.005 0.099 3453 Dihedral : 11.871 81.441 4628 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 0.24 % Allowed : 4.02 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.83 (0.17), residues: 2370 helix: -1.42 (0.25), residues: 358 sheet: -0.47 (0.20), residues: 707 loop : -1.57 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 596 HIS 0.012 0.001 HIS D 68 PHE 0.019 0.002 PHE F 382 TYR 0.014 0.002 TYR F 486 ARG 0.011 0.001 ARG J 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 114 time to evaluate : 2.263 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: G 95 MET cc_start: 0.9553 (ptm) cc_final: 0.7903 (ppp) REVERT: G 373 MET cc_start: 0.8535 (mmt) cc_final: 0.8133 (tpp) REVERT: G 475 MET cc_start: 0.8603 (tpp) cc_final: 0.8332 (mmm) REVERT: B 577 GLN cc_start: 0.9450 (OUTLIER) cc_final: 0.9238 (pt0) REVERT: A 373 MET cc_start: 0.8905 (mtm) cc_final: 0.7947 (mtt) REVERT: A 426 MET cc_start: 0.8659 (ttt) cc_final: 0.8395 (tpp) REVERT: A 434 MET cc_start: 0.9353 (ttt) cc_final: 0.8995 (tmm) REVERT: C 581 LEU cc_start: 0.9553 (tp) cc_final: 0.9344 (tp) REVERT: C 626 MET cc_start: 0.8741 (ttm) cc_final: 0.8093 (tpp) REVERT: C 630 GLU cc_start: 0.9581 (tp30) cc_final: 0.8839 (tp30) REVERT: F 61 TYR cc_start: 0.8611 (m-80) cc_final: 0.8369 (m-10) REVERT: F 373 MET cc_start: 0.8659 (ptp) cc_final: 0.8152 (mtt) REVERT: I 577 GLN cc_start: 0.9194 (pt0) cc_final: 0.8306 (tm-30) REVERT: I 626 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8104 (tmm) REVERT: I 643 TYR cc_start: 0.9496 (m-80) cc_final: 0.9202 (m-80) REVERT: H 90 TYR cc_start: 0.8939 (m-80) cc_final: 0.8670 (m-10) REVERT: L 95 ASN cc_start: 0.9384 (m110) cc_final: 0.9005 (t0) REVERT: L 100 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8749 (pm20) REVERT: D 101 ASP cc_start: 0.9037 (t0) cc_final: 0.8816 (m-30) REVERT: J 90 TYR cc_start: 0.8325 (m-80) cc_final: 0.7803 (m-80) outliers start: 5 outliers final: 0 residues processed: 118 average time/residue: 0.3974 time to fit residues: 68.7141 Evaluate side-chains 77 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 119 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 179 optimal weight: 8.9990 chunk 146 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 215 optimal weight: 8.9990 chunk 232 optimal weight: 4.9990 chunk 192 optimal weight: 0.0970 chunk 213 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 chunk 172 optimal weight: 9.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN C 658 GLN F 72 HIS ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 GLN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20773 Z= 0.218 Angle : 0.609 12.872 28237 Z= 0.306 Chirality : 0.047 0.403 3458 Planarity : 0.004 0.071 3453 Dihedral : 9.575 67.410 4628 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.05 % Allowed : 4.02 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.53 (0.17), residues: 2370 helix: -0.94 (0.27), residues: 359 sheet: -0.24 (0.20), residues: 683 loop : -1.47 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 631 HIS 0.003 0.001 HIS D 52 PHE 0.024 0.001 PHE K 67 TYR 0.023 0.001 TYR H 90 ARG 0.009 0.000 ARG J 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 99 time to evaluate : 2.200 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: G 95 MET cc_start: 0.9571 (ptm) cc_final: 0.8544 (ppp) REVERT: G 373 MET cc_start: 0.8558 (mmt) cc_final: 0.8249 (tpp) REVERT: A 373 MET cc_start: 0.8746 (mtm) cc_final: 0.7974 (mtt) REVERT: A 434 MET cc_start: 0.9232 (ttt) cc_final: 0.8896 (tmm) REVERT: C 589 ASP cc_start: 0.9140 (p0) cc_final: 0.8891 (p0) REVERT: C 626 MET cc_start: 0.8754 (ttm) cc_final: 0.8062 (tpp) REVERT: C 630 GLU cc_start: 0.9576 (tp30) cc_final: 0.8830 (tp30) REVERT: F 61 TYR cc_start: 0.8572 (m-80) cc_final: 0.8345 (m-10) REVERT: F 373 MET cc_start: 0.8768 (ptp) cc_final: 0.8275 (mtm) REVERT: F 434 MET cc_start: 0.9090 (tmm) cc_final: 0.8667 (tmm) REVERT: I 530 MET cc_start: 0.9008 (mmp) cc_final: 0.8581 (mmp) REVERT: I 577 GLN cc_start: 0.9114 (pt0) cc_final: 0.8182 (tm-30) REVERT: I 626 MET cc_start: 0.8624 (ttp) cc_final: 0.8406 (tmm) REVERT: I 643 TYR cc_start: 0.9476 (m-80) cc_final: 0.9195 (m-80) REVERT: L 95 ASN cc_start: 0.9412 (m110) cc_final: 0.8922 (t0) REVERT: L 100 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8780 (pm20) REVERT: D 101 ASP cc_start: 0.9077 (t0) cc_final: 0.8824 (m-30) REVERT: J 90 TYR cc_start: 0.8296 (m-80) cc_final: 0.7795 (m-80) outliers start: 1 outliers final: 0 residues processed: 100 average time/residue: 0.3787 time to fit residues: 57.2871 Evaluate side-chains 70 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 213 optimal weight: 8.9990 chunk 162 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 144 optimal weight: 10.0000 chunk 216 optimal weight: 10.0000 chunk 229 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 205 optimal weight: 9.9990 chunk 61 optimal weight: 0.0970 overall best weight: 4.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 229 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN C 590 GLN ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 20773 Z= 0.334 Angle : 0.698 11.545 28237 Z= 0.347 Chirality : 0.049 0.460 3458 Planarity : 0.004 0.065 3453 Dihedral : 8.453 58.352 4628 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.74 (0.17), residues: 2370 helix: -0.98 (0.27), residues: 361 sheet: -0.63 (0.20), residues: 698 loop : -1.50 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 479 HIS 0.005 0.001 HIS F 374 PHE 0.018 0.002 PHE G 468 TYR 0.016 0.002 TYR C 586 ARG 0.008 0.001 ARG D 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 MET cc_start: 0.9740 (ptm) cc_final: 0.8916 (ppp) REVERT: G 373 MET cc_start: 0.8410 (mmt) cc_final: 0.8060 (tpp) REVERT: B 629 MET cc_start: 0.9151 (mmt) cc_final: 0.8731 (mmt) REVERT: A 373 MET cc_start: 0.8773 (mtm) cc_final: 0.7860 (ttm) REVERT: A 434 MET cc_start: 0.9365 (ttt) cc_final: 0.9030 (tmm) REVERT: C 589 ASP cc_start: 0.9316 (p0) cc_final: 0.9094 (p0) REVERT: C 626 MET cc_start: 0.8847 (ttm) cc_final: 0.8183 (tpp) REVERT: F 61 TYR cc_start: 0.8486 (m-80) cc_final: 0.8164 (m-80) REVERT: F 373 MET cc_start: 0.8805 (ptp) cc_final: 0.8387 (mtm) REVERT: I 530 MET cc_start: 0.9278 (mmp) cc_final: 0.8898 (mmp) REVERT: I 577 GLN cc_start: 0.9133 (pt0) cc_final: 0.8140 (tm-30) REVERT: I 626 MET cc_start: 0.8676 (ttp) cc_final: 0.8415 (tmm) REVERT: I 643 TYR cc_start: 0.9499 (m-80) cc_final: 0.9188 (m-80) REVERT: L 95 ASN cc_start: 0.9078 (m110) cc_final: 0.8875 (t0) REVERT: L 100 GLU cc_start: 0.9274 (mt-10) cc_final: 0.8936 (pm20) REVERT: D 101 ASP cc_start: 0.9171 (t0) cc_final: 0.8914 (m-30) REVERT: J 90 TYR cc_start: 0.8421 (m-80) cc_final: 0.7931 (m-80) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.3493 time to fit residues: 46.3328 Evaluate side-chains 58 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 190 optimal weight: 0.2980 chunk 130 optimal weight: 9.9990 chunk 3 optimal weight: 0.0770 chunk 170 optimal weight: 0.6980 chunk 94 optimal weight: 8.9990 chunk 195 optimal weight: 8.9990 chunk 158 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 116 optimal weight: 6.9990 chunk 205 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN C 658 GLN F 72 HIS H 1 GLN ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20773 Z= 0.167 Angle : 0.580 12.835 28237 Z= 0.290 Chirality : 0.047 0.400 3458 Planarity : 0.004 0.065 3453 Dihedral : 7.652 58.347 4628 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.09 % Allowed : 2.08 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.44 (0.17), residues: 2370 helix: -0.64 (0.28), residues: 353 sheet: -0.33 (0.20), residues: 716 loop : -1.41 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP I 596 HIS 0.003 0.001 HIS A 216 PHE 0.011 0.001 PHE F 391 TYR 0.014 0.001 TYR H 90 ARG 0.007 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 MET cc_start: 0.9726 (ptm) cc_final: 0.8846 (ppp) REVERT: G 373 MET cc_start: 0.8302 (mmt) cc_final: 0.7884 (tpp) REVERT: B 629 MET cc_start: 0.9044 (mmt) cc_final: 0.8592 (mmt) REVERT: B 630 GLU cc_start: 0.9583 (mt-10) cc_final: 0.9272 (mt-10) REVERT: A 373 MET cc_start: 0.8757 (mtm) cc_final: 0.8078 (mtt) REVERT: A 434 MET cc_start: 0.9344 (ttt) cc_final: 0.8996 (tmm) REVERT: C 589 ASP cc_start: 0.9137 (p0) cc_final: 0.8812 (p0) REVERT: C 626 MET cc_start: 0.8787 (ttm) cc_final: 0.8170 (tpp) REVERT: F 61 TYR cc_start: 0.8435 (m-80) cc_final: 0.8118 (m-80) REVERT: F 373 MET cc_start: 0.8808 (ptp) cc_final: 0.8366 (mtm) REVERT: F 434 MET cc_start: 0.9020 (tmm) cc_final: 0.8666 (tmm) REVERT: I 530 MET cc_start: 0.9109 (mmp) cc_final: 0.8884 (mmp) REVERT: I 577 GLN cc_start: 0.9060 (pt0) cc_final: 0.8125 (tm-30) REVERT: I 626 MET cc_start: 0.8660 (ttp) cc_final: 0.8447 (tmm) REVERT: L 100 GLU cc_start: 0.9255 (mt-10) cc_final: 0.8922 (pm20) REVERT: D 101 ASP cc_start: 0.9163 (t0) cc_final: 0.8904 (m-30) REVERT: J 90 TYR cc_start: 0.8392 (m-80) cc_final: 0.7886 (m-80) REVERT: J 100 MET cc_start: 0.6915 (pmm) cc_final: 0.6666 (pmm) outliers start: 2 outliers final: 0 residues processed: 86 average time/residue: 0.3446 time to fit residues: 46.1885 Evaluate side-chains 59 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 77 optimal weight: 8.9990 chunk 206 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 134 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 229 optimal weight: 4.9990 chunk 190 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20773 Z= 0.298 Angle : 0.661 12.907 28237 Z= 0.329 Chirality : 0.048 0.458 3458 Planarity : 0.004 0.062 3453 Dihedral : 7.634 59.009 4628 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.58 (0.17), residues: 2370 helix: -0.86 (0.27), residues: 379 sheet: -0.42 (0.20), residues: 689 loop : -1.45 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 571 HIS 0.004 0.001 HIS F 374 PHE 0.015 0.002 PHE A 353 TYR 0.019 0.002 TYR C 586 ARG 0.012 0.001 ARG K 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 2.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 95 MET cc_start: 0.9784 (ptm) cc_final: 0.8029 (ppp) REVERT: G 373 MET cc_start: 0.8387 (mmt) cc_final: 0.8056 (tpp) REVERT: A 373 MET cc_start: 0.8666 (mtm) cc_final: 0.8009 (mtt) REVERT: A 434 MET cc_start: 0.9364 (ttt) cc_final: 0.9039 (tmm) REVERT: C 589 ASP cc_start: 0.9322 (p0) cc_final: 0.9047 (p0) REVERT: C 626 MET cc_start: 0.8835 (ttm) cc_final: 0.8136 (tpp) REVERT: F 61 TYR cc_start: 0.8522 (m-80) cc_final: 0.8197 (m-80) REVERT: F 373 MET cc_start: 0.8795 (ptp) cc_final: 0.8440 (mtm) REVERT: I 530 MET cc_start: 0.9403 (mmp) cc_final: 0.9117 (mmp) REVERT: I 577 GLN cc_start: 0.9107 (pt0) cc_final: 0.8142 (tm-30) REVERT: L 100 GLU cc_start: 0.9348 (mt-10) cc_final: 0.9021 (pp20) REVERT: D 101 ASP cc_start: 0.9237 (t0) cc_final: 0.8958 (m-30) REVERT: J 90 TYR cc_start: 0.8472 (m-80) cc_final: 0.8032 (m-80) REVERT: J 100 MET cc_start: 0.7155 (pmm) cc_final: 0.6810 (pmm) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.3466 time to fit residues: 43.4867 Evaluate side-chains 55 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 221 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 167 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 193 optimal weight: 30.0000 chunk 128 optimal weight: 4.9990 chunk 228 optimal weight: 5.9990 chunk 142 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 105 optimal weight: 0.3980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20773 Z= 0.203 Angle : 0.597 13.196 28237 Z= 0.299 Chirality : 0.047 0.410 3458 Planarity : 0.004 0.060 3453 Dihedral : 7.244 58.807 4628 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.45 (0.17), residues: 2370 helix: -0.53 (0.29), residues: 355 sheet: -0.48 (0.20), residues: 704 loop : -1.34 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 571 HIS 0.004 0.001 HIS D 52 PHE 0.010 0.001 PHE F 391 TYR 0.010 0.001 TYR H 90 ARG 0.005 0.000 ARG D 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 2.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 95 MET cc_start: 0.9776 (ptm) cc_final: 0.8064 (ppp) REVERT: G 373 MET cc_start: 0.8296 (mmt) cc_final: 0.7947 (tpp) REVERT: B 535 MET cc_start: 0.8854 (pmm) cc_final: 0.8589 (pmm) REVERT: A 373 MET cc_start: 0.8618 (mtm) cc_final: 0.8039 (mtt) REVERT: A 434 MET cc_start: 0.9357 (ttt) cc_final: 0.8967 (tmm) REVERT: C 589 ASP cc_start: 0.9222 (p0) cc_final: 0.8907 (p0) REVERT: C 626 MET cc_start: 0.8803 (ttm) cc_final: 0.8158 (tpp) REVERT: F 61 TYR cc_start: 0.8456 (m-80) cc_final: 0.8144 (m-80) REVERT: F 373 MET cc_start: 0.8756 (ptp) cc_final: 0.8430 (ptm) REVERT: I 577 GLN cc_start: 0.9070 (pt0) cc_final: 0.8117 (tm-30) REVERT: I 643 TYR cc_start: 0.9449 (m-10) cc_final: 0.9205 (m-80) REVERT: L 100 GLU cc_start: 0.9327 (mt-10) cc_final: 0.9007 (pp20) REVERT: D 101 ASP cc_start: 0.9238 (t0) cc_final: 0.8973 (m-30) REVERT: J 90 TYR cc_start: 0.8462 (m-80) cc_final: 0.8034 (m-80) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.3289 time to fit residues: 40.9296 Evaluate side-chains 57 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 141 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 179 optimal weight: 8.9990 chunk 207 optimal weight: 0.1980 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20773 Z= 0.205 Angle : 0.591 12.678 28237 Z= 0.296 Chirality : 0.047 0.402 3458 Planarity : 0.004 0.059 3453 Dihedral : 6.981 56.865 4628 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.42 (0.17), residues: 2370 helix: -0.61 (0.28), residues: 375 sheet: -0.36 (0.20), residues: 689 loop : -1.36 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 45 HIS 0.004 0.001 HIS D 52 PHE 0.010 0.001 PHE F 391 TYR 0.012 0.001 TYR C 586 ARG 0.005 0.000 ARG D 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 2.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 95 MET cc_start: 0.9777 (ptm) cc_final: 0.9208 (ppp) REVERT: G 373 MET cc_start: 0.8304 (mmt) cc_final: 0.7941 (tpp) REVERT: A 104 MET cc_start: 0.9477 (tpt) cc_final: 0.9242 (tpp) REVERT: A 373 MET cc_start: 0.8576 (mtm) cc_final: 0.8021 (mtt) REVERT: A 434 MET cc_start: 0.9347 (ttt) cc_final: 0.8970 (tmm) REVERT: C 589 ASP cc_start: 0.9243 (p0) cc_final: 0.8925 (p0) REVERT: C 626 MET cc_start: 0.8852 (ttm) cc_final: 0.8174 (tpp) REVERT: F 61 TYR cc_start: 0.8478 (m-80) cc_final: 0.8182 (m-80) REVERT: F 373 MET cc_start: 0.8730 (ptp) cc_final: 0.8427 (ptm) REVERT: I 530 MET cc_start: 0.9236 (mmp) cc_final: 0.8980 (mmp) REVERT: I 577 GLN cc_start: 0.9055 (pt0) cc_final: 0.8580 (tm-30) REVERT: I 626 MET cc_start: 0.8218 (tmm) cc_final: 0.7922 (tmm) REVERT: I 643 TYR cc_start: 0.9459 (m-10) cc_final: 0.9216 (m-80) REVERT: L 100 GLU cc_start: 0.9355 (mt-10) cc_final: 0.9014 (pp20) REVERT: D 101 ASP cc_start: 0.9236 (t0) cc_final: 0.8973 (m-30) REVERT: J 90 TYR cc_start: 0.8548 (m-80) cc_final: 0.8120 (m-80) REVERT: K 83 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7702 (mm-30) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.3490 time to fit residues: 42.9959 Evaluate side-chains 60 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 218 optimal weight: 3.9990 chunk 199 optimal weight: 20.0000 chunk 212 optimal weight: 9.9990 chunk 128 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 167 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 192 optimal weight: 20.0000 chunk 201 optimal weight: 4.9990 chunk 139 optimal weight: 20.0000 chunk 225 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN C 658 GLN ** F 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 HIS ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 20773 Z= 0.353 Angle : 0.704 12.681 28237 Z= 0.351 Chirality : 0.049 0.463 3458 Planarity : 0.005 0.065 3453 Dihedral : 7.461 58.178 4628 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.68 (0.17), residues: 2370 helix: -0.90 (0.27), residues: 379 sheet: -0.59 (0.20), residues: 689 loop : -1.47 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 631 HIS 0.005 0.001 HIS D 52 PHE 0.017 0.002 PHE L 67 TYR 0.028 0.002 TYR F 217 ARG 0.007 0.001 ARG G 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 2.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 MET cc_start: 0.9765 (ptm) cc_final: 0.8873 (ppp) REVERT: G 373 MET cc_start: 0.8398 (mmt) cc_final: 0.8038 (tpp) REVERT: A 100 MET cc_start: 0.9129 (mtm) cc_final: 0.8812 (mtm) REVERT: A 373 MET cc_start: 0.8596 (mtm) cc_final: 0.7839 (ttm) REVERT: A 434 MET cc_start: 0.9376 (ttt) cc_final: 0.8986 (tmm) REVERT: C 530 MET cc_start: 0.8482 (tmm) cc_final: 0.8200 (tmm) REVERT: C 589 ASP cc_start: 0.9336 (p0) cc_final: 0.9069 (p0) REVERT: C 626 MET cc_start: 0.8939 (ttm) cc_final: 0.8274 (tpp) REVERT: F 61 TYR cc_start: 0.8561 (m-80) cc_final: 0.8240 (m-10) REVERT: F 373 MET cc_start: 0.8721 (ptp) cc_final: 0.8371 (ptm) REVERT: I 530 MET cc_start: 0.9378 (mmp) cc_final: 0.9100 (mmp) REVERT: I 577 GLN cc_start: 0.9123 (pt0) cc_final: 0.8567 (tm-30) REVERT: I 626 MET cc_start: 0.8065 (tmm) cc_final: 0.7786 (tmm) REVERT: I 643 TYR cc_start: 0.9501 (m-10) cc_final: 0.9243 (m-80) REVERT: L 100 GLU cc_start: 0.9491 (mt-10) cc_final: 0.9129 (pp20) REVERT: D 101 ASP cc_start: 0.9300 (t0) cc_final: 0.8975 (m-30) REVERT: J 90 TYR cc_start: 0.8695 (m-80) cc_final: 0.8324 (m-80) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.3311 time to fit residues: 37.5173 Evaluate side-chains 57 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 2.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 137 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 156 optimal weight: 10.0000 chunk 236 optimal weight: 0.9980 chunk 217 optimal weight: 10.0000 chunk 188 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 115 optimal weight: 0.0040 chunk 149 optimal weight: 6.9990 chunk 200 optimal weight: 7.9990 overall best weight: 2.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20773 Z= 0.231 Angle : 0.620 12.566 28237 Z= 0.310 Chirality : 0.048 0.426 3458 Planarity : 0.004 0.059 3453 Dihedral : 7.133 57.213 4628 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.62 (0.17), residues: 2370 helix: -0.78 (0.27), residues: 381 sheet: -0.53 (0.20), residues: 689 loop : -1.46 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 112 HIS 0.005 0.001 HIS D 52 PHE 0.011 0.001 PHE E 62 TYR 0.023 0.001 TYR F 217 ARG 0.007 0.000 ARG A 476 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 2.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 95 MET cc_start: 0.9763 (ptm) cc_final: 0.8867 (ppp) REVERT: G 373 MET cc_start: 0.8390 (mmt) cc_final: 0.8028 (tpp) REVERT: A 100 MET cc_start: 0.9131 (mtm) cc_final: 0.8886 (mtm) REVERT: A 373 MET cc_start: 0.8580 (mtm) cc_final: 0.7828 (ttm) REVERT: A 434 MET cc_start: 0.9382 (ttt) cc_final: 0.9014 (tmm) REVERT: C 530 MET cc_start: 0.8517 (tmm) cc_final: 0.8283 (tmm) REVERT: C 589 ASP cc_start: 0.9249 (p0) cc_final: 0.8955 (p0) REVERT: C 626 MET cc_start: 0.8917 (ttm) cc_final: 0.8244 (tpp) REVERT: F 61 TYR cc_start: 0.8515 (m-80) cc_final: 0.8207 (m-10) REVERT: F 373 MET cc_start: 0.8739 (ptp) cc_final: 0.8427 (ptm) REVERT: I 530 MET cc_start: 0.9319 (mmp) cc_final: 0.9079 (mmp) REVERT: I 577 GLN cc_start: 0.9070 (pt0) cc_final: 0.8522 (tm-30) REVERT: I 643 TYR cc_start: 0.9505 (m-10) cc_final: 0.9246 (m-80) REVERT: L 100 GLU cc_start: 0.9491 (mt-10) cc_final: 0.9143 (pp20) REVERT: D 101 ASP cc_start: 0.9308 (t0) cc_final: 0.8977 (m-30) REVERT: J 90 TYR cc_start: 0.8713 (m-80) cc_final: 0.8341 (m-80) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.3410 time to fit residues: 39.7483 Evaluate side-chains 59 residues out of total 2117 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 2.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 57 optimal weight: 6.9990 chunk 173 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 188 optimal weight: 30.0000 chunk 78 optimal weight: 10.0000 chunk 193 optimal weight: 30.0000 chunk 23 optimal weight: 7.9990 chunk 34 optimal weight: 0.0970 chunk 165 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.029867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.023779 restraints weight = 269031.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.024371 restraints weight = 163485.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.024780 restraints weight = 117387.630| |-----------------------------------------------------------------------------| r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.5467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20773 Z= 0.287 Angle : 0.655 12.497 28237 Z= 0.327 Chirality : 0.048 0.431 3458 Planarity : 0.004 0.059 3453 Dihedral : 7.236 57.802 4628 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.65 (0.17), residues: 2370 helix: -0.82 (0.27), residues: 381 sheet: -0.53 (0.20), residues: 692 loop : -1.50 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP G 45 HIS 0.005 0.001 HIS D 52 PHE 0.014 0.001 PHE E 62 TYR 0.025 0.001 TYR F 217 ARG 0.007 0.001 ARG E 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2907.34 seconds wall clock time: 54 minutes 40.12 seconds (3280.12 seconds total)