Starting phenix.real_space_refine on Wed Feb 21 21:51:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtf_32784/02_2024/7wtf_32784.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtf_32784/02_2024/7wtf_32784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtf_32784/02_2024/7wtf_32784.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtf_32784/02_2024/7wtf_32784.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtf_32784/02_2024/7wtf_32784.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtf_32784/02_2024/7wtf_32784.pdb" } resolution = 3.0 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= -0.002 sd= 0.100 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 144 5.16 5 C 20372 2.51 5 N 5254 2.21 5 O 6279 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 663": "OE1" <-> "OE2" Residue "B GLU 750": "OE1" <-> "OE2" Residue "B GLU 775": "OE1" <-> "OE2" Residue "B PHE 900": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "B TYR 1069": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1094": "OE1" <-> "OE2" Residue "B TYR 1140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C TYR 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 727": "OE1" <-> "OE2" Residue "C ASP 739": "OD1" <-> "OD2" Residue "C ASP 869": "OD1" <-> "OD2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C ASP 1043": "OD1" <-> "OD2" Residue "C TYR 1069": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 153": "OE1" <-> "OE2" Residue "D TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 195": "OD1" <-> "OD2" Residue "D TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 952": "OD1" <-> "OD2" Residue "D TYR 1069": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1113": "OE1" <-> "OE2" Residue "D ASP 1120": "OD1" <-> "OD2" Residue "G ASP 107": "OD1" <-> "OD2" Residue "G TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32049 Number of models: 1 Model: "" Number of chains: 32 Chain: "H" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "B" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 61, 'TRANS': 1036} Chain breaks: 4 Chain: "C" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 61, 'TRANS': 1036} Chain breaks: 4 Chain: "D" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 61, 'TRANS': 1036} Chain breaks: 4 Chain: "G" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "J" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "I" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "K" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 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: "B" 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: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 16.00, per 1000 atoms: 0.50 Number of scatterers: 32049 At special positions: 0 Unit cell: (150.8, 145.6, 251.68, 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 144 16.00 O 6279 8.00 N 5254 7.00 C 20372 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 293 " - pdb=" SG CYS B 303 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 381 " - pdb=" SG CYS B 434 " distance=2.03 Simple disulfide: pdb=" SG CYS B 393 " - pdb=" SG CYS B 527 " distance=2.03 Simple disulfide: pdb=" SG CYS B 482 " - pdb=" SG CYS B 490 " distance=2.03 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 651 " distance=2.02 Simple disulfide: pdb=" SG CYS B 664 " - pdb=" SG CYS B 673 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 762 " distance=2.03 Simple disulfide: pdb=" SG CYS B 745 " - pdb=" SG CYS B 751 " distance=2.03 Simple disulfide: pdb=" SG CYS B1034 " - pdb=" SG CYS B1045 " distance=2.03 Simple disulfide: pdb=" SG CYS B1084 " - pdb=" SG CYS B1128 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 293 " - pdb=" SG CYS C 303 " distance=2.03 Simple disulfide: pdb=" SG CYS C 338 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 381 " - pdb=" SG CYS C 434 " distance=2.03 Simple disulfide: pdb=" SG CYS C 393 " - pdb=" SG CYS C 527 " distance=2.03 Simple disulfide: pdb=" SG CYS C 482 " - pdb=" SG CYS C 490 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 651 " distance=2.02 Simple disulfide: pdb=" SG CYS C 664 " - pdb=" SG CYS C 673 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 762 " distance=2.03 Simple disulfide: pdb=" SG CYS C 745 " - pdb=" SG CYS C 751 " distance=2.03 Simple disulfide: pdb=" SG CYS C1034 " - pdb=" SG CYS C1045 " distance=2.03 Simple disulfide: pdb=" SG CYS C1084 " - pdb=" SG CYS C1128 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 136 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 163 " distance=2.03 Simple disulfide: pdb=" SG CYS D 293 " - pdb=" SG CYS D 303 " distance=2.03 Simple disulfide: pdb=" SG CYS D 338 " - pdb=" SG CYS D 363 " distance=2.04 Simple disulfide: pdb=" SG CYS D 381 " - pdb=" SG CYS D 434 " distance=2.04 Simple disulfide: pdb=" SG CYS D 393 " - pdb=" SG CYS D 527 " distance=2.03 Simple disulfide: pdb=" SG CYS D 482 " - pdb=" SG CYS D 490 " distance=2.03 Simple disulfide: pdb=" SG CYS D 619 " - pdb=" SG CYS D 651 " distance=2.03 Simple disulfide: pdb=" SG CYS D 664 " - pdb=" SG CYS D 673 " distance=2.03 Simple disulfide: pdb=" SG CYS D 740 " - pdb=" SG CYS D 762 " distance=2.04 Simple disulfide: pdb=" SG CYS D 745 " - pdb=" SG CYS D 751 " distance=2.03 Simple disulfide: pdb=" SG CYS D1034 " - pdb=" SG CYS D1045 " distance=2.03 Simple disulfide: pdb=" SG CYS D1084 " - pdb=" SG CYS D1128 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " NAG-ASN " NAG A 1 " - " ASN B 719 " " NAG B1201 " - " ASN B1160 " " NAG B1202 " - " ASN B 17 " " NAG B1203 " - " ASN B 61 " " NAG B1204 " - " ASN B 605 " " NAG B1205 " - " ASN B 659 " " NAG B1206 " - " ASN B 618 " " NAG B1207 " - " ASN B 711 " " NAG B1208 " - " ASN B 122 " " NAG B1209 " - " ASN B 149 " " NAG B1210 " - " ASN B 333 " " NAG B1211 " - " ASN B 284 " " NAG C1201 " - " ASN C1160 " " NAG C1202 " - " ASN C 125 " " NAG C1203 " - " ASN C 17 " " NAG C1204 " - " ASN C 61 " " NAG C1205 " - " ASN C 605 " " NAG C1206 " - " ASN C 659 " " NAG C1207 " - " ASN C 711 " " NAG C1208 " - " ASN C 146 " " NAG C1209 " - " ASN C 162 " " NAG C1210 " - " ASN C 618 " " NAG D1201 " - " ASN D1160 " " NAG D1202 " - " ASN D 17 " " NAG D1203 " - " ASN D 61 " " NAG D1204 " - " ASN D 605 " " NAG D1205 " - " ASN D 659 " " NAG D1206 " - " ASN D 711 " " NAG D1207 " - " ASN D 146 " " NAG D1208 " - " ASN D 284 " " NAG D1209 " - " ASN D 618 " " NAG E 1 " - " ASN B 803 " " NAG F 1 " - " ASN B1100 " " NAG M 1 " - " ASN B1136 " " NAG N 1 " - " ASN B1076 " " NAG P 1 " - " ASN C 719 " " NAG Q 1 " - " ASN C 803 " " NAG R 1 " - " ASN C1100 " " NAG S 1 " - " ASN C1136 " " NAG T 1 " - " ASN C 284 " " NAG U 1 " - " ASN C1076 " " NAG V 1 " - " ASN C 333 " " NAG W 1 " - " ASN D 233 " " NAG X 1 " - " ASN D 719 " " NAG Y 1 " - " ASN D1076 " " NAG Z 1 " - " ASN D 803 " " NAG a 1 " - " ASN D1100 " " NAG b 1 " - " ASN D1136 " " NAG c 1 " - " ASN D 333 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.09 Conformation dependent library (CDL) restraints added in 5.5 seconds 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7398 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 61 sheets defined 20.0% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'B' and resid 296 through 306 Processing helix chain 'B' and resid 339 through 345 removed outlier: 4.041A pdb=" N VAL B 343 " --> pdb=" O PRO B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.575A pdb=" N LEU B 389 " --> pdb=" O PRO B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.666A pdb=" N ALA B 413 " --> pdb=" O ARG B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 423 Processing helix chain 'B' and resid 545 through 548 Processing helix chain 'B' and resid 635 through 640 removed outlier: 4.090A pdb=" N THR B 640 " --> pdb=" O VAL B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 744 Processing helix chain 'B' and resid 748 through 755 Processing helix chain 'B' and resid 756 through 759 removed outlier: 3.713A pdb=" N GLY B 759 " --> pdb=" O LEU B 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 756 through 759' Processing helix chain 'B' and resid 760 through 785 removed outlier: 3.843A pdb=" N ASP B 777 " --> pdb=" O ALA B 773 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 783 " --> pdb=" O ASN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 825 Processing helix chain 'B' and resid 851 through 855 removed outlier: 3.532A pdb=" N ALA B 854 " --> pdb=" O LEU B 851 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN B 855 " --> pdb=" O ILE B 852 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 851 through 855' Processing helix chain 'B' and resid 868 through 886 removed outlier: 3.886A pdb=" N GLN B 874 " --> pdb=" O GLU B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 892 Processing helix chain 'B' and resid 899 through 912 removed outlier: 3.751A pdb=" N ALA B 905 " --> pdb=" O PRO B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 920 removed outlier: 3.915A pdb=" N TYR B 919 " --> pdb=" O GLN B 915 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU B 920 " --> pdb=" O ASN B 916 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 915 through 920' Processing helix chain 'B' and resid 921 through 942 removed outlier: 3.628A pdb=" N LYS B 935 " --> pdb=" O SER B 931 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE B 936 " --> pdb=" O ALA B 932 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN B 937 " --> pdb=" O ILE B 933 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP B 938 " --> pdb=" O GLY B 934 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 941 " --> pdb=" O GLN B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 947 through 967 removed outlier: 3.794A pdb=" N ASP B 952 " --> pdb=" O GLY B 948 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL B 953 " --> pdb=" O LYS B 949 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL B 954 " --> pdb=" O LEU B 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 970 No H-bonds generated for 'chain 'B' and resid 968 through 970' Processing helix chain 'B' and resid 979 through 984 Processing helix chain 'B' and resid 987 through 995 removed outlier: 3.540A pdb=" N GLU B 992 " --> pdb=" O PRO B 988 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL B 993 " --> pdb=" O PRO B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1000 removed outlier: 3.512A pdb=" N THR B1000 " --> pdb=" O ASP B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1002 through 1034 removed outlier: 3.515A pdb=" N THR B1008 " --> pdb=" O GLN B1004 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR B1009 " --> pdb=" O SER B1005 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B1023 " --> pdb=" O GLU B1019 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B1026 " --> pdb=" O ALA B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1149 removed outlier: 4.180A pdb=" N GLU B1146 " --> pdb=" O PRO B1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 1150 through 1163 removed outlier: 3.592A pdb=" N ASP B1155 " --> pdb=" O LYS B1151 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS B1156 " --> pdb=" O GLU B1152 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N HIS B1161 " --> pdb=" O TYR B1157 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR B1162 " --> pdb=" O PHE B1158 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER B1163 " --> pdb=" O LYS B1159 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 306 Processing helix chain 'C' and resid 340 through 345 Processing helix chain 'C' and resid 367 through 372 removed outlier: 4.029A pdb=" N ASN C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 removed outlier: 3.524A pdb=" N ILE C 412 " --> pdb=" O GLU C 408 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA C 413 " --> pdb=" O VAL C 409 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 408 through 413' Processing helix chain 'C' and resid 419 through 424 removed outlier: 3.598A pdb=" N TYR C 423 " --> pdb=" O ASN C 419 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN C 424 " --> pdb=" O ILE C 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 419 through 424' Processing helix chain 'C' and resid 440 through 445 removed outlier: 3.788A pdb=" N SER C 445 " --> pdb=" O ASN C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 746 removed outlier: 3.952A pdb=" N ILE C 744 " --> pdb=" O CYS C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 756 removed outlier: 3.697A pdb=" N SER C 752 " --> pdb=" O SER C 748 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASN C 753 " --> pdb=" O THR C 749 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU C 754 " --> pdb=" O GLU C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 759 No H-bonds generated for 'chain 'C' and resid 757 through 759' Processing helix chain 'C' and resid 762 through 784 removed outlier: 3.553A pdb=" N ASP C 777 " --> pdb=" O ALA C 773 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR C 780 " --> pdb=" O GLN C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 825 removed outlier: 3.569A pdb=" N LEU C 823 " --> pdb=" O PRO C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 886 removed outlier: 3.544A pdb=" N ALA C 873 " --> pdb=" O ASP C 869 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN C 874 " --> pdb=" O GLU C 870 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C 884 " --> pdb=" O LEU C 880 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR C 885 " --> pdb=" O ALA C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 899 through 912 removed outlier: 3.956A pdb=" N ALA C 905 " --> pdb=" O PRO C 901 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE C 911 " --> pdb=" O ARG C 907 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY C 912 " --> pdb=" O PHE C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 920 removed outlier: 3.697A pdb=" N TYR C 919 " --> pdb=" O GLN C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 940 removed outlier: 3.569A pdb=" N LYS C 935 " --> pdb=" O SER C 931 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE C 936 " --> pdb=" O ALA C 932 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN C 937 " --> pdb=" O ILE C 933 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP C 938 " --> pdb=" O GLY C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 946 removed outlier: 3.911A pdb=" N ALA C 946 " --> pdb=" O THR C 943 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 943 through 946' Processing helix chain 'C' and resid 947 through 966 removed outlier: 4.151A pdb=" N VAL C 953 " --> pdb=" O LYS C 949 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL C 954 " --> pdb=" O LEU C 950 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN C 957 " --> pdb=" O VAL C 953 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 985 removed outlier: 3.615A pdb=" N PHE C 983 " --> pdb=" O LEU C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 995 removed outlier: 3.646A pdb=" N GLU C 992 " --> pdb=" O PRO C 988 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL C 993 " --> pdb=" O PRO C 989 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1034 removed outlier: 3.806A pdb=" N ARG C1002 " --> pdb=" O LEU C 998 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU C1003 " --> pdb=" O ILE C 999 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C1026 " --> pdb=" O ALA C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1142 through 1149 removed outlier: 3.917A pdb=" N GLU C1146 " --> pdb=" O PRO C1142 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER C1149 " --> pdb=" O PRO C1145 " (cutoff:3.500A) Processing helix chain 'C' and resid 1150 through 1159 removed outlier: 3.701A pdb=" N ASP C1155 " --> pdb=" O LYS C1151 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS C1156 " --> pdb=" O GLU C1152 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 306 Processing helix chain 'D' and resid 340 through 345 removed outlier: 3.930A pdb=" N PHE D 344 " --> pdb=" O PHE D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'D' and resid 385 through 389 Processing helix chain 'D' and resid 407 through 413 removed outlier: 4.120A pdb=" N GLN D 411 " --> pdb=" O ASP D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 626 removed outlier: 3.947A pdb=" N ILE D 626 " --> pdb=" O PRO D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 746 removed outlier: 3.520A pdb=" N TYR D 743 " --> pdb=" O ASP D 739 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS D 745 " --> pdb=" O THR D 741 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY D 746 " --> pdb=" O MET D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 756 removed outlier: 4.096A pdb=" N ASN D 753 " --> pdb=" O THR D 749 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU D 754 " --> pdb=" O GLU D 750 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 759 No H-bonds generated for 'chain 'D' and resid 757 through 759' Processing helix chain 'D' and resid 760 through 785 removed outlier: 3.650A pdb=" N GLN D 764 " --> pdb=" O SER D 760 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU D 765 " --> pdb=" O PHE D 761 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS D 766 " --> pdb=" O CYS D 762 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN D 776 " --> pdb=" O ILE D 772 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP D 777 " --> pdb=" O ALA D 773 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR D 780 " --> pdb=" O GLN D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 828 removed outlier: 3.523A pdb=" N ASN D 826 " --> pdb=" O ASP D 822 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL D 828 " --> pdb=" O LEU D 824 " (cutoff:3.500A) Processing helix chain 'D' and resid 868 through 886 removed outlier: 3.814A pdb=" N THR D 885 " --> pdb=" O ALA D 881 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 892 removed outlier: 3.535A pdb=" N GLY D 891 " --> pdb=" O TRP D 888 " (cutoff:3.500A) Processing helix chain 'D' and resid 899 through 912 removed outlier: 3.709A pdb=" N ALA D 905 " --> pdb=" O PRO D 901 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR D 906 " --> pdb=" O MET D 902 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE D 911 " --> pdb=" O ARG D 907 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY D 912 " --> pdb=" O PHE D 908 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 920 removed outlier: 3.696A pdb=" N TYR D 919 " --> pdb=" O GLN D 915 " (cutoff:3.500A) Processing helix chain 'D' and resid 921 through 943 removed outlier: 3.550A pdb=" N ILE D 936 " --> pdb=" O ALA D 932 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN D 937 " --> pdb=" O ILE D 933 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP D 938 " --> pdb=" O GLY D 934 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR D 943 " --> pdb=" O SER D 939 " (cutoff:3.500A) Processing helix chain 'D' and resid 944 through 946 No H-bonds generated for 'chain 'D' and resid 944 through 946' Processing helix chain 'D' and resid 947 through 967 removed outlier: 3.828A pdb=" N VAL D 953 " --> pdb=" O LYS D 949 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR D 963 " --> pdb=" O GLN D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 968 through 970 No H-bonds generated for 'chain 'D' and resid 968 through 970' Processing helix chain 'D' and resid 980 through 985 removed outlier: 3.750A pdb=" N SER D 984 " --> pdb=" O ASN D 980 " (cutoff:3.500A) Processing helix chain 'D' and resid 990 through 1000 removed outlier: 3.657A pdb=" N LEU D 998 " --> pdb=" O GLN D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1000 through 1034 removed outlier: 3.536A pdb=" N LEU D1026 " --> pdb=" O ALA D1022 " (cutoff:3.500A) Processing helix chain 'D' and resid 1142 through 1162 removed outlier: 4.259A pdb=" N GLU D1146 " --> pdb=" O PRO D1142 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 4.426A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'H' and resid 46 through 49 removed outlier: 5.903A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 19 through 23 removed outlier: 3.657A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE L 75 " --> pdb=" O VAL L 19 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 44 through 46 Processing sheet with id=AA5, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.023A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N ASN B 61 " --> pdb=" O TYR B 271 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N TYR B 271 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.248A pdb=" N ASP B 289 " --> pdb=" O LYS B 280 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 168 through 172 removed outlier: 4.089A pdb=" N ILE B 105 " --> pdb=" O GLN B 241 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN B 241 " --> pdb=" O ILE B 105 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 313 through 320 removed outlier: 5.769A pdb=" N ILE B 314 " --> pdb=" O THR B 601 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N THR B 601 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLN B 316 " --> pdb=" O VAL B 599 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL B 599 " --> pdb=" O GLN B 316 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER B 318 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AB1, first strand: chain 'B' and resid 358 through 360 Processing sheet with id=AB2, first strand: chain 'B' and resid 358 through 360 Processing sheet with id=AB3, first strand: chain 'B' and resid 454 through 456 Processing sheet with id=AB4, first strand: chain 'B' and resid 475 through 476 Processing sheet with id=AB5, first strand: chain 'B' and resid 567 through 569 Processing sheet with id=AB6, first strand: chain 'B' and resid 656 through 657 removed outlier: 5.972A pdb=" N GLU B 656 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N THR B 698 " --> pdb=" O GLU B 656 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR B 697 " --> pdb=" O CYS B 673 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE B 672 " --> pdb=" O ILE B 668 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 703 through 706 Processing sheet with id=AB8, first strand: chain 'B' and resid 713 through 721 removed outlier: 6.521A pdb=" N SER B 713 " --> pdb=" O THR B1078 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR B1078 " --> pdb=" O SER B 713 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA B 715 " --> pdb=" O ASN B1076 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ASN B1076 " --> pdb=" O ALA B 715 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU B1074 " --> pdb=" O PRO B 717 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASN B 719 " --> pdb=" O ALA B1072 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B1078 " --> pdb=" O SER B1099 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA B1080 " --> pdb=" O PHE B1097 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N PHE B1097 " --> pdb=" O ALA B1080 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 724 through 730 Processing sheet with id=AC1, first strand: chain 'B' and resid 736 through 738 removed outlier: 3.550A pdb=" N THR B 861 " --> pdb=" O SER B 737 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 790 through 792 removed outlier: 5.406A pdb=" N ILE B 790 " --> pdb=" O ASN C 705 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 1122 through 1124 Processing sheet with id=AC4, first strand: chain 'C' and resid 27 through 31 removed outlier: 7.830A pdb=" N ASN C 61 " --> pdb=" O TYR C 271 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N TYR C 271 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU C 96 " --> pdb=" O ASN C 185 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN C 185 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE C 198 " --> pdb=" O ASP C 227 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ASP C 227 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ILE C 200 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU C 225 " --> pdb=" O ILE C 200 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 42 through 43 removed outlier: 3.573A pdb=" N ALA D 577 " --> pdb=" O GLY D 568 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR D 590 " --> pdb=" O VAL D 553 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.805A pdb=" N ASP C 289 " --> pdb=" O LYS C 280 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AC8, first strand: chain 'C' and resid 165 through 169 removed outlier: 5.701A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLY C 103 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 313 through 321 removed outlier: 5.283A pdb=" N ILE C 314 " --> pdb=" O THR C 601 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N THR C 601 " --> pdb=" O ILE C 314 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N GLN C 316 " --> pdb=" O VAL C 599 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL C 599 " --> pdb=" O GLN C 316 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N SER C 318 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 597 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 652 " --> pdb=" O PHE C 645 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE C 645 " --> pdb=" O LEU C 652 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 326 through 330 removed outlier: 7.454A pdb=" N GLU C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N ASN C 544 " --> pdb=" O GLU C 326 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ILE C 328 " --> pdb=" O ASN C 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 358 through 360 removed outlier: 3.952A pdb=" N ILE C 360 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL C 397 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG C 511 " --> pdb=" O TRP C 438 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TRP C 438 " --> pdb=" O ARG C 511 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 475 through 476 removed outlier: 3.630A pdb=" N TYR C 475 " --> pdb=" O TYR C 491 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 553 through 556 removed outlier: 3.656A pdb=" N THR C 590 " --> pdb=" O VAL C 553 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA C 577 " --> pdb=" O GLY C 568 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 656 through 657 removed outlier: 6.118A pdb=" N GLU C 656 " --> pdb=" O ALA C 696 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N THR C 698 " --> pdb=" O GLU C 656 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE C 672 " --> pdb=" O ILE C 668 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 713 through 730 removed outlier: 6.548A pdb=" N SER C 713 " --> pdb=" O THR C1078 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR C1078 " --> pdb=" O SER C 713 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA C 715 " --> pdb=" O ASN C1076 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASN C1076 " --> pdb=" O ALA C 715 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLU C1074 " --> pdb=" O PRO C 717 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N GLY C1061 " --> pdb=" O SER C1057 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N SER C1057 " --> pdb=" O GLY C1061 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL C1063 " --> pdb=" O PRO C1055 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU C1065 " --> pdb=" O SER C1053 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N SER C1053 " --> pdb=" O LEU C1065 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL C1067 " --> pdb=" O LEU C1051 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 713 through 730 removed outlier: 6.548A pdb=" N SER C 713 " --> pdb=" O THR C1078 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR C1078 " --> pdb=" O SER C 713 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA C 715 " --> pdb=" O ASN C1076 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ASN C1076 " --> pdb=" O ALA C 715 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLU C1074 " --> pdb=" O PRO C 717 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA C1080 " --> pdb=" O PHE C1097 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE C1097 " --> pdb=" O ALA C1080 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 737 through 738 Processing sheet with id=AD9, first strand: chain 'C' and resid 789 through 792 removed outlier: 6.033A pdb=" N ILE C 790 " --> pdb=" O ASN D 705 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 1122 through 1124 Processing sheet with id=AE2, first strand: chain 'D' and resid 27 through 31 removed outlier: 7.993A pdb=" N ASN D 61 " --> pdb=" O TYR D 271 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N TYR D 271 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA D 266 " --> pdb=" O ILE D 95 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N SER D 202 " --> pdb=" O PRO D 224 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N HIS D 204 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N LEU D 222 " --> pdb=" O HIS D 204 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL D 36 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 48 through 55 removed outlier: 3.722A pdb=" N ASP D 289 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 84 through 85 Processing sheet with id=AE5, first strand: chain 'D' and resid 168 through 169 Processing sheet with id=AE6, first strand: chain 'D' and resid 313 through 321 removed outlier: 5.214A pdb=" N ILE D 314 " --> pdb=" O THR D 601 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR D 601 " --> pdb=" O ILE D 314 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLN D 316 " --> pdb=" O VAL D 599 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL D 599 " --> pdb=" O GLN D 316 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N SER D 318 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL D 597 " --> pdb=" O SER D 318 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N CYS D 651 " --> pdb=" O TYR D 614 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY D 650 " --> pdb=" O THR D 647 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 358 through 360 removed outlier: 3.982A pdb=" N ALA D 399 " --> pdb=" O LYS D 358 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE D 360 " --> pdb=" O VAL D 397 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 363 through 364 removed outlier: 6.832A pdb=" N CYS D 363 " --> pdb=" O CYS D 527 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'D' and resid 402 through 404 removed outlier: 3.878A pdb=" N ILE D 404 " --> pdb=" O TYR D 510 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG D 511 " --> pdb=" O TRP D 438 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TRP D 438 " --> pdb=" O ARG D 511 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL D 513 " --> pdb=" O ILE D 436 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE D 436 " --> pdb=" O VAL D 513 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 454 through 456 Processing sheet with id=AF2, first strand: chain 'D' and resid 475 through 476 Processing sheet with id=AF3, first strand: chain 'D' and resid 544 through 545 Processing sheet with id=AF4, first strand: chain 'D' and resid 656 through 657 removed outlier: 6.142A pdb=" N GLU D 656 " --> pdb=" O ALA D 696 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N THR D 698 " --> pdb=" O GLU D 656 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR D 697 " --> pdb=" O CYS D 673 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE D 672 " --> pdb=" O ILE D 668 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 713 through 721 removed outlier: 6.536A pdb=" N SER D 713 " --> pdb=" O THR D1078 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR D1078 " --> pdb=" O SER D 713 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA D 715 " --> pdb=" O ASN D1076 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASN D1076 " --> pdb=" O ALA D 715 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLU D1074 " --> pdb=" O PRO D 717 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N TYR D1069 " --> pdb=" O HIS D1050 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N HIS D1050 " --> pdb=" O TYR D1069 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 724 through 730 removed outlier: 3.627A pdb=" N ALA D1080 " --> pdb=" O PHE D1097 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE D1097 " --> pdb=" O ALA D1080 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 737 through 738 Processing sheet with id=AF8, first strand: chain 'D' and resid 1122 through 1127 removed outlier: 3.603A pdb=" N SER D1125 " --> pdb=" O ALA D1089 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ALA D1089 " --> pdb=" O SER D1125 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 3 through 6 removed outlier: 4.898A pdb=" N SER G 77 " --> pdb=" O ALA G 24 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N THR G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 46 through 51 removed outlier: 6.096A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 19 through 24 removed outlier: 3.786A pdb=" N VAL J 19 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE J 75 " --> pdb=" O VAL J 19 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 45 through 46 Processing sheet with id=AG4, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AG5, first strand: chain 'I' and resid 47 through 51 removed outlier: 7.171A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 21 through 24 Processing sheet with id=AG7, first strand: chain 'K' and resid 44 through 48 removed outlier: 6.572A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 950 hydrogen bonds defined for protein. 2535 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: 13.62 Time building geometry restraints manager: 13.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 5146 1.28 - 1.41: 8250 1.41 - 1.55: 19155 1.55 - 1.69: 56 1.69 - 1.82: 186 Bond restraints: 32793 Sorted by residual: bond pdb=" C PRO C 899 " pdb=" O PRO C 899 " ideal model delta sigma weight residual 1.233 1.140 0.093 1.13e-02 7.83e+03 6.82e+01 bond pdb=" C PRO B 899 " pdb=" O PRO B 899 " ideal model delta sigma weight residual 1.233 1.144 0.089 1.13e-02 7.83e+03 6.19e+01 bond pdb=" C PRO D 899 " pdb=" O PRO D 899 " ideal model delta sigma weight residual 1.233 1.150 0.084 1.10e-02 8.26e+03 5.79e+01 bond pdb=" C PRO C 901 " pdb=" O PRO C 901 " ideal model delta sigma weight residual 1.237 1.142 0.096 1.32e-02 5.74e+03 5.25e+01 bond pdb=" C PRO D 901 " pdb=" O PRO D 901 " ideal model delta sigma weight residual 1.238 1.154 0.083 1.24e-02 6.50e+03 4.51e+01 ... (remaining 32788 not shown) Histogram of bond angle deviations from ideal: 97.71 - 105.68: 796 105.68 - 113.65: 18103 113.65 - 121.62: 17593 121.62 - 129.58: 7944 129.58 - 137.55: 154 Bond angle restraints: 44590 Sorted by residual: angle pdb=" N PRO D 988 " pdb=" CA PRO D 988 " pdb=" C PRO D 988 " ideal model delta sigma weight residual 110.70 123.15 -12.45 1.22e+00 6.72e-01 1.04e+02 angle pdb=" C ASN C 544 " pdb=" CA ASN C 544 " pdb=" CB ASN C 544 " ideal model delta sigma weight residual 111.82 101.11 10.71 1.38e+00 5.25e-01 6.02e+01 angle pdb=" N SER B 942 " pdb=" CA SER B 942 " pdb=" C SER B 942 " ideal model delta sigma weight residual 113.20 103.92 9.28 1.21e+00 6.83e-01 5.88e+01 angle pdb=" N ALA B 946 " pdb=" CA ALA B 946 " pdb=" C ALA B 946 " ideal model delta sigma weight residual 111.82 103.44 8.38 1.16e+00 7.43e-01 5.21e+01 angle pdb=" C THR B 943 " pdb=" CA THR B 943 " pdb=" CB THR B 943 " ideal model delta sigma weight residual 110.71 121.56 -10.85 1.53e+00 4.27e-01 5.03e+01 ... (remaining 44585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.62: 19104 23.62 - 47.24: 1186 47.24 - 70.86: 142 70.86 - 94.49: 65 94.49 - 118.11: 34 Dihedral angle restraints: 20531 sinusoidal: 9008 harmonic: 11523 Sorted by residual: dihedral pdb=" CA ASN D 145 " pdb=" C ASN D 145 " pdb=" N ASN D 146 " pdb=" CA ASN D 146 " ideal model delta harmonic sigma weight residual -180.00 -70.15 -109.85 0 5.00e+00 4.00e-02 4.83e+02 dihedral pdb=" CA ASP C 142 " pdb=" C ASP C 142 " pdb=" N HIS C 143 " pdb=" CA HIS C 143 " ideal model delta harmonic sigma weight residual 180.00 70.18 109.82 0 5.00e+00 4.00e-02 4.82e+02 dihedral pdb=" CB CYS D 740 " pdb=" SG CYS D 740 " pdb=" SG CYS D 762 " pdb=" CB CYS D 762 " ideal model delta sinusoidal sigma weight residual 93.00 3.84 89.16 1 1.00e+01 1.00e-02 9.46e+01 ... (remaining 20528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.155: 5051 0.155 - 0.309: 141 0.309 - 0.464: 6 0.464 - 0.618: 2 0.618 - 0.773: 1 Chirality restraints: 5201 Sorted by residual: chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN D 333 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-01 2.50e+01 1.49e+01 chirality pdb=" C1 NAG C1208 " pdb=" ND2 ASN C 146 " pdb=" C2 NAG C1208 " pdb=" O5 NAG C1208 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.40e+00 chirality pdb=" CA PRO D 988 " pdb=" N PRO D 988 " pdb=" C PRO D 988 " pdb=" CB PRO D 988 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.80e+00 ... (remaining 5198 not shown) Planarity restraints: 5717 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 147 " 0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C LYS D 147 " -0.063 2.00e-02 2.50e+03 pdb=" O LYS D 147 " 0.023 2.00e-02 2.50e+03 pdb=" N SER D 148 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 941 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.19e+01 pdb=" C SER B 941 " -0.060 2.00e-02 2.50e+03 pdb=" O SER B 941 " 0.022 2.00e-02 2.50e+03 pdb=" N SER B 942 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS D 762 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C CYS D 762 " -0.056 2.00e-02 2.50e+03 pdb=" O CYS D 762 " 0.020 2.00e-02 2.50e+03 pdb=" N THR D 763 " 0.019 2.00e-02 2.50e+03 ... (remaining 5714 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 8677 2.80 - 3.33: 26820 3.33 - 3.85: 52153 3.85 - 4.38: 58528 4.38 - 4.90: 101123 Nonbonded interactions: 247301 Sorted by model distance: nonbonded pdb=" O GLY C 882 " pdb=" OG SER C 886 " model vdw 2.278 2.440 nonbonded pdb=" O VAL D 610 " pdb=" OH TYR D 638 " model vdw 2.284 2.440 nonbonded pdb=" OG1 THR B 647 " pdb=" O GLY B 650 " model vdw 2.286 2.440 nonbonded pdb=" O ASP H 112 " pdb=" OH TYR L 49 " model vdw 2.290 2.440 nonbonded pdb=" OG SER H 21 " pdb=" OG1 THR H 78 " model vdw 2.298 2.440 ... (remaining 247296 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' } ncs_group { reference = (chain 'B' and (resid 14 through 1164 or resid 1201 through 1209)) selection = (chain 'C' and (resid 14 through 1164 or resid 1201 through 1209)) selection = chain 'D' } ncs_group { reference = chain 'F' selection = chain 'M' selection = chain 'R' selection = chain 'S' selection = chain 'a' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 11.540 Check model and map are aligned: 0.450 Set scattering table: 0.250 Process input model: 81.580 Find NCS groups from input model: 2.510 Set up NCS constraints: 0.490 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:13.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 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 : 0.006 0.103 32793 Z= 0.419 Angle : 1.009 12.890 44590 Z= 0.576 Chirality : 0.065 0.773 5201 Planarity : 0.007 0.082 5668 Dihedral : 15.823 118.107 12998 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.06 % Favored : 92.74 % Rotamer: Outliers : 0.52 % Allowed : 1.16 % Favored : 98.32 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.12), residues: 3924 helix: -3.29 (0.12), residues: 669 sheet: -0.40 (0.19), residues: 783 loop : -2.30 (0.11), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 260 HIS 0.013 0.001 HIS B 49 PHE 0.030 0.002 PHE C 106 TYR 0.045 0.002 TYR B 455 ARG 0.016 0.001 ARG D 187 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 436 time to evaluate : 3.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 81 MET cc_start: 0.1742 (tpt) cc_final: 0.1149 (mtm) REVERT: B 360 ILE cc_start: 0.7982 (mt) cc_final: 0.7736 (mm) REVERT: B 367 TYR cc_start: 0.7255 (m-80) cc_final: 0.6929 (m-80) REVERT: B 983 PHE cc_start: 0.6700 (m-10) cc_final: 0.6393 (m-10) REVERT: C 117 LEU cc_start: 0.6081 (mt) cc_final: 0.5561 (tt) REVERT: C 142 ASP cc_start: 0.1998 (OUTLIER) cc_final: 0.1050 (t0) REVERT: C 823 LEU cc_start: 0.8218 (mt) cc_final: 0.7938 (mp) REVERT: D 1074 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7222 (pt0) outliers start: 18 outliers final: 8 residues processed: 449 average time/residue: 1.2132 time to fit residues: 662.1776 Evaluate side-chains 221 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 211 time to evaluate : 3.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 ASN Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 1074 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 331 optimal weight: 7.9990 chunk 297 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 200 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 308 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 229 optimal weight: 0.8980 chunk 356 optimal weight: 20.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN L 91 GLN B 49 HIS ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 GLN B 753 ASN B 757 GLN B 764 GLN B 903 GLN B 909 ASN B1121 ASN ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 ASN C 582 GLN ** C 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 855 GLN C 903 GLN C 927 ASN C 967 GLN C1012 GLN C1115 GLN D 14 GLN D 99 ASN D 273 GLN ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 582 GLN D1004 GLN D1121 ASN ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 ASN K 31 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 32793 Z= 0.256 Angle : 0.656 11.717 44590 Z= 0.326 Chirality : 0.048 0.456 5201 Planarity : 0.005 0.056 5668 Dihedral : 10.238 104.810 5851 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.78 % Favored : 94.14 % Rotamer: Outliers : 2.23 % Allowed : 10.34 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.20 (0.12), residues: 3924 helix: -1.10 (0.18), residues: 690 sheet: -0.15 (0.19), residues: 787 loop : -2.14 (0.11), residues: 2447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 260 HIS 0.015 0.001 HIS C 143 PHE 0.021 0.002 PHE B 594 TYR 0.020 0.001 TYR B 170 ARG 0.005 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 199 time to evaluate : 3.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 81 MET cc_start: 0.1661 (tpt) cc_final: 0.1398 (mtm) REVERT: B 360 ILE cc_start: 0.8131 (mt) cc_final: 0.7931 (mm) REVERT: B 367 TYR cc_start: 0.7771 (m-80) cc_final: 0.7515 (m-80) REVERT: C 174 MET cc_start: 0.2832 (mtt) cc_final: 0.1055 (mmt) REVERT: C 197 TYR cc_start: 0.7554 (OUTLIER) cc_final: 0.7142 (t80) REVERT: D 1074 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7251 (pt0) REVERT: G 81 MET cc_start: 0.1958 (tpt) cc_final: 0.0806 (ptm) outliers start: 77 outliers final: 31 residues processed: 259 average time/residue: 1.2139 time to fit residues: 405.2665 Evaluate side-chains 195 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 162 time to evaluate : 3.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 260 TRP Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 860 LEU Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 1052 MET Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain D residue 363 CYS Chi-restraints excluded: chain D residue 590 THR Chi-restraints excluded: chain D residue 737 SER Chi-restraints excluded: chain D residue 739 ASP Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 979 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1074 GLU Chi-restraints excluded: chain D residue 1138 THR Chi-restraints excluded: chain G residue 88 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 198 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 297 optimal weight: 4.9990 chunk 243 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 357 optimal weight: 0.8980 chunk 386 optimal weight: 30.0000 chunk 318 optimal weight: 5.9990 chunk 354 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 286 optimal weight: 6.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN B 49 HIS ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN B 362 ASN ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 753 ASN B1073 GLN ** B1103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1121 ASN ** C 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 ASN C 615 GLN C 789 GLN C 855 GLN D 14 GLN D 273 GLN ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 903 GLN ** D 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 ASN J 37 GLN J 55 GLN I 31 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 32793 Z= 0.322 Angle : 0.666 11.635 44590 Z= 0.331 Chirality : 0.049 0.484 5201 Planarity : 0.004 0.054 5668 Dihedral : 8.226 102.445 5842 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.73 % Favored : 93.25 % Rotamer: Outliers : 2.87 % Allowed : 13.96 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.96 (0.13), residues: 3924 helix: -0.39 (0.19), residues: 703 sheet: -0.17 (0.18), residues: 817 loop : -2.11 (0.11), residues: 2404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 149 HIS 0.011 0.001 HIS C 143 PHE 0.028 0.002 PHE C 106 TYR 0.022 0.002 TYR D 267 ARG 0.006 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 185 time to evaluate : 3.348 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: B 360 ILE cc_start: 0.8288 (mt) cc_final: 0.8040 (mm) REVERT: B 367 TYR cc_start: 0.7748 (m-80) cc_final: 0.7498 (m-80) REVERT: C 117 LEU cc_start: 0.6510 (mt) cc_final: 0.6176 (tt) REVERT: C 120 VAL cc_start: 0.7073 (t) cc_final: 0.6749 (p) REVERT: C 174 MET cc_start: 0.3403 (mtt) cc_final: 0.1783 (mmt) REVERT: C 197 TYR cc_start: 0.7823 (OUTLIER) cc_final: 0.7290 (t80) REVERT: C 570 ASP cc_start: 0.7600 (p0) cc_final: 0.7262 (p0) REVERT: C 978 VAL cc_start: 0.8622 (OUTLIER) cc_final: 0.8374 (m) REVERT: D 549 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7459 (mmmt) REVERT: D 567 PHE cc_start: 0.6679 (OUTLIER) cc_final: 0.5912 (m-80) REVERT: D 1074 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7422 (pt0) REVERT: K 4 MET cc_start: 0.0940 (ptp) cc_final: -0.0477 (ptt) outliers start: 99 outliers final: 54 residues processed: 266 average time/residue: 1.0111 time to fit residues: 339.2944 Evaluate side-chains 212 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 153 time to evaluate : 3.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 588 ASP Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 904 MET Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1076 ASN Chi-restraints excluded: chain B residue 1086 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 573 ASP Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 942 SER Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1052 MET Chi-restraints excluded: chain C residue 1107 THR Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain D residue 363 CYS Chi-restraints excluded: chain D residue 549 LYS Chi-restraints excluded: chain D residue 567 PHE Chi-restraints excluded: chain D residue 643 ASN Chi-restraints excluded: chain D residue 737 SER Chi-restraints excluded: chain D residue 751 CYS Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 918 LEU Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 979 LEU Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1074 GLU Chi-restraints excluded: chain D residue 1138 THR Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain J residue 77 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 353 optimal weight: 7.9990 chunk 268 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 170 optimal weight: 0.0270 chunk 240 optimal weight: 10.0000 chunk 358 optimal weight: 2.9990 chunk 379 optimal weight: 7.9990 chunk 187 optimal weight: 0.2980 chunk 340 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 overall best weight: 1.0642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 55 GLN B 49 HIS ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1073 GLN ** B1103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 HIS ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 GLN D 14 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 903 GLN D 915 GLN D 916 ASN D 994 GLN D1108 GLN D1121 ASN J 37 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32793 Z= 0.205 Angle : 0.591 11.082 44590 Z= 0.291 Chirality : 0.046 0.434 5201 Planarity : 0.004 0.066 5668 Dihedral : 7.179 105.753 5841 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.66 % Favored : 94.29 % Rotamer: Outliers : 3.16 % Allowed : 15.41 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.73 (0.13), residues: 3924 helix: 0.12 (0.20), residues: 699 sheet: -0.13 (0.18), residues: 805 loop : -2.01 (0.12), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 104 HIS 0.007 0.001 HIS C 143 PHE 0.020 0.001 PHE C 106 TYR 0.019 0.001 TYR B 170 ARG 0.003 0.000 ARG C 155 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 165 time to evaluate : 3.421 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: B 44 ARG cc_start: 0.6882 (mmt90) cc_final: 0.6671 (mmt90) REVERT: B 360 ILE cc_start: 0.8305 (mt) cc_final: 0.8059 (mm) REVERT: B 367 TYR cc_start: 0.7723 (m-80) cc_final: 0.7493 (m-80) REVERT: B 733 MET cc_start: 0.9017 (ptp) cc_final: 0.8731 (ptm) REVERT: B 857 PHE cc_start: 0.6304 (m-80) cc_final: 0.6082 (m-80) REVERT: C 120 VAL cc_start: 0.7004 (t) cc_final: 0.6747 (p) REVERT: C 197 TYR cc_start: 0.7736 (OUTLIER) cc_final: 0.7232 (t80) REVERT: C 570 ASP cc_start: 0.7511 (p0) cc_final: 0.7240 (p0) REVERT: D 549 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7381 (mmmt) REVERT: D 916 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8559 (p0) outliers start: 109 outliers final: 48 residues processed: 252 average time/residue: 0.9784 time to fit residues: 314.9002 Evaluate side-chains 199 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 148 time to evaluate : 3.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 763 THR Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 868 THR Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1076 ASN Chi-restraints excluded: chain B residue 1086 ASP Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 1076 ASN Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain D residue 363 CYS Chi-restraints excluded: chain D residue 549 LYS Chi-restraints excluded: chain D residue 567 PHE Chi-restraints excluded: chain D residue 622 VAL Chi-restraints excluded: chain D residue 643 ASN Chi-restraints excluded: chain D residue 737 SER Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 916 ASN Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 979 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1138 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 316 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 282 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 chunk 324 optimal weight: 0.0970 chunk 262 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 193 optimal weight: 4.9990 chunk 340 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 55 GLN B 49 HIS ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 GLN ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 903 GLN D 994 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 32793 Z= 0.236 Angle : 0.593 12.911 44590 Z= 0.292 Chirality : 0.046 0.402 5201 Planarity : 0.004 0.054 5668 Dihedral : 6.725 107.817 5838 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.01 % Favored : 93.93 % Rotamer: Outliers : 3.13 % Allowed : 16.68 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.13), residues: 3924 helix: 0.36 (0.21), residues: 694 sheet: -0.14 (0.18), residues: 815 loop : -1.96 (0.12), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 438 HIS 0.006 0.001 HIS C 143 PHE 0.022 0.001 PHE C 106 TYR 0.017 0.001 TYR D 267 ARG 0.003 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 163 time to evaluate : 3.499 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: B 44 ARG cc_start: 0.7086 (mmt90) cc_final: 0.6860 (mmt90) REVERT: B 360 ILE cc_start: 0.8324 (mt) cc_final: 0.8083 (mm) REVERT: B 733 MET cc_start: 0.9028 (ptp) cc_final: 0.8731 (ptm) REVERT: B 857 PHE cc_start: 0.6371 (m-80) cc_final: 0.6142 (m-80) REVERT: C 117 LEU cc_start: 0.6739 (mt) cc_final: 0.6374 (tt) REVERT: C 197 TYR cc_start: 0.7815 (OUTLIER) cc_final: 0.7311 (t80) REVERT: C 570 ASP cc_start: 0.7488 (p0) cc_final: 0.7267 (p0) REVERT: C 660 ASN cc_start: 0.8216 (OUTLIER) cc_final: 0.7673 (p0) REVERT: C 1052 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8248 (ptm) REVERT: D 549 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7402 (mmmt) REVERT: D 567 PHE cc_start: 0.6578 (OUTLIER) cc_final: 0.5874 (m-80) REVERT: G 81 MET cc_start: 0.1402 (tpt) cc_final: 0.1194 (tpp) REVERT: I 48 MET cc_start: 0.2287 (mpt) cc_final: 0.1185 (mmm) outliers start: 108 outliers final: 57 residues processed: 257 average time/residue: 0.9742 time to fit residues: 321.8798 Evaluate side-chains 213 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 151 time to evaluate : 3.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 868 THR Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 904 MET Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1076 ASN Chi-restraints excluded: chain B residue 1086 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1052 MET Chi-restraints excluded: chain C residue 1076 ASN Chi-restraints excluded: chain C residue 1107 THR Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1138 THR Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain D residue 549 LYS Chi-restraints excluded: chain D residue 567 PHE Chi-restraints excluded: chain D residue 643 ASN Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 918 LEU Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 979 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1138 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain J residue 77 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 127 optimal weight: 0.4980 chunk 342 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 380 optimal weight: 30.0000 chunk 315 optimal weight: 0.8980 chunk 176 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 199 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 HIS ** B 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1103 HIS ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 GLN D 14 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 903 GLN D 994 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 32793 Z= 0.180 Angle : 0.569 12.076 44590 Z= 0.279 Chirality : 0.045 0.385 5201 Planarity : 0.004 0.054 5668 Dihedral : 6.191 110.783 5836 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.45 % Favored : 94.47 % Rotamer: Outliers : 2.64 % Allowed : 18.39 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.52 (0.13), residues: 3924 helix: 0.58 (0.21), residues: 694 sheet: -0.12 (0.18), residues: 820 loop : -1.92 (0.12), residues: 2410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 149 HIS 0.005 0.001 HIS C 204 PHE 0.017 0.001 PHE C 106 TYR 0.022 0.001 TYR B 170 ARG 0.003 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 164 time to evaluate : 3.375 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: B 360 ILE cc_start: 0.8341 (mt) cc_final: 0.8098 (mm) REVERT: B 733 MET cc_start: 0.8993 (ptp) cc_final: 0.8677 (ptm) REVERT: C 197 TYR cc_start: 0.7869 (OUTLIER) cc_final: 0.7338 (t80) REVERT: C 570 ASP cc_start: 0.7438 (p0) cc_final: 0.7227 (p0) REVERT: C 660 ASN cc_start: 0.8187 (OUTLIER) cc_final: 0.7662 (p0) REVERT: C 978 VAL cc_start: 0.8486 (OUTLIER) cc_final: 0.8208 (m) REVERT: C 1052 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8076 (ptm) REVERT: D 549 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7317 (mmmt) REVERT: D 711 ASN cc_start: 0.8353 (OUTLIER) cc_final: 0.7591 (p0) REVERT: G 81 MET cc_start: 0.1398 (tpt) cc_final: 0.1107 (tpp) REVERT: G 114 MET cc_start: 0.0813 (ttm) cc_final: 0.0444 (ttp) REVERT: I 48 MET cc_start: 0.2317 (mpt) cc_final: 0.1237 (mmm) outliers start: 91 outliers final: 46 residues processed: 238 average time/residue: 0.9914 time to fit residues: 302.2702 Evaluate side-chains 199 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 147 time to evaluate : 3.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1076 ASN Chi-restraints excluded: chain B residue 1086 ASP Chi-restraints excluded: chain B residue 1113 GLU Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1052 MET Chi-restraints excluded: chain C residue 1076 ASN Chi-restraints excluded: chain C residue 1107 THR Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1138 THR Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain D residue 549 LYS Chi-restraints excluded: chain D residue 567 PHE Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 711 ASN Chi-restraints excluded: chain D residue 726 THR Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 918 LEU Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 979 LEU Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1138 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain J residue 77 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 366 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 216 optimal weight: 1.9990 chunk 277 optimal weight: 20.0000 chunk 215 optimal weight: 1.9990 chunk 320 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 378 optimal weight: 50.0000 chunk 237 optimal weight: 1.9990 chunk 230 optimal weight: 0.8980 chunk 174 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 GLN C 967 GLN C1121 ASN ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 994 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 32793 Z= 0.320 Angle : 0.638 12.573 44590 Z= 0.314 Chirality : 0.047 0.357 5201 Planarity : 0.004 0.054 5668 Dihedral : 6.348 111.584 5836 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.75 % Favored : 93.14 % Rotamer: Outliers : 2.95 % Allowed : 18.80 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.59 (0.13), residues: 3924 helix: 0.41 (0.21), residues: 698 sheet: -0.13 (0.18), residues: 833 loop : -1.96 (0.12), residues: 2393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 149 HIS 0.007 0.001 HIS B 49 PHE 0.033 0.002 PHE C 106 TYR 0.020 0.001 TYR B 267 ARG 0.005 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 160 time to evaluate : 3.789 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: L 35 TRP cc_start: 0.5787 (t-100) cc_final: 0.5562 (t-100) REVERT: B 360 ILE cc_start: 0.8252 (mt) cc_final: 0.7999 (mm) REVERT: C 117 LEU cc_start: 0.6629 (mt) cc_final: 0.6263 (tt) REVERT: C 197 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.7289 (t80) REVERT: C 660 ASN cc_start: 0.8234 (OUTLIER) cc_final: 0.7733 (p0) REVERT: D 193 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.8024 (m-40) REVERT: D 549 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7360 (mmmt) REVERT: D 711 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.7625 (p0) REVERT: D 1143 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8590 (tm) REVERT: I 48 MET cc_start: 0.2269 (mpt) cc_final: 0.1244 (mmm) outliers start: 102 outliers final: 67 residues processed: 245 average time/residue: 0.9715 time to fit residues: 308.2481 Evaluate side-chains 217 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 144 time to evaluate : 3.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 868 THR Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 904 MET Chi-restraints excluded: chain B residue 911 ILE Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1076 ASN Chi-restraints excluded: chain B residue 1086 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 942 SER Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1052 MET Chi-restraints excluded: chain C residue 1076 ASN Chi-restraints excluded: chain C residue 1107 THR Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1138 THR Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain D residue 549 LYS Chi-restraints excluded: chain D residue 567 PHE Chi-restraints excluded: chain D residue 643 ASN Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 711 ASN Chi-restraints excluded: chain D residue 726 THR Chi-restraints excluded: chain D residue 739 ASP Chi-restraints excluded: chain D residue 756 LEU Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 918 LEU Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 979 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1138 THR Chi-restraints excluded: chain D residue 1143 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain J residue 77 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 234 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 226 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 240 optimal weight: 9.9990 chunk 258 optimal weight: 0.0970 chunk 187 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 297 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN ** B 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 GLN B1073 GLN ** B1103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 GLN ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 HIS ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 994 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 32793 Z= 0.202 Angle : 0.592 11.750 44590 Z= 0.290 Chirality : 0.045 0.362 5201 Planarity : 0.004 0.054 5668 Dihedral : 6.043 111.932 5836 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.66 % Favored : 94.24 % Rotamer: Outliers : 3.01 % Allowed : 19.29 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.13), residues: 3924 helix: 0.63 (0.21), residues: 691 sheet: -0.04 (0.18), residues: 808 loop : -1.87 (0.12), residues: 2425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 149 HIS 0.005 0.001 HIS C 204 PHE 0.021 0.001 PHE B 499 TYR 0.024 0.001 TYR B 170 ARG 0.004 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 151 time to evaluate : 3.220 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: L 35 TRP cc_start: 0.5842 (t-100) cc_final: 0.5004 (t-100) REVERT: B 360 ILE cc_start: 0.8301 (mt) cc_final: 0.8048 (mm) REVERT: B 733 MET cc_start: 0.8987 (ptp) cc_final: 0.8707 (ptm) REVERT: C 117 LEU cc_start: 0.6599 (mt) cc_final: 0.6203 (tt) REVERT: C 197 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.7250 (t80) REVERT: C 328 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7913 (pt) REVERT: C 660 ASN cc_start: 0.8189 (OUTLIER) cc_final: 0.7703 (p0) REVERT: C 1052 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8186 (ptm) REVERT: D 193 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.8050 (m-40) REVERT: D 549 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7342 (mmmt) REVERT: D 711 ASN cc_start: 0.8323 (OUTLIER) cc_final: 0.7527 (p0) REVERT: D 1143 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8559 (tm) REVERT: G 81 MET cc_start: 0.0541 (tpp) cc_final: 0.0270 (ttt) REVERT: I 48 MET cc_start: 0.2152 (mpt) cc_final: 0.1190 (mmm) outliers start: 104 outliers final: 66 residues processed: 240 average time/residue: 1.0471 time to fit residues: 321.6584 Evaluate side-chains 216 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 142 time to evaluate : 3.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 36 TRP Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 868 THR Chi-restraints excluded: chain B residue 904 MET Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1076 ASN Chi-restraints excluded: chain B residue 1086 ASP Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 938 ASP Chi-restraints excluded: chain C residue 942 SER Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1052 MET Chi-restraints excluded: chain C residue 1076 ASN Chi-restraints excluded: chain C residue 1107 THR Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1138 THR Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain D residue 220 SER Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain D residue 549 LYS Chi-restraints excluded: chain D residue 567 PHE Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 711 ASN Chi-restraints excluded: chain D residue 726 THR Chi-restraints excluded: chain D residue 739 ASP Chi-restraints excluded: chain D residue 756 LEU Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 918 LEU Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 979 LEU Chi-restraints excluded: chain D residue 994 GLN Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1135 VAL Chi-restraints excluded: chain D residue 1138 THR Chi-restraints excluded: chain D residue 1143 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain J residue 77 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 344 optimal weight: 1.9990 chunk 362 optimal weight: 20.0000 chunk 331 optimal weight: 4.9990 chunk 352 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 153 optimal weight: 30.0000 chunk 277 optimal weight: 20.0000 chunk 108 optimal weight: 1.9990 chunk 318 optimal weight: 0.3980 chunk 333 optimal weight: 6.9990 chunk 351 optimal weight: 30.0000 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN B1073 GLN ** B1103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 GLN C 565 GLN C 677 GLN ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 HIS ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 897 GLN D 994 GLN D1007 GLN G 62 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 32793 Z= 0.388 Angle : 0.685 12.605 44590 Z= 0.339 Chirality : 0.049 0.345 5201 Planarity : 0.004 0.054 5668 Dihedral : 6.434 111.498 5836 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.36 % Favored : 92.53 % Rotamer: Outliers : 3.24 % Allowed : 19.46 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.61 (0.13), residues: 3924 helix: 0.44 (0.21), residues: 686 sheet: -0.07 (0.18), residues: 817 loop : -2.00 (0.12), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 149 HIS 0.007 0.001 HIS C1050 PHE 0.040 0.002 PHE C 106 TYR 0.024 0.002 TYR B 267 ARG 0.007 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 152 time to evaluate : 3.560 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: B 548 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7421 (pp) REVERT: B 567 PHE cc_start: 0.6401 (OUTLIER) cc_final: 0.5896 (m-10) REVERT: C 117 LEU cc_start: 0.6493 (mt) cc_final: 0.6293 (tt) REVERT: C 197 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.7346 (t80) REVERT: C 273 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.8058 (mp10) REVERT: C 328 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7972 (pt) REVERT: C 660 ASN cc_start: 0.8218 (OUTLIER) cc_final: 0.7565 (p0) REVERT: C 996 ASP cc_start: 0.7422 (t0) cc_final: 0.7192 (t0) REVERT: C 1052 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8474 (ptm) REVERT: D 549 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7400 (mmmt) REVERT: D 711 ASN cc_start: 0.8527 (OUTLIER) cc_final: 0.7712 (p0) REVERT: D 1143 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8678 (tm) REVERT: G 81 MET cc_start: 0.0281 (tpp) cc_final: -0.0135 (ttt) REVERT: I 48 MET cc_start: 0.2165 (mpt) cc_final: 0.1212 (mmm) outliers start: 112 outliers final: 72 residues processed: 247 average time/residue: 0.9663 time to fit residues: 306.0395 Evaluate side-chains 221 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 139 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 567 PHE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 868 THR Chi-restraints excluded: chain B residue 911 ILE Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1076 ASN Chi-restraints excluded: chain B residue 1086 ASP Chi-restraints excluded: chain B residue 1135 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 565 GLN Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 938 ASP Chi-restraints excluded: chain C residue 942 SER Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1052 MET Chi-restraints excluded: chain C residue 1076 ASN Chi-restraints excluded: chain C residue 1107 THR Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1138 THR Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 220 SER Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain D residue 549 LYS Chi-restraints excluded: chain D residue 567 PHE Chi-restraints excluded: chain D residue 643 ASN Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 711 ASN Chi-restraints excluded: chain D residue 726 THR Chi-restraints excluded: chain D residue 739 ASP Chi-restraints excluded: chain D residue 756 LEU Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 979 LEU Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1119 THR Chi-restraints excluded: chain D residue 1129 ASP Chi-restraints excluded: chain D residue 1135 VAL Chi-restraints excluded: chain D residue 1138 THR Chi-restraints excluded: chain D residue 1143 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain J residue 77 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 231 optimal weight: 0.5980 chunk 373 optimal weight: 50.0000 chunk 227 optimal weight: 0.7980 chunk 177 optimal weight: 5.9990 chunk 259 optimal weight: 0.7980 chunk 391 optimal weight: 9.9990 chunk 360 optimal weight: 10.0000 chunk 311 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 240 optimal weight: 10.0000 chunk 191 optimal weight: 4.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1073 GLN ** B1103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 GLN C 677 GLN ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 HIS ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 897 GLN D 994 GLN D1007 GLN D1121 ASN G 62 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.394 32793 Z= 0.455 Angle : 0.853 59.197 44590 Z= 0.463 Chirality : 0.050 0.600 5201 Planarity : 0.004 0.054 5668 Dihedral : 6.439 111.506 5836 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.36 % Favored : 92.53 % Rotamer: Outliers : 2.66 % Allowed : 20.24 % Favored : 77.09 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.63 (0.13), residues: 3924 helix: 0.41 (0.21), residues: 686 sheet: -0.08 (0.18), residues: 817 loop : -2.01 (0.12), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP H 36 HIS 0.007 0.001 HIS B 49 PHE 0.040 0.002 PHE C 106 TYR 0.023 0.002 TYR B 267 ARG 0.007 0.000 ARG D 236 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7848 Ramachandran restraints generated. 3924 Oldfield, 0 Emsley, 3924 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 141 time to evaluate : 3.176 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: B 548 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7422 (pp) REVERT: B 567 PHE cc_start: 0.6401 (OUTLIER) cc_final: 0.5896 (m-10) REVERT: C 197 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.7345 (t80) REVERT: C 328 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7972 (pt) REVERT: C 567 PHE cc_start: 0.6604 (OUTLIER) cc_final: 0.6249 (m-10) REVERT: C 660 ASN cc_start: 0.8216 (OUTLIER) cc_final: 0.7563 (p0) REVERT: C 996 ASP cc_start: 0.7418 (t0) cc_final: 0.7192 (t0) REVERT: C 1052 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8474 (ptm) REVERT: D 193 ASN cc_start: 0.8399 (OUTLIER) cc_final: 0.8060 (m-40) REVERT: D 549 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7401 (mmmt) REVERT: D 711 ASN cc_start: 0.8524 (OUTLIER) cc_final: 0.7711 (p0) REVERT: D 1143 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8654 (tm) REVERT: G 81 MET cc_start: 0.0265 (tpp) cc_final: -0.0114 (ttt) REVERT: I 48 MET cc_start: 0.2170 (mpt) cc_final: 0.1214 (mmm) outliers start: 92 outliers final: 74 residues processed: 216 average time/residue: 0.9801 time to fit residues: 273.2985 Evaluate side-chains 224 residues out of total 3453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 139 time to evaluate : 3.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 567 PHE Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 643 ASN Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 868 THR Chi-restraints excluded: chain B residue 877 SER Chi-restraints excluded: chain B residue 904 MET Chi-restraints excluded: chain B residue 917 VAL Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 1019 GLU Chi-restraints excluded: chain B residue 1042 VAL Chi-restraints excluded: chain B residue 1076 ASN Chi-restraints excluded: chain B residue 1086 ASP Chi-restraints excluded: chain B residue 1135 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 197 TYR Chi-restraints excluded: chain C residue 237 PHE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 567 PHE Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 938 ASP Chi-restraints excluded: chain C residue 942 SER Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1052 MET Chi-restraints excluded: chain C residue 1076 ASN Chi-restraints excluded: chain C residue 1107 THR Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1138 THR Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 193 ASN Chi-restraints excluded: chain D residue 220 SER Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 283 GLU Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 309 THR Chi-restraints excluded: chain D residue 320 PHE Chi-restraints excluded: chain D residue 549 LYS Chi-restraints excluded: chain D residue 567 PHE Chi-restraints excluded: chain D residue 643 ASN Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 711 ASN Chi-restraints excluded: chain D residue 726 THR Chi-restraints excluded: chain D residue 739 ASP Chi-restraints excluded: chain D residue 756 LEU Chi-restraints excluded: chain D residue 788 LYS Chi-restraints excluded: chain D residue 978 VAL Chi-restraints excluded: chain D residue 979 LEU Chi-restraints excluded: chain D residue 994 GLN Chi-restraints excluded: chain D residue 1042 VAL Chi-restraints excluded: chain D residue 1129 ASP Chi-restraints excluded: chain D residue 1135 VAL Chi-restraints excluded: chain D residue 1138 THR Chi-restraints excluded: chain D residue 1143 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain J residue 77 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 247 optimal weight: 3.9990 chunk 332 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 287 optimal weight: 20.0000 chunk 46 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 312 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 320 optimal weight: 0.2980 chunk 39 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1073 GLN ** B1103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 GLN ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 HIS ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 786 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 897 GLN D 994 GLN D1007 GLN G 62 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.207091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.151971 restraints weight = 47346.640| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 2.63 r_work: 0.3433 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.366 32793 Z= 0.425 Angle : 0.913 59.198 44590 Z= 0.507 Chirality : 0.049 0.525 5201 Planarity : 0.004 0.054 5668 Dihedral : 6.434 111.561 5836 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.36 % Favored : 92.53 % Rotamer: Outliers : 2.66 % Allowed : 20.30 % Favored : 77.03 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.13), residues: 3924 helix: 0.44 (0.21), residues: 684 sheet: -0.08 (0.18), residues: 817 loop : -2.00 (0.12), residues: 2423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 36 HIS 0.006 0.001 HIS B 49 PHE 0.037 0.002 PHE C 106 TYR 0.022 0.001 TYR B 267 ARG 0.007 0.000 ARG D 236 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8321.52 seconds wall clock time: 151 minutes 25.94 seconds (9085.94 seconds total)