Starting phenix.real_space_refine on Tue Mar 19 04:50:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7edh_31071/03_2024/7edh_31071.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7edh_31071/03_2024/7edh_31071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7edh_31071/03_2024/7edh_31071.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7edh_31071/03_2024/7edh_31071.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7edh_31071/03_2024/7edh_31071.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7edh_31071/03_2024/7edh_31071.pdb" } resolution = 3.6 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= -0.001 sd= 0.041 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 100 5.16 5 C 14801 2.51 5 N 3763 2.21 5 O 4612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 212": "OD1" <-> "OD2" Residue "A ASP 225": "OD1" <-> "OD2" Residue "A PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 987": "OE1" <-> "OE2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 86": "OD1" <-> "OD2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 295": "OE1" <-> "OE2" Residue "B PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 770": "OE1" <-> "OE2" Residue "B PHE 1059": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1092": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 86": "OD1" <-> "OD2" Residue "C PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 306": "OE1" <-> "OE2" Residue "C TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 425": "OD1" <-> "OD2" Residue "C TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 722": "OE1" <-> "OE2" Residue "C PHE 1059": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23276 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 6366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 819, 6366 Classifications: {'peptide': 819} Link IDs: {'PTRANS': 39, 'TRANS': 779} Chain breaks: 8 Chain: "B" Number of atoms: 7957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1019, 7957 Classifications: {'peptide': 1019} Link IDs: {'PTRANS': 51, 'TRANS': 967} Chain breaks: 7 Chain: "C" Number of atoms: 7878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7878 Classifications: {'peptide': 1008} Link IDs: {'PTRANS': 51, 'TRANS': 956} Chain breaks: 8 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 12.82, per 1000 atoms: 0.55 Number of scatterers: 23276 At special positions: 0 Unit cell: (132, 140.8, 177.1, 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 100 16.00 O 4612 8.00 N 3763 7.00 C 14801 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.04 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.04 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 163 " distance=2.04 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.04 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.04 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 279 " " NAG A2003 " - " ASN A 600 " " NAG A2004 " - " ASN A 654 " " NAG A2005 " - " ASN A 706 " " NAG A2006 " - " ASN A1071 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 162 " " NAG B2003 " - " ASN B 231 " " NAG B2004 " - " ASN B 328 " " NAG B2005 " - " ASN B 600 " " NAG B2006 " - " ASN B 654 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 328 " " NAG C2003 " - " ASN C 600 " " NAG D 1 " - " ASN A 120 " " NAG E 1 " - " ASN A 162 " " NAG F 1 " - " ASN A 231 " " NAG G 1 " - " ASN A 613 " " NAG H 1 " - " ASN A 714 " " NAG I 1 " - " ASN A 798 " " NAG J 1 " - " ASN A1095 " " NAG K 1 " - " ASN A1131 " " NAG L 1 " - " ASN B 120 " " NAG M 1 " - " ASN B 279 " " NAG N 1 " - " ASN B 340 " " NAG O 1 " - " ASN B 613 " " NAG P 1 " - " ASN B 706 " " NAG Q 1 " - " ASN B 714 " " NAG R 1 " - " ASN B 798 " " NAG S 1 " - " ASN B1071 " " NAG T 1 " - " ASN B1095 " " NAG U 1 " - " ASN B1131 " " NAG V 1 " - " ASN C 120 " " NAG W 1 " - " ASN C 162 " " NAG X 1 " - " ASN C 231 " " NAG Y 1 " - " ASN C 279 " " NAG Z 1 " - " ASN C 340 " " NAG a 1 " - " ASN C 613 " " NAG b 1 " - " ASN C 706 " " NAG c 1 " - " ASN C 714 " " NAG d 1 " - " ASN C 798 " " NAG e 1 " - " ASN C1071 " " NAG f 1 " - " ASN C1095 " " NAG g 1 " - " ASN C1131 " Time building additional restraints: 10.20 Conformation dependent library (CDL) restraints added in 4.0 seconds 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5336 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 41 sheets defined 23.3% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.52 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 734 through 740 removed outlier: 3.654A pdb=" N TYR A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 751 Processing helix chain 'A' and resid 758 through 780 removed outlier: 3.612A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 773 " --> pdb=" O VAL A 769 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR A 775 " --> pdb=" O GLN A 771 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL A 778 " --> pdb=" O ASN A 774 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A 779 " --> pdb=" O THR A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 822 Processing helix chain 'A' and resid 863 through 882 removed outlier: 3.622A pdb=" N GLY A 882 " --> pdb=" O THR A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 912 through 915 removed outlier: 3.559A pdb=" N GLU A 915 " --> pdb=" O VAL A 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 912 through 915' Processing helix chain 'A' and resid 916 through 938 removed outlier: 3.512A pdb=" N ILE A 931 " --> pdb=" O ALA A 927 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN A 932 " --> pdb=" O ILE A 928 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 934 " --> pdb=" O LYS A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 962 Processing helix chain 'A' and resid 973 through 979 removed outlier: 3.716A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 991 removed outlier: 3.803A pdb=" N GLU A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1030 removed outlier: 3.607A pdb=" N GLN A 999 " --> pdb=" O THR A 995 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU A1014 " --> pdb=" O ILE A1010 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A1015 " --> pdb=" O ARG A1011 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A1030 " --> pdb=" O MET A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1143 removed outlier: 4.415A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 removed outlier: 3.738A pdb=" N GLU B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 340 removed outlier: 4.356A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B 339 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 380 through 384 removed outlier: 3.695A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 419 Processing helix chain 'B' and resid 734 through 740 removed outlier: 3.621A pdb=" N TYR B 738 " --> pdb=" O ASP B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 752 removed outlier: 3.884A pdb=" N GLN B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 780 removed outlier: 4.119A pdb=" N PHE B 779 " --> pdb=" O THR B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 removed outlier: 3.731A pdb=" N VAL B 823 " --> pdb=" O LEU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 881 Processing helix chain 'B' and resid 883 through 887 removed outlier: 3.599A pdb=" N ALA B 887 " --> pdb=" O THR B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 904 removed outlier: 3.555A pdb=" N ASN B 904 " --> pdb=" O ALA B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 915 removed outlier: 3.744A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 942 through 962 removed outlier: 3.706A pdb=" N GLN B 962 " --> pdb=" O THR B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 removed outlier: 4.036A pdb=" N ILE B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 979 " --> pdb=" O ASN B 975 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 981 " --> pdb=" O ILE B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.215A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 341 Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 414 through 419 removed outlier: 3.668A pdb=" N TYR C 418 " --> pdb=" O LYS C 414 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN C 419 " --> pdb=" O ILE C 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 414 through 419' Processing helix chain 'C' and resid 735 through 740 Processing helix chain 'C' and resid 743 through 752 removed outlier: 3.964A pdb=" N GLN C 752 " --> pdb=" O ASN C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 780 removed outlier: 3.903A pdb=" N GLN C 759 " --> pdb=" O SER C 755 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG C 762 " --> pdb=" O THR C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 821 removed outlier: 3.502A pdb=" N ASP C 817 " --> pdb=" O SER C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 881 Processing helix chain 'C' and resid 883 through 887 removed outlier: 3.788A pdb=" N ALA C 887 " --> pdb=" O THR C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 906 removed outlier: 3.682A pdb=" N ILE C 906 " --> pdb=" O ARG C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 915 removed outlier: 3.694A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU C 915 " --> pdb=" O ASN C 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 910 through 915' Processing helix chain 'C' and resid 916 through 938 Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.557A pdb=" N GLN C 946 " --> pdb=" O LEU C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 981 removed outlier: 3.571A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1030 removed outlier: 4.433A pdb=" N GLU C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1143 removed outlier: 3.736A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.525A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.806A pdb=" N GLN A 268 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.655A pdb=" N PHE A 104 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 87 through 89 removed outlier: 3.888A pdb=" N VAL A 190 " --> pdb=" O TYR A 201 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 133 through 140 removed outlier: 10.188A pdb=" N ASP A 136 " --> pdb=" O TYR A 157 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N TYR A 157 " --> pdb=" O ASP A 136 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.615A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER A 313 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 321 through 325 removed outlier: 4.175A pdb=" N GLU A 321 " --> pdb=" O CYS A 535 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG A 325 " --> pdb=" O ASN A 539 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR A 569 " --> pdb=" O ASP A 565 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLY A 563 " --> pdb=" O ASP A 571 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.120A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 708 through 712 Processing sheet with id=AB2, first strand: chain 'A' and resid 715 through 725 removed outlier: 3.716A pdb=" N MET A1047 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 731 through 733 Processing sheet with id=AB4, first strand: chain 'A' and resid 1117 through 1119 removed outlier: 3.514A pdb=" N ILE A1078 " --> pdb=" O HIS A1085 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N CYS A1079 " --> pdb=" O VAL A1130 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.725A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.783A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.635A pdb=" N PHE B 104 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 125 " --> pdb=" O VAL B 118 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 87 through 89 removed outlier: 3.520A pdb=" N VAL B 190 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N SER B 202 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 131 through 140 removed outlier: 6.525A pdb=" N GLN B 132 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N CYS B 134 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N VAL B 156 " --> pdb=" O CYS B 134 " (cutoff:3.500A) removed outlier: 10.585A pdb=" N ASP B 136 " --> pdb=" O PHE B 154 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N PHE B 154 " --> pdb=" O ASP B 136 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 308 through 316 removed outlier: 5.328A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER B 313 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY B 645 " --> pdb=" O THR B 642 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 322 through 325 removed outlier: 6.837A pdb=" N ILE B 323 " --> pdb=" O ASN B 539 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AC5, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC6, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.312A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 698 through 700 removed outlier: 6.769A pdb=" N ALA B 698 " --> pdb=" O ILE C 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 714 through 725 removed outlier: 3.768A pdb=" N MET B1047 " --> pdb=" O VAL B1062 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.559A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1073 through 1075 removed outlier: 3.520A pdb=" N THR B1073 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA B1075 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE B1092 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.621A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS B1079 " --> pdb=" O VAL B1130 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 30 through 31 removed outlier: 3.611A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.753A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.526A pdb=" N SER C 169 " --> pdb=" O VAL C 124 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 221 through 227 removed outlier: 6.003A pdb=" N SER C 202 " --> pdb=" O PRO C 222 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL C 190 " --> pdb=" O TYR C 201 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY C 265 " --> pdb=" O TYR C 89 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.284A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SER C 313 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY C 590 " --> pdb=" O PHE C 315 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 323 through 325 Processing sheet with id=AD9, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.946A pdb=" N ASN C 351 " --> pdb=" O SER C 396 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER C 396 " --> pdb=" O ASN C 351 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASN C 391 " --> pdb=" O GLU C 513 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU C 513 " --> pdb=" O ASN C 391 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.216A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 709 through 725 removed outlier: 6.925A pdb=" N GLN C1068 " --> pdb=" O ILE C 713 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N PHE C 715 " --> pdb=" O PRO C1066 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE C 717 " --> pdb=" O TYR C1064 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR C1064 " --> pdb=" O ILE C 717 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL C 719 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL C1062 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR C 721 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU C1060 " --> pdb=" O THR C 721 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE C 723 " --> pdb=" O VAL C1058 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL C1058 " --> pdb=" O ILE C 723 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY C1056 " --> pdb=" O PRO C 725 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET C1047 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.657A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 1117 through 1119 removed outlier: 3.958A pdb=" N CYS C1079 " --> pdb=" O VAL C1130 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1091 through 1094 782 hydrogen bonds defined for protein. 2181 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.13 Time building geometry restraints manager: 10.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7333 1.35 - 1.47: 5990 1.47 - 1.59: 10321 1.59 - 1.71: 0 1.71 - 1.83: 124 Bond restraints: 23768 Sorted by residual: bond pdb=" C1 NAG L 2 " pdb=" O5 NAG L 2 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.39e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.02e+00 bond pdb=" N VAL A 141 " pdb=" CA VAL A 141 " ideal model delta sigma weight residual 1.458 1.417 0.041 1.90e-02 2.77e+03 4.71e+00 bond pdb=" C1 NAG A2001 " pdb=" O5 NAG A2001 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.43e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.29e+00 ... (remaining 23763 not shown) Histogram of bond angle deviations from ideal: 99.27 - 106.49: 608 106.49 - 113.72: 13522 113.72 - 120.94: 10678 120.94 - 128.17: 7433 128.17 - 135.39: 90 Bond angle restraints: 32331 Sorted by residual: angle pdb=" N VAL A 128 " pdb=" CA VAL A 128 " pdb=" C VAL A 128 " ideal model delta sigma weight residual 112.17 107.35 4.82 9.50e-01 1.11e+00 2.57e+01 angle pdb=" N LYS B 851 " pdb=" CA LYS B 851 " pdb=" C LYS B 851 " ideal model delta sigma weight residual 110.80 102.07 8.73 2.13e+00 2.20e-01 1.68e+01 angle pdb=" N THR C 122 " pdb=" CA THR C 122 " pdb=" C THR C 122 " ideal model delta sigma weight residual 114.56 109.99 4.57 1.27e+00 6.20e-01 1.30e+01 angle pdb=" N VAL B 128 " pdb=" CA VAL B 128 " pdb=" C VAL B 128 " ideal model delta sigma weight residual 111.77 108.21 3.56 1.04e+00 9.25e-01 1.17e+01 angle pdb=" CA TRP A 64 " pdb=" CB TRP A 64 " pdb=" CG TRP A 64 " ideal model delta sigma weight residual 113.60 120.07 -6.47 1.90e+00 2.77e-01 1.16e+01 ... (remaining 32326 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.81: 14195 23.81 - 47.62: 752 47.62 - 71.42: 121 71.42 - 95.23: 42 95.23 - 119.04: 43 Dihedral angle restraints: 15153 sinusoidal: 6878 harmonic: 8275 Sorted by residual: dihedral pdb=" CB CYS C 288 " pdb=" SG CYS C 288 " pdb=" SG CYS C 298 " pdb=" CB CYS C 298 " ideal model delta sinusoidal sigma weight residual -86.00 -170.87 84.87 1 1.00e+01 1.00e-02 8.74e+01 dihedral pdb=" CB CYS A1029 " pdb=" SG CYS A1029 " pdb=" SG CYS A1040 " pdb=" CB CYS A1040 " ideal model delta sinusoidal sigma weight residual 93.00 173.80 -80.80 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS B 659 " pdb=" SG CYS B 659 " pdb=" SG CYS B 668 " pdb=" CB CYS B 668 " ideal model delta sinusoidal sigma weight residual 93.00 170.94 -77.94 1 1.00e+01 1.00e-02 7.59e+01 ... (remaining 15150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 3863 0.122 - 0.244: 46 0.244 - 0.367: 5 0.367 - 0.489: 3 0.489 - 0.611: 2 Chirality restraints: 3919 Sorted by residual: chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN C 162 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.33e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 162 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.91e+00 chirality pdb=" C1 NAG Z 1 " pdb=" ND2 ASN C 340 " pdb=" C2 NAG Z 1 " pdb=" O5 NAG Z 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.91e+00 ... (remaining 3916 not shown) Planarity restraints: 4122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 140 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.84e+00 pdb=" C GLY A 140 " 0.038 2.00e-02 2.50e+03 pdb=" O GLY A 140 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL A 141 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 983 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.83e+00 pdb=" N PRO A 984 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 984 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 984 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 983 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO C 984 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 984 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 984 " -0.031 5.00e-02 4.00e+02 ... (remaining 4119 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1319 2.73 - 3.27: 22613 3.27 - 3.82: 35340 3.82 - 4.36: 39297 4.36 - 4.90: 70471 Nonbonded interactions: 169040 Sorted by model distance: nonbonded pdb=" OH TYR C 753 " pdb=" OD1 ASP C 991 " model vdw 2.189 2.440 nonbonded pdb=" OD2 ASP C 575 " pdb=" OG1 THR C 578 " model vdw 2.203 2.440 nonbonded pdb=" OG SER A 110 " pdb=" OE1 GLN A 132 " model vdw 2.214 2.440 nonbonded pdb=" OH TYR B 498 " pdb=" O TYR B 502 " model vdw 2.219 2.440 nonbonded pdb=" OG SER B 110 " pdb=" OE1 GLN B 132 " model vdw 2.222 2.440 ... (remaining 169035 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 'B' and (resid 27 through 139 or resid 152 through 173 or resid 184 throu \ gh 208 or resid 214 through 240 or resid 261 through 618 or resid 638 through 11 \ 43 or resid 2001 through 2004)) selection = (chain 'C' and (resid 27 through 824 or resid 842 through 1143 or resid 2001 thr \ ough 2004)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 13.000 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 62.730 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23768 Z= 0.244 Angle : 0.668 10.390 32331 Z= 0.349 Chirality : 0.050 0.611 3919 Planarity : 0.004 0.055 4077 Dihedral : 15.724 119.039 9721 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.37 % Favored : 93.34 % Rotamer: Outliers : 0.16 % Allowed : 0.48 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.16), residues: 2794 helix: 1.88 (0.23), residues: 608 sheet: -0.68 (0.22), residues: 549 loop : -2.08 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 102 HIS 0.003 0.000 HIS B 204 PHE 0.022 0.001 PHE B 138 TYR 0.014 0.001 TYR A 89 ARG 0.005 0.000 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 165 time to evaluate : 2.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 742 ASP cc_start: 0.6118 (t70) cc_final: 0.5882 (t70) REVERT: C 1028 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7399 (tm-30) REVERT: C 1132 ASN cc_start: 0.8223 (t0) cc_final: 0.7571 (t0) outliers start: 4 outliers final: 0 residues processed: 166 average time/residue: 0.3346 time to fit residues: 89.8008 Evaluate side-chains 107 residues out of total 2485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 238 optimal weight: 4.9990 chunk 213 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 144 optimal weight: 0.1980 chunk 114 optimal weight: 0.7980 chunk 221 optimal weight: 4.9990 chunk 85 optimal weight: 0.0970 chunk 134 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 256 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN A 776 GLN A 962 GLN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 ASN ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.0740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 23768 Z= 0.174 Angle : 0.585 10.245 32331 Z= 0.289 Chirality : 0.047 0.380 3919 Planarity : 0.004 0.056 4077 Dihedral : 11.844 110.115 4645 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.87 % Favored : 92.84 % Rotamer: Outliers : 0.48 % Allowed : 6.80 % Favored : 92.72 % 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: -1.13 (0.16), residues: 2794 helix: 1.98 (0.22), residues: 615 sheet: -0.50 (0.21), residues: 596 loop : -2.09 (0.15), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 102 HIS 0.003 0.000 HIS C 204 PHE 0.015 0.001 PHE B 138 TYR 0.019 0.001 TYR C 505 ARG 0.005 0.000 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 2.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 405 ARG cc_start: 0.8116 (ttp80) cc_final: 0.7816 (ttp80) REVERT: C 505 TYR cc_start: 0.7898 (m-80) cc_final: 0.7461 (m-80) REVERT: C 742 ASP cc_start: 0.6334 (t70) cc_final: 0.6059 (t70) REVERT: C 1132 ASN cc_start: 0.8267 (t0) cc_final: 0.7624 (t0) outliers start: 12 outliers final: 9 residues processed: 129 average time/residue: 0.3113 time to fit residues: 67.5994 Evaluate side-chains 115 residues out of total 2485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 962 GLN Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 846 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 142 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 213 optimal weight: 6.9990 chunk 174 optimal weight: 0.9990 chunk 70 optimal weight: 0.0070 chunk 256 optimal weight: 0.7980 chunk 277 optimal weight: 0.7980 chunk 228 optimal weight: 0.9980 chunk 254 optimal weight: 0.3980 chunk 87 optimal weight: 7.9990 chunk 205 optimal weight: 4.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23768 Z= 0.149 Angle : 0.553 10.103 32331 Z= 0.270 Chirality : 0.046 0.370 3919 Planarity : 0.004 0.056 4077 Dihedral : 10.286 109.692 4645 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.62 % Favored : 93.09 % Rotamer: Outliers : 0.68 % Allowed : 9.78 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.02 (0.16), residues: 2794 helix: 2.10 (0.22), residues: 612 sheet: -0.47 (0.20), residues: 621 loop : -2.03 (0.15), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 102 HIS 0.002 0.000 HIS A1085 PHE 0.015 0.001 PHE B 138 TYR 0.013 0.001 TYR C 89 ARG 0.002 0.000 ARG A1016 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 2.734 Fit side-chains REVERT: A 187 ARG cc_start: 0.6974 (mtp180) cc_final: 0.6673 (tpp-160) REVERT: C 52 GLN cc_start: 0.7630 (tm-30) cc_final: 0.6931 (tm-30) REVERT: C 742 ASP cc_start: 0.6338 (t70) cc_final: 0.6018 (t70) REVERT: C 1132 ASN cc_start: 0.8286 (t0) cc_final: 0.7628 (t0) outliers start: 17 outliers final: 8 residues processed: 130 average time/residue: 0.3153 time to fit residues: 69.6088 Evaluate side-chains 111 residues out of total 2485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 2.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 846 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 253 optimal weight: 9.9990 chunk 192 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 257 optimal weight: 0.7980 chunk 272 optimal weight: 3.9990 chunk 134 optimal weight: 0.2980 chunk 244 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 801 GLN A 932 GLN ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 ASN ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23768 Z= 0.166 Angle : 0.552 10.081 32331 Z= 0.270 Chirality : 0.046 0.373 3919 Planarity : 0.004 0.057 4077 Dihedral : 9.390 109.882 4645 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.94 % Favored : 92.73 % Rotamer: Outliers : 1.17 % Allowed : 12.31 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.16), residues: 2794 helix: 2.16 (0.22), residues: 615 sheet: -0.40 (0.21), residues: 611 loop : -2.05 (0.15), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 102 HIS 0.002 0.000 HIS C1085 PHE 0.024 0.001 PHE B 131 TYR 0.014 0.001 TYR C 89 ARG 0.004 0.000 ARG B 405 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 114 time to evaluate : 2.506 Fit side-chains REVERT: A 187 ARG cc_start: 0.7077 (mtp180) cc_final: 0.6848 (tpp-160) REVERT: C 52 GLN cc_start: 0.7642 (tm-30) cc_final: 0.6943 (tm-30) REVERT: C 537 ASN cc_start: 0.7109 (OUTLIER) cc_final: 0.6847 (p0) REVERT: C 847 ILE cc_start: 0.6618 (mt) cc_final: 0.6374 (mt) REVERT: C 1132 ASN cc_start: 0.8328 (t0) cc_final: 0.7650 (t0) outliers start: 29 outliers final: 14 residues processed: 137 average time/residue: 0.2969 time to fit residues: 69.9948 Evaluate side-chains 123 residues out of total 2485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 2.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 846 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 227 optimal weight: 7.9990 chunk 154 optimal weight: 0.0970 chunk 3 optimal weight: 5.9990 chunk 202 optimal weight: 0.0670 chunk 112 optimal weight: 8.9990 chunk 232 optimal weight: 0.7980 chunk 188 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 244 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 overall best weight: 0.5916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 HIS ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23768 Z= 0.147 Angle : 0.536 9.975 32331 Z= 0.261 Chirality : 0.045 0.371 3919 Planarity : 0.004 0.058 4077 Dihedral : 8.806 109.331 4645 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.37 % Favored : 93.31 % Rotamer: Outliers : 1.09 % Allowed : 13.48 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.16), residues: 2794 helix: 2.24 (0.22), residues: 610 sheet: -0.38 (0.21), residues: 597 loop : -1.98 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 102 HIS 0.002 0.000 HIS A1085 PHE 0.016 0.001 PHE B 138 TYR 0.013 0.001 TYR C 89 ARG 0.002 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 117 time to evaluate : 2.764 Fit side-chains REVERT: A 187 ARG cc_start: 0.7069 (mtp180) cc_final: 0.6752 (tpp-160) REVERT: B 448 TYR cc_start: 0.7270 (m-10) cc_final: 0.7025 (m-80) REVERT: C 52 GLN cc_start: 0.7638 (tm-30) cc_final: 0.6936 (tm-30) REVERT: C 1132 ASN cc_start: 0.8268 (t0) cc_final: 0.7612 (t0) outliers start: 27 outliers final: 19 residues processed: 139 average time/residue: 0.2977 time to fit residues: 70.8887 Evaluate side-chains 127 residues out of total 2485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 2.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 487 PHE Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 91 optimal weight: 10.0000 chunk 245 optimal weight: 1.9990 chunk 53 optimal weight: 0.0980 chunk 160 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 272 optimal weight: 5.9990 chunk 226 optimal weight: 9.9990 chunk 126 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 90 optimal weight: 0.0370 chunk 143 optimal weight: 2.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23768 Z= 0.186 Angle : 0.552 9.873 32331 Z= 0.270 Chirality : 0.046 0.370 3919 Planarity : 0.004 0.058 4077 Dihedral : 8.481 110.028 4645 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.05 % Favored : 92.63 % Rotamer: Outliers : 1.45 % Allowed : 14.41 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.16), residues: 2794 helix: 2.23 (0.22), residues: 610 sheet: -0.37 (0.21), residues: 591 loop : -2.01 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 64 HIS 0.002 0.000 HIS C1085 PHE 0.021 0.001 PHE B 131 TYR 0.015 0.001 TYR C 418 ARG 0.004 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 109 time to evaluate : 2.765 Fit side-chains REVERT: A 187 ARG cc_start: 0.7143 (mtp180) cc_final: 0.6887 (tpp-160) REVERT: A 189 PHE cc_start: 0.7431 (m-10) cc_final: 0.6886 (m-10) REVERT: A 239 LEU cc_start: 0.7386 (mm) cc_final: 0.6906 (pp) REVERT: C 52 GLN cc_start: 0.7651 (tm-30) cc_final: 0.6933 (tm-30) REVERT: C 847 ILE cc_start: 0.6617 (mt) cc_final: 0.6406 (mt) REVERT: C 1132 ASN cc_start: 0.8321 (t0) cc_final: 0.7670 (t0) outliers start: 36 outliers final: 26 residues processed: 140 average time/residue: 0.2977 time to fit residues: 71.5098 Evaluate side-chains 131 residues out of total 2485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 105 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 487 PHE Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 263 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 199 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 229 optimal weight: 2.9990 chunk 152 optimal weight: 0.0570 chunk 271 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 125 optimal weight: 0.0060 overall best weight: 0.5716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 23768 Z= 0.144 Angle : 0.532 9.839 32331 Z= 0.260 Chirality : 0.045 0.364 3919 Planarity : 0.004 0.058 4077 Dihedral : 8.076 108.984 4645 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.12 % Favored : 93.56 % Rotamer: Outliers : 1.29 % Allowed : 14.81 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.16), residues: 2794 helix: 2.34 (0.22), residues: 604 sheet: -0.38 (0.21), residues: 597 loop : -1.94 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 102 HIS 0.002 0.000 HIS A1085 PHE 0.018 0.001 PHE B 138 TYR 0.013 0.001 TYR C 89 ARG 0.004 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 114 time to evaluate : 2.646 Fit side-chains REVERT: A 167 TYR cc_start: 0.7389 (t80) cc_final: 0.6867 (t80) REVERT: A 187 ARG cc_start: 0.7063 (mtp180) cc_final: 0.6777 (tpp-160) REVERT: A 239 LEU cc_start: 0.7193 (mm) cc_final: 0.6837 (pp) REVERT: B 187 ARG cc_start: 0.5800 (tpm170) cc_final: 0.5462 (tpm170) REVERT: B 189 PHE cc_start: 0.7341 (m-80) cc_final: 0.7088 (m-80) REVERT: B 448 TYR cc_start: 0.7324 (m-10) cc_final: 0.7073 (m-80) REVERT: C 52 GLN cc_start: 0.7621 (tm-30) cc_final: 0.6910 (tm-30) outliers start: 32 outliers final: 22 residues processed: 141 average time/residue: 0.2891 time to fit residues: 70.9175 Evaluate side-chains 132 residues out of total 2485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 2.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 487 PHE Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 168 optimal weight: 0.0870 chunk 108 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 52 optimal weight: 8.9990 chunk 172 optimal weight: 3.9990 chunk 185 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 25 optimal weight: 0.0970 chunk 213 optimal weight: 10.0000 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 23768 Z= 0.158 Angle : 0.538 9.805 32331 Z= 0.262 Chirality : 0.045 0.364 3919 Planarity : 0.004 0.058 4077 Dihedral : 7.803 109.242 4645 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.76 % Favored : 92.95 % Rotamer: Outliers : 1.17 % Allowed : 15.17 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.16), residues: 2794 helix: 2.35 (0.22), residues: 604 sheet: -0.37 (0.21), residues: 597 loop : -1.94 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 64 HIS 0.002 0.000 HIS A1085 PHE 0.015 0.001 PHE B1072 TYR 0.014 0.001 TYR C 89 ARG 0.003 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 109 time to evaluate : 2.517 Fit side-chains REVERT: A 187 ARG cc_start: 0.7048 (mtp180) cc_final: 0.6817 (tpp-160) REVERT: A 239 LEU cc_start: 0.7193 (mm) cc_final: 0.6851 (pp) REVERT: B 189 PHE cc_start: 0.7364 (m-80) cc_final: 0.7099 (m-80) REVERT: C 52 GLN cc_start: 0.7664 (tm-30) cc_final: 0.6886 (tm-30) outliers start: 29 outliers final: 26 residues processed: 133 average time/residue: 0.2862 time to fit residues: 65.9600 Evaluate side-chains 130 residues out of total 2485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 104 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 487 PHE Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 247 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 chunk 237 optimal weight: 0.1980 chunk 253 optimal weight: 4.9990 chunk 152 optimal weight: 0.0980 chunk 110 optimal weight: 7.9990 chunk 198 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 228 optimal weight: 9.9990 chunk 239 optimal weight: 0.0980 chunk 252 optimal weight: 4.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23768 Z= 0.134 Angle : 0.528 9.788 32331 Z= 0.257 Chirality : 0.045 0.359 3919 Planarity : 0.004 0.058 4077 Dihedral : 7.566 108.466 4645 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.08 % Favored : 93.59 % Rotamer: Outliers : 1.29 % Allowed : 15.33 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.16), residues: 2794 helix: 2.48 (0.22), residues: 597 sheet: -0.32 (0.21), residues: 595 loop : -1.91 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 102 HIS 0.002 0.000 HIS A1085 PHE 0.020 0.001 PHE B 138 TYR 0.014 0.001 TYR A 167 ARG 0.004 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 112 time to evaluate : 2.739 Fit side-chains revert: symmetry clash REVERT: A 187 ARG cc_start: 0.6910 (mtp180) cc_final: 0.6662 (tpp-160) REVERT: A 239 LEU cc_start: 0.7142 (mm) cc_final: 0.6852 (pp) REVERT: B 189 PHE cc_start: 0.7312 (m-80) cc_final: 0.7062 (m-80) REVERT: C 52 GLN cc_start: 0.7640 (tm-30) cc_final: 0.6868 (tm-30) outliers start: 32 outliers final: 25 residues processed: 140 average time/residue: 0.2989 time to fit residues: 72.7014 Evaluate side-chains 132 residues out of total 2485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 2.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 487 PHE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 166 optimal weight: 2.9990 chunk 267 optimal weight: 0.7980 chunk 163 optimal weight: 0.6980 chunk 127 optimal weight: 0.9990 chunk 186 optimal weight: 4.9990 chunk 280 optimal weight: 1.9990 chunk 258 optimal weight: 0.6980 chunk 223 optimal weight: 0.0270 chunk 23 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23768 Z= 0.151 Angle : 0.532 9.763 32331 Z= 0.259 Chirality : 0.045 0.361 3919 Planarity : 0.004 0.058 4077 Dihedral : 7.451 108.736 4645 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.44 % Favored : 93.20 % Rotamer: Outliers : 1.21 % Allowed : 15.49 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), residues: 2794 helix: 2.48 (0.22), residues: 597 sheet: -0.32 (0.21), residues: 595 loop : -1.91 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 102 HIS 0.002 0.000 HIS A1085 PHE 0.015 0.001 PHE B1072 TYR 0.013 0.001 TYR C 89 ARG 0.004 0.000 ARG B 187 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5588 Ramachandran restraints generated. 2794 Oldfield, 0 Emsley, 2794 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 108 time to evaluate : 2.650 Fit side-chains revert: symmetry clash REVERT: A 187 ARG cc_start: 0.7012 (mtp180) cc_final: 0.6695 (tpp-160) REVERT: A 239 LEU cc_start: 0.7213 (mm) cc_final: 0.6906 (pp) REVERT: A 300 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7316 (tt) REVERT: B 189 PHE cc_start: 0.7264 (m-80) cc_final: 0.6986 (m-80) REVERT: C 52 GLN cc_start: 0.7646 (tm-30) cc_final: 0.6870 (tm-30) outliers start: 30 outliers final: 26 residues processed: 133 average time/residue: 0.2940 time to fit residues: 67.7649 Evaluate side-chains 131 residues out of total 2485 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 104 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 567 ASP Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 487 PHE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 377 TYR Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 846 LEU Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 177 optimal weight: 1.9990 chunk 238 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 206 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 224 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 230 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 ASN ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.147741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.118635 restraints weight = 45961.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.120908 restraints weight = 37752.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.121110 restraints weight = 37964.186| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23768 Z= 0.232 Angle : 0.585 18.735 32331 Z= 0.287 Chirality : 0.046 0.358 3919 Planarity : 0.004 0.058 4077 Dihedral : 7.576 110.135 4645 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.44 % Favored : 92.20 % Rotamer: Outliers : 1.29 % Allowed : 15.41 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.16), residues: 2794 helix: 2.29 (0.22), residues: 608 sheet: -0.39 (0.21), residues: 588 loop : -2.01 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 64 HIS 0.003 0.001 HIS B1085 PHE 0.022 0.002 PHE A 235 TYR 0.020 0.001 TYR C 89 ARG 0.003 0.000 ARG B 187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3340.97 seconds wall clock time: 62 minutes 36.27 seconds (3756.27 seconds total)