Starting phenix.real_space_refine on Mon Feb 19 14:07:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7edi_31072/02_2024/7edi_31072.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7edi_31072/02_2024/7edi_31072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7edi_31072/02_2024/7edi_31072.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7edi_31072/02_2024/7edi_31072.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7edi_31072/02_2024/7edi_31072.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7edi_31072/02_2024/7edi_31072.pdb" } resolution = 3.3 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= 0.051 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 108 5.16 5 C 15835 2.51 5 N 4034 2.21 5 O 4918 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A GLU 306": "OE1" <-> "OE2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A GLU 770": "OE1" <-> "OE2" Residue "B TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1089": "OE1" <-> "OE2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C GLU 658": "OE1" <-> "OE2" Residue "C GLU 745": "OE1" <-> "OE2" Residue "C GLU 777": "OE1" <-> "OE2" Residue "C GLU 816": "OE1" <-> "OE2" Residue "C PHE 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24895 Number of models: 1 Model: "" Number of chains: 37 Chain: "A" Number of atoms: 7992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7992 Classifications: {'peptide': 1024} Link IDs: {'PTRANS': 51, 'TRANS': 972} Chain breaks: 7 Chain: "B" Number of atoms: 7933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1016, 7933 Classifications: {'peptide': 1016} Link IDs: {'PTRANS': 51, 'TRANS': 964} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: "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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 13.76, per 1000 atoms: 0.55 Number of scatterers: 24895 At special positions: 0 Unit cell: (132, 140.8, 200.2, 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 108 16.00 O 4918 8.00 N 4034 7.00 C 15835 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, 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 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.02 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=2.04 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=2.03 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 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=2.02 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 O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 162 " " NAG A2003 " - " ASN A 231 " " NAG A2004 " - " ASN A 600 " " 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 120 " " NAG C2003 " - " ASN C 162 " " NAG C2004 " - " ASN C 600 " " NAG C2005 " - " ASN C 654 " " NAG D 1 " - " ASN A 120 " " NAG E 1 " - " ASN A 279 " " NAG F 1 " - " ASN A 328 " " NAG G 1 " - " ASN A 613 " " NAG H 1 " - " ASN A 706 " " NAG I 1 " - " ASN A 714 " " NAG J 1 " - " ASN A 798 " " NAG K 1 " - " ASN A1071 " " NAG L 1 " - " ASN A1095 " " NAG M 1 " - " ASN A1131 " " NAG N 1 " - " ASN B 120 " " NAG O 1 " - " ASN B 279 " " NAG P 1 " - " ASN B 340 " " NAG Q 1 " - " ASN B 613 " " NAG R 1 " - " ASN B 706 " " NAG S 1 " - " ASN B 714 " " NAG T 1 " - " ASN B 798 " " NAG U 1 " - " ASN B1071 " " NAG V 1 " - " ASN B1095 " " NAG W 1 " - " ASN B1131 " " NAG X 1 " - " ASN C 231 " " NAG Y 1 " - " ASN C 279 " " NAG Z 1 " - " ASN C 328 " " NAG a 1 " - " ASN C 340 " " NAG b 1 " - " ASN C 613 " " NAG c 1 " - " ASN C 706 " " NAG d 1 " - " ASN C 714 " " NAG e 1 " - " ASN C 798 " " NAG f 1 " - " ASN C1071 " " NAG g 1 " - " ASN C1095 " " NAG h 1 " - " ASN C1131 " Time building additional restraints: 10.70 Conformation dependent library (CDL) restraints added in 4.4 seconds 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5710 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 49 sheets defined 23.4% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 382 through 387 removed outlier: 3.642A pdb=" N LEU A 387 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 540 through 543 Processing helix chain 'A' and resid 734 through 740 removed outlier: 3.630A pdb=" N TYR A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 739 " --> pdb=" O CYS A 735 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS A 740 " --> pdb=" O THR A 736 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 734 through 740' Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.588A pdb=" N SER A 747 " --> pdb=" O SER A 743 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 780 removed outlier: 4.029A pdb=" N ASN A 761 " --> pdb=" O CYS A 757 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A 778 " --> pdb=" O ASN A 774 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 779 " --> pdb=" O THR A 775 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 780 " --> pdb=" O GLN A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 822 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 888 removed outlier: 4.327A pdb=" N ALA A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY A 888 " --> pdb=" O THR A 884 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 883 through 888' Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 916 through 938 removed outlier: 3.649A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 962 removed outlier: 4.234A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 981 removed outlier: 3.569A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 1030 removed outlier: 3.723A pdb=" N GLU A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG A 992 " --> pdb=" O VAL A 988 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A 993 " --> pdb=" O GLN A 989 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N THR A 995 " --> pdb=" O ASP A 991 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 998 " --> pdb=" O ILE A 994 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU A1014 " --> pdb=" O ILE A1010 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A1015 " --> pdb=" O ARG A1011 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A1030 " --> pdb=" O MET A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1143 removed outlier: 4.515A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 removed outlier: 3.511A pdb=" N GLU B 295 " --> pdb=" O ASP B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.996A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 380 through 384 Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 752 removed outlier: 4.004A pdb=" N GLN B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 780 removed outlier: 4.080A pdb=" N PHE B 779 " --> pdb=" O THR B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 removed outlier: 3.523A pdb=" N ASP B 817 " --> pdb=" O SER B 813 " (cutoff:3.500A) removed outlier: 3.658A 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 894 through 904 Processing helix chain 'B' and resid 905 through 907 No H-bonds generated for 'chain 'B' and resid 905 through 907' Processing helix chain 'B' and resid 910 through 916 Processing helix chain 'B' and resid 916 through 938 removed outlier: 3.699A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 961 removed outlier: 3.555A pdb=" N GLN B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 965 removed outlier: 3.635A pdb=" N SER B 965 " --> pdb=" O GLN B 962 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 962 through 965' Processing helix chain 'B' and resid 973 through 981 removed outlier: 3.934A pdb=" N ILE B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B 981 " --> pdb=" O ILE B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1030 removed outlier: 3.996A 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 362 through 367 removed outlier: 3.706A pdb=" N TYR C 366 " --> pdb=" O TYR C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 387 removed outlier: 3.571A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU C 387 " --> pdb=" O LEU C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 404 No H-bonds generated for 'chain 'C' and resid 402 through 404' Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 435 through 440 removed outlier: 3.749A pdb=" N SER C 440 " --> pdb=" O ASN C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 740 Processing helix chain 'C' and resid 743 through 751 Processing helix chain 'C' and resid 752 through 754 No H-bonds generated for 'chain 'C' and resid 752 through 754' Processing helix chain 'C' and resid 755 through 780 removed outlier: 3.745A pdb=" N GLN C 759 " --> pdb=" O SER C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 821 Processing helix chain 'C' and resid 863 through 881 Processing helix chain 'C' and resid 883 through 887 removed outlier: 3.659A pdb=" N ALA C 887 " --> pdb=" O THR C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 905 Processing helix chain 'C' and resid 910 through 915 removed outlier: 3.773A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) removed outlier: 3.523A 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 Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 981 removed outlier: 3.770A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 1030 removed outlier: 3.748A pdb=" N ILE C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL C1030 " --> pdb=" O MET C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1113 through 1115 No H-bonds generated for 'chain 'C' and resid 1113 through 1115' Processing helix chain 'C' and resid 1137 through 1143 removed outlier: 3.888A 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: 3.750A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.557A pdb=" N ARG A 270 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA4, first strand: chain 'A' and resid 221 through 226 removed outlier: 6.757A pdb=" N SER A 202 " --> pdb=" O PRO A 222 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 224 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 205 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129 removed outlier: 7.008A pdb=" N VAL A 128 " --> pdb=" O THR A 164 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 164 " --> pdb=" O VAL A 128 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.348A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER A 313 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 321 through 323 removed outlier: 3.930A pdb=" N GLU A 321 " --> pdb=" O CYS A 535 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 351 through 355 removed outlier: 4.148A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A 396 " --> pdb=" O ASN A 351 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 358 through 359 removed outlier: 7.100A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB2, first strand: chain 'A' and resid 470 through 471 removed outlier: 3.540A pdb=" N TYR A 486 " --> pdb=" O TYR A 470 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 562 through 563 removed outlier: 7.112A pdb=" N PHE A 562 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 651 through 652 removed outlier: 5.920A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 698 through 699 removed outlier: 6.831A pdb=" N ALA A 698 " --> pdb=" O ILE B 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 708 through 712 Processing sheet with id=AB7, first strand: chain 'A' and resid 715 through 725 removed outlier: 3.632A pdb=" N MET A1047 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 730 through 732 removed outlier: 4.651A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1117 through 1119 removed outlier: 3.816A pdb=" N CYS A1079 " --> pdb=" O VAL A1130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AC2, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.822A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.682A pdb=" N THR B 271 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ASP B 287 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU B 273 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA B 285 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LYS B 275 " --> pdb=" O THR B 283 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.654A pdb=" N LEU B 82 " --> pdb=" O PHE B 235 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL B 118 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL B 125 " --> pdb=" O VAL B 118 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 87 through 92 removed outlier: 3.547A pdb=" N GLU B 188 " --> pdb=" O LYS B 203 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL B 190 " --> pdb=" O TYR B 201 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE B 200 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL B 224 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N SER B 202 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 308 through 316 removed outlier: 5.212A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER B 313 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY B 645 " --> pdb=" O THR B 642 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 322 through 325 Processing sheet with id=AC8, first strand: chain 'B' and resid 351 through 355 removed outlier: 4.041A pdb=" N ASN B 351 " --> pdb=" O SER B 396 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER B 396 " --> pdb=" O ASN B 351 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP B 395 " --> pdb=" O VAL B 509 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AD1, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.299A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 699 through 701 removed outlier: 3.677A pdb=" N LYS C 787 " --> pdb=" O ASN B 700 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 714 through 725 removed outlier: 3.506A pdb=" N SER B 718 " --> pdb=" O THR B1063 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B1062 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 714 through 725 removed outlier: 3.506A pdb=" N SER B 718 " --> pdb=" O THR B1063 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.681A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.877A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1091 through 1094 Processing sheet with id=AD8, first strand: chain 'C' and resid 30 through 31 removed outlier: 3.887A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.706A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.536A pdb=" N LEU C 238 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY C 101 " --> pdb=" O LEU C 238 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 221 through 227 removed outlier: 6.214A pdb=" N SER C 202 " --> pdb=" O PRO C 222 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL C 224 " --> pdb=" O ILE C 200 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL C 190 " --> pdb=" O TYR C 201 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.699A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 313 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 322 through 325 removed outlier: 3.675A pdb=" N ARG C 325 " --> pdb=" O ASN C 539 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 351 through 355 removed outlier: 4.048A pdb=" N ASN C 351 " --> pdb=" O SER C 396 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER C 396 " --> pdb=" O ASN C 351 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 358 through 359 removed outlier: 7.238A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AE8, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AE9, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.029A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 709 through 725 removed outlier: 7.013A pdb=" N GLN C1068 " --> pdb=" O ILE C 713 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N PHE C 715 " --> pdb=" O PRO C1066 " (cutoff:3.500A) removed outlier: 6.990A 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: 6.916A pdb=" N VAL C 719 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL C1062 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR C 721 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU C1060 " --> pdb=" O THR C 721 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE C 723 " --> pdb=" O VAL C1058 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL C1058 " --> pdb=" O ILE C 723 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLY C1056 " --> pdb=" O PRO C 725 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1044 through 1047 removed outlier: 6.762A pdb=" N VAL C1062 " --> pdb=" O LEU C1046 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR C1073 " --> pdb=" O SER C1094 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.636A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1117 through 1119 removed outlier: 3.679A pdb=" N CYS C1079 " --> pdb=" O VAL C1130 " (cutoff:3.500A) 832 hydrogen bonds defined for protein. 2286 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: 10.38 Time building geometry restraints manager: 11.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7846 1.34 - 1.46: 6299 1.46 - 1.58: 11157 1.58 - 1.71: 0 1.71 - 1.83: 132 Bond restraints: 25434 Sorted by residual: bond pdb=" C1 NAG R 1 " pdb=" O5 NAG R 1 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.93e+00 bond pdb=" C1 NAG H 1 " pdb=" O5 NAG H 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.55e+00 bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.82e+00 bond pdb=" C ASN A 79 " pdb=" N PRO A 80 " ideal model delta sigma weight residual 1.332 1.357 -0.025 1.12e-02 7.97e+03 4.81e+00 bond pdb=" C1 NAG C2003 " pdb=" O5 NAG C2003 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.90e+00 ... (remaining 25429 not shown) Histogram of bond angle deviations from ideal: 98.85 - 106.03: 565 106.03 - 113.22: 14154 113.22 - 120.41: 9321 120.41 - 127.60: 10393 127.60 - 134.79: 168 Bond angle restraints: 34601 Sorted by residual: angle pdb=" N THR A 615 " pdb=" CA THR A 615 " pdb=" C THR A 615 " ideal model delta sigma weight residual 114.75 107.70 7.05 1.26e+00 6.30e-01 3.13e+01 angle pdb=" N ARG A 992 " pdb=" CA ARG A 992 " pdb=" C ARG A 992 " ideal model delta sigma weight residual 113.18 106.58 6.60 1.33e+00 5.65e-01 2.46e+01 angle pdb=" C THR B 112 " pdb=" CA THR B 112 " pdb=" CB THR B 112 " ideal model delta sigma weight residual 115.79 109.93 5.86 1.19e+00 7.06e-01 2.42e+01 angle pdb=" C ASP B 567 " pdb=" CA ASP B 567 " pdb=" CB ASP B 567 " ideal model delta sigma weight residual 115.89 110.06 5.83 1.32e+00 5.74e-01 1.95e+01 angle pdb=" N ASN B1071 " pdb=" CA ASN B1071 " pdb=" C ASN B1071 " ideal model delta sigma weight residual 111.96 117.66 -5.70 1.41e+00 5.03e-01 1.63e+01 ... (remaining 34596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.77: 15153 23.77 - 47.54: 813 47.54 - 71.31: 128 71.31 - 95.08: 28 95.08 - 118.84: 35 Dihedral angle restraints: 16157 sinusoidal: 7289 harmonic: 8868 Sorted by residual: dihedral pdb=" CB CYS A1029 " pdb=" SG CYS A1029 " pdb=" SG CYS A1040 " pdb=" CB CYS A1040 " ideal model delta sinusoidal sigma weight residual 93.00 179.82 -86.82 1 1.00e+01 1.00e-02 9.07e+01 dihedral pdb=" CB CYS A 659 " pdb=" SG CYS A 659 " pdb=" SG CYS A 668 " pdb=" CB CYS A 668 " ideal model delta sinusoidal sigma weight residual -86.00 -6.09 -79.91 1 1.00e+01 1.00e-02 7.92e+01 dihedral pdb=" CB CYS A 288 " pdb=" SG CYS A 288 " pdb=" SG CYS A 298 " pdb=" CB CYS A 298 " ideal model delta sinusoidal sigma weight residual -86.00 -165.56 79.56 1 1.00e+01 1.00e-02 7.86e+01 ... (remaining 16154 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 4136 0.163 - 0.326: 13 0.326 - 0.489: 7 0.489 - 0.651: 0 0.651 - 0.814: 2 Chirality restraints: 4158 Sorted by residual: chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN A1131 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.59 -0.81 2.00e-01 2.50e+01 1.66e+01 chirality pdb=" C1 NAG f 1 " pdb=" ND2 ASN C1071 " pdb=" C2 NAG f 1 " pdb=" O5 NAG f 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" C1 NAG B2003 " pdb=" ND2 ASN B 231 " pdb=" C2 NAG B2003 " pdb=" O5 NAG B2003 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.69e+00 ... (remaining 4155 not shown) Planarity restraints: 4422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1131 " 0.009 2.00e-02 2.50e+03 2.47e-02 7.63e+00 pdb=" CG ASN A1131 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN A1131 " 0.028 2.00e-02 2.50e+03 pdb=" ND2 ASN A1131 " -0.016 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1131 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.24e+00 pdb=" CG ASN A1131 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN A1131 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN A1131 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 162 " -0.020 2.00e-02 2.50e+03 1.82e-02 4.16e+00 pdb=" CG ASN C 162 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN C 162 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN C 162 " 0.019 2.00e-02 2.50e+03 pdb=" C1 NAG C2003 " -0.020 2.00e-02 2.50e+03 ... (remaining 4419 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 387 2.66 - 3.22: 22689 3.22 - 3.78: 35275 3.78 - 4.34: 46341 4.34 - 4.90: 79165 Nonbonded interactions: 183857 Sorted by model distance: nonbonded pdb=" OH TYR B 89 " pdb=" OE2 GLU B 188 " model vdw 2.097 2.440 nonbonded pdb=" O ASP B 565 " pdb=" OG1 THR B 569 " model vdw 2.107 2.440 nonbonded pdb=" O THR A 390 " pdb=" OG1 THR A 520 " model vdw 2.133 2.440 nonbonded pdb=" OD1 ASP B 439 " pdb=" OH TYR B 448 " model vdw 2.134 2.440 nonbonded pdb=" O THR C 390 " pdb=" OG1 THR C 520 " model vdw 2.181 2.440 ... (remaining 183852 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 139 or resid 152 through 208 or resid 214 throu \ gh 240 or resid 261 through 618 or resid 638 through 672 or resid 688 through 11 \ 43 or resid 2001 through 2005)) selection = (chain 'B' and (resid 27 through 139 or resid 152 through 208 or resid 214 throu \ gh 618 or resid 638 through 1143 or resid 2002 through 2006)) selection = (chain 'C' and (resid 27 through 824 or resid 842 through 1143 or resid 2001 thr \ ough 2005)) } 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 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.080 Check model and map are aligned: 0.350 Set scattering table: 0.250 Process input model: 67.760 Find NCS groups from input model: 2.050 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 25434 Z= 0.295 Angle : 0.695 9.788 34601 Z= 0.365 Chirality : 0.053 0.814 4158 Planarity : 0.004 0.071 4376 Dihedral : 15.139 118.844 10336 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.10 % Favored : 93.40 % Rotamer: Outliers : 0.19 % Allowed : 0.34 % Favored : 99.47 % 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 (0.15), residues: 2998 helix: 1.69 (0.22), residues: 622 sheet: -0.52 (0.20), residues: 654 loop : -1.72 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 64 HIS 0.009 0.001 HIS C 204 PHE 0.029 0.002 PHE B 344 TYR 0.017 0.001 TYR C1064 ARG 0.008 0.001 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 173 time to evaluate : 2.982 Fit side-chains REVERT: A 188 GLU cc_start: 0.7744 (tt0) cc_final: 0.7516 (tt0) REVERT: A 226 LEU cc_start: 0.5090 (tp) cc_final: 0.4886 (tp) REVERT: A 883 TRP cc_start: 0.7891 (p90) cc_final: 0.6889 (p90) REVERT: B 357 ASN cc_start: 0.8281 (m-40) cc_final: 0.8075 (p0) REVERT: B 728 MET cc_start: 0.8402 (ptt) cc_final: 0.8072 (ptt) REVERT: B 1026 MET cc_start: 0.8125 (tmm) cc_final: 0.7798 (tpp) REVERT: B 1129 ILE cc_start: 0.8122 (pt) cc_final: 0.7683 (pt) REVERT: C 234 ARG cc_start: 0.7528 (mtm-85) cc_final: 0.7284 (mtm-85) REVERT: C 315 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8398 (p90) outliers start: 5 outliers final: 0 residues processed: 175 average time/residue: 0.3531 time to fit residues: 100.9833 Evaluate side-chains 124 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 2.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 315 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 255 optimal weight: 2.9990 chunk 229 optimal weight: 20.0000 chunk 127 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 154 optimal weight: 0.0970 chunk 122 optimal weight: 4.9990 chunk 237 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 chunk 176 optimal weight: 2.9990 chunk 275 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 GLN A 989 GLN A1103 GLN B 950 ASN C 603 ASN C 966 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 25434 Z= 0.330 Angle : 0.656 9.736 34601 Z= 0.331 Chirality : 0.051 0.619 4158 Planarity : 0.004 0.048 4376 Dihedral : 11.000 102.931 4899 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.40 % Favored : 93.10 % Rotamer: Outliers : 0.68 % Allowed : 7.63 % Favored : 91.69 % 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: -1.12 (0.15), residues: 2998 helix: 1.57 (0.22), residues: 629 sheet: -0.59 (0.19), residues: 683 loop : -1.80 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 64 HIS 0.009 0.001 HIS B 66 PHE 0.033 0.002 PHE A1118 TYR 0.022 0.002 TYR C 167 ARG 0.008 0.001 ARG B1036 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 2.758 Fit side-chains REVERT: A 55 PHE cc_start: 0.7032 (m-80) cc_final: 0.6693 (m-80) REVERT: A 188 GLU cc_start: 0.7616 (tt0) cc_final: 0.7019 (tt0) REVERT: A 301 LYS cc_start: 0.8700 (tppt) cc_final: 0.8485 (tppp) REVERT: A 883 TRP cc_start: 0.7871 (p90) cc_final: 0.6901 (p90) REVERT: B 425 ASP cc_start: 0.7525 (m-30) cc_final: 0.7296 (m-30) REVERT: B 1129 ILE cc_start: 0.8339 (pt) cc_final: 0.8048 (pt) REVERT: C 315 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8720 (p90) outliers start: 18 outliers final: 9 residues processed: 156 average time/residue: 0.3244 time to fit residues: 85.3446 Evaluate side-chains 132 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 122 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 948 VAL Chi-restraints excluded: chain C residue 1089 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 152 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 229 optimal weight: 10.0000 chunk 187 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 275 optimal weight: 1.9990 chunk 297 optimal weight: 3.9990 chunk 245 optimal weight: 40.0000 chunk 273 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 221 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 954 GLN ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 25434 Z= 0.275 Angle : 0.620 9.905 34601 Z= 0.310 Chirality : 0.050 0.607 4158 Planarity : 0.004 0.049 4376 Dihedral : 10.178 99.705 4899 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.00 % Favored : 93.53 % Rotamer: Outliers : 1.32 % Allowed : 10.61 % Favored : 88.08 % 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: -1.10 (0.15), residues: 2998 helix: 1.67 (0.21), residues: 639 sheet: -0.59 (0.19), residues: 685 loop : -1.83 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 64 HIS 0.005 0.001 HIS A1085 PHE 0.029 0.002 PHE A1118 TYR 0.018 0.001 TYR A1064 ARG 0.005 0.000 ARG B1036 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 139 time to evaluate : 3.026 Fit side-chains REVERT: A 55 PHE cc_start: 0.7119 (m-80) cc_final: 0.6679 (m-80) REVERT: A 188 GLU cc_start: 0.7433 (tt0) cc_final: 0.6810 (tt0) REVERT: A 883 TRP cc_start: 0.7805 (p90) cc_final: 0.6905 (p90) REVERT: A 998 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8614 (mm) REVERT: B 189 PHE cc_start: 0.7164 (m-80) cc_final: 0.6954 (m-80) REVERT: B 395 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.6780 (p0) REVERT: B 425 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7271 (m-30) REVERT: B 529 ASN cc_start: 0.8134 (t0) cc_final: 0.7800 (t0) REVERT: B 728 MET cc_start: 0.8358 (ptt) cc_final: 0.8048 (ptm) REVERT: B 875 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8204 (tt) REVERT: B 1129 ILE cc_start: 0.8192 (pt) cc_final: 0.7984 (pt) outliers start: 35 outliers final: 14 residues processed: 169 average time/residue: 0.3240 time to fit residues: 94.2276 Evaluate side-chains 146 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 128 time to evaluate : 2.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 272 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 chunk 185 optimal weight: 0.0970 chunk 276 optimal weight: 0.8980 chunk 292 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 262 optimal weight: 0.0870 chunk 78 optimal weight: 0.9980 overall best weight: 0.8158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 GLN A1103 GLN B 641 GLN C 85 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25434 Z= 0.182 Angle : 0.590 10.312 34601 Z= 0.289 Chirality : 0.049 0.612 4158 Planarity : 0.004 0.045 4376 Dihedral : 9.514 95.175 4897 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.67 % Favored : 93.83 % Rotamer: Outliers : 1.35 % Allowed : 12.56 % Favored : 86.08 % 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: -0.90 (0.16), residues: 2998 helix: 1.88 (0.22), residues: 639 sheet: -0.43 (0.19), residues: 687 loop : -1.75 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 64 HIS 0.004 0.001 HIS A1085 PHE 0.024 0.001 PHE B 84 TYR 0.016 0.001 TYR A1064 ARG 0.003 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 135 time to evaluate : 2.477 Fit side-chains REVERT: A 55 PHE cc_start: 0.7061 (m-80) cc_final: 0.6678 (m-80) REVERT: A 188 GLU cc_start: 0.7389 (tt0) cc_final: 0.6650 (tt0) REVERT: A 883 TRP cc_start: 0.7787 (p90) cc_final: 0.6932 (p90) REVERT: A 1047 MET cc_start: 0.7709 (ptp) cc_final: 0.7447 (ptp) REVERT: B 393 TYR cc_start: 0.7177 (m-10) cc_final: 0.6964 (m-80) REVERT: B 395 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.6657 (p0) REVERT: B 425 ASP cc_start: 0.7494 (m-30) cc_final: 0.7284 (m-30) REVERT: B 529 ASN cc_start: 0.8084 (t0) cc_final: 0.7761 (t0) REVERT: B 728 MET cc_start: 0.8313 (ptt) cc_final: 0.8078 (ptm) outliers start: 36 outliers final: 16 residues processed: 166 average time/residue: 0.3046 time to fit residues: 87.3433 Evaluate side-chains 146 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 2.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 1089 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 243 optimal weight: 40.0000 chunk 166 optimal weight: 0.6980 chunk 4 optimal weight: 10.0000 chunk 218 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 249 optimal weight: 6.9990 chunk 202 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 262 optimal weight: 0.0980 chunk 73 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 GLN B 910 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25434 Z= 0.221 Angle : 0.602 11.332 34601 Z= 0.295 Chirality : 0.049 0.615 4158 Planarity : 0.004 0.046 4376 Dihedral : 8.952 94.439 4897 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.97 % Favored : 93.56 % Rotamer: Outliers : 1.73 % Allowed : 13.73 % Favored : 84.54 % 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: -0.91 (0.16), residues: 2998 helix: 1.81 (0.22), residues: 643 sheet: -0.44 (0.20), residues: 679 loop : -1.73 (0.15), residues: 1676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 64 HIS 0.005 0.001 HIS A1085 PHE 0.025 0.001 PHE A1118 TYR 0.017 0.001 TYR B 418 ARG 0.004 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 135 time to evaluate : 3.001 Fit side-chains revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7121 (m-80) cc_final: 0.6680 (m-80) REVERT: A 188 GLU cc_start: 0.7423 (tt0) cc_final: 0.7178 (mt-10) REVERT: A 883 TRP cc_start: 0.7794 (p90) cc_final: 0.7003 (p90) REVERT: A 998 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8568 (mm) REVERT: B 167 TYR cc_start: 0.7094 (t80) cc_final: 0.6843 (t80) REVERT: B 332 LEU cc_start: 0.8968 (tp) cc_final: 0.8767 (tt) REVERT: B 395 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.6718 (p0) REVERT: B 529 ASN cc_start: 0.8114 (t0) cc_final: 0.7784 (t0) outliers start: 46 outliers final: 29 residues processed: 172 average time/residue: 0.3014 time to fit residues: 90.7330 Evaluate side-chains 158 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 2.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 910 GLN Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 98 optimal weight: 1.9990 chunk 263 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 171 optimal weight: 0.0270 chunk 72 optimal weight: 5.9990 chunk 293 optimal weight: 0.9980 chunk 243 optimal weight: 8.9990 chunk 135 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 overall best weight: 1.0042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 654 ASN A 954 GLN A1103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25434 Z= 0.204 Angle : 0.596 12.474 34601 Z= 0.290 Chirality : 0.048 0.618 4158 Planarity : 0.004 0.045 4376 Dihedral : 8.514 93.524 4897 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.80 % Favored : 93.73 % Rotamer: Outliers : 1.81 % Allowed : 13.99 % Favored : 84.20 % 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: 2998 helix: 1.82 (0.22), residues: 649 sheet: -0.38 (0.20), residues: 679 loop : -1.70 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 64 HIS 0.004 0.001 HIS A1085 PHE 0.025 0.001 PHE B 84 TYR 0.016 0.001 TYR A1064 ARG 0.003 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 130 time to evaluate : 2.888 Fit side-chains REVERT: A 55 PHE cc_start: 0.7155 (m-80) cc_final: 0.6731 (m-80) REVERT: A 188 GLU cc_start: 0.7393 (tt0) cc_final: 0.7159 (mt-10) REVERT: A 883 TRP cc_start: 0.7785 (p90) cc_final: 0.7012 (p90) REVERT: A 998 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8567 (mm) REVERT: B 167 TYR cc_start: 0.7011 (t80) cc_final: 0.6760 (t80) REVERT: B 395 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.6731 (p0) REVERT: B 529 ASN cc_start: 0.8135 (t0) cc_final: 0.7807 (t0) outliers start: 48 outliers final: 32 residues processed: 172 average time/residue: 0.3159 time to fit residues: 95.8484 Evaluate side-chains 158 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 124 time to evaluate : 2.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 903 PHE Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 282 optimal weight: 0.9980 chunk 33 optimal weight: 30.0000 chunk 167 optimal weight: 0.7980 chunk 214 optimal weight: 4.9990 chunk 165 optimal weight: 0.9990 chunk 246 optimal weight: 30.0000 chunk 163 optimal weight: 0.0370 chunk 292 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25434 Z= 0.230 Angle : 0.608 11.302 34601 Z= 0.297 Chirality : 0.048 0.621 4158 Planarity : 0.004 0.056 4376 Dihedral : 8.051 92.255 4897 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.04 % Favored : 93.50 % Rotamer: Outliers : 1.77 % Allowed : 14.86 % 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: -0.87 (0.16), residues: 2998 helix: 1.78 (0.21), residues: 648 sheet: -0.34 (0.20), residues: 672 loop : -1.72 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 64 HIS 0.005 0.001 HIS A1085 PHE 0.025 0.001 PHE A1118 TYR 0.017 0.001 TYR A1064 ARG 0.004 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 130 time to evaluate : 2.787 Fit side-chains REVERT: A 55 PHE cc_start: 0.7186 (m-80) cc_final: 0.6738 (m-80) REVERT: A 188 GLU cc_start: 0.7404 (tt0) cc_final: 0.7176 (mt-10) REVERT: A 751 LEU cc_start: 0.9110 (tp) cc_final: 0.8840 (tp) REVERT: A 883 TRP cc_start: 0.7771 (p90) cc_final: 0.6986 (p90) REVERT: A 998 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8585 (mm) REVERT: B 167 TYR cc_start: 0.7125 (t80) cc_final: 0.6848 (t80) REVERT: B 395 ASP cc_start: 0.7320 (OUTLIER) cc_final: 0.6808 (p0) REVERT: B 529 ASN cc_start: 0.8139 (t0) cc_final: 0.7808 (t0) outliers start: 47 outliers final: 34 residues processed: 170 average time/residue: 0.3054 time to fit residues: 90.5056 Evaluate side-chains 163 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 127 time to evaluate : 3.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 903 PHE Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 180 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 87 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 185 optimal weight: 0.0770 chunk 198 optimal weight: 0.5980 chunk 144 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 229 optimal weight: 30.0000 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN A 954 GLN A1103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25434 Z= 0.152 Angle : 0.564 10.638 34601 Z= 0.276 Chirality : 0.046 0.608 4158 Planarity : 0.004 0.054 4376 Dihedral : 7.702 90.535 4897 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.37 % Favored : 94.13 % Rotamer: Outliers : 1.69 % Allowed : 14.97 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.16), residues: 2998 helix: 2.03 (0.22), residues: 636 sheet: -0.13 (0.20), residues: 660 loop : -1.63 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 64 HIS 0.004 0.001 HIS C 204 PHE 0.025 0.001 PHE B 84 TYR 0.015 0.001 TYR A1064 ARG 0.003 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 138 time to evaluate : 3.023 Fit side-chains revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7130 (m-80) cc_final: 0.6854 (m-80) REVERT: A 751 LEU cc_start: 0.9063 (tp) cc_final: 0.8802 (tp) REVERT: A 883 TRP cc_start: 0.7747 (p90) cc_final: 0.6885 (p90) REVERT: A 998 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8612 (mm) REVERT: A 1102 THR cc_start: 0.8858 (OUTLIER) cc_final: 0.8466 (p) REVERT: B 167 TYR cc_start: 0.6937 (t80) cc_final: 0.6705 (t80) REVERT: B 332 LEU cc_start: 0.8983 (tp) cc_final: 0.8775 (tt) REVERT: B 395 ASP cc_start: 0.7273 (OUTLIER) cc_final: 0.6758 (p0) REVERT: B 529 ASN cc_start: 0.8108 (t0) cc_final: 0.7774 (t0) outliers start: 45 outliers final: 29 residues processed: 174 average time/residue: 0.2967 time to fit residues: 90.2950 Evaluate side-chains 158 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 126 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1068 GLN Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 1024 THR Chi-restraints excluded: chain B residue 1103 GLN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 903 PHE Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1069 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 265 optimal weight: 3.9990 chunk 279 optimal weight: 0.5980 chunk 255 optimal weight: 0.8980 chunk 272 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 118 optimal weight: 0.0970 chunk 213 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 245 optimal weight: 8.9990 chunk 257 optimal weight: 0.6980 chunk 271 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25434 Z= 0.165 Angle : 0.572 10.843 34601 Z= 0.281 Chirality : 0.046 0.602 4158 Planarity : 0.004 0.053 4376 Dihedral : 7.476 85.864 4897 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.37 % Favored : 94.13 % Rotamer: Outliers : 1.35 % Allowed : 15.42 % Favored : 83.23 % 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: -0.65 (0.16), residues: 2998 helix: 1.99 (0.22), residues: 635 sheet: -0.13 (0.20), residues: 661 loop : -1.59 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 64 HIS 0.004 0.001 HIS A1085 PHE 0.026 0.001 PHE B 84 TYR 0.014 0.001 TYR A1064 ARG 0.003 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 133 time to evaluate : 2.997 Fit side-chains REVERT: A 55 PHE cc_start: 0.7159 (m-80) cc_final: 0.6842 (m-80) REVERT: A 883 TRP cc_start: 0.7727 (p90) cc_final: 0.6962 (p90) REVERT: A 998 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8606 (mm) REVERT: B 167 TYR cc_start: 0.6958 (t80) cc_final: 0.6688 (t80) REVERT: B 395 ASP cc_start: 0.7302 (OUTLIER) cc_final: 0.6837 (p0) REVERT: B 529 ASN cc_start: 0.8103 (t0) cc_final: 0.7778 (t0) REVERT: B 875 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8238 (tt) REVERT: C 170 GLN cc_start: 0.7764 (mm110) cc_final: 0.7440 (tp40) REVERT: C 186 LEU cc_start: 0.8386 (tp) cc_final: 0.8039 (pp) outliers start: 36 outliers final: 31 residues processed: 163 average time/residue: 0.2957 time to fit residues: 84.7473 Evaluate side-chains 164 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 130 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 702 VAL Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 1103 GLN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 903 PHE Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 178 optimal weight: 1.9990 chunk 287 optimal weight: 0.9980 chunk 175 optimal weight: 0.0980 chunk 136 optimal weight: 7.9990 chunk 200 optimal weight: 2.9990 chunk 301 optimal weight: 0.9980 chunk 277 optimal weight: 0.2980 chunk 240 optimal weight: 20.0000 chunk 24 optimal weight: 0.9980 chunk 185 optimal weight: 0.0470 chunk 147 optimal weight: 5.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 ASN A 954 GLN B1008 GLN C 916 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 25434 Z= 0.149 Angle : 0.569 11.754 34601 Z= 0.276 Chirality : 0.046 0.592 4158 Planarity : 0.004 0.052 4376 Dihedral : 7.196 71.383 4897 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.24 % Favored : 94.26 % Rotamer: Outliers : 1.39 % Allowed : 15.57 % Favored : 83.04 % 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: -0.60 (0.16), residues: 2998 helix: 2.02 (0.22), residues: 630 sheet: -0.07 (0.20), residues: 666 loop : -1.55 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 64 HIS 0.004 0.000 HIS A1085 PHE 0.025 0.001 PHE B 84 TYR 0.014 0.001 TYR B1064 ARG 0.003 0.000 ARG A 234 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5996 Ramachandran restraints generated. 2998 Oldfield, 0 Emsley, 2998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 140 time to evaluate : 2.711 Fit side-chains REVERT: A 55 PHE cc_start: 0.7123 (m-80) cc_final: 0.6891 (m-80) REVERT: A 883 TRP cc_start: 0.7731 (p90) cc_final: 0.6890 (p90) REVERT: A 998 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8598 (mm) REVERT: B 167 TYR cc_start: 0.6921 (t80) cc_final: 0.6674 (t80) REVERT: B 395 ASP cc_start: 0.7310 (OUTLIER) cc_final: 0.6848 (p0) REVERT: B 529 ASN cc_start: 0.8070 (t0) cc_final: 0.7750 (t0) REVERT: B 875 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8216 (tt) REVERT: C 186 LEU cc_start: 0.8398 (tp) cc_final: 0.8059 (pp) outliers start: 37 outliers final: 33 residues processed: 171 average time/residue: 0.3006 time to fit residues: 89.4648 Evaluate side-chains 165 residues out of total 2659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 129 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 395 ASP Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 583 ASP Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 709 ILE Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 1103 GLN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 903 PHE Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 190 optimal weight: 0.6980 chunk 256 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 221 optimal weight: 1.9990 chunk 35 optimal weight: 30.0000 chunk 66 optimal weight: 0.7980 chunk 240 optimal weight: 20.0000 chunk 100 optimal weight: 0.2980 chunk 247 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 44 optimal weight: 40.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN B 910 GLN C 916 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.188355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.127113 restraints weight = 40767.213| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 4.08 r_work: 0.3716 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25434 Z= 0.176 Angle : 0.571 10.996 34601 Z= 0.280 Chirality : 0.046 0.595 4158 Planarity : 0.004 0.052 4376 Dihedral : 6.964 62.295 4897 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.37 % Favored : 94.16 % Rotamer: Outliers : 1.35 % Allowed : 15.76 % Favored : 82.89 % 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: -0.60 (0.16), residues: 2998 helix: 2.01 (0.22), residues: 631 sheet: -0.07 (0.20), residues: 664 loop : -1.56 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 64 HIS 0.004 0.001 HIS A1085 PHE 0.026 0.001 PHE B 84 TYR 0.014 0.001 TYR A1064 ARG 0.004 0.000 ARG B 325 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4394.82 seconds wall clock time: 82 minutes 14.41 seconds (4934.41 seconds total)