Starting phenix.real_space_refine on Thu Mar 21 14:05:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtp_34261/03_2024/8gtp_34261.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtp_34261/03_2024/8gtp_34261.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtp_34261/03_2024/8gtp_34261.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtp_34261/03_2024/8gtp_34261.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtp_34261/03_2024/8gtp_34261.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtp_34261/03_2024/8gtp_34261.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.107 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 132 5.16 5 C 19257 2.51 5 N 4959 2.21 5 O 5901 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B ASP 985": "OD1" <-> "OD2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H GLU 81": "OE1" <-> "OE2" Residue "L GLU 84": "OE1" <-> "OE2" Residue "I GLU 10": "OE1" <-> "OE2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I GLU 81": "OE1" <-> "OE2" Residue "M GLU 84": "OE1" <-> "OE2" Residue "J GLU 10": "OE1" <-> "OE2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J GLU 81": "OE1" <-> "OE2" Residue "N GLU 84": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30249 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8043 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 8 Chain: "B" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8043 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 8 Chain: "C" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8043 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 8 Chain: "H" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 902 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 816 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "I" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 902 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "M" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 816 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Chain: "J" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 902 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "N" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 816 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} 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: "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: "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: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 16.21, per 1000 atoms: 0.54 Number of scatterers: 30249 At special positions: 0 Unit cell: (134.625, 178.782, 224.016, 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 132 16.00 O 5901 8.00 N 4959 7.00 C 19257 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.08 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.87 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.20 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=1.99 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.50 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.26 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=1.97 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.17 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.10 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.08 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.66 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.02 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=1.80 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=1.99 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.51 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.26 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=1.97 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.17 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.10 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.08 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.10 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.02 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=1.89 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=1.98 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.74 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.26 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=1.97 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.17 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.10 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.17 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 89 " distance=2.17 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 95 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 89 " distance=2.17 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 A1410 " - " NAG A1411 " " NAG B1410 " - " NAG B1411 " " NAG C1410 " - " NAG C1411 " " 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 K 1 " - " NAG K 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-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " ASN A 709 " " NAG A1410 " - " ASN A1074 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG B1409 " - " ASN B 709 " " NAG B1410 " - " ASN B1074 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG C1409 " - " ASN C 709 " " NAG C1410 " - " ASN C1074 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG O 1 " - " ASN A1134 " " NAG P 1 " - " ASN B 331 " " NAG Q 1 " - " ASN B 343 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 331 " " NAG W 1 " - " ASN C 343 " " NAG X 1 " - " ASN C 717 " " NAG Y 1 " - " ASN C 801 " " NAG Z 1 " - " ASN C1098 " " NAG a 1 " - " ASN C1134 " Time building additional restraints: 11.71 Conformation dependent library (CDL) restraints added in 6.7 seconds 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6984 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 61 sheets defined 18.8% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.91 Creating SS restraints... Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 4.352A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.918A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.653A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 754 removed outlier: 4.087A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.986A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 removed outlier: 3.589A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.514A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.577A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.652A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.590A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 4.080A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.757A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.324A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.953A pdb=" N GLU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.831A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.919A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.654A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 4.089A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.986A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 removed outlier: 3.590A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.514A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.577A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.651A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.591A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 4.078A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.757A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1033 removed outlier: 4.288A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.719A pdb=" N GLU C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 342 removed outlier: 4.351A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.919A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.654A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 754 removed outlier: 4.088A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.985A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 removed outlier: 3.591A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.515A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.577A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.651A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.592A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 4.078A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.757A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.322A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.682A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N HIS H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.507A pdb=" N ARG H 64 " --> pdb=" O GLN H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.682A pdb=" N SER I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N HIS I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 61 through 64 removed outlier: 3.506A pdb=" N ARG I 64 " --> pdb=" O GLN I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.683A pdb=" N SER J 31 " --> pdb=" O THR J 28 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N HIS J 32 " --> pdb=" O PHE J 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 28 through 32' Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.506A pdb=" N ARG J 64 " --> pdb=" O GLN J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.701A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.815A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN C 542 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.012A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 310 through 318 removed outlier: 4.554A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER A 596 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 611 " --> pdb=" O SER A 596 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.547A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.576A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.694A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 538 through 543 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.956A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.868A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.151A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.151A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.499A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.666A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.945A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.701A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.011A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN B 164 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 310 through 314 removed outlier: 4.079A pdb=" N SER B 596 " --> pdb=" O LEU B 611 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 611 " --> pdb=" O SER B 596 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 327 through 328 removed outlier: 5.615A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.546A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.695A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.024A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.748A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.150A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.150A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.499A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.944A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.701A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.011A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.502A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.502A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.632A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER C 596 " --> pdb=" O LEU C 611 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU C 611 " --> pdb=" O SER C 596 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.546A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.694A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.820A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.151A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.151A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.498A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.945A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.555A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.360A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 9 through 11 removed outlier: 3.696A pdb=" N VAL L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 9 through 11 Processing sheet with id=AF6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AF7, first strand: chain 'I' and resid 3 through 5 removed outlier: 3.555A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.360A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE I 34 " --> pdb=" O ILE I 50 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 9 through 11 removed outlier: 3.696A pdb=" N VAL M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLN M 38 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU M 47 " --> pdb=" O GLN M 38 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 9 through 11 Processing sheet with id=AG2, first strand: chain 'M' and resid 17 through 23 Processing sheet with id=AG3, first strand: chain 'J' and resid 3 through 5 removed outlier: 3.555A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 57 through 59 removed outlier: 6.360A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE J 34 " --> pdb=" O ILE J 50 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 9 through 11 removed outlier: 3.696A pdb=" N VAL N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLN N 38 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU N 47 " --> pdb=" O GLN N 38 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 9 through 11 Processing sheet with id=AG7, first strand: chain 'N' and resid 17 through 23 1103 hydrogen bonds defined for protein. 2958 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: 14.92 Time building geometry restraints manager: 12.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5136 1.32 - 1.44: 8634 1.44 - 1.57: 17021 1.57 - 1.69: 1 1.69 - 1.81: 171 Bond restraints: 30963 Sorted by residual: bond pdb=" N PRO B 561 " pdb=" CD PRO B 561 " ideal model delta sigma weight residual 1.473 1.539 -0.066 1.40e-02 5.10e+03 2.22e+01 bond pdb=" C PHE C 329 " pdb=" N PRO C 330 " ideal model delta sigma weight residual 1.329 1.388 -0.058 1.25e-02 6.40e+03 2.17e+01 bond pdb=" N PRO C 561 " pdb=" CD PRO C 561 " ideal model delta sigma weight residual 1.473 1.538 -0.065 1.40e-02 5.10e+03 2.17e+01 bond pdb=" C ILE C 664 " pdb=" N PRO C 665 " ideal model delta sigma weight residual 1.331 1.387 -0.055 1.20e-02 6.94e+03 2.14e+01 bond pdb=" C ILE A 664 " pdb=" N PRO A 665 " ideal model delta sigma weight residual 1.331 1.386 -0.055 1.20e-02 6.94e+03 2.11e+01 ... (remaining 30958 not shown) Histogram of bond angle deviations from ideal: 98.17 - 106.28: 1002 106.28 - 114.38: 17943 114.38 - 122.49: 18343 122.49 - 130.60: 4746 130.60 - 138.70: 110 Bond angle restraints: 42144 Sorted by residual: angle pdb=" N LYS A 310 " pdb=" CA LYS A 310 " pdb=" C LYS A 310 " ideal model delta sigma weight residual 109.15 120.36 -11.21 1.44e+00 4.82e-01 6.06e+01 angle pdb=" N PHE A 559 " pdb=" CA PHE A 559 " pdb=" C PHE A 559 " ideal model delta sigma weight residual 110.32 98.17 12.15 1.59e+00 3.96e-01 5.84e+01 angle pdb=" N PHE C 338 " pdb=" CA PHE C 338 " pdb=" C PHE C 338 " ideal model delta sigma weight residual 111.40 102.37 9.03 1.22e+00 6.72e-01 5.48e+01 angle pdb=" N PHE A 338 " pdb=" CA PHE A 338 " pdb=" C PHE A 338 " ideal model delta sigma weight residual 111.40 102.46 8.94 1.22e+00 6.72e-01 5.37e+01 angle pdb=" N LEU A 560 " pdb=" CA LEU A 560 " pdb=" C LEU A 560 " ideal model delta sigma weight residual 110.40 100.89 9.51 1.31e+00 5.83e-01 5.28e+01 ... (remaining 42139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 17456 17.92 - 35.84: 1337 35.84 - 53.76: 337 53.76 - 71.68: 75 71.68 - 89.60: 37 Dihedral angle restraints: 19242 sinusoidal: 8349 harmonic: 10893 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual 93.00 14.84 78.16 1 1.00e+01 1.00e-02 7.63e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual 93.00 170.54 -77.54 1 1.00e+01 1.00e-02 7.53e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual 93.00 20.28 72.72 1 1.00e+01 1.00e-02 6.75e+01 ... (remaining 19239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.296: 4896 0.296 - 0.592: 11 0.592 - 0.888: 4 0.888 - 1.183: 2 1.183 - 1.479: 1 Chirality restraints: 4914 Sorted by residual: chirality pdb=" C1 NAG A1411 " pdb=" O4 NAG A1410 " pdb=" C2 NAG A1411 " pdb=" O5 NAG A1411 " both_signs ideal model delta sigma weight residual False -2.40 -3.09 0.69 2.00e-02 2.50e+03 1.19e+03 chirality pdb=" C1 NAG C1411 " pdb=" O4 NAG C1410 " pdb=" C2 NAG C1411 " pdb=" O5 NAG C1411 " both_signs ideal model delta sigma weight residual False -2.40 -3.09 0.69 2.00e-02 2.50e+03 1.18e+03 chirality pdb=" C1 NAG B1411 " pdb=" O4 NAG B1410 " pdb=" C2 NAG B1411 " pdb=" O5 NAG B1411 " both_signs ideal model delta sigma weight residual False -2.40 -3.09 0.69 2.00e-02 2.50e+03 1.17e+03 ... (remaining 4911 not shown) Planarity restraints: 5406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.099 2.00e-02 2.50e+03 4.03e-01 2.03e+03 pdb=" CG ASN A 331 " -0.118 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.235 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.703 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.488 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " 0.104 2.00e-02 2.50e+03 1.25e-01 1.94e+02 pdb=" CG ASN C 331 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.213 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " 0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.051 2.00e-02 2.50e+03 9.28e-02 1.08e+02 pdb=" CG ASN B 331 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " 0.037 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.167 2.00e-02 2.50e+03 pdb=" C1 NAG P 1 " 0.103 2.00e-02 2.50e+03 ... (remaining 5403 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 250 2.51 - 3.11: 21951 3.11 - 3.70: 42673 3.70 - 4.30: 62688 4.30 - 4.90: 104496 Nonbonded interactions: 232058 Sorted by model distance: nonbonded pdb=" O SER B 530 " pdb=" OG1 THR B 531 " model vdw 1.912 2.440 nonbonded pdb=" O ASN B 603 " pdb=" OG1 THR B 604 " model vdw 1.915 2.440 nonbonded pdb=" O ALA A 522 " pdb=" OG1 THR A 523 " model vdw 1.972 2.440 nonbonded pdb=" O ILE B 332 " pdb=" CG2 THR B 333 " model vdw 1.978 3.460 nonbonded pdb=" O ASN B 856 " pdb=" ND2 ASN B 856 " model vdw 1.986 2.520 ... (remaining 232053 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'K' 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' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 2.150 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: 0.040 Extract box with map and model: 7.590 Check model and map are aligned: 0.480 Set scattering table: 0.300 Process input model: 85.350 Find NCS groups from input model: 2.000 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.067 30963 Z= 0.598 Angle : 1.089 13.704 42144 Z= 0.641 Chirality : 0.078 1.479 4914 Planarity : 0.007 0.119 5358 Dihedral : 13.836 89.599 12123 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 2.73 % Allowed : 7.81 % Favored : 89.47 % Rotamer: Outliers : 4.36 % Allowed : 9.05 % Favored : 86.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.12), residues: 3702 helix: -1.30 (0.17), residues: 662 sheet: -1.48 (0.15), residues: 987 loop : -2.80 (0.11), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 36 HIS 0.005 0.001 HIS C 505 PHE 0.025 0.002 PHE A 400 TYR 0.024 0.002 TYR B 453 ARG 0.004 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 586 time to evaluate : 2.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7603 (tt0) REVERT: A 382 VAL cc_start: 0.9216 (OUTLIER) cc_final: 0.9005 (m) REVERT: A 580 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8385 (pt0) REVERT: A 675 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6387 (mp10) REVERT: A 856 ASN cc_start: 0.8591 (OUTLIER) cc_final: 0.8383 (p0) REVERT: C 321 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7366 (mm110) REVERT: C 324 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6556 (pm20) REVERT: C 529 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7296 (tptp) REVERT: C 690 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7556 (mm110) REVERT: H 22 CYS cc_start: 0.0196 (t) cc_final: -0.0899 (t) REVERT: H 80 MET cc_start: 0.3888 (tmm) cc_final: 0.2972 (tmm) REVERT: L 92 TRP cc_start: 0.6705 (t-100) cc_final: 0.5953 (t-100) outliers start: 141 outliers final: 54 residues processed: 708 average time/residue: 0.4191 time to fit residues: 462.6073 Evaluate side-chains 358 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 295 time to evaluate : 2.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 328 ARG Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 561 PRO Chi-restraints excluded: chain B residue 606 ASN Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 690 GLN Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain L residue 16 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 7.9990 chunk 284 optimal weight: 2.9990 chunk 157 optimal weight: 0.0870 chunk 97 optimal weight: 0.9990 chunk 191 optimal weight: 0.6980 chunk 151 optimal weight: 5.9990 chunk 293 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 178 optimal weight: 1.9990 chunk 218 optimal weight: 7.9990 chunk 340 optimal weight: 30.0000 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 121 ASN A 164 ASN A 173 GLN A 334 ASN A 360 ASN A 422 ASN A 450 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 GLN A 690 GLN A 907 ASN A1005 GLN B 121 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN B 173 GLN B 414 GLN B 422 ASN B 450 ASN B 606 ASN B 690 GLN B 779 GLN B 914 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 173 GLN C 207 HIS C 422 ASN C 450 ASN C 607 GLN C 644 GLN C 955 ASN C1002 GLN C1005 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 30963 Z= 0.220 Angle : 0.728 16.148 42144 Z= 0.366 Chirality : 0.052 1.193 4914 Planarity : 0.006 0.092 5358 Dihedral : 7.804 83.569 5622 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.19 % Favored : 92.46 % Rotamer: Outliers : 3.71 % Allowed : 14.21 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.13), residues: 3702 helix: 0.28 (0.20), residues: 666 sheet: -0.86 (0.16), residues: 947 loop : -2.39 (0.12), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 36 HIS 0.010 0.001 HIS A 519 PHE 0.020 0.001 PHE B 371 TYR 0.020 0.001 TYR C 170 ARG 0.009 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 324 time to evaluate : 3.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ILE cc_start: 0.7969 (mp) cc_final: 0.7645 (mt) REVERT: A 386 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.7683 (mtpm) REVERT: A 516 GLU cc_start: 0.7063 (tm-30) cc_final: 0.6788 (tm-30) REVERT: A 675 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.6460 (mp10) REVERT: A 855 PHE cc_start: 0.7678 (m-80) cc_final: 0.7445 (m-80) REVERT: B 523 THR cc_start: 0.3251 (OUTLIER) cc_final: 0.2941 (m) REVERT: B 854 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.6088 (tptt) REVERT: C 321 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7367 (mm-40) REVERT: C 523 THR cc_start: 0.4435 (OUTLIER) cc_final: 0.4217 (t) REVERT: C 529 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7587 (mmmt) REVERT: C 693 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8292 (pp) REVERT: H 22 CYS cc_start: -0.0059 (t) cc_final: -0.0479 (t) REVERT: L 92 TRP cc_start: 0.6308 (t-100) cc_final: 0.5827 (t-100) REVERT: J 48 MET cc_start: 0.1647 (mpp) cc_final: 0.1093 (mpp) outliers start: 120 outliers final: 53 residues processed: 417 average time/residue: 0.3902 time to fit residues: 266.9926 Evaluate side-chains 309 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 248 time to evaluate : 3.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 40 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 107 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 189 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 283 optimal weight: 3.9990 chunk 231 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 341 optimal weight: 50.0000 chunk 368 optimal weight: 30.0000 chunk 303 optimal weight: 2.9990 chunk 338 optimal weight: 50.0000 chunk 116 optimal weight: 7.9990 chunk 273 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A 751 ASN A 856 ASN A 907 ASN A 914 ASN B 121 ASN B 644 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C 955 ASN C1002 GLN L 16 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 30963 Z= 0.414 Angle : 0.756 13.520 42144 Z= 0.382 Chirality : 0.052 0.678 4914 Planarity : 0.006 0.071 5358 Dihedral : 6.872 57.999 5544 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.43 % Favored : 92.30 % Rotamer: Outliers : 4.57 % Allowed : 14.43 % Favored : 81.00 % 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: -1.84 (0.13), residues: 3702 helix: 0.56 (0.20), residues: 646 sheet: -0.63 (0.15), residues: 1001 loop : -2.21 (0.12), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP H 36 HIS 0.011 0.002 HIS A1064 PHE 0.030 0.002 PHE A 86 TYR 0.023 0.002 TYR A 380 ARG 0.012 0.001 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 258 time to evaluate : 3.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 THR cc_start: 0.7897 (OUTLIER) cc_final: 0.7652 (p) REVERT: A 515 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.7890 (p90) REVERT: A 516 GLU cc_start: 0.7231 (tm-30) cc_final: 0.6795 (tm-30) REVERT: A 675 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.6724 (mp10) REVERT: B 523 THR cc_start: 0.3246 (OUTLIER) cc_final: 0.2892 (m) REVERT: B 725 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7592 (tp30) REVERT: C 324 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.5713 (pp20) REVERT: C 529 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7745 (mmmt) REVERT: C 1002 GLN cc_start: 0.7567 (tt0) cc_final: 0.7342 (tt0) REVERT: L 92 TRP cc_start: 0.6651 (t-100) cc_final: 0.5830 (t-100) REVERT: J 48 MET cc_start: 0.1948 (mpp) cc_final: 0.1370 (mpp) REVERT: N 23 SER cc_start: 0.4809 (m) cc_final: 0.4467 (p) outliers start: 148 outliers final: 88 residues processed: 377 average time/residue: 0.3621 time to fit residues: 230.4118 Evaluate side-chains 312 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 217 time to evaluate : 2.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain I residue 2 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 337 optimal weight: 0.3980 chunk 256 optimal weight: 5.9990 chunk 177 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 229 optimal weight: 0.9990 chunk 342 optimal weight: 8.9990 chunk 362 optimal weight: 9.9990 chunk 178 optimal weight: 0.7980 chunk 324 optimal weight: 30.0000 chunk 97 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 641 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 30963 Z= 0.181 Angle : 0.631 12.474 42144 Z= 0.313 Chirality : 0.047 0.585 4914 Planarity : 0.004 0.049 5358 Dihedral : 6.261 59.743 5531 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.24 % Favored : 93.60 % Rotamer: Outliers : 2.93 % Allowed : 16.43 % Favored : 80.63 % 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: -1.38 (0.13), residues: 3702 helix: 1.05 (0.21), residues: 646 sheet: -0.35 (0.16), residues: 1000 loop : -1.94 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP H 36 HIS 0.005 0.001 HIS A 519 PHE 0.016 0.001 PHE H 63 TYR 0.016 0.001 TYR A 365 ARG 0.005 0.000 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 255 time to evaluate : 3.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.7299 (tp30) cc_final: 0.7094 (tp30) REVERT: A 323 THR cc_start: 0.7803 (OUTLIER) cc_final: 0.7563 (p) REVERT: A 386 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.7896 (mtpm) REVERT: A 515 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.7714 (p90) REVERT: A 516 GLU cc_start: 0.7091 (tm-30) cc_final: 0.6413 (tm-30) REVERT: A 675 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.6780 (mp10) REVERT: B 523 THR cc_start: 0.3202 (OUTLIER) cc_final: 0.2789 (m) REVERT: B 854 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.6099 (tptt) REVERT: B 1113 GLN cc_start: 0.8177 (mp10) cc_final: 0.7627 (mt0) REVERT: C 324 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.5751 (pp20) REVERT: C 529 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7785 (mmmt) REVERT: C 1002 GLN cc_start: 0.7525 (tt0) cc_final: 0.7295 (tt0) REVERT: H 93 TYR cc_start: 0.6762 (m-10) cc_final: 0.6498 (m-10) REVERT: L 92 TRP cc_start: 0.6709 (t-100) cc_final: 0.6215 (t-100) REVERT: J 48 MET cc_start: 0.2046 (mpp) cc_final: 0.1536 (mpp) REVERT: N 23 SER cc_start: 0.4789 (m) cc_final: 0.4448 (p) outliers start: 95 outliers final: 59 residues processed: 332 average time/residue: 0.3767 time to fit residues: 207.9345 Evaluate side-chains 291 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 224 time to evaluate : 2.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain I residue 2 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 301 optimal weight: 0.6980 chunk 205 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 269 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 309 optimal weight: 30.0000 chunk 250 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 185 optimal weight: 4.9990 chunk 325 optimal weight: 50.0000 chunk 91 optimal weight: 2.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 196 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 30963 Z= 0.336 Angle : 0.674 11.404 42144 Z= 0.336 Chirality : 0.048 0.535 4914 Planarity : 0.005 0.052 5358 Dihedral : 6.001 55.529 5522 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.81 % Favored : 92.06 % Rotamer: Outliers : 3.61 % Allowed : 15.91 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.13), residues: 3702 helix: 0.95 (0.21), residues: 649 sheet: -0.29 (0.16), residues: 1038 loop : -1.84 (0.13), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP L 36 HIS 0.008 0.001 HIS A1064 PHE 0.024 0.002 PHE A 86 TYR 0.018 0.001 TYR B 655 ARG 0.006 0.000 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 231 time to evaluate : 3.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5702 (tpp) cc_final: 0.5130 (tpt) REVERT: A 298 GLU cc_start: 0.7384 (tp30) cc_final: 0.7145 (tp30) REVERT: A 515 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.8083 (p90) REVERT: A 675 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.6752 (mp10) REVERT: B 375 PHE cc_start: 0.2000 (OUTLIER) cc_final: 0.0408 (t80) REVERT: B 854 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.6076 (tptt) REVERT: B 1113 GLN cc_start: 0.8035 (mp10) cc_final: 0.7442 (mt0) REVERT: C 324 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.5914 (pp20) REVERT: C 353 TRP cc_start: 0.5531 (p-90) cc_final: 0.5300 (p-90) REVERT: C 529 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7808 (mmmt) REVERT: C 1002 GLN cc_start: 0.7696 (tt0) cc_final: 0.7492 (tt0) REVERT: H 23 ARG cc_start: 0.6410 (mmm160) cc_final: 0.6108 (tpt-90) REVERT: H 33 PHE cc_start: 0.6894 (m-80) cc_final: 0.6561 (m-10) REVERT: H 69 MET cc_start: 0.6670 (ttm) cc_final: 0.6383 (ttt) REVERT: H 94 TYR cc_start: 0.5291 (OUTLIER) cc_final: 0.4509 (m-80) REVERT: H 103 TRP cc_start: 0.6868 (p90) cc_final: 0.6566 (p90) REVERT: L 92 TRP cc_start: 0.7013 (t-100) cc_final: 0.6407 (t-100) REVERT: L 101 TRP cc_start: 0.6171 (t-100) cc_final: 0.5877 (t-100) REVERT: J 48 MET cc_start: 0.2069 (mpp) cc_final: 0.1627 (mpp) REVERT: N 23 SER cc_start: 0.4813 (m) cc_final: 0.4449 (p) outliers start: 117 outliers final: 77 residues processed: 325 average time/residue: 0.3739 time to fit residues: 204.2437 Evaluate side-chains 301 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 217 time to evaluate : 3.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain J residue 17 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 121 optimal weight: 10.0000 chunk 326 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 212 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 362 optimal weight: 30.0000 chunk 301 optimal weight: 0.7980 chunk 167 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 chunk 190 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C1002 GLN C1010 GLN J 52 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 30963 Z= 0.238 Angle : 0.622 10.719 42144 Z= 0.307 Chirality : 0.046 0.500 4914 Planarity : 0.004 0.066 5358 Dihedral : 5.746 56.201 5519 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.51 % Favored : 93.35 % Rotamer: Outliers : 3.00 % Allowed : 16.99 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.13), residues: 3702 helix: 1.13 (0.21), residues: 647 sheet: -0.13 (0.16), residues: 1015 loop : -1.75 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP L 36 HIS 0.004 0.001 HIS A1064 PHE 0.019 0.001 PHE A 86 TYR 0.021 0.001 TYR H 93 ARG 0.004 0.000 ARG M 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 232 time to evaluate : 3.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PRO cc_start: 0.7064 (Cg_endo) cc_final: 0.6817 (Cg_exo) REVERT: A 177 MET cc_start: 0.5651 (tpp) cc_final: 0.5037 (tpt) REVERT: A 298 GLU cc_start: 0.7371 (tp30) cc_final: 0.7111 (tp30) REVERT: A 357 ARG cc_start: 0.7350 (ttm-80) cc_final: 0.7028 (ttm-80) REVERT: A 386 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.7896 (mtpm) REVERT: A 490 PHE cc_start: 0.6575 (t80) cc_final: 0.6331 (t80) REVERT: A 515 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.7922 (p90) REVERT: A 675 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.6774 (mp10) REVERT: B 854 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.5977 (tptt) REVERT: B 1113 GLN cc_start: 0.7986 (mp10) cc_final: 0.7460 (mt0) REVERT: C 324 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.5855 (pp20) REVERT: C 353 TRP cc_start: 0.5539 (p-90) cc_final: 0.5285 (p-90) REVERT: C 529 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7841 (mmmt) REVERT: H 69 MET cc_start: 0.6538 (ttm) cc_final: 0.6310 (ttt) REVERT: H 94 TYR cc_start: 0.5460 (OUTLIER) cc_final: 0.4560 (m-80) REVERT: H 103 TRP cc_start: 0.6884 (p90) cc_final: 0.6670 (p90) REVERT: L 92 TRP cc_start: 0.7087 (t-100) cc_final: 0.6502 (t-100) REVERT: L 101 TRP cc_start: 0.6141 (t-100) cc_final: 0.5936 (t-100) REVERT: J 48 MET cc_start: 0.2097 (mpp) cc_final: 0.1645 (mpp) REVERT: N 23 SER cc_start: 0.4803 (m) cc_final: 0.4444 (p) outliers start: 97 outliers final: 70 residues processed: 312 average time/residue: 0.4140 time to fit residues: 216.7053 Evaluate side-chains 296 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 219 time to evaluate : 3.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 17 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 349 optimal weight: 0.8980 chunk 40 optimal weight: 0.4980 chunk 206 optimal weight: 10.0000 chunk 264 optimal weight: 3.9990 chunk 205 optimal weight: 0.0040 chunk 305 optimal weight: 2.9990 chunk 202 optimal weight: 0.8980 chunk 361 optimal weight: 20.0000 chunk 226 optimal weight: 0.9990 chunk 220 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 30963 Z= 0.157 Angle : 0.581 12.581 42144 Z= 0.286 Chirality : 0.045 0.476 4914 Planarity : 0.004 0.062 5358 Dihedral : 5.285 57.866 5515 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.67 % Favored : 93.19 % Rotamer: Outliers : 2.63 % Allowed : 17.64 % Favored : 79.73 % 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: -0.83 (0.14), residues: 3702 helix: 1.43 (0.21), residues: 649 sheet: 0.08 (0.16), residues: 999 loop : -1.60 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP L 36 HIS 0.003 0.000 HIS A 519 PHE 0.018 0.001 PHE A 86 TYR 0.010 0.001 TYR C1067 ARG 0.018 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 231 time to evaluate : 3.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.4998 (OUTLIER) cc_final: 0.4476 (t0) REVERT: A 177 MET cc_start: 0.5538 (tpp) cc_final: 0.4912 (tpt) REVERT: A 515 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.7880 (p90) REVERT: A 675 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.6915 (mp10) REVERT: B 375 PHE cc_start: 0.2031 (OUTLIER) cc_final: 0.0395 (t80) REVERT: B 854 LYS cc_start: 0.7441 (OUTLIER) cc_final: 0.5887 (tptt) REVERT: B 960 ASN cc_start: 0.7863 (t0) cc_final: 0.7619 (t0) REVERT: B 1113 GLN cc_start: 0.7934 (mp10) cc_final: 0.7680 (mt0) REVERT: C 226 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.8010 (mm) REVERT: C 324 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.5836 (pp20) REVERT: C 353 TRP cc_start: 0.5509 (p-90) cc_final: 0.5243 (p-90) REVERT: C 529 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7871 (mmmt) REVERT: H 69 MET cc_start: 0.6747 (ttm) cc_final: 0.6504 (ttt) REVERT: H 94 TYR cc_start: 0.5337 (OUTLIER) cc_final: 0.4443 (m-80) REVERT: H 103 TRP cc_start: 0.6982 (p90) cc_final: 0.6765 (p90) REVERT: L 92 TRP cc_start: 0.6944 (t-100) cc_final: 0.6419 (t-100) REVERT: J 48 MET cc_start: 0.2079 (mpp) cc_final: 0.1652 (mpp) REVERT: N 23 SER cc_start: 0.4793 (m) cc_final: 0.4446 (p) outliers start: 85 outliers final: 60 residues processed: 300 average time/residue: 0.3835 time to fit residues: 191.5011 Evaluate side-chains 288 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 219 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 118 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 223 optimal weight: 9.9990 chunk 144 optimal weight: 0.0970 chunk 215 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 70 optimal weight: 0.0370 chunk 229 optimal weight: 2.9990 chunk 246 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 284 optimal weight: 3.9990 overall best weight: 1.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 30963 Z= 0.251 Angle : 0.608 10.278 42144 Z= 0.302 Chirality : 0.046 0.459 4914 Planarity : 0.004 0.073 5358 Dihedral : 5.359 56.963 5510 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.02 % Favored : 92.87 % Rotamer: Outliers : 3.06 % Allowed : 17.18 % Favored : 79.77 % 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: -0.81 (0.14), residues: 3702 helix: 1.34 (0.21), residues: 652 sheet: 0.13 (0.16), residues: 1020 loop : -1.59 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 36 HIS 0.005 0.001 HIS A1064 PHE 0.018 0.001 PHE A 86 TYR 0.020 0.001 TYR A 453 ARG 0.009 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 218 time to evaluate : 3.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.4949 (OUTLIER) cc_final: 0.4473 (t0) REVERT: A 177 MET cc_start: 0.5276 (tpp) cc_final: 0.4844 (tpt) REVERT: A 357 ARG cc_start: 0.7511 (ttm-80) cc_final: 0.7258 (ttm-80) REVERT: A 515 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.8108 (p90) REVERT: A 675 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.6882 (mp10) REVERT: B 375 PHE cc_start: 0.1924 (OUTLIER) cc_final: 0.0317 (t80) REVERT: B 854 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.5922 (tptt) REVERT: B 960 ASN cc_start: 0.7887 (t0) cc_final: 0.7634 (t0) REVERT: B 1113 GLN cc_start: 0.7961 (mp10) cc_final: 0.7703 (mt0) REVERT: C 324 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.5866 (pp20) REVERT: C 353 TRP cc_start: 0.5568 (p-90) cc_final: 0.5284 (p-90) REVERT: C 529 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7900 (mmmt) REVERT: H 69 MET cc_start: 0.6626 (ttm) cc_final: 0.6396 (ttt) REVERT: H 94 TYR cc_start: 0.5488 (OUTLIER) cc_final: 0.4557 (m-80) REVERT: J 48 MET cc_start: 0.2272 (mpp) cc_final: 0.1764 (mpp) REVERT: N 23 SER cc_start: 0.4806 (m) cc_final: 0.4459 (p) outliers start: 99 outliers final: 79 residues processed: 296 average time/residue: 0.3817 time to fit residues: 192.1426 Evaluate side-chains 301 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 214 time to evaluate : 3.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain N residue 25 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 328 optimal weight: 20.0000 chunk 346 optimal weight: 0.0370 chunk 315 optimal weight: 5.9990 chunk 336 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 264 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 304 optimal weight: 6.9990 chunk 318 optimal weight: 8.9990 chunk 335 optimal weight: 4.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 173 GLN C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 30963 Z= 0.344 Angle : 0.648 12.309 42144 Z= 0.322 Chirality : 0.048 0.487 4914 Planarity : 0.004 0.067 5358 Dihedral : 5.608 56.219 5510 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.46 % Favored : 92.44 % Rotamer: Outliers : 3.37 % Allowed : 16.90 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.14), residues: 3702 helix: 1.11 (0.21), residues: 646 sheet: 0.02 (0.16), residues: 1027 loop : -1.60 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP L 92 HIS 0.008 0.001 HIS A1064 PHE 0.022 0.002 PHE A 86 TYR 0.016 0.001 TYR A 453 ARG 0.009 0.000 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 211 time to evaluate : 3.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.6408 (m) cc_final: 0.6089 (m) REVERT: A 137 ASN cc_start: 0.5021 (OUTLIER) cc_final: 0.4539 (t0) REVERT: A 177 MET cc_start: 0.5276 (tpp) cc_final: 0.4838 (tpt) REVERT: A 515 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.8353 (p90) REVERT: A 675 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.6823 (mp10) REVERT: B 375 PHE cc_start: 0.1870 (OUTLIER) cc_final: 0.0304 (t80) REVERT: B 517 LEU cc_start: 0.4041 (OUTLIER) cc_final: 0.3797 (mt) REVERT: B 854 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.5932 (tptt) REVERT: B 960 ASN cc_start: 0.7903 (t0) cc_final: 0.7648 (t0) REVERT: B 1113 GLN cc_start: 0.8001 (mp10) cc_final: 0.7679 (mt0) REVERT: C 324 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.5854 (pp20) REVERT: C 353 TRP cc_start: 0.5732 (p-90) cc_final: 0.5495 (p-90) REVERT: C 529 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7904 (mmmt) REVERT: H 94 TYR cc_start: 0.5467 (OUTLIER) cc_final: 0.4255 (m-80) REVERT: L 101 TRP cc_start: 0.6534 (t-100) cc_final: 0.6215 (m100) REVERT: I 69 MET cc_start: -0.1102 (tpt) cc_final: -0.2670 (mtt) REVERT: J 48 MET cc_start: 0.2220 (mpp) cc_final: 0.1693 (mpp) REVERT: N 23 SER cc_start: 0.4832 (m) cc_final: 0.4488 (p) outliers start: 109 outliers final: 85 residues processed: 299 average time/residue: 0.3827 time to fit residues: 193.3109 Evaluate side-chains 297 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 203 time to evaluate : 3.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 93 ASP Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain N residue 25 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 221 optimal weight: 0.1980 chunk 356 optimal weight: 10.0000 chunk 217 optimal weight: 5.9990 chunk 168 optimal weight: 0.8980 chunk 247 optimal weight: 30.0000 chunk 373 optimal weight: 20.0000 chunk 343 optimal weight: 6.9990 chunk 297 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 229 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.5750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30963 Z= 0.186 Angle : 0.602 11.833 42144 Z= 0.297 Chirality : 0.045 0.462 4914 Planarity : 0.004 0.065 5358 Dihedral : 5.389 59.742 5510 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.54 % Favored : 93.35 % Rotamer: Outliers : 2.66 % Allowed : 17.64 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3702 helix: 1.33 (0.21), residues: 647 sheet: 0.21 (0.16), residues: 1047 loop : -1.61 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP L 92 HIS 0.004 0.001 HIS A1064 PHE 0.017 0.001 PHE C 106 TYR 0.017 0.001 TYR A 453 ARG 0.009 0.000 ARG C 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7404 Ramachandran restraints generated. 3702 Oldfield, 0 Emsley, 3702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 214 time to evaluate : 2.942 Fit side-chains revert: symmetry clash REVERT: A 137 ASN cc_start: 0.5072 (OUTLIER) cc_final: 0.4610 (t0) REVERT: A 177 MET cc_start: 0.5294 (tpp) cc_final: 0.4817 (tpt) REVERT: A 386 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.7897 (mtpm) REVERT: A 515 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.8163 (p90) REVERT: A 675 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.6889 (mp10) REVERT: B 375 PHE cc_start: 0.1756 (OUTLIER) cc_final: 0.0247 (t80) REVERT: B 517 LEU cc_start: 0.3925 (OUTLIER) cc_final: 0.3678 (mt) REVERT: B 854 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.5914 (tptt) REVERT: B 960 ASN cc_start: 0.7883 (t0) cc_final: 0.7642 (t0) REVERT: C 324 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.5779 (pp20) REVERT: C 353 TRP cc_start: 0.5753 (p-90) cc_final: 0.5481 (p-90) REVERT: C 529 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7932 (mmmt) REVERT: H 94 TYR cc_start: 0.5470 (OUTLIER) cc_final: 0.4262 (m-80) REVERT: L 101 TRP cc_start: 0.6515 (t-100) cc_final: 0.6064 (m100) REVERT: I 69 MET cc_start: -0.1040 (tpt) cc_final: -0.2645 (mtt) REVERT: J 48 MET cc_start: 0.2220 (mpp) cc_final: 0.1914 (mpp) REVERT: N 23 SER cc_start: 0.4798 (m) cc_final: 0.4461 (p) outliers start: 86 outliers final: 72 residues processed: 282 average time/residue: 0.3917 time to fit residues: 183.9977 Evaluate side-chains 281 residues out of total 3249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 199 time to evaluate : 2.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 375 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 52 ASN Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 94 TYR Chi-restraints excluded: chain L residue 28 ASN Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 17 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 236 optimal weight: 0.7980 chunk 316 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 274 optimal weight: 0.0470 chunk 43 optimal weight: 0.2980 chunk 82 optimal weight: 3.9990 chunk 297 optimal weight: 0.2980 chunk 124 optimal weight: 6.9990 chunk 305 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 196 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.199179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.123386 restraints weight = 45580.997| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 3.74 r_work: 0.3334 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.5806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30963 Z= 0.171 Angle : 0.584 12.261 42144 Z= 0.288 Chirality : 0.045 0.467 4914 Planarity : 0.004 0.067 5358 Dihedral : 5.200 58.161 5510 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.73 % Favored : 93.17 % Rotamer: Outliers : 2.59 % Allowed : 17.70 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.14), residues: 3702 helix: 1.50 (0.21), residues: 647 sheet: 0.29 (0.16), residues: 1007 loop : -1.51 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP L 36 HIS 0.003 0.000 HIS A1064 PHE 0.015 0.001 PHE C 106 TYR 0.017 0.001 TYR A 453 ARG 0.009 0.000 ARG C 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6620.78 seconds wall clock time: 123 minutes 0.75 seconds (7380.75 seconds total)