Starting phenix.real_space_refine on Sun Feb 25 09:15:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xco_33124/02_2024/7xco_33124.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xco_33124/02_2024/7xco_33124.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xco_33124/02_2024/7xco_33124.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xco_33124/02_2024/7xco_33124.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xco_33124/02_2024/7xco_33124.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xco_33124/02_2024/7xco_33124.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14604 atoms to isotropic. 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 147 5.16 5 C 22734 2.51 5 N 5919 2.21 5 O 7002 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 35802 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 8330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8330 Classifications: {'peptide': 1062} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 59, 'TRANS': 1002} Chain breaks: 7 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Chain: "B" Number of atoms: 8351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8351 Classifications: {'peptide': 1065} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 59, 'TRANS': 1005} Chain breaks: 7 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Chain: "C" Number of atoms: 8330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8330 Classifications: {'peptide': 1062} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 59, 'TRANS': 1002} Chain breaks: 7 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Chain: "H" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1688 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 210} Chain breaks: 1 Chain: "L" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1615 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 200} Chain: "M" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1688 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 210} Chain breaks: 1 Chain: "N" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1615 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 200} Chain: "O" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1688 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 210} Chain breaks: 1 Chain: "P" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1615 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 200} 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 18.47, per 1000 atoms: 0.52 Number of scatterers: 35802 At special positions: 0 Unit cell: (158.79, 209.04, 223.78, 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 147 16.00 O 7002 8.00 N 5919 7.00 C 22734 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.04 Simple disulfide: pdb=" SG CYS M 154 " - pdb=" SG CYS M 210 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 89 " distance=2.03 Simple disulfide: pdb=" SG CYS N 134 " - pdb=" SG CYS N 194 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.04 Simple disulfide: pdb=" SG CYS O 154 " - pdb=" SG CYS O 210 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 89 " distance=2.03 Simple disulfide: pdb=" SG CYS P 134 " - pdb=" SG CYS P 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " NAG-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 331 " " NAG A1308 " - " ASN A 616 " " NAG B1301 " - " ASN B 17 " " NAG B1302 " - " ASN B 61 " " NAG B1303 " - " ASN B 122 " " NAG B1304 " - " ASN B 165 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 234 " " NAG C1301 " - " ASN C 17 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C 234 " " NAG C1306 " - " ASN C 282 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 616 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 282 " " NAG F 1 " - " ASN A 709 " " NAG G 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG Q 1 " - " ASN B 709 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B1074 " " NAG U 1 " - " ASN B1098 " " NAG V 1 " - " ASN B1134 " " NAG W 1 " - " ASN C 717 " " NAG X 1 " - " ASN C 801 " " NAG Y 1 " - " ASN C1074 " " NAG Z 1 " - " ASN C1098 " " NAG a 1 " - " ASN C1134 " " NAG b 1 " - " ASN C 331 " Time building additional restraints: 14.34 Conformation dependent library (CDL) restraints added in 7.2 seconds 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8388 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 74 sheets defined 18.7% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.99 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.127A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.521A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.922A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.746A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 826 Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.087A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.596A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.795A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.724A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.503A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.877A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 640 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 748 through 754 removed outlier: 4.143A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 753 " --> pdb=" O CYS B 749 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 748 through 754' 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 760 through 783 removed outlier: 3.614A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.781A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.075A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.791A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.334A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.915A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.518A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.548A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.629A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.520A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.145A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 938 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.362A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.621A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 170 through 172 No H-bonds generated for 'chain 'H' and resid 170 through 172' Processing helix chain 'H' and resid 199 through 203 removed outlier: 4.182A pdb=" N LEU H 203 " --> pdb=" O SER H 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.536A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.560A pdb=" N LYS L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N HIS L 189 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 91 removed outlier: 3.970A pdb=" N THR M 91 " --> pdb=" O SER M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 170 through 172 No H-bonds generated for 'chain 'M' and resid 170 through 172' Processing helix chain 'M' and resid 199 through 203 removed outlier: 4.123A pdb=" N LEU M 203 " --> pdb=" O SER M 200 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 32 No H-bonds generated for 'chain 'N' and resid 30 through 32' Processing helix chain 'N' and resid 121 through 125 Processing helix chain 'N' and resid 183 through 187 Processing helix chain 'O' and resid 170 through 172 No H-bonds generated for 'chain 'O' and resid 170 through 172' Processing helix chain 'P' and resid 80 through 84 removed outlier: 3.764A pdb=" N PHE P 84 " --> pdb=" O PRO P 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 127 removed outlier: 3.660A pdb=" N SER P 127 " --> pdb=" O GLN P 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 8.299A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.650A 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 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.976A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.796A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.946A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 removed outlier: 5.717A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.688A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.086A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.803A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.658A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.658A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.641A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.735A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 31 removed outlier: 7.997A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.306A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.311A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.058A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.891A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 140 through 142 Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.220A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.783A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.058A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.682A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.682A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.640A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 31 removed outlier: 7.915A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.551A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.755A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 135 through 141 removed outlier: 10.534A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.229A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.988A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ASN C 437 " --> pdb=" O PHE C 374 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N PHE C 374 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 removed outlier: 4.083A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.986A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.680A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.680A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.601A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.518A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AF2, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.792A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 134 through 138 removed outlier: 6.311A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 134 through 138 removed outlier: 6.311A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 165 through 168 Processing sheet with id=AF6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.219A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.219A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR L 97 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 116 through 118 removed outlier: 3.873A pdb=" N ASN L 138 " --> pdb=" O TYR L 173 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 154 through 155 removed outlier: 4.504A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 3 through 5 Processing sheet with id=AG3, first strand: chain 'M' and resid 58 through 59 removed outlier: 6.679A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N TRP M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY M 33 " --> pdb=" O ASP M 99 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ASN M 116 " --> pdb=" O ARG M 98 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'M' and resid 58 through 59 removed outlier: 6.679A pdb=" N TRP M 36 " --> pdb=" O MET M 48 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N TRP M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE M 34 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY M 33 " --> pdb=" O ASP M 99 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'M' and resid 134 through 138 Processing sheet with id=AG6, first strand: chain 'M' and resid 134 through 138 Processing sheet with id=AG7, first strand: chain 'M' and resid 165 through 168 Processing sheet with id=AG8, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AG9, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.298A pdb=" N LEU N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLN N 38 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LEU N 47 " --> pdb=" O GLN N 38 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 116 through 118 removed outlier: 3.913A pdb=" N ASN N 138 " --> pdb=" O TYR N 173 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N TYR N 173 " --> pdb=" O ASN N 138 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'N' and resid 144 through 149 Processing sheet with id=AH3, first strand: chain 'O' and resid 3 through 6 Processing sheet with id=AH4, first strand: chain 'O' and resid 58 through 60 removed outlier: 6.841A pdb=" N TRP O 36 " --> pdb=" O MET O 48 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N TRP O 50 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE O 34 " --> pdb=" O TRP O 50 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY O 33 " --> pdb=" O ASP O 99 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'O' and resid 134 through 138 removed outlier: 6.117A pdb=" N TYR O 190 " --> pdb=" O ASP O 158 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'O' and resid 134 through 138 removed outlier: 6.117A pdb=" N TYR O 190 " --> pdb=" O ASP O 158 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'O' and resid 165 through 168 Processing sheet with id=AH8, first strand: chain 'P' and resid 4 through 7 Processing sheet with id=AH9, first strand: chain 'P' and resid 11 through 13 removed outlier: 3.816A pdb=" N THR P 102 " --> pdb=" O TYR P 87 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N TRP P 36 " --> pdb=" O LEU P 48 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU P 48 " --> pdb=" O TRP P 36 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'P' and resid 116 through 118 removed outlier: 3.735A pdb=" N VAL P 133 " --> pdb=" O PHE P 118 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN P 138 " --> pdb=" O TYR P 173 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR P 173 " --> pdb=" O ASN P 138 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'P' and resid 144 through 149 1497 hydrogen bonds defined for protein. 3999 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: 18.16 Time building geometry restraints manager: 15.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 5894 1.32 - 1.46: 14608 1.46 - 1.61: 15930 1.61 - 1.75: 0 1.75 - 1.89: 183 Bond restraints: 36615 Sorted by residual: bond pdb=" C PRO A 817 " pdb=" O PRO A 817 " ideal model delta sigma weight residual 1.235 1.179 0.056 1.30e-02 5.92e+03 1.85e+01 bond pdb=" C PRO C 817 " pdb=" O PRO C 817 " ideal model delta sigma weight residual 1.237 1.192 0.045 1.29e-02 6.01e+03 1.21e+01 bond pdb=" N ILE C 818 " pdb=" CA ILE C 818 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.23e-02 6.61e+03 1.10e+01 bond pdb=" C PRO B 817 " pdb=" O PRO B 817 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.30e-02 5.92e+03 1.05e+01 bond pdb=" N ILE A 818 " pdb=" CA ILE A 818 " ideal model delta sigma weight residual 1.456 1.498 -0.041 1.30e-02 5.92e+03 1.01e+01 ... (remaining 36610 not shown) Histogram of bond angle deviations from ideal: 96.13 - 103.72: 495 103.72 - 111.30: 15905 111.30 - 118.89: 13461 118.89 - 126.47: 19485 126.47 - 134.06: 467 Bond angle restraints: 49813 Sorted by residual: angle pdb=" N PRO C 892 " pdb=" CA PRO C 892 " pdb=" CB PRO C 892 " ideal model delta sigma weight residual 103.34 110.35 -7.01 9.30e-01 1.16e+00 5.68e+01 angle pdb=" N PRO B 892 " pdb=" CA PRO B 892 " pdb=" CB PRO B 892 " ideal model delta sigma weight residual 103.34 110.33 -6.99 9.30e-01 1.16e+00 5.66e+01 angle pdb=" N PRO A 892 " pdb=" CA PRO A 892 " pdb=" CB PRO A 892 " ideal model delta sigma weight residual 103.34 110.33 -6.99 9.30e-01 1.16e+00 5.64e+01 angle pdb=" N PRO A 942 " pdb=" CA PRO A 942 " pdb=" CB PRO A 942 " ideal model delta sigma weight residual 103.25 110.23 -6.98 1.05e+00 9.07e-01 4.41e+01 angle pdb=" N PRO C 942 " pdb=" CA PRO C 942 " pdb=" CB PRO C 942 " ideal model delta sigma weight residual 103.25 110.16 -6.91 1.05e+00 9.07e-01 4.33e+01 ... (remaining 49808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 19928 17.98 - 35.95: 2022 35.95 - 53.93: 554 53.93 - 71.91: 114 71.91 - 89.88: 49 Dihedral angle restraints: 22667 sinusoidal: 9620 harmonic: 13047 Sorted by residual: 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 10.77 82.23 1 1.00e+01 1.00e-02 8.30e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -12.31 -73.69 1 1.00e+01 1.00e-02 6.90e+01 dihedral pdb=" CA CYS A 617 " pdb=" C CYS A 617 " pdb=" N THR A 618 " pdb=" CA THR A 618 " ideal model delta harmonic sigma weight residual 180.00 150.63 29.37 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 22664 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 5157 0.076 - 0.153: 649 0.153 - 0.229: 14 0.229 - 0.305: 5 0.305 - 0.381: 1 Chirality restraints: 5826 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 709 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CA PRO B 942 " pdb=" N PRO B 942 " pdb=" C PRO B 942 " pdb=" CB PRO B 942 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA PRO C 942 " pdb=" N PRO C 942 " pdb=" C PRO C 942 " pdb=" CB PRO C 942 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 5823 not shown) Planarity restraints: 6372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 675 " 0.020 2.00e-02 2.50e+03 3.98e-02 1.58e+01 pdb=" C GLN B 675 " -0.069 2.00e-02 2.50e+03 pdb=" O GLN B 675 " 0.026 2.00e-02 2.50e+03 pdb=" N THR B 676 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.039 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO B 987 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " 0.036 5.00e-02 4.00e+02 5.47e-02 4.78e+00 pdb=" N PRO A 987 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " 0.031 5.00e-02 4.00e+02 ... (remaining 6369 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1750 2.73 - 3.27: 32967 3.27 - 3.81: 56921 3.81 - 4.36: 68109 4.36 - 4.90: 119185 Nonbonded interactions: 278932 Sorted by model distance: nonbonded pdb=" O ILE N 106 " pdb=" OH TYR N 140 " model vdw 2.183 2.440 nonbonded pdb=" OG SER O 52 " pdb=" O ALA O 104 " model vdw 2.194 2.440 nonbonded pdb=" OG SER C 438 " pdb=" OD2 ASP C 442 " model vdw 2.202 2.440 nonbonded pdb=" OH TYR C 91 " pdb=" OE1 GLU C 191 " model vdw 2.241 2.440 nonbonded pdb=" OG SER A 359 " pdb=" OD1 ASN A 394 " model vdw 2.252 2.440 ... (remaining 278927 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' and (resid 14 through 827 or resid 848 through 1147 or resid 1301 thr \ ough 1308)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'P' } 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: 10.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.290 Construct map_model_manager: 0.030 Extract box with map and model: 30.220 Check model and map are aligned: 0.560 Set scattering table: 0.340 Process input model: 94.930 Find NCS groups from input model: 2.520 Set up NCS constraints: 0.560 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 153.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 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 : 0.003 0.085 36615 Z= 0.220 Angle : 0.586 8.541 49813 Z= 0.320 Chirality : 0.046 0.381 5826 Planarity : 0.004 0.068 6328 Dihedral : 15.809 89.883 14117 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.06 % Favored : 94.78 % Rotamer: Outliers : 2.72 % Allowed : 17.48 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 0.04 (0.13), residues: 4428 helix: 1.68 (0.21), residues: 654 sheet: 0.73 (0.14), residues: 1314 loop : -0.85 (0.13), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 633 HIS 0.005 0.001 HIS B 519 PHE 0.019 0.001 PHE C 32 TYR 0.017 0.001 TYR A1067 ARG 0.015 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 184 time to evaluate : 3.947 Fit side-chains REVERT: B 436 TRP cc_start: 0.5099 (OUTLIER) cc_final: 0.4898 (p-90) REVERT: C 190 ARG cc_start: 0.6762 (mmt90) cc_final: 0.6461 (mmt90) REVERT: C 821 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8064 (tt) REVERT: L 49 ILE cc_start: 0.5772 (tt) cc_final: 0.5448 (mp) REVERT: O 81 MET cc_start: 0.1058 (mtm) cc_final: -0.0748 (ptp) outliers start: 106 outliers final: 95 residues processed: 285 average time/residue: 1.0225 time to fit residues: 378.8154 Evaluate side-chains 268 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 171 time to evaluate : 3.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 167 SER Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 27 TYR Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 156 VAL Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 219 THR Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 64 SER Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 21 SER Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 71 THR Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain O residue 164 VAL Chi-restraints excluded: chain O residue 165 THR Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain P residue 68 SER Chi-restraints excluded: chain P residue 77 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 377 optimal weight: 30.0000 chunk 338 optimal weight: 5.9990 chunk 187 optimal weight: 0.3980 chunk 115 optimal weight: 0.6980 chunk 228 optimal weight: 9.9990 chunk 181 optimal weight: 2.9990 chunk 350 optimal weight: 5.9990 chunk 135 optimal weight: 9.9990 chunk 213 optimal weight: 0.0570 chunk 260 optimal weight: 4.9990 chunk 405 optimal weight: 0.6980 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 978 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN H 57 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.0384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 36615 Z= 0.150 Angle : 0.507 10.968 49813 Z= 0.263 Chirality : 0.044 0.257 5826 Planarity : 0.004 0.057 6328 Dihedral : 8.064 62.658 6270 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.81 % Favored : 95.10 % Rotamer: Outliers : 3.38 % Allowed : 17.23 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % 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: 0.21 (0.13), residues: 4428 helix: 2.21 (0.21), residues: 661 sheet: 0.87 (0.14), residues: 1283 loop : -0.86 (0.12), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 633 HIS 0.005 0.001 HIS B 519 PHE 0.013 0.001 PHE B 898 TYR 0.019 0.001 TYR A1067 ARG 0.012 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 183 time to evaluate : 3.783 Fit side-chains revert: symmetry clash REVERT: B 646 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7618 (mtt180) REVERT: B 856 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8320 (mttp) REVERT: C 127 VAL cc_start: 0.7638 (OUTLIER) cc_final: 0.7364 (p) REVERT: C 185 ASN cc_start: 0.1543 (OUTLIER) cc_final: 0.1301 (p0) REVERT: C 690 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7317 (tm-30) REVERT: L 49 ILE cc_start: 0.5771 (tt) cc_final: 0.5448 (mp) REVERT: N 54 SER cc_start: 0.6729 (m) cc_final: 0.6422 (p) REVERT: N 175 LEU cc_start: 0.3186 (OUTLIER) cc_final: 0.2938 (mp) REVERT: O 74 THR cc_start: 0.3010 (OUTLIER) cc_final: 0.2594 (t) REVERT: O 81 MET cc_start: 0.0450 (mtm) cc_final: -0.2959 (tpp) outliers start: 132 outliers final: 72 residues processed: 291 average time/residue: 1.0760 time to fit residues: 408.5448 Evaluate side-chains 251 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 172 time to evaluate : 3.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain O residue 164 VAL Chi-restraints excluded: chain O residue 165 THR Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 158 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 225 optimal weight: 9.9990 chunk 125 optimal weight: 7.9990 chunk 337 optimal weight: 0.9990 chunk 276 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 406 optimal weight: 20.0000 chunk 439 optimal weight: 3.9990 chunk 362 optimal weight: 0.2980 chunk 403 optimal weight: 30.0000 chunk 138 optimal weight: 5.9990 chunk 326 optimal weight: 7.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 87 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN A1135 ASN B 23 GLN B 437 ASN B 532 ASN B1135 ASN ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN H 57 ASN H 119 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 36615 Z= 0.287 Angle : 0.600 9.612 49813 Z= 0.312 Chirality : 0.047 0.268 5826 Planarity : 0.005 0.057 6328 Dihedral : 7.766 62.620 6210 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.80 % Favored : 94.06 % Rotamer: Outliers : 4.90 % Allowed : 16.66 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.04 (0.13), residues: 4428 helix: 2.04 (0.21), residues: 666 sheet: 0.65 (0.14), residues: 1327 loop : -0.94 (0.12), residues: 2435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 633 HIS 0.005 0.001 HIS L 92 PHE 0.019 0.002 PHE B 898 TYR 0.026 0.002 TYR B 265 ARG 0.006 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 186 time to evaluate : 4.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 820 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.7217 (m-30) REVERT: A 1127 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.7169 (p0) REVERT: B 115 GLN cc_start: 0.5547 (OUTLIER) cc_final: 0.5234 (tp-100) REVERT: B 544 ASN cc_start: 0.7969 (t0) cc_final: 0.7727 (t0) REVERT: B 564 GLN cc_start: 0.7218 (mm110) cc_final: 0.6961 (tp-100) REVERT: B 646 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7633 (mtt180) REVERT: B 702 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7340 (tt0) REVERT: B 763 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7961 (mp) REVERT: B 856 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8406 (mttp) REVERT: C 24 LEU cc_start: 0.2642 (OUTLIER) cc_final: 0.2346 (pp) REVERT: C 127 VAL cc_start: 0.7702 (OUTLIER) cc_final: 0.7463 (p) REVERT: C 185 ASN cc_start: 0.1258 (OUTLIER) cc_final: 0.0875 (p0) REVERT: C 690 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7346 (tm-30) REVERT: C 1045 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8198 (ttpt) REVERT: H 155 LEU cc_start: 0.2442 (OUTLIER) cc_final: 0.2049 (mt) REVERT: L 49 ILE cc_start: 0.5831 (tt) cc_final: 0.5564 (mp) REVERT: M 82 GLU cc_start: 0.3248 (OUTLIER) cc_final: 0.2855 (tm-30) REVERT: M 117 TRP cc_start: 0.5493 (m100) cc_final: 0.4968 (m100) REVERT: N 175 LEU cc_start: 0.3130 (OUTLIER) cc_final: 0.2886 (mp) REVERT: O 70 MET cc_start: -0.0704 (tmt) cc_final: -0.1496 (mtp) outliers start: 191 outliers final: 106 residues processed: 352 average time/residue: 1.0297 time to fit residues: 470.5903 Evaluate side-chains 293 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 172 time to evaluate : 3.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 219 THR Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 22 SER Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 71 THR Chi-restraints excluded: chain O residue 164 VAL Chi-restraints excluded: chain O residue 165 THR Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain O residue 174 THR Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 158 ASN Chi-restraints excluded: chain P residue 163 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 401 optimal weight: 20.0000 chunk 305 optimal weight: 0.7980 chunk 211 optimal weight: 0.8980 chunk 45 optimal weight: 20.0000 chunk 194 optimal weight: 0.7980 chunk 273 optimal weight: 0.9990 chunk 408 optimal weight: 0.0030 chunk 432 optimal weight: 30.0000 chunk 213 optimal weight: 0.3980 chunk 386 optimal weight: 30.0000 chunk 116 optimal weight: 6.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 188 ASN A 239 GLN A 978 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN H 57 ASN H 119 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 36615 Z= 0.141 Angle : 0.508 9.624 49813 Z= 0.263 Chirality : 0.044 0.269 5826 Planarity : 0.004 0.053 6328 Dihedral : 7.082 62.049 6204 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.74 % Favored : 95.19 % Rotamer: Outliers : 3.28 % Allowed : 18.48 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.18 (0.13), residues: 4428 helix: 2.31 (0.21), residues: 659 sheet: 0.80 (0.14), residues: 1288 loop : -0.89 (0.12), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 633 HIS 0.004 0.001 HIS B 519 PHE 0.013 0.001 PHE B 318 TYR 0.024 0.001 TYR A 170 ARG 0.008 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 187 time to evaluate : 4.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1127 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.7086 (p0) REVERT: B 544 ASN cc_start: 0.7825 (t0) cc_final: 0.7581 (t0) REVERT: B 564 GLN cc_start: 0.7121 (mm110) cc_final: 0.6882 (tp-100) REVERT: B 646 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7581 (mtt180) REVERT: B 702 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7321 (tt0) REVERT: B 856 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8358 (mttp) REVERT: B 964 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7393 (mtpt) REVERT: C 14 GLN cc_start: 0.5727 (OUTLIER) cc_final: 0.3306 (tp-100) REVERT: C 24 LEU cc_start: 0.2708 (OUTLIER) cc_final: 0.2476 (pp) REVERT: C 68 ILE cc_start: 0.6204 (OUTLIER) cc_final: 0.5917 (mp) REVERT: C 185 ASN cc_start: 0.1337 (OUTLIER) cc_final: 0.0825 (p0) REVERT: C 690 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7375 (tm-30) REVERT: H 155 LEU cc_start: 0.2428 (OUTLIER) cc_final: 0.2045 (mt) REVERT: L 49 ILE cc_start: 0.5841 (tt) cc_final: 0.5540 (mp) REVERT: M 82 GLU cc_start: 0.3219 (OUTLIER) cc_final: 0.2890 (tm-30) REVERT: M 117 TRP cc_start: 0.5357 (m100) cc_final: 0.4478 (m100) REVERT: N 54 SER cc_start: 0.6760 (m) cc_final: 0.6439 (p) REVERT: N 175 LEU cc_start: 0.3102 (OUTLIER) cc_final: 0.2858 (mp) REVERT: O 70 MET cc_start: -0.0742 (tmt) cc_final: -0.1618 (mtp) REVERT: O 81 MET cc_start: 0.0525 (mtm) cc_final: 0.0291 (ptp) outliers start: 128 outliers final: 72 residues processed: 298 average time/residue: 1.0608 time to fit residues: 409.2736 Evaluate side-chains 263 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 178 time to evaluate : 3.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 48 MET Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain O residue 164 VAL Chi-restraints excluded: chain O residue 165 THR Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 158 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 359 optimal weight: 20.0000 chunk 245 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 321 optimal weight: 10.0000 chunk 178 optimal weight: 1.9990 chunk 368 optimal weight: 9.9990 chunk 298 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 220 optimal weight: 10.0000 chunk 387 optimal weight: 7.9990 chunk 109 optimal weight: 0.4980 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 239 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN H 57 ASN H 116 ASN H 119 GLN H 218 ASN ** L 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 169 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 36615 Z= 0.347 Angle : 0.640 9.713 49813 Z= 0.333 Chirality : 0.049 0.270 5826 Planarity : 0.005 0.056 6328 Dihedral : 7.551 63.473 6193 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.21 % Favored : 93.65 % Rotamer: Outliers : 4.38 % Allowed : 18.51 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.08 (0.13), residues: 4428 helix: 1.93 (0.21), residues: 666 sheet: 0.56 (0.14), residues: 1329 loop : -1.00 (0.12), residues: 2433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 633 HIS 0.005 0.001 HIS L 92 PHE 0.022 0.002 PHE B 898 TYR 0.027 0.002 TYR C 265 ARG 0.010 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 183 time to evaluate : 3.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7331 (ttp80) REVERT: A 820 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.7265 (m-30) REVERT: A 1127 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7277 (p0) REVERT: B 52 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7259 (tm-30) REVERT: B 115 GLN cc_start: 0.5557 (OUTLIER) cc_final: 0.5237 (tp-100) REVERT: B 544 ASN cc_start: 0.8162 (t0) cc_final: 0.7766 (t0) REVERT: B 564 GLN cc_start: 0.7318 (mm110) cc_final: 0.7093 (tp40) REVERT: B 646 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7641 (mtt180) REVERT: B 702 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7367 (tt0) REVERT: B 763 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7997 (mp) REVERT: B 856 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8432 (mttp) REVERT: B 964 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7522 (mppt) REVERT: C 24 LEU cc_start: 0.2655 (OUTLIER) cc_final: 0.2314 (pp) REVERT: C 127 VAL cc_start: 0.7726 (OUTLIER) cc_final: 0.7508 (p) REVERT: C 185 ASN cc_start: 0.1475 (OUTLIER) cc_final: 0.0890 (p0) REVERT: C 690 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7336 (tm-30) REVERT: C 1045 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8221 (ttpt) REVERT: H 155 LEU cc_start: 0.2449 (OUTLIER) cc_final: 0.2114 (mt) REVERT: L 49 ILE cc_start: 0.5940 (tt) cc_final: 0.5688 (mp) REVERT: L 169 LYS cc_start: 0.4422 (OUTLIER) cc_final: 0.3695 (mptt) REVERT: M 63 LYS cc_start: 0.5332 (OUTLIER) cc_final: 0.4958 (mptt) REVERT: M 82 GLU cc_start: 0.3418 (OUTLIER) cc_final: 0.3061 (tm-30) REVERT: M 117 TRP cc_start: 0.5514 (m100) cc_final: 0.5001 (m100) REVERT: M 131 LYS cc_start: 0.5169 (OUTLIER) cc_final: 0.4516 (pmtt) REVERT: N 175 LEU cc_start: 0.3160 (OUTLIER) cc_final: 0.2909 (mp) REVERT: O 70 MET cc_start: -0.0902 (tmt) cc_final: -0.1825 (mtp) REVERT: P 209 PHE cc_start: 0.1088 (OUTLIER) cc_final: 0.0183 (t80) outliers start: 171 outliers final: 104 residues processed: 327 average time/residue: 1.0280 time to fit residues: 435.6596 Evaluate side-chains 302 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 176 time to evaluate : 3.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 357 ARG Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 941 THR Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 169 LYS Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 63 LYS Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain M residue 131 LYS Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 219 THR Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 97 THR Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 163 VAL Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain O residue 164 VAL Chi-restraints excluded: chain O residue 165 THR Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain O residue 174 THR Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 158 ASN Chi-restraints excluded: chain P residue 209 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 145 optimal weight: 5.9990 chunk 389 optimal weight: 0.9990 chunk 85 optimal weight: 0.4980 chunk 253 optimal weight: 1.9990 chunk 106 optimal weight: 40.0000 chunk 432 optimal weight: 9.9990 chunk 359 optimal weight: 6.9990 chunk 200 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 143 optimal weight: 10.0000 chunk 227 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 188 ASN A 239 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN H 57 ASN H 119 GLN N 166 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 36615 Z= 0.161 Angle : 0.543 9.604 49813 Z= 0.281 Chirality : 0.044 0.262 5826 Planarity : 0.004 0.054 6328 Dihedral : 7.125 63.233 6191 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.01 % Favored : 94.90 % Rotamer: Outliers : 3.82 % Allowed : 19.25 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.07 (0.13), residues: 4428 helix: 2.17 (0.21), residues: 667 sheet: 0.72 (0.14), residues: 1286 loop : -0.96 (0.12), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 633 HIS 0.005 0.001 HIS L 92 PHE 0.016 0.001 PHE B 592 TYR 0.021 0.001 TYR M 27 ARG 0.014 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 184 time to evaluate : 3.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 820 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.7020 (m-30) REVERT: A 1127 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.7184 (p0) REVERT: B 24 LEU cc_start: 0.4596 (OUTLIER) cc_final: 0.4206 (mm) REVERT: B 52 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7258 (tt0) REVERT: B 115 GLN cc_start: 0.5587 (OUTLIER) cc_final: 0.5246 (tp-100) REVERT: B 544 ASN cc_start: 0.8070 (t0) cc_final: 0.7687 (t0) REVERT: B 564 GLN cc_start: 0.7233 (mm110) cc_final: 0.7009 (tp40) REVERT: B 646 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7591 (mtt180) REVERT: B 702 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7325 (tt0) REVERT: B 856 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8372 (mttp) REVERT: B 964 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7351 (mppt) REVERT: C 14 GLN cc_start: 0.5768 (OUTLIER) cc_final: 0.3394 (tp-100) REVERT: C 24 LEU cc_start: 0.2692 (OUTLIER) cc_final: 0.2427 (pp) REVERT: C 68 ILE cc_start: 0.6112 (OUTLIER) cc_final: 0.5837 (mp) REVERT: C 185 ASN cc_start: 0.1310 (OUTLIER) cc_final: 0.0648 (p0) REVERT: C 190 ARG cc_start: 0.6813 (mmt90) cc_final: 0.6572 (mmt90) REVERT: C 690 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7244 (tm-30) REVERT: H 155 LEU cc_start: 0.2378 (OUTLIER) cc_final: 0.2045 (mt) REVERT: L 49 ILE cc_start: 0.5877 (tt) cc_final: 0.5600 (mp) REVERT: L 96 LEU cc_start: 0.5125 (OUTLIER) cc_final: 0.4824 (mm) REVERT: M 82 GLU cc_start: 0.3271 (OUTLIER) cc_final: 0.2886 (tm-30) REVERT: M 117 TRP cc_start: 0.5438 (m100) cc_final: 0.4746 (m100) REVERT: M 131 LYS cc_start: 0.5146 (OUTLIER) cc_final: 0.4517 (pmtt) REVERT: N 175 LEU cc_start: 0.3149 (OUTLIER) cc_final: 0.2908 (mp) REVERT: O 70 MET cc_start: -0.0984 (tmt) cc_final: -0.2272 (tpp) REVERT: O 81 MET cc_start: 0.0748 (mtm) cc_final: -0.0163 (ptp) REVERT: O 189 LEU cc_start: 0.2682 (tp) cc_final: 0.2361 (mt) REVERT: P 209 PHE cc_start: 0.1057 (OUTLIER) cc_final: 0.0167 (t80) outliers start: 149 outliers final: 95 residues processed: 315 average time/residue: 1.0104 time to fit residues: 414.9425 Evaluate side-chains 294 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 179 time to evaluate : 3.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 131 LYS Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 48 MET Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 71 THR Chi-restraints excluded: chain O residue 164 VAL Chi-restraints excluded: chain O residue 165 THR Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain P residue 97 THR Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 158 ASN Chi-restraints excluded: chain P residue 209 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 416 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 246 optimal weight: 6.9990 chunk 315 optimal weight: 6.9990 chunk 244 optimal weight: 0.0170 chunk 364 optimal weight: 9.9990 chunk 241 optimal weight: 4.9990 chunk 430 optimal weight: 0.9990 chunk 269 optimal weight: 0.3980 chunk 262 optimal weight: 6.9990 chunk 198 optimal weight: 0.6980 overall best weight: 1.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 239 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN H 57 ASN H 116 ASN L 189 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 36615 Z= 0.179 Angle : 0.544 9.646 49813 Z= 0.280 Chirality : 0.045 0.265 5826 Planarity : 0.004 0.060 6328 Dihedral : 6.995 62.756 6191 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.22 % Favored : 94.69 % Rotamer: Outliers : 3.87 % Allowed : 19.28 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.08 (0.13), residues: 4428 helix: 2.20 (0.21), residues: 669 sheet: 0.70 (0.14), residues: 1290 loop : -0.96 (0.12), residues: 2469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 633 HIS 0.005 0.001 HIS L 92 PHE 0.015 0.001 PHE B 592 TYR 0.020 0.001 TYR C 265 ARG 0.014 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 185 time to evaluate : 3.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8067 (tt) REVERT: A 1127 ASP cc_start: 0.7487 (OUTLIER) cc_final: 0.7175 (p0) REVERT: B 24 LEU cc_start: 0.4595 (OUTLIER) cc_final: 0.4206 (mm) REVERT: B 52 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7257 (tt0) REVERT: B 115 GLN cc_start: 0.5617 (OUTLIER) cc_final: 0.5257 (tp-100) REVERT: B 544 ASN cc_start: 0.8055 (t0) cc_final: 0.7647 (t0) REVERT: B 564 GLN cc_start: 0.7232 (mm110) cc_final: 0.7014 (tp40) REVERT: B 646 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7595 (mtt180) REVERT: B 702 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7335 (tt0) REVERT: B 856 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8375 (mttp) REVERT: B 964 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7330 (mppt) REVERT: C 14 GLN cc_start: 0.5764 (OUTLIER) cc_final: 0.3416 (tp-100) REVERT: C 24 LEU cc_start: 0.2686 (OUTLIER) cc_final: 0.2423 (pp) REVERT: C 68 ILE cc_start: 0.6114 (OUTLIER) cc_final: 0.5836 (mp) REVERT: C 127 VAL cc_start: 0.7553 (OUTLIER) cc_final: 0.7310 (p) REVERT: C 185 ASN cc_start: 0.1372 (OUTLIER) cc_final: 0.0685 (p0) REVERT: C 190 ARG cc_start: 0.6831 (mmt90) cc_final: 0.6582 (mmt90) REVERT: C 690 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7325 (tm-30) REVERT: H 155 LEU cc_start: 0.2374 (OUTLIER) cc_final: 0.2042 (mt) REVERT: L 49 ILE cc_start: 0.5922 (tt) cc_final: 0.5654 (mp) REVERT: L 96 LEU cc_start: 0.5157 (OUTLIER) cc_final: 0.4846 (mm) REVERT: M 82 GLU cc_start: 0.3278 (OUTLIER) cc_final: 0.2902 (tm-30) REVERT: M 117 TRP cc_start: 0.5394 (m100) cc_final: 0.4471 (m100) REVERT: M 131 LYS cc_start: 0.5142 (OUTLIER) cc_final: 0.4511 (pmtt) REVERT: N 54 SER cc_start: 0.6831 (m) cc_final: 0.6464 (p) REVERT: N 175 LEU cc_start: 0.3119 (OUTLIER) cc_final: 0.2884 (mp) REVERT: O 68 VAL cc_start: 0.1595 (OUTLIER) cc_final: 0.1382 (m) REVERT: O 70 MET cc_start: -0.1082 (tmt) cc_final: -0.2427 (tpp) REVERT: O 81 MET cc_start: 0.0640 (mtm) cc_final: -0.0253 (ptp) REVERT: O 189 LEU cc_start: 0.2700 (tp) cc_final: 0.2408 (mt) REVERT: P 209 PHE cc_start: 0.1039 (OUTLIER) cc_final: 0.0148 (t80) outliers start: 151 outliers final: 106 residues processed: 318 average time/residue: 1.0241 time to fit residues: 423.5268 Evaluate side-chains 309 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 181 time to evaluate : 3.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 116 ASN Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 131 LYS Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 48 MET Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 68 VAL Chi-restraints excluded: chain O residue 71 THR Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain O residue 164 VAL Chi-restraints excluded: chain O residue 165 THR Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 158 ASN Chi-restraints excluded: chain P residue 209 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 266 optimal weight: 7.9990 chunk 172 optimal weight: 3.9990 chunk 257 optimal weight: 40.0000 chunk 129 optimal weight: 5.9990 chunk 84 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 273 optimal weight: 1.9990 chunk 293 optimal weight: 5.9990 chunk 213 optimal weight: 0.0370 chunk 40 optimal weight: 20.0000 chunk 338 optimal weight: 8.9990 overall best weight: 2.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 188 ASN A 239 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN H 57 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 36615 Z= 0.241 Angle : 0.576 9.870 49813 Z= 0.297 Chirality : 0.046 0.263 5826 Planarity : 0.004 0.065 6328 Dihedral : 7.096 62.760 6191 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.58 % Favored : 94.33 % Rotamer: Outliers : 4.15 % Allowed : 19.17 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.02 (0.13), residues: 4428 helix: 2.12 (0.21), residues: 669 sheet: 0.58 (0.14), residues: 1315 loop : -0.99 (0.12), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 633 HIS 0.005 0.001 HIS L 92 PHE 0.018 0.001 PHE B 898 TYR 0.023 0.001 TYR B 265 ARG 0.014 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 183 time to evaluate : 3.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8086 (tt) REVERT: A 733 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8248 (mtmt) REVERT: A 1127 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.7217 (p0) REVERT: B 24 LEU cc_start: 0.4607 (OUTLIER) cc_final: 0.4221 (mm) REVERT: B 52 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7282 (tt0) REVERT: B 115 GLN cc_start: 0.5632 (OUTLIER) cc_final: 0.5269 (tp-100) REVERT: B 544 ASN cc_start: 0.8113 (t0) cc_final: 0.7669 (t0) REVERT: B 564 GLN cc_start: 0.7263 (mm110) cc_final: 0.7031 (tp40) REVERT: B 646 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7599 (mtt180) REVERT: B 702 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7348 (tt0) REVERT: B 763 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7884 (mp) REVERT: B 856 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8436 (mttp) REVERT: B 964 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7364 (mppt) REVERT: C 14 GLN cc_start: 0.5777 (OUTLIER) cc_final: 0.3413 (tp-100) REVERT: C 24 LEU cc_start: 0.2687 (OUTLIER) cc_final: 0.2405 (pp) REVERT: C 68 ILE cc_start: 0.6072 (OUTLIER) cc_final: 0.5793 (mp) REVERT: C 127 VAL cc_start: 0.7625 (OUTLIER) cc_final: 0.7374 (p) REVERT: C 185 ASN cc_start: 0.1448 (OUTLIER) cc_final: 0.0749 (p0) REVERT: C 190 ARG cc_start: 0.6878 (OUTLIER) cc_final: 0.6615 (mmt90) REVERT: C 690 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7247 (tm-30) REVERT: H 116 ASN cc_start: 0.6290 (OUTLIER) cc_final: 0.5630 (m-40) REVERT: H 155 LEU cc_start: 0.2405 (OUTLIER) cc_final: 0.2068 (mt) REVERT: L 49 ILE cc_start: 0.5923 (tt) cc_final: 0.5676 (mp) REVERT: L 96 LEU cc_start: 0.5163 (OUTLIER) cc_final: 0.4839 (mm) REVERT: L 169 LYS cc_start: 0.4481 (OUTLIER) cc_final: 0.3749 (mptt) REVERT: M 82 GLU cc_start: 0.3299 (OUTLIER) cc_final: 0.2905 (tm-30) REVERT: M 117 TRP cc_start: 0.5428 (m100) cc_final: 0.4650 (m100) REVERT: M 131 LYS cc_start: 0.5156 (OUTLIER) cc_final: 0.4513 (pmtt) REVERT: N 175 LEU cc_start: 0.3126 (OUTLIER) cc_final: 0.2888 (mp) REVERT: O 70 MET cc_start: -0.0995 (tmt) cc_final: -0.2420 (tpp) REVERT: O 81 MET cc_start: 0.0617 (mtm) cc_final: -0.0361 (ptp) REVERT: O 189 LEU cc_start: 0.2707 (tp) cc_final: 0.2465 (mt) REVERT: P 209 PHE cc_start: 0.0988 (OUTLIER) cc_final: 0.0107 (t80) outliers start: 162 outliers final: 108 residues processed: 325 average time/residue: 1.0403 time to fit residues: 438.7793 Evaluate side-chains 315 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 181 time to evaluate : 3.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 995 ARG Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 116 ASN Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 169 LYS Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 131 LYS Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 71 THR Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain O residue 164 VAL Chi-restraints excluded: chain O residue 165 THR Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 150 VAL Chi-restraints excluded: chain P residue 158 ASN Chi-restraints excluded: chain P residue 209 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 391 optimal weight: 8.9990 chunk 412 optimal weight: 0.9990 chunk 376 optimal weight: 4.9990 chunk 401 optimal weight: 6.9990 chunk 241 optimal weight: 20.0000 chunk 174 optimal weight: 0.3980 chunk 315 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 362 optimal weight: 0.0970 chunk 379 optimal weight: 6.9990 chunk 400 optimal weight: 6.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 239 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN H 57 ASN H 116 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36615 Z= 0.181 Angle : 0.543 9.955 49813 Z= 0.280 Chirality : 0.045 0.266 5826 Planarity : 0.004 0.060 6328 Dihedral : 6.906 61.739 6191 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.13 % Favored : 94.81 % Rotamer: Outliers : 3.56 % Allowed : 19.89 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.05 (0.13), residues: 4428 helix: 2.17 (0.21), residues: 671 sheet: 0.69 (0.14), residues: 1291 loop : -0.98 (0.12), residues: 2466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 633 HIS 0.005 0.001 HIS L 92 PHE 0.016 0.001 PHE B 592 TYR 0.019 0.001 TYR C 265 ARG 0.015 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 188 time to evaluate : 3.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 733 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8397 (mtmt) REVERT: A 1127 ASP cc_start: 0.7487 (OUTLIER) cc_final: 0.7176 (p0) REVERT: B 24 LEU cc_start: 0.4592 (OUTLIER) cc_final: 0.4203 (mm) REVERT: B 52 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7241 (tt0) REVERT: B 115 GLN cc_start: 0.5599 (OUTLIER) cc_final: 0.5259 (tp-100) REVERT: B 564 GLN cc_start: 0.7259 (mm110) cc_final: 0.7034 (tp40) REVERT: B 646 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7599 (mtt180) REVERT: B 702 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7343 (tt0) REVERT: B 856 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8378 (mttp) REVERT: B 964 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7290 (mppt) REVERT: C 14 GLN cc_start: 0.5793 (OUTLIER) cc_final: 0.3458 (tp-100) REVERT: C 24 LEU cc_start: 0.2687 (OUTLIER) cc_final: 0.2436 (pp) REVERT: C 68 ILE cc_start: 0.6074 (OUTLIER) cc_final: 0.5795 (mp) REVERT: C 127 VAL cc_start: 0.7571 (OUTLIER) cc_final: 0.7319 (p) REVERT: C 185 ASN cc_start: 0.1546 (OUTLIER) cc_final: 0.0798 (p0) REVERT: C 190 ARG cc_start: 0.6850 (mmt90) cc_final: 0.6600 (mmt90) REVERT: C 690 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7201 (tm-30) REVERT: H 155 LEU cc_start: 0.2383 (OUTLIER) cc_final: 0.2056 (mt) REVERT: L 49 ILE cc_start: 0.5964 (tt) cc_final: 0.5722 (mp) REVERT: L 96 LEU cc_start: 0.5167 (OUTLIER) cc_final: 0.4831 (mm) REVERT: L 169 LYS cc_start: 0.4450 (OUTLIER) cc_final: 0.3711 (mptt) REVERT: M 82 GLU cc_start: 0.3333 (OUTLIER) cc_final: 0.2949 (tm-30) REVERT: M 117 TRP cc_start: 0.5381 (m100) cc_final: 0.4547 (m100) REVERT: M 131 LYS cc_start: 0.5154 (OUTLIER) cc_final: 0.4533 (pmtt) REVERT: M 165 THR cc_start: 0.1582 (OUTLIER) cc_final: 0.1291 (t) REVERT: N 54 SER cc_start: 0.6843 (m) cc_final: 0.6477 (p) REVERT: N 175 LEU cc_start: 0.3124 (OUTLIER) cc_final: 0.2885 (mp) REVERT: O 48 MET cc_start: 0.1099 (ppp) cc_final: -0.0361 (tpp) REVERT: O 70 MET cc_start: -0.0953 (tmt) cc_final: -0.2415 (tpp) REVERT: O 81 MET cc_start: 0.0779 (mtm) cc_final: -0.0240 (ptp) REVERT: O 189 LEU cc_start: 0.2817 (tp) cc_final: 0.2607 (mt) REVERT: P 209 PHE cc_start: 0.0941 (OUTLIER) cc_final: 0.0057 (t80) outliers start: 139 outliers final: 97 residues processed: 311 average time/residue: 1.0369 time to fit residues: 421.2035 Evaluate side-chains 298 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 178 time to evaluate : 3.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 169 LYS Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 131 LYS Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 152 LEU Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 175 LEU Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 71 THR Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain O residue 164 VAL Chi-restraints excluded: chain O residue 165 THR Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 158 ASN Chi-restraints excluded: chain P residue 209 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 263 optimal weight: 2.9990 chunk 424 optimal weight: 8.9990 chunk 259 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 295 optimal weight: 2.9990 chunk 445 optimal weight: 7.9990 chunk 409 optimal weight: 5.9990 chunk 354 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 273 optimal weight: 3.9990 chunk 217 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 239 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 ASN H 119 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 36615 Z= 0.312 Angle : 0.620 10.041 49813 Z= 0.321 Chirality : 0.048 0.258 5826 Planarity : 0.005 0.070 6328 Dihedral : 7.263 62.122 6188 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.35 % Favored : 93.52 % Rotamer: Outliers : 3.64 % Allowed : 19.84 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.15 (0.13), residues: 4428 helix: 1.98 (0.21), residues: 674 sheet: 0.51 (0.14), residues: 1285 loop : -1.07 (0.12), residues: 2469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 633 HIS 0.005 0.001 HIS L 92 PHE 0.021 0.002 PHE B 898 TYR 0.026 0.002 TYR B 265 ARG 0.015 0.001 ARG C 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8856 Ramachandran restraints generated. 4428 Oldfield, 0 Emsley, 4428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 181 time to evaluate : 3.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 733 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8246 (mtmt) REVERT: A 820 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.7193 (m-30) REVERT: A 1127 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7287 (p0) REVERT: B 24 LEU cc_start: 0.4667 (OUTLIER) cc_final: 0.4264 (mm) REVERT: B 52 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7262 (tt0) REVERT: B 115 GLN cc_start: 0.5625 (OUTLIER) cc_final: 0.5252 (tp-100) REVERT: B 564 GLN cc_start: 0.7311 (mm110) cc_final: 0.7081 (tp40) REVERT: B 646 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7627 (mtt180) REVERT: B 702 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7337 (tt0) REVERT: B 856 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8478 (mttp) REVERT: B 964 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7422 (mppt) REVERT: C 14 GLN cc_start: 0.5719 (OUTLIER) cc_final: 0.3446 (tp-100) REVERT: C 24 LEU cc_start: 0.2705 (OUTLIER) cc_final: 0.2403 (pp) REVERT: C 68 ILE cc_start: 0.6027 (OUTLIER) cc_final: 0.5749 (mp) REVERT: C 127 VAL cc_start: 0.7696 (OUTLIER) cc_final: 0.7461 (p) REVERT: C 185 ASN cc_start: 0.1694 (OUTLIER) cc_final: 0.0910 (p0) REVERT: C 190 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6652 (mmt90) REVERT: C 690 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7300 (tm-30) REVERT: C 1045 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8208 (ttpt) REVERT: H 48 MET cc_start: 0.6218 (ttm) cc_final: 0.4602 (tmm) REVERT: H 155 LEU cc_start: 0.2356 (OUTLIER) cc_final: 0.2036 (mt) REVERT: L 49 ILE cc_start: 0.5992 (tt) cc_final: 0.5788 (mp) REVERT: L 96 LEU cc_start: 0.5142 (OUTLIER) cc_final: 0.4769 (mp) REVERT: L 169 LYS cc_start: 0.4441 (OUTLIER) cc_final: 0.3740 (mptt) REVERT: M 48 MET cc_start: 0.6706 (mtm) cc_final: 0.6480 (mtt) REVERT: M 82 GLU cc_start: 0.3436 (OUTLIER) cc_final: 0.3096 (tm-30) REVERT: M 117 TRP cc_start: 0.5412 (m100) cc_final: 0.4660 (m100) REVERT: M 131 LYS cc_start: 0.5131 (OUTLIER) cc_final: 0.4482 (pmtt) REVERT: M 165 THR cc_start: 0.1574 (OUTLIER) cc_final: 0.1273 (t) REVERT: O 70 MET cc_start: -0.0877 (tmt) cc_final: -0.2393 (tpp) REVERT: O 81 MET cc_start: 0.0874 (mtm) cc_final: 0.0292 (mtm) REVERT: P 209 PHE cc_start: 0.0908 (OUTLIER) cc_final: 0.0036 (t80) outliers start: 142 outliers final: 105 residues processed: 307 average time/residue: 1.0687 time to fit residues: 424.1550 Evaluate side-chains 304 residues out of total 3910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 174 time to evaluate : 3.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 702 GLU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 856 LYS Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 630 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 821 LEU Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 183 VAL Chi-restraints excluded: chain H residue 219 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 28 THR Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 109 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 169 LYS Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 191 VAL Chi-restraints excluded: chain M residue 2 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 131 LYS Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 152 LEU Chi-restraints excluded: chain M residue 164 VAL Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 183 VAL Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain N residue 6 GLN Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 127 SER Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 191 VAL Chi-restraints excluded: chain O residue 11 VAL Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 37 VAL Chi-restraints excluded: chain O residue 58 THR Chi-restraints excluded: chain O residue 71 THR Chi-restraints excluded: chain O residue 74 THR Chi-restraints excluded: chain O residue 164 VAL Chi-restraints excluded: chain O residue 165 THR Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 147 GLN Chi-restraints excluded: chain P residue 158 ASN Chi-restraints excluded: chain P residue 209 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 281 optimal weight: 1.9990 chunk 377 optimal weight: 20.0000 chunk 108 optimal weight: 0.7980 chunk 326 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 355 optimal weight: 7.9990 chunk 148 optimal weight: 20.0000 chunk 364 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 ASN H 116 ASN H 119 GLN O 169 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.211407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.130355 restraints weight = 50620.811| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 4.05 r_work: 0.3212 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 36615 Z= 0.307 Angle : 0.702 59.171 49813 Z= 0.385 Chirality : 0.049 0.944 5826 Planarity : 0.005 0.068 6328 Dihedral : 7.271 62.127 6187 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.37 % Favored : 93.52 % Rotamer: Outliers : 3.74 % Allowed : 19.82 % Favored : 76.44 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.16 (0.13), residues: 4428 helix: 1.96 (0.21), residues: 674 sheet: 0.50 (0.14), residues: 1285 loop : -1.07 (0.12), residues: 2469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 633 HIS 0.005 0.001 HIS L 92 PHE 0.020 0.002 PHE B 898 TYR 0.026 0.002 TYR B 265 ARG 0.015 0.000 ARG C 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12578.47 seconds wall clock time: 226 minutes 30.26 seconds (13590.26 seconds total)