Starting phenix.real_space_refine on Wed Mar 20 22:34:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swx_25488/03_2024/7swx_25488.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swx_25488/03_2024/7swx_25488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swx_25488/03_2024/7swx_25488.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swx_25488/03_2024/7swx_25488.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swx_25488/03_2024/7swx_25488.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7swx_25488/03_2024/7swx_25488.pdb" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 125 5.16 5 C 18208 2.51 5 N 4674 2.21 5 O 5662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28669 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 8557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8557 Classifications: {'peptide': 1095} Link IDs: {'PTRANS': 56, 'TRANS': 1038} Chain breaks: 4 Chain: "B" Number of atoms: 8595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8595 Classifications: {'peptide': 1099} Link IDs: {'PTRANS': 56, 'TRANS': 1042} Chain breaks: 4 Chain: "C" Number of atoms: 8595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1099, 8595 Classifications: {'peptide': 1099} Link IDs: {'PTRANS': 56, 'TRANS': 1042} Chain breaks: 4 Chain: "H" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 916 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "L" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 872 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 106} 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 14.67, per 1000 atoms: 0.51 Number of scatterers: 28669 At special positions: 0 Unit cell: (154, 171.6, 183.7, 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 125 16.00 O 5662 8.00 N 4674 7.00 C 18208 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=47, 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=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 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=2.02 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 A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 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 C 840 " - pdb=" SG CYS C 851 " 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 L 23 " - pdb=" SG CYS L 94 " distance=2.04 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 M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A1401 " - " ASN A 17 " " NAG A1402 " - " ASN A 61 " " NAG A1403 " - " ASN A 125 " " NAG A1404 " - " ASN A 149 " " NAG A1405 " - " ASN A 603 " " NAG A1406 " - " ASN A 657 " " NAG A1407 " - " ASN A 709 " " NAG B1201 " - " ASN B 61 " " NAG B1202 " - " ASN B 122 " " NAG B1203 " - " ASN B 149 " " NAG B1204 " - " ASN B 165 " " NAG B1205 " - " ASN B 234 " " NAG B1206 " - " ASN B 282 " " NAG B1207 " - " ASN B 603 " " NAG B1208 " - " ASN B 657 " " NAG B1209 " - " ASN B 709 " " NAG C1201 " - " ASN C 61 " " NAG C1202 " - " ASN C 122 " " NAG C1203 " - " ASN C 149 " " NAG C1204 " - " ASN C 165 " " NAG C1205 " - " ASN C 234 " " NAG C1206 " - " ASN C 282 " " NAG C1207 " - " ASN C 603 " " NAG C1208 " - " ASN C 657 " " NAG C1209 " - " ASN C 709 " " NAG D 1 " - " ASN A 165 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN A 343 " " NAG G 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN A 616 " " NAG K 1 " - " ASN B 17 " " NAG M 1 " - " ASN B 343 " " NAG N 1 " - " ASN B 616 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1074 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN C 17 " " NAG S 1 " - " ASN C 616 " " NAG T 1 " - " ASN C 801 " " NAG U 1 " - " ASN C1074 " " NAG V 1 " - " ASN C1134 " " NAG W 1 " - " ASN A 331 " " NAG X 1 " - " ASN A 717 " " NAG Y 1 " - " ASN A1074 " " NAG Z 1 " - " ASN A1098 " " NAG a 1 " - " ASN B 717 " " NAG b 1 " - " ASN B1098 " " NAG c 1 " - " ASN C 331 " " NAG d 1 " - " ASN C 717 " " NAG e 1 " - " ASN C1098 " " NAG f 1 " - " ASN B 331 " " NAG g 1 " - " ASN C 343 " Time building additional restraints: 12.10 Conformation dependent library (CDL) restraints added in 5.1 seconds 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6570 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 52 sheets defined 22.1% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.45 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.518A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.726A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.536A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 756 through 783 removed outlier: 3.535A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.518A pdb=" N ASN A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.658A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 890' Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.256A 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 945 through 965 removed outlier: 4.075A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) 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 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.504A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.679A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.636A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.660A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 753 Processing helix chain 'B' and resid 756 through 783 removed outlier: 3.577A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 848 through 856 removed outlier: 3.583A pdb=" N ASN B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.539A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.598A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.359A 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: 3.798A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (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 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.927A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 342 removed outlier: 3.522A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.827A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.658A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.530A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.619A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 756 through 783 removed outlier: 3.538A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.738A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.582A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 941 removed outlier: 4.358A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.119A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) 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 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.859A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'H' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.468A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.177A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.402A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.517A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.881A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.536A pdb=" N LEU A 141 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.070A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 11.380A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.933A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.335A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.633A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.258A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.401A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.391A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.332A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.332A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.304A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.416A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.197A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.440A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.517A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.784A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.784A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.428A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.554A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.540A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) 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 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.009A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.516A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.516A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.530A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.997A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.104A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.106A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.997A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.253A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 83 through 85 removed outlier: 13.007A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 11.971A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.087A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.916A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.278A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.493A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.386A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.386A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.583A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.553A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.913A pdb=" N VAL H 18 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.543A pdb=" N VAL H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TRP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS H 38 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN H 57 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.141A pdb=" N CYS H 96 " --> pdb=" O TRP H 108 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TRP H 108 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ARG H 98 " --> pdb=" O ASP H 106 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.348A pdb=" N LEU L 11 " --> pdb=" O GLU L 111 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA L 90 " --> pdb=" O LEU L 110 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN L 43 " --> pdb=" O LYS L 51 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS L 51 " --> pdb=" O GLN L 43 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.526A pdb=" N TYR L 31 " --> pdb=" O LYS L 36 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS L 36 " --> pdb=" O TYR L 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 1141 hydrogen bonds defined for protein. 3150 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.05 Time building geometry restraints manager: 13.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9059 1.34 - 1.47: 7519 1.47 - 1.59: 12587 1.59 - 1.72: 0 1.72 - 1.84: 156 Bond restraints: 29321 Sorted by residual: bond pdb=" N PRO C 817 " pdb=" CD PRO C 817 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.49e+01 bond pdb=" N LEU A 303 " pdb=" CA LEU A 303 " ideal model delta sigma weight residual 1.456 1.503 -0.046 1.31e-02 5.83e+03 1.24e+01 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C1 NAG A1403 " pdb=" O5 NAG A1403 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.94e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.74e+00 ... (remaining 29316 not shown) Histogram of bond angle deviations from ideal: 97.97 - 105.20: 543 105.20 - 112.44: 15135 112.44 - 119.67: 9518 119.67 - 126.90: 14417 126.90 - 134.13: 298 Bond angle restraints: 39911 Sorted by residual: angle pdb=" C SER B 659 " pdb=" CA SER B 659 " pdb=" CB SER B 659 " ideal model delta sigma weight residual 110.24 117.20 -6.96 1.46e+00 4.69e-01 2.27e+01 angle pdb=" N LEU L 53 " pdb=" CA LEU L 53 " pdb=" C LEU L 53 " ideal model delta sigma weight residual 110.42 103.85 6.57 1.55e+00 4.16e-01 1.79e+01 angle pdb=" CA PHE B 377 " pdb=" CB PHE B 377 " pdb=" CG PHE B 377 " ideal model delta sigma weight residual 113.80 117.84 -4.04 1.00e+00 1.00e+00 1.63e+01 angle pdb=" N ILE B1018 " pdb=" CA ILE B1018 " pdb=" C ILE B1018 " ideal model delta sigma weight residual 110.62 114.60 -3.98 1.02e+00 9.61e-01 1.52e+01 angle pdb=" N GLN B 774 " pdb=" CA GLN B 774 " pdb=" C GLN B 774 " ideal model delta sigma weight residual 111.07 106.94 4.13 1.07e+00 8.73e-01 1.49e+01 ... (remaining 39906 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 16504 17.98 - 35.97: 1492 35.97 - 53.95: 394 53.95 - 71.93: 72 71.93 - 89.91: 30 Dihedral angle restraints: 18492 sinusoidal: 8253 harmonic: 10239 Sorted by residual: dihedral pdb=" CB CYS C 15 " pdb=" SG CYS C 15 " pdb=" SG CYS C 136 " pdb=" CB CYS C 136 " ideal model delta sinusoidal sigma weight residual -86.00 -151.41 65.41 1 1.00e+01 1.00e-02 5.61e+01 dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual -86.00 -145.42 59.42 1 1.00e+01 1.00e-02 4.72e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 142.50 -49.50 1 1.00e+01 1.00e-02 3.36e+01 ... (remaining 18489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 4532 0.106 - 0.212: 175 0.212 - 0.319: 12 0.319 - 0.425: 3 0.425 - 0.531: 1 Chirality restraints: 4723 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.65e+01 chirality pdb=" C1 NAG A1401 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG A1401 " pdb=" O5 NAG A1401 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.05e+00 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.35 -0.05 2.00e-02 2.50e+03 5.19e+00 ... (remaining 4720 not shown) Planarity restraints: 5117 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1201 " 0.347 2.00e-02 2.50e+03 3.00e-01 1.12e+03 pdb=" C7 NAG C1201 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG C1201 " 0.106 2.00e-02 2.50e+03 pdb=" N2 NAG C1201 " -0.534 2.00e-02 2.50e+03 pdb=" O7 NAG C1201 " 0.162 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG Y 2 " 0.346 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG Y 2 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG Y 2 " 0.097 2.00e-02 2.50e+03 pdb=" N2 NAG Y 2 " -0.532 2.00e-02 2.50e+03 pdb=" O7 NAG Y 2 " 0.169 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1208 " -0.346 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG B1208 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG B1208 " -0.106 2.00e-02 2.50e+03 pdb=" N2 NAG B1208 " 0.533 2.00e-02 2.50e+03 pdb=" O7 NAG B1208 " -0.161 2.00e-02 2.50e+03 ... (remaining 5114 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3669 2.75 - 3.29: 26190 3.29 - 3.83: 45602 3.83 - 4.36: 53438 4.36 - 4.90: 94833 Nonbonded interactions: 223732 Sorted by model distance: nonbonded pdb=" OH TYR A 248 " pdb=" O SER A 256 " model vdw 2.217 2.440 nonbonded pdb=" OG SER A 711 " pdb=" OE1 GLN B 895 " model vdw 2.260 2.440 nonbonded pdb=" OD1 ASN B1135 " pdb=" N THR B1136 " model vdw 2.279 2.520 nonbonded pdb=" O TYR A 145 " pdb=" OH TYR H 102 " model vdw 2.286 2.440 nonbonded pdb=" OE2 GLU A 406 " pdb=" NZ LYS A 417 " model vdw 2.292 2.520 ... (remaining 223727 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 70 or resid 76 through 1146 or resid 1401 throu \ gh 1407)) selection = (chain 'B' and (resid 14 through 175 or resid 185 through 1146 or resid 1201 thr \ ough 1207)) selection = (chain 'C' and (resid 14 through 175 or resid 185 through 1146 or resid 1201 thr \ ough 1207)) } 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 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } 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=0.00 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.260 Check model and map are aligned: 0.430 Set scattering table: 0.270 Process input model: 78.100 Find NCS groups from input model: 2.180 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 29321 Z= 0.281 Angle : 0.662 8.956 39911 Z= 0.343 Chirality : 0.050 0.531 4723 Planarity : 0.013 0.300 5064 Dihedral : 14.732 89.913 11781 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.03 % Allowed : 13.07 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % 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: -0.62 (0.13), residues: 3488 helix: 1.23 (0.20), residues: 692 sheet: 0.90 (0.18), residues: 797 loop : -1.67 (0.12), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 50 HIS 0.012 0.001 HIS B1048 PHE 0.029 0.002 PHE C 377 TYR 0.028 0.001 TYR L 55 ARG 0.008 0.001 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 631 time to evaluate : 3.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.8121 (m) cc_final: 0.7804 (p) REVERT: A 324 GLU cc_start: 0.8213 (pt0) cc_final: 0.8006 (pt0) REVERT: A 450 ASN cc_start: 0.7725 (m-40) cc_final: 0.7277 (m110) REVERT: A 695 TYR cc_start: 0.7883 (p90) cc_final: 0.7156 (p90) REVERT: A 949 GLN cc_start: 0.8454 (mm110) cc_final: 0.8001 (mm-40) REVERT: A 1072 GLU cc_start: 0.7459 (pm20) cc_final: 0.7241 (pm20) REVERT: B 28 TYR cc_start: 0.8219 (m-80) cc_final: 0.7907 (m-80) REVERT: B 202 LYS cc_start: 0.7641 (mttt) cc_final: 0.7421 (mttm) REVERT: B 271 GLN cc_start: 0.7735 (mt0) cc_final: 0.7491 (mt0) REVERT: B 373 SER cc_start: 0.8151 (p) cc_final: 0.7847 (t) REVERT: B 378 LYS cc_start: 0.7926 (mttt) cc_final: 0.7680 (ttmm) REVERT: B 571 ASP cc_start: 0.7505 (t0) cc_final: 0.7225 (t0) REVERT: B 714 ILE cc_start: 0.7961 (mm) cc_final: 0.7753 (mt) REVERT: B 772 VAL cc_start: 0.8458 (m) cc_final: 0.8249 (t) REVERT: B 882 ILE cc_start: 0.8448 (pt) cc_final: 0.8132 (mt) REVERT: B 979 ASP cc_start: 0.7506 (t70) cc_final: 0.7109 (t0) REVERT: C 191 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7828 (mt-10) REVERT: C 296 LEU cc_start: 0.7763 (tp) cc_final: 0.7465 (tt) REVERT: C 378 LYS cc_start: 0.8019 (mtpp) cc_final: 0.7638 (mtpp) REVERT: C 440 ASN cc_start: 0.7716 (m110) cc_final: 0.7499 (m110) REVERT: C 529 LYS cc_start: 0.8128 (mmtt) cc_final: 0.7881 (mmtt) REVERT: C 558 LYS cc_start: 0.8163 (mtmt) cc_final: 0.7905 (mtmt) REVERT: C 571 ASP cc_start: 0.7921 (t70) cc_final: 0.6987 (t0) REVERT: C 736 VAL cc_start: 0.8435 (t) cc_final: 0.8208 (p) REVERT: C 772 VAL cc_start: 0.8675 (p) cc_final: 0.8416 (m) REVERT: C 1005 GLN cc_start: 0.8216 (mm-40) cc_final: 0.7999 (tp40) REVERT: C 1072 GLU cc_start: 0.7857 (pm20) cc_final: 0.7564 (pm20) REVERT: C 1075 PHE cc_start: 0.7578 (m-80) cc_final: 0.7271 (m-80) outliers start: 1 outliers final: 0 residues processed: 632 average time/residue: 0.4408 time to fit residues: 437.5344 Evaluate side-chains 591 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 591 time to evaluate : 3.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 294 optimal weight: 0.2980 chunk 264 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 178 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 chunk 273 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 166 optimal weight: 0.6980 chunk 203 optimal weight: 1.9990 chunk 316 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 115 GLN ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A 658 ASN B 501 ASN B 613 GLN C 388 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1101 HIS ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 29321 Z= 0.210 Angle : 0.589 11.186 39911 Z= 0.298 Chirality : 0.047 0.395 4723 Planarity : 0.004 0.055 5064 Dihedral : 8.230 59.402 5491 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.02 % Allowed : 13.17 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % 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: -0.47 (0.14), residues: 3488 helix: 1.47 (0.20), residues: 690 sheet: 0.87 (0.18), residues: 818 loop : -1.58 (0.12), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 47 HIS 0.007 0.001 HIS A 655 PHE 0.027 0.001 PHE C 970 TYR 0.018 0.001 TYR B1067 ARG 0.005 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 608 time to evaluate : 3.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.8140 (m) cc_final: 0.7754 (p) REVERT: A 266 TYR cc_start: 0.8433 (m-80) cc_final: 0.8148 (m-80) REVERT: A 306 PHE cc_start: 0.8927 (m-80) cc_final: 0.8634 (m-10) REVERT: A 450 ASN cc_start: 0.7711 (m-40) cc_final: 0.7279 (m110) REVERT: A 695 TYR cc_start: 0.7876 (p90) cc_final: 0.7060 (p90) REVERT: A 949 GLN cc_start: 0.8472 (mm110) cc_final: 0.8050 (mm-40) REVERT: B 28 TYR cc_start: 0.8256 (m-80) cc_final: 0.8054 (m-80) REVERT: B 66 HIS cc_start: 0.6567 (OUTLIER) cc_final: 0.6184 (p-80) REVERT: B 188 ASN cc_start: 0.7431 (m-40) cc_final: 0.7048 (m-40) REVERT: B 373 SER cc_start: 0.8134 (p) cc_final: 0.7878 (t) REVERT: B 378 LYS cc_start: 0.7824 (mttt) cc_final: 0.7530 (ttmm) REVERT: B 398 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7478 (m-30) REVERT: B 571 ASP cc_start: 0.7618 (t0) cc_final: 0.7226 (t0) REVERT: C 66 HIS cc_start: 0.7427 (m-70) cc_final: 0.7186 (m170) REVERT: C 81 ASN cc_start: 0.8264 (p0) cc_final: 0.8036 (p0) REVERT: C 158 ARG cc_start: 0.7954 (mtt90) cc_final: 0.7655 (mtt90) REVERT: C 200 TYR cc_start: 0.7930 (m-80) cc_final: 0.7661 (m-80) REVERT: C 296 LEU cc_start: 0.7736 (tp) cc_final: 0.7435 (tt) REVERT: C 304 LYS cc_start: 0.8136 (mmtp) cc_final: 0.7922 (mptt) REVERT: C 430 THR cc_start: 0.7667 (m) cc_final: 0.7160 (p) REVERT: C 440 ASN cc_start: 0.7716 (m110) cc_final: 0.7497 (m110) REVERT: C 495 TYR cc_start: 0.7530 (m-80) cc_final: 0.6682 (m-80) REVERT: C 529 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7883 (mmtt) REVERT: C 558 LYS cc_start: 0.8155 (mtmt) cc_final: 0.7899 (mtmt) REVERT: C 571 ASP cc_start: 0.7874 (t70) cc_final: 0.6977 (t0) REVERT: C 772 VAL cc_start: 0.8681 (p) cc_final: 0.8419 (m) REVERT: C 1005 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7952 (tp40) REVERT: C 1072 GLU cc_start: 0.7888 (pm20) cc_final: 0.7563 (pm20) REVERT: C 1141 LEU cc_start: 0.8187 (tt) cc_final: 0.7950 (tt) outliers start: 62 outliers final: 40 residues processed: 639 average time/residue: 0.4153 time to fit residues: 418.0703 Evaluate side-chains 603 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 561 time to evaluate : 3.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 176 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 263 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 317 optimal weight: 4.9990 chunk 342 optimal weight: 9.9990 chunk 282 optimal weight: 3.9990 chunk 314 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 254 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 207 HIS A 321 GLN B 501 ASN B 613 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 422 ASN C1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 29321 Z= 0.437 Angle : 0.680 13.997 39911 Z= 0.346 Chirality : 0.051 0.395 4723 Planarity : 0.005 0.057 5064 Dihedral : 7.697 59.990 5491 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.55 % Allowed : 14.22 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % 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: -0.74 (0.13), residues: 3488 helix: 1.09 (0.20), residues: 689 sheet: 0.64 (0.18), residues: 785 loop : -1.62 (0.12), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 47 HIS 0.008 0.002 HIS A 207 PHE 0.027 0.002 PHE C1121 TYR 0.031 0.002 TYR B 204 ARG 0.006 0.001 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 604 time to evaluate : 3.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.8257 (m) cc_final: 0.7814 (p) REVERT: A 266 TYR cc_start: 0.8392 (m-80) cc_final: 0.8120 (m-80) REVERT: A 420 ASP cc_start: 0.7561 (m-30) cc_final: 0.7243 (t0) REVERT: A 450 ASN cc_start: 0.7779 (m-40) cc_final: 0.7386 (m110) REVERT: A 695 TYR cc_start: 0.8146 (p90) cc_final: 0.7360 (p90) REVERT: A 803 SER cc_start: 0.8372 (t) cc_final: 0.8047 (p) REVERT: A 804 GLN cc_start: 0.8416 (mm-40) cc_final: 0.7858 (mm-40) REVERT: A 904 TYR cc_start: 0.7880 (m-10) cc_final: 0.7626 (m-80) REVERT: A 979 ASP cc_start: 0.7755 (t0) cc_final: 0.7450 (t0) REVERT: A 1130 ILE cc_start: 0.8247 (pt) cc_final: 0.7780 (mt) REVERT: B 153 MET cc_start: 0.6837 (mmm) cc_final: 0.6635 (mmm) REVERT: B 188 ASN cc_start: 0.7645 (m-40) cc_final: 0.7170 (m-40) REVERT: B 207 HIS cc_start: 0.7678 (t70) cc_final: 0.7475 (t-170) REVERT: B 376 THR cc_start: 0.8125 (OUTLIER) cc_final: 0.7878 (p) REVERT: B 378 LYS cc_start: 0.7976 (mttt) cc_final: 0.7693 (ttmm) REVERT: B 398 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7637 (m-30) REVERT: B 571 ASP cc_start: 0.7716 (t0) cc_final: 0.7231 (t0) REVERT: B 773 GLU cc_start: 0.7774 (tt0) cc_final: 0.7487 (tt0) REVERT: B 780 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6928 (mt-10) REVERT: C 132 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7178 (mt-10) REVERT: C 158 ARG cc_start: 0.7950 (mtt90) cc_final: 0.7504 (mtt90) REVERT: C 304 LYS cc_start: 0.8201 (mmtp) cc_final: 0.7978 (mptt) REVERT: C 430 THR cc_start: 0.7751 (m) cc_final: 0.7395 (p) REVERT: C 440 ASN cc_start: 0.7748 (m110) cc_final: 0.7524 (m110) REVERT: C 458 LYS cc_start: 0.8308 (mtpt) cc_final: 0.8106 (mtpt) REVERT: C 529 LYS cc_start: 0.8176 (mmtt) cc_final: 0.7908 (mmtt) REVERT: C 558 LYS cc_start: 0.8170 (mtmt) cc_final: 0.7853 (mtmt) REVERT: C 772 VAL cc_start: 0.8715 (p) cc_final: 0.8461 (m) REVERT: C 796 ASP cc_start: 0.7237 (t0) cc_final: 0.6996 (t70) REVERT: C 801 ASN cc_start: 0.7639 (m-40) cc_final: 0.7439 (m-40) REVERT: C 804 GLN cc_start: 0.8194 (mt0) cc_final: 0.7884 (mp10) REVERT: C 954 GLN cc_start: 0.8109 (mt0) cc_final: 0.7889 (mt0) REVERT: C 1005 GLN cc_start: 0.8263 (mm-40) cc_final: 0.8059 (mm-40) REVERT: C 1072 GLU cc_start: 0.7973 (pm20) cc_final: 0.7746 (pm20) REVERT: C 1141 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7856 (tt) REVERT: C 1142 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7253 (mp10) outliers start: 109 outliers final: 74 residues processed: 659 average time/residue: 0.4168 time to fit residues: 430.4537 Evaluate side-chains 651 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 573 time to evaluate : 3.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 127 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 501 ASN Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 313 optimal weight: 1.9990 chunk 238 optimal weight: 9.9990 chunk 164 optimal weight: 1.9990 chunk 35 optimal weight: 0.0870 chunk 151 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 chunk 318 optimal weight: 0.8980 chunk 337 optimal weight: 9.9990 chunk 166 optimal weight: 3.9990 chunk 301 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 658 ASN A1101 HIS A1106 GLN B 30 ASN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 613 GLN B 675 GLN C 949 GLN C1101 HIS ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 29321 Z= 0.333 Angle : 0.618 11.704 39911 Z= 0.313 Chirality : 0.048 0.362 4723 Planarity : 0.004 0.057 5064 Dihedral : 7.208 57.756 5491 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.39 % Allowed : 15.72 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % 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: -0.68 (0.13), residues: 3488 helix: 1.19 (0.20), residues: 688 sheet: 0.67 (0.18), residues: 773 loop : -1.59 (0.12), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 64 HIS 0.005 0.001 HIS B 146 PHE 0.035 0.002 PHE A 140 TYR 0.020 0.002 TYR C 495 ARG 0.007 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 581 time to evaluate : 2.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.8198 (m) cc_final: 0.7745 (p) REVERT: A 306 PHE cc_start: 0.9028 (m-80) cc_final: 0.8746 (m-10) REVERT: A 420 ASP cc_start: 0.7521 (m-30) cc_final: 0.7202 (t0) REVERT: A 450 ASN cc_start: 0.7771 (m-40) cc_final: 0.7369 (m110) REVERT: A 484 GLU cc_start: 0.8529 (pt0) cc_final: 0.8258 (pt0) REVERT: A 516 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7183 (mm-30) REVERT: A 654 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7482 (mt-10) REVERT: A 803 SER cc_start: 0.8337 (t) cc_final: 0.8010 (p) REVERT: A 904 TYR cc_start: 0.7865 (m-10) cc_final: 0.7619 (m-80) REVERT: A 979 ASP cc_start: 0.7729 (t0) cc_final: 0.7374 (t0) REVERT: B 66 HIS cc_start: 0.6921 (OUTLIER) cc_final: 0.6125 (p-80) REVERT: B 78 ARG cc_start: 0.7576 (ttm-80) cc_final: 0.6823 (ttp-110) REVERT: B 153 MET cc_start: 0.6844 (mmm) cc_final: 0.6621 (mmm) REVERT: B 188 ASN cc_start: 0.7595 (m-40) cc_final: 0.7121 (m-40) REVERT: B 207 HIS cc_start: 0.7651 (t70) cc_final: 0.7445 (t-170) REVERT: B 281 GLU cc_start: 0.7533 (pm20) cc_final: 0.7226 (pm20) REVERT: B 378 LYS cc_start: 0.7985 (mttt) cc_final: 0.7666 (ttmm) REVERT: B 398 ASP cc_start: 0.7835 (OUTLIER) cc_final: 0.7565 (m-30) REVERT: B 571 ASP cc_start: 0.7716 (t0) cc_final: 0.7204 (t0) REVERT: B 773 GLU cc_start: 0.7650 (tt0) cc_final: 0.7259 (tt0) REVERT: C 132 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7120 (mt-10) REVERT: C 158 ARG cc_start: 0.7957 (mtt90) cc_final: 0.7489 (mtt90) REVERT: C 304 LYS cc_start: 0.8153 (mmtp) cc_final: 0.7929 (mptt) REVERT: C 440 ASN cc_start: 0.7740 (m110) cc_final: 0.7522 (m110) REVERT: C 458 LYS cc_start: 0.8314 (mtpt) cc_final: 0.8114 (mtpt) REVERT: C 529 LYS cc_start: 0.8129 (mmtt) cc_final: 0.7863 (mmtt) REVERT: C 571 ASP cc_start: 0.7782 (t0) cc_final: 0.7408 (t0) REVERT: C 772 VAL cc_start: 0.8667 (p) cc_final: 0.8416 (m) REVERT: C 804 GLN cc_start: 0.8117 (mt0) cc_final: 0.7828 (mp10) REVERT: C 1005 GLN cc_start: 0.8231 (mm-40) cc_final: 0.8028 (mm-40) REVERT: C 1072 GLU cc_start: 0.8007 (pm20) cc_final: 0.7566 (pm20) REVERT: C 1141 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7749 (tt) REVERT: C 1142 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7285 (mp10) outliers start: 104 outliers final: 75 residues processed: 636 average time/residue: 0.4125 time to fit residues: 412.1975 Evaluate side-chains 650 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 571 time to evaluate : 3.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 245 HIS Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 280 optimal weight: 0.7980 chunk 191 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 251 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 287 optimal weight: 0.6980 chunk 233 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 172 optimal weight: 2.9990 chunk 302 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 245 HIS A1083 HIS B 30 ASN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 613 GLN C1101 HIS ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 29321 Z= 0.201 Angle : 0.603 19.771 39911 Z= 0.299 Chirality : 0.051 1.251 4723 Planarity : 0.004 0.054 5064 Dihedral : 6.868 58.791 5491 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.06 % Allowed : 16.50 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.13), residues: 3488 helix: 1.45 (0.20), residues: 688 sheet: 0.64 (0.18), residues: 786 loop : -1.49 (0.12), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 64 HIS 0.010 0.001 HIS C 207 PHE 0.017 0.001 PHE A 133 TYR 0.017 0.001 TYR A 265 ARG 0.007 0.000 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 584 time to evaluate : 3.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.8156 (m) cc_final: 0.7701 (p) REVERT: A 296 LEU cc_start: 0.7937 (tt) cc_final: 0.7734 (tp) REVERT: A 306 PHE cc_start: 0.8994 (m-80) cc_final: 0.8743 (m-10) REVERT: A 420 ASP cc_start: 0.7505 (m-30) cc_final: 0.7187 (t0) REVERT: A 450 ASN cc_start: 0.7746 (m-40) cc_final: 0.7345 (m110) REVERT: A 484 GLU cc_start: 0.8532 (pt0) cc_final: 0.8273 (pt0) REVERT: A 516 GLU cc_start: 0.7360 (mm-30) cc_final: 0.7130 (mm-30) REVERT: A 803 SER cc_start: 0.8276 (t) cc_final: 0.7963 (p) REVERT: A 825 LYS cc_start: 0.8790 (ttmm) cc_final: 0.8457 (mttm) REVERT: A 979 ASP cc_start: 0.7763 (t0) cc_final: 0.7346 (t0) REVERT: B 66 HIS cc_start: 0.6827 (OUTLIER) cc_final: 0.6131 (p-80) REVERT: B 78 ARG cc_start: 0.7520 (ttm-80) cc_final: 0.6913 (ttm110) REVERT: B 153 MET cc_start: 0.6884 (mmm) cc_final: 0.6637 (mmm) REVERT: B 188 ASN cc_start: 0.7510 (m-40) cc_final: 0.7050 (m-40) REVERT: B 281 GLU cc_start: 0.7501 (pm20) cc_final: 0.7223 (pm20) REVERT: B 376 THR cc_start: 0.8107 (OUTLIER) cc_final: 0.7873 (p) REVERT: B 378 LYS cc_start: 0.7972 (mttt) cc_final: 0.7703 (ttmm) REVERT: B 398 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7523 (m-30) REVERT: B 571 ASP cc_start: 0.7699 (t0) cc_final: 0.7191 (t0) REVERT: B 773 GLU cc_start: 0.7475 (tt0) cc_final: 0.7138 (tt0) REVERT: B 1073 LYS cc_start: 0.8114 (mmmm) cc_final: 0.7863 (mmtp) REVERT: C 132 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7096 (mt-10) REVERT: C 158 ARG cc_start: 0.7910 (mtt90) cc_final: 0.7445 (mtt90) REVERT: C 287 ASP cc_start: 0.8075 (t0) cc_final: 0.7544 (t0) REVERT: C 440 ASN cc_start: 0.7733 (m110) cc_final: 0.7514 (m110) REVERT: C 516 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7410 (mt-10) REVERT: C 529 LYS cc_start: 0.8119 (mmtt) cc_final: 0.7849 (mmtt) REVERT: C 571 ASP cc_start: 0.7783 (t0) cc_final: 0.7396 (t0) REVERT: C 772 VAL cc_start: 0.8654 (p) cc_final: 0.8363 (m) REVERT: C 1005 GLN cc_start: 0.8238 (mm-40) cc_final: 0.8022 (mm-40) REVERT: C 1072 GLU cc_start: 0.7992 (pm20) cc_final: 0.7557 (pm20) REVERT: C 1141 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7685 (tt) REVERT: C 1142 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7235 (mp10) outliers start: 94 outliers final: 63 residues processed: 639 average time/residue: 0.4291 time to fit residues: 432.0025 Evaluate side-chains 643 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 575 time to evaluate : 3.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 113 optimal weight: 2.9990 chunk 303 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 337 optimal weight: 8.9990 chunk 280 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 177 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 764 ASN B 30 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 613 GLN C1101 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 29321 Z= 0.406 Angle : 0.669 18.505 39911 Z= 0.336 Chirality : 0.054 1.212 4723 Planarity : 0.005 0.056 5064 Dihedral : 6.911 57.625 5491 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.04 % Favored : 95.93 % Rotamer: Outliers : 3.81 % Allowed : 16.89 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.13), residues: 3488 helix: 1.22 (0.20), residues: 693 sheet: 0.51 (0.18), residues: 780 loop : -1.53 (0.12), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 64 HIS 0.007 0.001 HIS B 207 PHE 0.027 0.002 PHE C 377 TYR 0.024 0.002 TYR B 204 ARG 0.007 0.001 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 593 time to evaluate : 3.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.8184 (m) cc_final: 0.7722 (p) REVERT: A 266 TYR cc_start: 0.8419 (m-80) cc_final: 0.8095 (m-80) REVERT: A 306 PHE cc_start: 0.9021 (m-80) cc_final: 0.8755 (m-10) REVERT: A 420 ASP cc_start: 0.7533 (m-30) cc_final: 0.7227 (t0) REVERT: A 450 ASN cc_start: 0.7783 (m-40) cc_final: 0.7422 (m110) REVERT: A 484 GLU cc_start: 0.8549 (pt0) cc_final: 0.8295 (pt0) REVERT: A 516 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7142 (mm-30) REVERT: A 666 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7849 (mt) REVERT: A 803 SER cc_start: 0.8351 (t) cc_final: 0.8009 (p) REVERT: A 825 LYS cc_start: 0.8863 (ttmm) cc_final: 0.8517 (mttm) REVERT: A 979 ASP cc_start: 0.7762 (t0) cc_final: 0.7338 (t0) REVERT: B 66 HIS cc_start: 0.6991 (OUTLIER) cc_final: 0.6059 (p-80) REVERT: B 78 ARG cc_start: 0.7644 (ttm-80) cc_final: 0.6842 (ttp-110) REVERT: B 188 ASN cc_start: 0.7627 (m-40) cc_final: 0.7098 (m-40) REVERT: B 281 GLU cc_start: 0.7537 (pm20) cc_final: 0.7220 (pm20) REVERT: B 376 THR cc_start: 0.8135 (OUTLIER) cc_final: 0.7913 (p) REVERT: B 378 LYS cc_start: 0.7970 (mttt) cc_final: 0.7684 (ttmm) REVERT: B 398 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7638 (m-30) REVERT: B 406 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6832 (mt-10) REVERT: B 571 ASP cc_start: 0.7729 (t0) cc_final: 0.7181 (t0) REVERT: B 773 GLU cc_start: 0.7526 (tt0) cc_final: 0.7157 (tt0) REVERT: B 900 MET cc_start: 0.7769 (mtt) cc_final: 0.7270 (mtt) REVERT: B 1073 LYS cc_start: 0.8091 (mmmm) cc_final: 0.7848 (mmtp) REVERT: C 158 ARG cc_start: 0.7918 (mtt90) cc_final: 0.7399 (mtt90) REVERT: C 458 LYS cc_start: 0.8330 (mtpt) cc_final: 0.8123 (mtpt) REVERT: C 571 ASP cc_start: 0.7888 (t0) cc_final: 0.7636 (t0) REVERT: C 772 VAL cc_start: 0.8658 (p) cc_final: 0.8409 (m) REVERT: C 796 ASP cc_start: 0.7190 (t0) cc_final: 0.6935 (t70) REVERT: C 1005 GLN cc_start: 0.8229 (mm-40) cc_final: 0.8022 (mm-40) REVERT: C 1072 GLU cc_start: 0.8052 (pm20) cc_final: 0.7784 (pm20) REVERT: C 1141 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7725 (tt) REVERT: C 1142 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7322 (mp10) outliers start: 117 outliers final: 90 residues processed: 662 average time/residue: 0.4078 time to fit residues: 424.8474 Evaluate side-chains 678 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 581 time to evaluate : 3.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 605 SER Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 325 optimal weight: 0.2980 chunk 38 optimal weight: 0.9990 chunk 192 optimal weight: 0.9990 chunk 246 optimal weight: 0.9990 chunk 191 optimal weight: 0.7980 chunk 284 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 336 optimal weight: 20.0000 chunk 210 optimal weight: 0.8980 chunk 205 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 314 GLN A 935 GLN B 30 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 613 GLN C 949 GLN C1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 29321 Z= 0.213 Angle : 0.596 13.665 39911 Z= 0.298 Chirality : 0.049 0.963 4723 Planarity : 0.004 0.054 5064 Dihedral : 6.567 57.514 5491 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.93 % Allowed : 18.32 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.14), residues: 3488 helix: 1.49 (0.20), residues: 688 sheet: 0.44 (0.18), residues: 793 loop : -1.39 (0.12), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.008 0.001 HIS B 207 PHE 0.042 0.001 PHE A 140 TYR 0.019 0.001 TYR A 265 ARG 0.006 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 579 time to evaluate : 3.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.8044 (m) cc_final: 0.7593 (p) REVERT: A 266 TYR cc_start: 0.8337 (m-80) cc_final: 0.8117 (m-80) REVERT: A 298 GLU cc_start: 0.7538 (tt0) cc_final: 0.7162 (tt0) REVERT: A 306 PHE cc_start: 0.8982 (m-80) cc_final: 0.8747 (m-10) REVERT: A 420 ASP cc_start: 0.7510 (m-30) cc_final: 0.7201 (t0) REVERT: A 450 ASN cc_start: 0.7736 (m-40) cc_final: 0.7375 (m110) REVERT: A 516 GLU cc_start: 0.7344 (mm-30) cc_final: 0.7104 (mm-30) REVERT: A 803 SER cc_start: 0.8297 (t) cc_final: 0.7972 (p) REVERT: A 825 LYS cc_start: 0.8725 (ttmm) cc_final: 0.8478 (mttm) REVERT: A 979 ASP cc_start: 0.7769 (t0) cc_final: 0.7324 (t0) REVERT: B 66 HIS cc_start: 0.6910 (OUTLIER) cc_final: 0.6033 (p-80) REVERT: B 78 ARG cc_start: 0.7525 (ttm-80) cc_final: 0.6819 (ttp-110) REVERT: B 188 ASN cc_start: 0.7524 (m-40) cc_final: 0.7078 (m-40) REVERT: B 376 THR cc_start: 0.8104 (OUTLIER) cc_final: 0.7889 (p) REVERT: B 378 LYS cc_start: 0.7977 (mttt) cc_final: 0.7722 (ttmm) REVERT: B 398 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7529 (m-30) REVERT: B 571 ASP cc_start: 0.7747 (t0) cc_final: 0.7185 (t0) REVERT: B 780 GLU cc_start: 0.7250 (mt-10) cc_final: 0.7002 (mt-10) REVERT: B 882 ILE cc_start: 0.8475 (pt) cc_final: 0.8131 (mt) REVERT: B 900 MET cc_start: 0.7739 (mtt) cc_final: 0.7503 (mtt) REVERT: B 1073 LYS cc_start: 0.8057 (mmmm) cc_final: 0.7829 (mmtp) REVERT: C 158 ARG cc_start: 0.7817 (mtt90) cc_final: 0.7347 (mtt90) REVERT: C 200 TYR cc_start: 0.7871 (m-80) cc_final: 0.7626 (m-80) REVERT: C 571 ASP cc_start: 0.7888 (t0) cc_final: 0.7635 (t0) REVERT: C 772 VAL cc_start: 0.8658 (p) cc_final: 0.8374 (m) REVERT: C 796 ASP cc_start: 0.7129 (t0) cc_final: 0.6855 (t0) REVERT: C 1005 GLN cc_start: 0.8227 (mm-40) cc_final: 0.8018 (mm-40) REVERT: C 1072 GLU cc_start: 0.8021 (pm20) cc_final: 0.7737 (pm20) REVERT: C 1141 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7642 (tt) REVERT: C 1142 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7293 (mp10) outliers start: 90 outliers final: 67 residues processed: 631 average time/residue: 0.4042 time to fit residues: 401.5371 Evaluate side-chains 643 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 571 time to evaluate : 3.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 208 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 213 optimal weight: 0.2980 chunk 229 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 264 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 GLN B 30 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 957 GLN C1101 HIS ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 29321 Z= 0.215 Angle : 0.588 15.405 39911 Z= 0.293 Chirality : 0.049 0.844 4723 Planarity : 0.004 0.054 5064 Dihedral : 6.496 59.913 5491 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.87 % Allowed : 18.98 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % 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: -0.45 (0.14), residues: 3488 helix: 1.51 (0.20), residues: 700 sheet: 0.47 (0.18), residues: 784 loop : -1.35 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.011 0.001 HIS B 207 PHE 0.037 0.001 PHE C 970 TYR 0.028 0.001 TYR C 707 ARG 0.008 0.000 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 578 time to evaluate : 3.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.8057 (m) cc_final: 0.7598 (p) REVERT: A 298 GLU cc_start: 0.7525 (tt0) cc_final: 0.7150 (tt0) REVERT: A 306 PHE cc_start: 0.8969 (m-80) cc_final: 0.8755 (m-10) REVERT: A 420 ASP cc_start: 0.7510 (m-30) cc_final: 0.7197 (t0) REVERT: A 450 ASN cc_start: 0.7741 (m-40) cc_final: 0.7378 (m110) REVERT: A 516 GLU cc_start: 0.7332 (mm-30) cc_final: 0.7118 (mm-30) REVERT: A 803 SER cc_start: 0.8295 (t) cc_final: 0.7969 (p) REVERT: A 825 LYS cc_start: 0.8751 (ttmm) cc_final: 0.8489 (mttm) REVERT: A 979 ASP cc_start: 0.7755 (t0) cc_final: 0.7337 (t0) REVERT: B 66 HIS cc_start: 0.6957 (OUTLIER) cc_final: 0.6067 (p-80) REVERT: B 78 ARG cc_start: 0.7539 (ttm-80) cc_final: 0.6827 (ttp-110) REVERT: B 188 ASN cc_start: 0.7542 (m-40) cc_final: 0.7053 (m-40) REVERT: B 378 LYS cc_start: 0.7954 (mttt) cc_final: 0.7702 (ttmm) REVERT: B 398 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7527 (m-30) REVERT: B 489 TYR cc_start: 0.7689 (m-80) cc_final: 0.7354 (m-80) REVERT: B 571 ASP cc_start: 0.7742 (t0) cc_final: 0.7183 (t0) REVERT: B 703 ASN cc_start: 0.8180 (t0) cc_final: 0.7486 (m-40) REVERT: B 780 GLU cc_start: 0.7240 (mt-10) cc_final: 0.7032 (mt-10) REVERT: B 882 ILE cc_start: 0.8405 (pt) cc_final: 0.8107 (mt) REVERT: B 900 MET cc_start: 0.7743 (mtt) cc_final: 0.7362 (mtt) REVERT: B 979 ASP cc_start: 0.7516 (t0) cc_final: 0.7212 (t0) REVERT: B 1073 LYS cc_start: 0.8083 (mmmm) cc_final: 0.7834 (mmtp) REVERT: C 158 ARG cc_start: 0.7965 (mtt90) cc_final: 0.7427 (mtt90) REVERT: C 316 SER cc_start: 0.8333 (p) cc_final: 0.8094 (m) REVERT: C 772 VAL cc_start: 0.8660 (p) cc_final: 0.8375 (m) REVERT: C 1005 GLN cc_start: 0.8226 (mm-40) cc_final: 0.8023 (mm-40) REVERT: C 1072 GLU cc_start: 0.8030 (pm20) cc_final: 0.7754 (pm20) REVERT: C 1141 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7582 (tt) REVERT: C 1142 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7319 (mp10) outliers start: 88 outliers final: 68 residues processed: 631 average time/residue: 0.4126 time to fit residues: 407.8064 Evaluate side-chains 644 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 572 time to evaluate : 3.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 CYS Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 691 SER Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 894 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 373 SER Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 305 optimal weight: 2.9990 chunk 322 optimal weight: 1.9990 chunk 294 optimal weight: 0.0170 chunk 313 optimal weight: 2.9990 chunk 188 optimal weight: 0.0970 chunk 136 optimal weight: 2.9990 chunk 246 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 283 optimal weight: 0.0040 chunk 296 optimal weight: 5.9990 chunk 312 optimal weight: 0.4980 overall best weight: 0.3228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 954 GLN A 965 GLN B 30 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 613 GLN B 762 GLN C 901 GLN C1010 GLN C1101 HIS ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 29321 Z= 0.155 Angle : 0.569 14.761 39911 Z= 0.283 Chirality : 0.047 0.709 4723 Planarity : 0.004 0.053 5064 Dihedral : 6.298 57.483 5491 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.31 % Allowed : 19.20 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % 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: -0.29 (0.14), residues: 3488 helix: 1.74 (0.20), residues: 694 sheet: 0.62 (0.18), residues: 772 loop : -1.28 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.012 0.001 HIS B 207 PHE 0.033 0.001 PHE A 140 TYR 0.023 0.001 TYR C 707 ARG 0.009 0.000 ARG B 158 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 592 time to evaluate : 2.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.8003 (m) cc_final: 0.7553 (p) REVERT: A 298 GLU cc_start: 0.7507 (tt0) cc_final: 0.7123 (tt0) REVERT: A 414 GLN cc_start: 0.8274 (mm-40) cc_final: 0.7741 (mm-40) REVERT: A 420 ASP cc_start: 0.7531 (m-30) cc_final: 0.7202 (t0) REVERT: A 450 ASN cc_start: 0.7733 (m-40) cc_final: 0.7381 (m110) REVERT: A 803 SER cc_start: 0.8253 (t) cc_final: 0.7937 (p) REVERT: A 825 LYS cc_start: 0.8691 (ttmm) cc_final: 0.8439 (mttm) REVERT: A 979 ASP cc_start: 0.7765 (t0) cc_final: 0.7396 (t0) REVERT: B 66 HIS cc_start: 0.6907 (OUTLIER) cc_final: 0.6373 (p-80) REVERT: B 188 ASN cc_start: 0.7470 (m-40) cc_final: 0.6997 (m-40) REVERT: B 378 LYS cc_start: 0.7917 (mttt) cc_final: 0.7671 (ttmm) REVERT: B 398 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7255 (m-30) REVERT: B 489 TYR cc_start: 0.7727 (m-80) cc_final: 0.7413 (m-80) REVERT: B 571 ASP cc_start: 0.7771 (t0) cc_final: 0.7167 (t0) REVERT: B 643 PHE cc_start: 0.7986 (t80) cc_final: 0.7714 (t80) REVERT: B 703 ASN cc_start: 0.8150 (t0) cc_final: 0.7468 (m-40) REVERT: B 773 GLU cc_start: 0.7396 (tt0) cc_final: 0.6915 (tt0) REVERT: B 780 GLU cc_start: 0.7237 (mt-10) cc_final: 0.7028 (mt-10) REVERT: B 882 ILE cc_start: 0.8369 (pt) cc_final: 0.8110 (mt) REVERT: B 933 LYS cc_start: 0.8441 (mtpt) cc_final: 0.8162 (mtpp) REVERT: B 979 ASP cc_start: 0.7523 (t0) cc_final: 0.7244 (t0) REVERT: B 1073 LYS cc_start: 0.8053 (mmmm) cc_final: 0.7814 (mmtp) REVERT: C 158 ARG cc_start: 0.7962 (mtt90) cc_final: 0.7456 (mtt90) REVERT: C 1072 GLU cc_start: 0.8036 (pm20) cc_final: 0.7763 (pm20) REVERT: C 1141 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7681 (tt) REVERT: C 1142 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.7327 (mp10) outliers start: 71 outliers final: 56 residues processed: 634 average time/residue: 0.4187 time to fit residues: 413.9014 Evaluate side-chains 634 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 574 time to evaluate : 3.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 516 GLU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 205 optimal weight: 0.6980 chunk 331 optimal weight: 5.9990 chunk 202 optimal weight: 0.2980 chunk 157 optimal weight: 0.8980 chunk 230 optimal weight: 0.9990 chunk 347 optimal weight: 5.9990 chunk 320 optimal weight: 2.9990 chunk 276 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 213 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 965 GLN B 30 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 658 ASN C 901 GLN C1101 HIS ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 29321 Z= 0.218 Angle : 0.589 14.446 39911 Z= 0.293 Chirality : 0.048 0.567 4723 Planarity : 0.004 0.053 5064 Dihedral : 6.253 59.933 5491 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.38 % Allowed : 19.56 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.14), residues: 3488 helix: 1.66 (0.20), residues: 695 sheet: 0.53 (0.18), residues: 780 loop : -1.26 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 64 HIS 0.013 0.001 HIS B 207 PHE 0.032 0.001 PHE C 970 TYR 0.019 0.001 TYR C 707 ARG 0.008 0.000 ARG C 567 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6976 Ramachandran restraints generated. 3488 Oldfield, 0 Emsley, 3488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 567 time to evaluate : 3.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.8031 (m) cc_final: 0.7584 (p) REVERT: A 298 GLU cc_start: 0.7523 (tt0) cc_final: 0.7160 (tt0) REVERT: A 306 PHE cc_start: 0.9010 (m-80) cc_final: 0.8745 (m-10) REVERT: A 414 GLN cc_start: 0.8274 (mm-40) cc_final: 0.7720 (mm-40) REVERT: A 420 ASP cc_start: 0.7543 (m-30) cc_final: 0.7227 (t0) REVERT: A 450 ASN cc_start: 0.7747 (m-40) cc_final: 0.7386 (m110) REVERT: A 803 SER cc_start: 0.8286 (t) cc_final: 0.7962 (p) REVERT: A 825 LYS cc_start: 0.8691 (ttmm) cc_final: 0.8460 (mttm) REVERT: A 979 ASP cc_start: 0.7757 (t0) cc_final: 0.7439 (t0) REVERT: B 66 HIS cc_start: 0.6989 (OUTLIER) cc_final: 0.6165 (p-80) REVERT: B 78 ARG cc_start: 0.7549 (ttm-80) cc_final: 0.6850 (ttp-110) REVERT: B 188 ASN cc_start: 0.7516 (m-40) cc_final: 0.7005 (m-40) REVERT: B 378 LYS cc_start: 0.7935 (mttt) cc_final: 0.7694 (ttmm) REVERT: B 398 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7484 (m-30) REVERT: B 489 TYR cc_start: 0.7723 (m-80) cc_final: 0.7406 (m-80) REVERT: B 571 ASP cc_start: 0.7741 (t0) cc_final: 0.7172 (t0) REVERT: B 703 ASN cc_start: 0.8184 (t0) cc_final: 0.7460 (m-40) REVERT: B 882 ILE cc_start: 0.8365 (pt) cc_final: 0.8121 (mt) REVERT: B 933 LYS cc_start: 0.8464 (mtpt) cc_final: 0.8184 (mtpp) REVERT: B 979 ASP cc_start: 0.7557 (t0) cc_final: 0.7275 (t0) REVERT: C 158 ARG cc_start: 0.7937 (mtt90) cc_final: 0.7382 (mtt90) REVERT: C 957 GLN cc_start: 0.8525 (tt0) cc_final: 0.8232 (tt0) REVERT: C 1072 GLU cc_start: 0.8056 (pm20) cc_final: 0.7784 (pm20) REVERT: C 1141 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7687 (tt) REVERT: C 1142 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7331 (mp10) outliers start: 73 outliers final: 58 residues processed: 614 average time/residue: 0.4139 time to fit residues: 398.6686 Evaluate side-chains 625 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 563 time to evaluate : 3.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 1028 LYS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 883 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1142 GLN Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 219 optimal weight: 0.7980 chunk 294 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 255 optimal weight: 0.4980 chunk 40 optimal weight: 4.9990 chunk 76 optimal weight: 0.2980 chunk 277 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 284 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 164 ASN A 207 HIS A 965 GLN B 30 ASN ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN C 901 GLN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.142390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.115934 restraints weight = 41286.790| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.53 r_work: 0.3357 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 29321 Z= 0.197 Angle : 0.579 14.312 39911 Z= 0.288 Chirality : 0.047 0.529 4723 Planarity : 0.004 0.053 5064 Dihedral : 6.114 59.670 5491 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.09 % Allowed : 20.05 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.13 % 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: -0.30 (0.14), residues: 3488 helix: 1.68 (0.20), residues: 695 sheet: 0.52 (0.18), residues: 764 loop : -1.22 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.013 0.001 HIS B 207 PHE 0.031 0.001 PHE A 140 TYR 0.021 0.001 TYR C 707 ARG 0.008 0.000 ARG C 567 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8149.88 seconds wall clock time: 146 minutes 5.90 seconds (8765.90 seconds total)