Starting phenix.real_space_refine on Sat Aug 10 18:08:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1d_18808/08_2024/8r1d_18808.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1d_18808/08_2024/8r1d_18808.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1d_18808/08_2024/8r1d_18808.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1d_18808/08_2024/8r1d_18808.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1d_18808/08_2024/8r1d_18808.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1d_18808/08_2024/8r1d_18808.cif" } resolution = 2.37 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= 0.008 sd= 0.083 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 138 5.16 5 C 19377 2.51 5 N 5043 2.21 5 O 5935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 109": "OD1" <-> "OD2" Residue "F TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 59": "OE1" <-> "OE2" Residue "L TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 91": "OD1" <-> "OD2" Residue "A PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A GLU 337": "OE1" <-> "OE2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 651": "OE1" <-> "OE2" Residue "A TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 777": "OE1" <-> "OE2" Residue "A PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 976": "OD1" <-> "OD2" Residue "A GLU 985": "OE1" <-> "OE2" Residue "A GLU 987": "OE1" <-> "OE2" Residue "A ASP 991": "OD1" <-> "OD2" Residue "A ASP 1081": "OD1" <-> "OD2" Residue "A GLU 1089": "OE1" <-> "OE2" Residue "A GLU 1108": "OE1" <-> "OE2" Residue "A PHE 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 93": "OE1" <-> "OE2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 284": "OD1" <-> "OD2" Residue "B GLU 295": "OE1" <-> "OE2" Residue "B GLU 306": "OE1" <-> "OE2" Residue "B PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 658": "OE1" <-> "OE2" Residue "B TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 865": "OE1" <-> "OE2" Residue "B PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 933": "OD1" <-> "OD2" Residue "B ASP 947": "OD1" <-> "OD2" Residue "B ASP 976": "OD1" <-> "OD2" Residue "B GLU 985": "OE1" <-> "OE2" Residue "B GLU 987": "OE1" <-> "OE2" Residue "B ASP 991": "OD1" <-> "OD2" Residue "B ASP 1081": "OD1" <-> "OD2" Residue "B GLU 1089": "OE1" <-> "OE2" Residue "B GLU 1108": "OE1" <-> "OE2" Residue "C PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 337": "OE1" <-> "OE2" Residue "C PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 513": "OE1" <-> "OE2" Residue "C PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 699": "OE1" <-> "OE2" Residue "C TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 777": "OE1" <-> "OE2" Residue "C PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 865": "OE1" <-> "OE2" Residue "C PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 933": "OD1" <-> "OD2" Residue "C GLU 985": "OE1" <-> "OE2" Residue "C ASP 991": "OD1" <-> "OD2" Residue "C ASP 1081": "OD1" <-> "OD2" Residue "C GLU 1108": "OE1" <-> "OE2" Residue "C TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 25": "OD1" <-> "OD2" Residue "E TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "E TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 25": "OD1" <-> "OD2" Residue "G TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 30493 Number of models: 1 Model: "" Number of chains: 18 Chain: "F" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 905 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "D" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 905 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "H" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 905 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 788 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "A" Number of atoms: 8317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8317 Classifications: {'peptide': 1065} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1014} Chain breaks: 6 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 8317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8317 Classifications: {'peptide': 1065} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1014} Chain breaks: 6 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 8317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8317 Classifications: {'peptide': 1065} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1014} Chain breaks: 6 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 788 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "G" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 788 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 14.92, per 1000 atoms: 0.49 Number of scatterers: 30493 At special positions: 0 Unit cell: (170.16, 162.857, 172.351, 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 138 16.00 O 5935 8.00 N 5043 7.00 C 19377 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 106 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 106 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A 837 " - pdb=" SG CYS A 848 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.04 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B 837 " - pdb=" SG CYS B 848 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C 837 " - pdb=" SG CYS C 848 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 87 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 87 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 58 " " NAG A1302 " - " ASN A 279 " " NAG A1303 " - " ASN A 613 " " NAG A1304 " - " ASN A 654 " " NAG A1305 " - " ASN A1071 " " NAG A1306 " - " ASN A 714 " " NAG A1307 " - " ASN A 798 " " NAG A1308 " - " ASN A1131 " " NAG A1309 " - " ASN A 231 " " NAG A1310 " - " ASN A 706 " " NAG B1301 " - " ASN B 58 " " NAG B1302 " - " ASN B 279 " " NAG B1303 " - " ASN B 613 " " NAG B1304 " - " ASN B 654 " " NAG B1305 " - " ASN B1071 " " NAG B1306 " - " ASN B 714 " " NAG B1307 " - " ASN B 798 " " NAG B1308 " - " ASN B1131 " " NAG B1309 " - " ASN B 231 " " NAG B1310 " - " ASN B 706 " " NAG C1301 " - " ASN C 58 " " NAG C1302 " - " ASN C 279 " " NAG C1303 " - " ASN C 613 " " NAG C1304 " - " ASN C 654 " " NAG C1305 " - " ASN C1071 " " NAG C1306 " - " ASN C 714 " " NAG C1307 " - " ASN C 798 " " NAG C1308 " - " ASN C1131 " " NAG C1309 " - " ASN C 231 " " NAG C1310 " - " ASN C 706 " Time building additional restraints: 11.54 Conformation dependent library (CDL) restraints added in 4.8 seconds 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7188 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 68 sheets defined 23.5% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.66 Creating SS restraints... Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 26 through 30 Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.641A pdb=" N PHE A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 369' Processing helix chain 'A' and resid 380 through 386 removed outlier: 3.529A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 4.665A pdb=" N SER A 405 " --> pdb=" O ASN A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 removed outlier: 3.607A pdb=" N SER A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 613 through 617 Processing helix chain 'A' and resid 734 through 741 Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 755 through 780 removed outlier: 3.637A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 823 removed outlier: 3.510A pdb=" N VAL A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 853 removed outlier: 3.889A pdb=" N ALA A 849 " --> pdb=" O ASP A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.880A pdb=" N ALA A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 906 Processing helix chain 'A' and resid 909 through 916 removed outlier: 3.987A pdb=" N LEU A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 Processing helix chain 'A' and resid 942 through 962 Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1030 removed outlier: 3.823A pdb=" N VAL A 988 " --> pdb=" O VAL A 984 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 4.222A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 361 through 363 No H-bonds generated for 'chain 'B' and resid 361 through 363' Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.709A pdb=" N PHE B 368 " --> pdb=" O VAL B 364 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 369 " --> pdb=" O LEU B 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 364 through 369' Processing helix chain 'B' and resid 380 through 386 removed outlier: 3.552A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 removed outlier: 4.502A pdb=" N SER B 405 " --> pdb=" O ASN B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 435 through 440 removed outlier: 3.642A pdb=" N SER B 440 " --> pdb=" O ASN B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 502 Processing helix chain 'B' and resid 613 through 617 Processing helix chain 'B' and resid 734 through 741 Processing helix chain 'B' and resid 743 through 752 removed outlier: 4.001A pdb=" N GLN B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 780 removed outlier: 3.673A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 845 through 853 removed outlier: 3.921A pdb=" N ALA B 849 " --> pdb=" O ASP B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.805A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 906 Processing helix chain 'B' and resid 909 through 916 removed outlier: 3.918A pdb=" N LEU B 913 " --> pdb=" O THR B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 942 through 962 Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 Processing helix chain 'B' and resid 982 through 1030 removed outlier: 3.782A pdb=" N VAL B 988 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 4.281A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 361 through 363 No H-bonds generated for 'chain 'C' and resid 361 through 363' Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.664A pdb=" N PHE C 368 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA C 369 " --> pdb=" O LEU C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 369' Processing helix chain 'C' and resid 380 through 386 removed outlier: 3.557A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 removed outlier: 4.631A pdb=" N SER C 405 " --> pdb=" O ASN C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 435 through 440 removed outlier: 3.604A pdb=" N SER C 440 " --> pdb=" O ASN C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 613 through 617 Processing helix chain 'C' and resid 734 through 741 Processing helix chain 'C' and resid 743 through 751 Processing helix chain 'C' and resid 752 through 754 No H-bonds generated for 'chain 'C' and resid 752 through 754' Processing helix chain 'C' and resid 755 through 780 removed outlier: 3.648A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 823 removed outlier: 3.508A pdb=" N VAL C 823 " --> pdb=" O LEU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 845 through 853 removed outlier: 3.915A pdb=" N ALA C 849 " --> pdb=" O ASP C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 888 removed outlier: 3.915A pdb=" N ALA C 887 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 906 Processing helix chain 'C' and resid 909 through 916 removed outlier: 3.947A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 Processing helix chain 'C' and resid 942 through 962 Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 981 Processing helix chain 'C' and resid 982 through 1030 removed outlier: 3.775A pdb=" N VAL C 988 " --> pdb=" O VAL C 984 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 4.276A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 30 Processing helix chain 'E' and resid 78 through 82 Processing helix chain 'G' and resid 26 through 30 Processing helix chain 'G' and resid 78 through 82 Processing sheet with id=AA1, first strand: chain 'F' and resid 3 through 7 removed outlier: 5.902A pdb=" N GLY F 16 " --> pdb=" O SER F 85 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.318A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.994A pdb=" N TYR F 110 " --> pdb=" O THR F 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.287A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.975A pdb=" N TYR D 110 " --> pdb=" O THR D 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.236A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.034A pdb=" N TYR H 110 " --> pdb=" O THR H 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.469A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AB3, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AB4, first strand: chain 'A' and resid 20 through 27 removed outlier: 7.833A pdb=" N ASN A 58 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N TYR A 266 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N PHE A 198 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP A 225 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE A 200 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 44 through 52 removed outlier: 3.845A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AB7, first strand: chain 'A' and resid 81 through 82 removed outlier: 4.096A pdb=" N GLY A 100 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA A 240 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE A 98 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ARG A 99 " --> pdb=" O ASN A 118 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 129 through 132 removed outlier: 6.313A pdb=" N GLU A 129 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA A 160 " --> pdb=" O GLU A 129 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLN A 131 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 626 through 627 removed outlier: 4.471A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASN A 314 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLY A 590 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 321 through 325 removed outlier: 4.259A pdb=" N GLU A 321 " --> pdb=" O CYS A 535 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AC3, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.743A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AC5, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AC6, first strand: chain 'A' and resid 651 through 657 removed outlier: 6.004A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N VAL A 653 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 699 through 701 Processing sheet with id=AC8, first strand: chain 'A' and resid 708 through 712 removed outlier: 3.754A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 715 through 725 removed outlier: 5.854A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.300A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 785 through 787 removed outlier: 6.115A pdb=" N ILE A 785 " --> pdb=" O ASN B 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'A' and resid 1117 through 1119 Processing sheet with id=AD4, first strand: chain 'B' and resid 20 through 27 removed outlier: 7.956A pdb=" N ASN B 58 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TYR B 266 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N PHE B 198 " --> pdb=" O ASP B 225 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASP B 225 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE B 200 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 44 through 52 removed outlier: 3.779A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 81 through 82 removed outlier: 12.689A pdb=" N PHE B 235 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 11.981A pdb=" N ASN B 134 " --> pdb=" O PHE B 235 " (cutoff:3.500A) removed outlier: 9.386A pdb=" N THR B 237 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU B 239 " --> pdb=" O PRO B 136 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLU B 129 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA B 160 " --> pdb=" O GLU B 129 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLN B 131 " --> pdb=" O SER B 158 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL B 156 " --> pdb=" O CYS B 133 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 81 through 82 removed outlier: 4.128A pdb=" N GLY B 100 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA B 240 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE B 98 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ARG B 99 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 626 through 627 removed outlier: 4.429A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASN B 314 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLY B 590 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 321 through 325 removed outlier: 4.247A pdb=" N GLU B 321 " --> pdb=" O CYS B 535 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AE2, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.641A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AE4, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AE5, first strand: chain 'B' and resid 651 through 657 removed outlier: 6.035A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N VAL B 653 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE B 667 " --> pdb=" O ILE B 663 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.798A pdb=" N ALA B1075 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE B1092 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 715 through 725 removed outlier: 5.906A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.352A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 785 through 787 removed outlier: 6.188A pdb=" N ILE B 785 " --> pdb=" O ASN C 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'B' and resid 1117 through 1119 Processing sheet with id=AF2, first strand: chain 'C' and resid 20 through 27 removed outlier: 7.903A pdb=" N ASN C 58 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N TYR C 266 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N PHE C 198 " --> pdb=" O ASP C 225 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP C 225 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE C 200 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 44 through 52 removed outlier: 3.849A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 81 through 82 Processing sheet with id=AF5, first strand: chain 'C' and resid 81 through 82 removed outlier: 4.281A pdb=" N GLY C 100 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA C 240 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE C 98 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ARG C 99 " --> pdb=" O ASN C 118 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 129 through 132 removed outlier: 3.735A pdb=" N ASN C 161 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER C 159 " --> pdb=" O GLN C 131 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 626 through 627 removed outlier: 4.542A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ASN C 314 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLY C 590 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 321 through 325 removed outlier: 4.285A pdb=" N GLU C 321 " --> pdb=" O CYS C 535 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 351 through 355 Processing sheet with id=AG1, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.671A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AG3, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AG4, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.054A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 708 through 712 removed outlier: 3.763A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 715 through 725 removed outlier: 5.860A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.404A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 1117 through 1119 Processing sheet with id=AG9, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.491A pdb=" N TRP E 34 " --> pdb=" O VAL E 46 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 9 through 12 Processing sheet with id=AH2, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AH3, first strand: chain 'G' and resid 9 through 12 removed outlier: 3.650A pdb=" N ALA G 83 " --> pdb=" O LEU G 103 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TRP G 34 " --> pdb=" O VAL G 46 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 9 through 12 removed outlier: 3.650A pdb=" N ALA G 83 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 18 through 23 1362 hydrogen bonds defined for protein. 3582 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.85 Time building geometry restraints manager: 12.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.69 - 0.91: 1 0.91 - 1.14: 1 1.14 - 1.37: 9872 1.37 - 1.59: 21089 1.59 - 1.82: 177 Bond restraints: 31140 Sorted by residual: bond pdb=" CG PRO L 8 " pdb=" CD PRO L 8 " ideal model delta sigma weight residual 1.503 0.686 0.817 3.40e-02 8.65e+02 5.77e+02 bond pdb=" CG PRO E 58 " pdb=" CD PRO E 58 " ideal model delta sigma weight residual 1.503 1.146 0.357 3.40e-02 8.65e+02 1.10e+02 bond pdb=" CG PRO H 41 " pdb=" CD PRO H 41 " ideal model delta sigma weight residual 1.503 1.156 0.347 3.40e-02 8.65e+02 1.04e+02 bond pdb=" CB PRO D 41 " pdb=" CG PRO D 41 " ideal model delta sigma weight residual 1.492 0.989 0.503 5.00e-02 4.00e+02 1.01e+02 bond pdb=" CG PRO G 58 " pdb=" CD PRO G 58 " ideal model delta sigma weight residual 1.503 1.183 0.320 3.40e-02 8.65e+02 8.86e+01 ... (remaining 31135 not shown) Histogram of bond angle deviations from ideal: 66.97 - 89.56: 10 89.56 - 112.14: 15982 112.14 - 134.73: 26376 134.73 - 157.31: 0 157.31 - 179.90: 1 Bond angle restraints: 42369 Sorted by residual: angle pdb=" N PRO L 8 " pdb=" CD PRO L 8 " pdb=" CG PRO L 8 " ideal model delta sigma weight residual 103.20 66.97 36.23 1.50e+00 4.44e-01 5.83e+02 angle pdb=" CB PRO D 41 " pdb=" CG PRO D 41 " pdb=" CD PRO D 41 " ideal model delta sigma weight residual 106.10 179.90 -73.80 3.20e+00 9.77e-02 5.32e+02 angle pdb=" N PRO D 41 " pdb=" CD PRO D 41 " pdb=" CG PRO D 41 " ideal model delta sigma weight residual 103.20 75.95 27.25 1.50e+00 4.44e-01 3.30e+02 angle pdb=" CA PRO D 41 " pdb=" CB PRO D 41 " pdb=" CG PRO D 41 " ideal model delta sigma weight residual 104.50 73.55 30.95 1.90e+00 2.77e-01 2.65e+02 angle pdb=" N PRO G 58 " pdb=" CD PRO G 58 " pdb=" CG PRO G 58 " ideal model delta sigma weight residual 103.20 79.50 23.70 1.50e+00 4.44e-01 2.50e+02 ... (remaining 42364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 17072 17.92 - 35.85: 1297 35.85 - 53.77: 366 53.77 - 71.70: 85 71.70 - 89.62: 50 Dihedral angle restraints: 18870 sinusoidal: 7650 harmonic: 11220 Sorted by residual: dihedral pdb=" N PRO D 41 " pdb=" CG PRO D 41 " pdb=" CD PRO D 41 " pdb=" CB PRO D 41 " ideal model delta sinusoidal sigma weight residual -30.00 -118.45 88.45 1 1.50e+01 4.44e-03 4.15e+01 dihedral pdb=" CA THR B 596 " pdb=" C THR B 596 " pdb=" N PRO B 597 " pdb=" CA PRO B 597 " ideal model delta harmonic sigma weight residual 180.00 148.86 31.14 0 5.00e+00 4.00e-02 3.88e+01 dihedral pdb=" CA THR C 596 " pdb=" C THR C 596 " pdb=" N PRO C 597 " pdb=" CA PRO C 597 " ideal model delta harmonic sigma weight residual 180.00 150.95 29.05 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 18867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 4111 0.063 - 0.126: 727 0.126 - 0.188: 41 0.188 - 0.251: 3 0.251 - 0.314: 2 Chirality restraints: 4884 Sorted by residual: chirality pdb=" C1 NAG A1307 " pdb=" ND2 ASN A 798 " pdb=" C2 NAG A1307 " pdb=" O5 NAG A1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 654 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 654 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 4881 not shown) Planarity restraints: 5460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E 13 " 0.105 5.00e-02 4.00e+02 1.50e-01 3.61e+01 pdb=" N PRO E 14 " -0.260 5.00e-02 4.00e+02 pdb=" CA PRO E 14 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO E 14 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 13 " -0.084 5.00e-02 4.00e+02 1.23e-01 2.40e+01 pdb=" N PRO L 14 " 0.212 5.00e-02 4.00e+02 pdb=" CA PRO L 14 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO L 14 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO G 7 " 0.083 5.00e-02 4.00e+02 1.21e-01 2.33e+01 pdb=" N PRO G 8 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO G 8 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO G 8 " 0.066 5.00e-02 4.00e+02 ... (remaining 5457 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 482 2.67 - 3.23: 27656 3.23 - 3.78: 47892 3.78 - 4.34: 69841 4.34 - 4.90: 111080 Nonbonded interactions: 256951 Sorted by model distance: nonbonded pdb=" OG1 THR A 596 " pdb=" O PRO A 597 " model vdw 2.112 3.040 nonbonded pdb=" OG1 THR B 596 " pdb=" O PRO B 597 " model vdw 2.186 3.040 nonbonded pdb=" OG1 THR C 596 " pdb=" O PRO C 597 " model vdw 2.191 3.040 nonbonded pdb=" OG1 THR A 106 " pdb=" OG1 THR A 111 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR C 753 " pdb=" OD1 ASP C 991 " model vdw 2.222 3.040 ... (remaining 256946 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 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: 0.030 Extract box with map and model: 1.530 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 80.030 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.180 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: 0.020 Load rotamer database and sin/cos tables:13.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 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 : 0.008 0.817 31140 Z= 0.424 Angle : 0.846 73.796 42369 Z= 0.455 Chirality : 0.047 0.314 4884 Planarity : 0.006 0.150 5430 Dihedral : 14.944 89.619 11529 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.11 % Allowed : 13.54 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: -0.07 (0.13), residues: 3822 helix: 1.57 (0.19), residues: 720 sheet: 0.17 (0.15), residues: 999 loop : -0.71 (0.12), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 630 HIS 0.004 0.001 HIS A1080 PHE 0.015 0.001 PHE C 315 TYR 0.018 0.002 TYR C1064 ARG 0.007 0.001 ARG B 992 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 331 time to evaluate : 3.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ASN cc_start: 0.6187 (t0) cc_final: 0.5625 (t0) REVERT: B 495 ARG cc_start: 0.7991 (mtp85) cc_final: 0.7576 (mtt90) REVERT: C 490 ARG cc_start: 0.7850 (tpp-160) cc_final: 0.7525 (tpp80) REVERT: G 11 SER cc_start: 0.6222 (OUTLIER) cc_final: 0.5929 (t) REVERT: G 58 PRO cc_start: 0.7150 (OUTLIER) cc_final: 0.6853 (Cg_exo) outliers start: 37 outliers final: 28 residues processed: 360 average time/residue: 1.3474 time to fit residues: 583.7689 Evaluate side-chains 353 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 323 time to evaluate : 3.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 999 GLN Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 58 PRO Chi-restraints excluded: chain G residue 71 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 2.9990 chunk 291 optimal weight: 4.9990 chunk 161 optimal weight: 30.0000 chunk 99 optimal weight: 9.9990 chunk 196 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 300 optimal weight: 0.0980 chunk 116 optimal weight: 4.9990 chunk 183 optimal weight: 10.0000 chunk 224 optimal weight: 20.0000 chunk 348 optimal weight: 7.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 236 GLN A 331 ASN A 687 GLN A 932 GLN B 236 GLN B 331 ASN B 484 ASN B 516 HIS B 687 GLN B 954 GLN C 236 GLN C 242 HIS C 331 ASN C 687 GLN C 954 GLN C1116 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.0713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31140 Z= 0.208 Angle : 0.583 10.997 42369 Z= 0.313 Chirality : 0.046 0.176 4884 Planarity : 0.004 0.079 5430 Dihedral : 6.057 56.225 4833 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.49 % Allowed : 11.17 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.13 (0.13), residues: 3822 helix: 1.90 (0.20), residues: 702 sheet: 0.25 (0.15), residues: 1002 loop : -0.60 (0.12), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 630 HIS 0.005 0.001 HIS B1061 PHE 0.016 0.001 PHE B 895 TYR 0.020 0.002 TYR C1064 ARG 0.005 0.001 ARG B 992 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 334 time to evaluate : 3.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 391 ASN cc_start: 0.7240 (m-40) cc_final: 0.6381 (p0) REVERT: B 495 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7646 (mtt90) REVERT: B 568 ASP cc_start: 0.8140 (m-30) cc_final: 0.7909 (m-30) REVERT: B 784 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8107 (mt0) REVERT: C 316 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7703 (ttt180) REVERT: C 323 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7670 (mp) REVERT: C 336 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7362 (p0) REVERT: C 490 ARG cc_start: 0.7775 (tpp-160) cc_final: 0.7558 (tpp80) REVERT: E 59 GLU cc_start: 0.6041 (OUTLIER) cc_final: 0.5610 (mm-30) REVERT: G 26 LYS cc_start: 0.7101 (OUTLIER) cc_final: 0.6793 (mtpt) outliers start: 83 outliers final: 33 residues processed: 379 average time/residue: 1.3062 time to fit residues: 590.4736 Evaluate side-chains 359 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 319 time to evaluate : 3.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 658 GLU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain G residue 26 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 9.9990 chunk 108 optimal weight: 0.9980 chunk 290 optimal weight: 10.0000 chunk 237 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 349 optimal weight: 2.9990 chunk 377 optimal weight: 9.9990 chunk 311 optimal weight: 20.0000 chunk 346 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 280 optimal weight: 5.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 236 GLN A 331 ASN A 484 ASN A 687 GLN A 932 GLN B 236 GLN B 331 ASN B 484 ASN B 516 HIS B 687 GLN B 951 HIS B 954 GLN C 236 GLN C 242 HIS C 331 ASN C 687 GLN C 954 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31140 Z= 0.234 Angle : 0.569 5.970 42369 Z= 0.307 Chirality : 0.046 0.164 4884 Planarity : 0.004 0.064 5430 Dihedral : 5.646 59.539 4802 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.58 % Allowed : 11.35 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.17 (0.13), residues: 3822 helix: 1.85 (0.20), residues: 705 sheet: 0.25 (0.15), residues: 1032 loop : -0.53 (0.13), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 630 HIS 0.005 0.001 HIS B1061 PHE 0.018 0.002 PHE B 895 TYR 0.020 0.002 TYR C1064 ARG 0.006 0.001 ARG A 992 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 323 time to evaluate : 3.253 Fit side-chains REVERT: A 787 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8507 (mmmt) REVERT: A 1110 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8833 (mm110) REVERT: B 495 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7636 (mtt90) REVERT: B 568 ASP cc_start: 0.8172 (m-30) cc_final: 0.7945 (m-30) REVERT: B 784 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8094 (mt0) REVERT: C 18 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7870 (pt) REVERT: C 316 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7715 (ttt180) REVERT: C 323 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7709 (mp) REVERT: C 336 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7338 (p0) REVERT: C 490 ARG cc_start: 0.7780 (tpp-160) cc_final: 0.7565 (tpp80) REVERT: C 627 THR cc_start: 0.7776 (p) cc_final: 0.7485 (t) REVERT: E 59 GLU cc_start: 0.6233 (OUTLIER) cc_final: 0.5758 (mm-30) REVERT: G 26 LYS cc_start: 0.7126 (OUTLIER) cc_final: 0.6852 (mtpt) outliers start: 86 outliers final: 47 residues processed: 372 average time/residue: 1.3430 time to fit residues: 594.5136 Evaluate side-chains 376 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 319 time to evaluate : 3.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 787 LYS Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 999 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 658 GLU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain G residue 26 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 20.0000 chunk 262 optimal weight: 10.0000 chunk 181 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 166 optimal weight: 20.0000 chunk 234 optimal weight: 9.9990 chunk 350 optimal weight: 4.9990 chunk 371 optimal weight: 30.0000 chunk 183 optimal weight: 10.0000 chunk 332 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 236 GLN A 331 ASN A 484 ASN A 687 GLN A 784 GLN A 932 GLN B 185 ASN B 236 GLN B 331 ASN B 484 ASN B 516 HIS B 687 GLN B 951 HIS B 954 GLN C 96 ASN C 236 GLN C 331 ASN C 484 ASN C 687 GLN C 954 GLN E 29 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.0966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 31140 Z= 0.373 Angle : 0.656 7.473 42369 Z= 0.355 Chirality : 0.051 0.230 4884 Planarity : 0.005 0.057 5430 Dihedral : 6.051 58.968 4802 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.36 % Allowed : 10.78 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: -0.01 (0.13), residues: 3822 helix: 1.55 (0.19), residues: 723 sheet: 0.20 (0.15), residues: 1032 loop : -0.65 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 630 HIS 0.007 0.002 HIS B1055 PHE 0.024 0.002 PHE B 895 TYR 0.021 0.002 TYR C 753 ARG 0.007 0.001 ARG C 902 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 311 time to evaluate : 3.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.7660 (m-80) cc_final: 0.7383 (m-80) REVERT: A 96 ASN cc_start: 0.7389 (t0) cc_final: 0.6637 (t0) REVERT: A 400 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.8018 (ptp90) REVERT: A 787 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8517 (mmmt) REVERT: A 1110 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8871 (mm110) REVERT: B 495 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7654 (mtt90) REVERT: B 568 ASP cc_start: 0.8242 (m-30) cc_final: 0.7971 (m-30) REVERT: B 784 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8084 (mt0) REVERT: C 18 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7837 (pt) REVERT: C 316 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7749 (ttt180) REVERT: C 323 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.7829 (mp) REVERT: C 336 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7395 (p0) REVERT: C 490 ARG cc_start: 0.7829 (tpp-160) cc_final: 0.7599 (tpp80) REVERT: E 59 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.6020 (mm-30) REVERT: G 26 LYS cc_start: 0.7159 (OUTLIER) cc_final: 0.6931 (mtpt) REVERT: G 30 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8460 (mtpp) REVERT: G 82 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6528 (pp20) outliers start: 112 outliers final: 59 residues processed: 376 average time/residue: 1.3388 time to fit residues: 596.9056 Evaluate side-chains 379 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 307 time to evaluate : 3.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 534 LYS Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 787 LYS Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 999 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 658 GLU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 26 LYS Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 104 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 8.9990 chunk 210 optimal weight: 10.0000 chunk 5 optimal weight: 0.4980 chunk 276 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 316 optimal weight: 10.0000 chunk 256 optimal weight: 2.9990 chunk 0 optimal weight: 50.0000 chunk 189 optimal weight: 10.0000 chunk 333 optimal weight: 0.0980 chunk 93 optimal weight: 7.9990 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 GLN A 185 ASN A 236 GLN A 331 ASN A 484 ASN A 687 GLN A 784 GLN A 932 GLN B 236 GLN B 331 ASN B 484 ASN B 516 HIS B 687 GLN ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN B1116 ASN C 236 GLN C 331 ASN C 687 GLN C 954 GLN E 29 ASN G 37 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31140 Z= 0.209 Angle : 0.551 5.951 42369 Z= 0.298 Chirality : 0.046 0.164 4884 Planarity : 0.004 0.055 5430 Dihedral : 5.595 56.472 4802 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.88 % Allowed : 11.29 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.18 (0.13), residues: 3822 helix: 1.85 (0.20), residues: 705 sheet: 0.24 (0.15), residues: 1062 loop : -0.53 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 630 HIS 0.004 0.001 HIS B1061 PHE 0.016 0.001 PHE B 895 TYR 0.018 0.002 TYR C1064 ARG 0.007 0.000 ARG A 992 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 316 time to evaluate : 3.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ASN cc_start: 0.7381 (m-40) cc_final: 0.6685 (t0) REVERT: A 400 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7965 (ptp90) REVERT: A 787 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8510 (mmmt) REVERT: B 383 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8068 (mmmt) REVERT: B 495 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7649 (mtt90) REVERT: B 568 ASP cc_start: 0.8202 (m-30) cc_final: 0.7966 (m-30) REVERT: B 784 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8086 (mt0) REVERT: C 18 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7833 (pt) REVERT: C 316 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7703 (ttt180) REVERT: C 323 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7747 (mp) REVERT: C 336 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7402 (p0) REVERT: C 383 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8117 (mmmt) REVERT: C 490 ARG cc_start: 0.7762 (tpp-160) cc_final: 0.7524 (tpp80) REVERT: C 627 THR cc_start: 0.7773 (p) cc_final: 0.7495 (t) REVERT: E 59 GLU cc_start: 0.6425 (OUTLIER) cc_final: 0.5962 (mm-30) REVERT: G 26 LYS cc_start: 0.7144 (OUTLIER) cc_final: 0.6911 (mtpt) REVERT: G 30 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8371 (mtpp) REVERT: G 82 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6556 (pp20) outliers start: 96 outliers final: 50 residues processed: 372 average time/residue: 1.3180 time to fit residues: 584.0301 Evaluate side-chains 377 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 313 time to evaluate : 3.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 787 LYS Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 999 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 658 GLU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 26 LYS Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 104 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 5.9990 chunk 334 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 217 optimal weight: 7.9990 chunk 91 optimal weight: 0.3980 chunk 371 optimal weight: 50.0000 chunk 308 optimal weight: 9.9990 chunk 172 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 195 optimal weight: 10.0000 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 236 GLN A 331 ASN A 484 ASN A 687 GLN A 784 GLN A 932 GLN B 236 GLN B 331 ASN B 484 ASN B 516 HIS B 687 GLN ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 HIS B 954 GLN C 236 GLN C 331 ASN C 687 GLN C 954 GLN E 29 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31140 Z= 0.250 Angle : 0.570 5.984 42369 Z= 0.309 Chirality : 0.047 0.167 4884 Planarity : 0.004 0.053 5430 Dihedral : 5.583 56.327 4801 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.91 % Allowed : 11.26 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.14 (0.13), residues: 3822 helix: 1.73 (0.20), residues: 723 sheet: 0.28 (0.15), residues: 1026 loop : -0.57 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 630 HIS 0.005 0.001 HIS A1061 PHE 0.018 0.002 PHE B 895 TYR 0.019 0.002 TYR C1064 ARG 0.006 0.000 ARG B 992 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 313 time to evaluate : 3.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 83 MET cc_start: 0.6781 (mtp) cc_final: 0.6544 (mtm) REVERT: A 96 ASN cc_start: 0.7318 (m-40) cc_final: 0.6622 (t0) REVERT: A 400 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7987 (ptp90) REVERT: A 787 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8503 (mmmt) REVERT: A 1088 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8177 (mtt-85) REVERT: A 1110 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8853 (mm110) REVERT: B 383 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8136 (mmmt) REVERT: B 495 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7645 (mtt90) REVERT: B 568 ASP cc_start: 0.8194 (m-30) cc_final: 0.7950 (m-30) REVERT: B 784 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8097 (mt0) REVERT: C 18 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7836 (pt) REVERT: C 316 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7723 (ttt180) REVERT: C 323 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.7770 (mp) REVERT: C 336 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7436 (p0) REVERT: C 383 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8256 (mmmt) REVERT: C 490 ARG cc_start: 0.7807 (tpp-160) cc_final: 0.7585 (tpp80) REVERT: C 627 THR cc_start: 0.7809 (p) cc_final: 0.7501 (t) REVERT: C 1088 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8109 (mtt-85) REVERT: E 59 GLU cc_start: 0.6408 (OUTLIER) cc_final: 0.5969 (mm-30) REVERT: G 26 LYS cc_start: 0.7158 (OUTLIER) cc_final: 0.6931 (mtpt) REVERT: G 30 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8377 (mtpp) REVERT: G 82 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6557 (pp20) outliers start: 97 outliers final: 54 residues processed: 369 average time/residue: 1.3566 time to fit residues: 593.3971 Evaluate side-chains 379 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 308 time to evaluate : 3.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 787 LYS Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1088 ARG Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 999 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 658 GLU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain C residue 1088 ARG Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 26 LYS Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 104 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 211 optimal weight: 20.0000 chunk 271 optimal weight: 30.0000 chunk 210 optimal weight: 10.0000 chunk 312 optimal weight: 10.0000 chunk 207 optimal weight: 20.0000 chunk 370 optimal weight: 50.0000 chunk 231 optimal weight: 10.0000 chunk 225 optimal weight: 3.9990 chunk 170 optimal weight: 20.0000 overall best weight: 8.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 204 HIS A 236 GLN A 331 ASN A 484 ASN A 687 GLN A 784 GLN A 932 GLN B 185 ASN B 236 GLN B 331 ASN B 484 ASN B 687 GLN ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 HIS B 954 GLN C 236 GLN C 331 ASN C 484 ASN C 655 ASN C 687 GLN C 954 GLN E 29 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 31140 Z= 0.358 Angle : 0.640 6.966 42369 Z= 0.347 Chirality : 0.050 0.215 4884 Planarity : 0.004 0.052 5430 Dihedral : 5.961 59.892 4799 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.18 % Allowed : 11.35 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.03 (0.13), residues: 3822 helix: 1.63 (0.20), residues: 723 sheet: 0.21 (0.15), residues: 1047 loop : -0.64 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 630 HIS 0.007 0.002 HIS A1061 PHE 0.023 0.002 PHE B 895 TYR 0.021 0.002 TYR B 393 ARG 0.007 0.001 ARG A 992 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 306 time to evaluate : 3.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.7649 (m-80) cc_final: 0.7401 (m-80) REVERT: H 87 ARG cc_start: 0.6104 (OUTLIER) cc_final: 0.5420 (mmt90) REVERT: A 96 ASN cc_start: 0.7319 (m-40) cc_final: 0.6645 (t0) REVERT: A 400 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.8002 (ptp90) REVERT: A 787 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8517 (mmmt) REVERT: A 1088 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8161 (mtt-85) REVERT: A 1110 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.8854 (mm110) REVERT: B 495 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7655 (mtt90) REVERT: B 784 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8085 (mt0) REVERT: C 18 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7810 (pt) REVERT: C 316 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7751 (ttt180) REVERT: C 323 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.7838 (mp) REVERT: C 336 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7447 (p0) REVERT: C 383 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8384 (mmmt) REVERT: E 59 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.5980 (mm-30) REVERT: G 26 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6953 (mtpt) REVERT: G 30 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8457 (mtpp) REVERT: G 82 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6603 (mm-30) outliers start: 106 outliers final: 62 residues processed: 370 average time/residue: 1.3369 time to fit residues: 587.2769 Evaluate side-chains 385 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 307 time to evaluate : 3.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 787 LYS Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1088 ARG Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 999 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 658 GLU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 26 LYS Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 104 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 10.0000 chunk 147 optimal weight: 8.9990 chunk 221 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 235 optimal weight: 2.9990 chunk 252 optimal weight: 7.9990 chunk 182 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 290 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 204 HIS A 236 GLN A 687 GLN A 784 GLN A 932 GLN B 236 GLN B 331 ASN B 484 ASN B 687 GLN ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 910 GLN B 954 GLN C 236 GLN C 331 ASN C 687 GLN ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN E 29 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31140 Z= 0.245 Angle : 0.574 7.005 42369 Z= 0.310 Chirality : 0.047 0.217 4884 Planarity : 0.004 0.053 5430 Dihedral : 5.674 59.988 4799 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.00 % Allowed : 11.71 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.10 (0.13), residues: 3822 helix: 1.73 (0.20), residues: 723 sheet: 0.23 (0.15), residues: 1047 loop : -0.61 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 630 HIS 0.005 0.001 HIS A1061 PHE 0.017 0.002 PHE B 895 TYR 0.019 0.002 TYR B 393 ARG 0.008 0.000 ARG A 992 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 306 time to evaluate : 2.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.7685 (m-80) cc_final: 0.7460 (m-80) REVERT: H 87 ARG cc_start: 0.6093 (OUTLIER) cc_final: 0.5427 (mmt90) REVERT: A 96 ASN cc_start: 0.7297 (m-40) cc_final: 0.6641 (t0) REVERT: A 400 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7971 (ptp90) REVERT: A 787 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8502 (mmmt) REVERT: A 1110 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8850 (mm110) REVERT: B 383 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8156 (mmmt) REVERT: B 495 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7657 (mtt90) REVERT: B 568 ASP cc_start: 0.8182 (m-30) cc_final: 0.7936 (m-30) REVERT: B 784 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8097 (mt0) REVERT: C 18 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7825 (pt) REVERT: C 316 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7717 (ttt180) REVERT: C 323 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7773 (mp) REVERT: C 336 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7444 (p0) REVERT: C 383 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8253 (mmmt) REVERT: C 490 ARG cc_start: 0.7784 (tpp-160) cc_final: 0.7536 (tpp80) REVERT: C 627 THR cc_start: 0.7791 (p) cc_final: 0.7499 (t) REVERT: E 59 GLU cc_start: 0.6404 (OUTLIER) cc_final: 0.5951 (mm-30) REVERT: G 26 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6943 (mtpt) REVERT: G 30 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8391 (mtpp) outliers start: 100 outliers final: 62 residues processed: 366 average time/residue: 1.3076 time to fit residues: 571.0370 Evaluate side-chains 381 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 304 time to evaluate : 3.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 787 LYS Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 999 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 225 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 658 GLU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 26 LYS Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 104 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 10.0000 chunk 354 optimal weight: 10.0000 chunk 323 optimal weight: 9.9990 chunk 344 optimal weight: 5.9990 chunk 207 optimal weight: 0.0980 chunk 150 optimal weight: 6.9990 chunk 270 optimal weight: 30.0000 chunk 105 optimal weight: 0.9980 chunk 311 optimal weight: 20.0000 chunk 326 optimal weight: 5.9990 chunk 343 optimal weight: 7.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 236 GLN A 784 GLN A 932 GLN B 236 GLN B 331 ASN B 687 GLN ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 HIS B 954 GLN C 236 GLN C 331 ASN C 687 GLN ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN E 29 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31140 Z= 0.206 Angle : 0.546 7.247 42369 Z= 0.295 Chirality : 0.046 0.178 4884 Planarity : 0.004 0.053 5430 Dihedral : 5.411 58.719 4799 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.67 % Allowed : 11.98 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.24 (0.13), residues: 3822 helix: 1.93 (0.20), residues: 705 sheet: 0.31 (0.15), residues: 1026 loop : -0.51 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 630 HIS 0.005 0.001 HIS B 951 PHE 0.015 0.001 PHE B 895 TYR 0.018 0.002 TYR B 393 ARG 0.007 0.000 ARG A 992 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 311 time to evaluate : 3.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 60 TYR cc_start: 0.7721 (m-80) cc_final: 0.7506 (m-80) REVERT: H 76 LYS cc_start: 0.7362 (OUTLIER) cc_final: 0.7079 (mtpp) REVERT: A 96 ASN cc_start: 0.7376 (m-40) cc_final: 0.6788 (t0) REVERT: A 336 ASP cc_start: 0.7685 (p0) cc_final: 0.7417 (p0) REVERT: A 400 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7949 (ptp90) REVERT: A 787 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8486 (mmmt) REVERT: A 1088 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8176 (mtt-85) REVERT: A 1110 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.8847 (mm110) REVERT: B 383 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8126 (mmmt) REVERT: B 495 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7649 (mtt90) REVERT: B 568 ASP cc_start: 0.8170 (m-30) cc_final: 0.7929 (m-30) REVERT: B 784 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8102 (mt0) REVERT: C 18 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7810 (pt) REVERT: C 316 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7705 (ttt180) REVERT: C 323 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7742 (mp) REVERT: C 336 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7448 (p0) REVERT: C 383 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8156 (mmmt) REVERT: C 490 ARG cc_start: 0.7776 (tpp-160) cc_final: 0.7552 (tpp80) REVERT: C 627 THR cc_start: 0.7790 (p) cc_final: 0.7545 (t) REVERT: C 851 LYS cc_start: 0.8740 (ttmm) cc_final: 0.8123 (mmtm) REVERT: E 59 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.5885 (mm-30) REVERT: G 26 LYS cc_start: 0.7155 (OUTLIER) cc_final: 0.6925 (mtpt) REVERT: G 30 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8383 (mtpp) outliers start: 89 outliers final: 58 residues processed: 361 average time/residue: 1.3728 time to fit residues: 592.0228 Evaluate side-chains 385 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 311 time to evaluate : 3.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 787 LYS Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1088 ARG Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 999 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 658 GLU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 26 LYS Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 104 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 9.9990 chunk 364 optimal weight: 40.0000 chunk 222 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 chunk 253 optimal weight: 10.0000 chunk 382 optimal weight: 10.0000 chunk 352 optimal weight: 9.9990 chunk 304 optimal weight: 20.0000 chunk 31 optimal weight: 50.0000 chunk 235 optimal weight: 3.9990 chunk 186 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 236 GLN A 784 GLN A 932 GLN B 236 GLN B 331 ASN B 484 ASN B 687 GLN ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 GLN C 236 GLN C 331 ASN C 484 ASN C 687 GLN ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN E 29 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 31140 Z= 0.302 Angle : 0.606 8.245 42369 Z= 0.328 Chirality : 0.049 0.202 4884 Planarity : 0.004 0.052 5430 Dihedral : 5.691 58.826 4799 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.70 % Allowed : 12.16 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.06 (0.13), residues: 3822 helix: 1.69 (0.20), residues: 723 sheet: 0.25 (0.15), residues: 1017 loop : -0.64 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 630 HIS 0.006 0.001 HIS A1061 PHE 0.021 0.002 PHE B 895 TYR 0.025 0.002 TYR B 393 ARG 0.007 0.001 ARG A 992 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7644 Ramachandran restraints generated. 3822 Oldfield, 0 Emsley, 3822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 306 time to evaluate : 3.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 76 LYS cc_start: 0.7346 (OUTLIER) cc_final: 0.7052 (mtpp) REVERT: H 87 ARG cc_start: 0.6112 (OUTLIER) cc_final: 0.5489 (mmt90) REVERT: A 96 ASN cc_start: 0.7355 (m-40) cc_final: 0.6757 (t0) REVERT: A 400 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7989 (ptp90) REVERT: A 787 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8506 (mmmt) REVERT: A 1088 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8172 (mtt-85) REVERT: A 1110 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8853 (mm110) REVERT: B 383 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8255 (mmmt) REVERT: B 495 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7658 (mtt90) REVERT: B 568 ASP cc_start: 0.8171 (m-30) cc_final: 0.7912 (m-30) REVERT: B 784 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8092 (mt0) REVERT: C 18 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7816 (pt) REVERT: C 316 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7737 (ttt180) REVERT: C 323 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7804 (mp) REVERT: C 336 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7454 (p0) REVERT: C 383 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8343 (mmmt) REVERT: C 627 THR cc_start: 0.7812 (p) cc_final: 0.7498 (t) REVERT: C 851 LYS cc_start: 0.8779 (ttmm) cc_final: 0.8086 (mmtm) REVERT: E 59 GLU cc_start: 0.6439 (OUTLIER) cc_final: 0.5976 (mm-30) REVERT: G 26 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6957 (mtpt) REVERT: G 30 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8403 (mtpp) outliers start: 90 outliers final: 59 residues processed: 358 average time/residue: 1.3525 time to fit residues: 574.2333 Evaluate side-chains 381 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 305 time to evaluate : 3.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 LYS Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 787 LYS Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1088 ARG Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 383 LYS Chi-restraints excluded: chain B residue 495 ARG Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 ILE Chi-restraints excluded: chain B residue 999 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 316 ARG Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain C residue 400 ARG Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 658 GLU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 824 THR Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 26 LYS Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 104 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 5.9990 chunk 324 optimal weight: 9.9990 chunk 93 optimal weight: 0.6980 chunk 280 optimal weight: 5.9990 chunk 44 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 305 optimal weight: 6.9990 chunk 127 optimal weight: 0.9980 chunk 313 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 56 optimal weight: 30.0000 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 236 GLN A 331 ASN A 784 GLN A 932 GLN B 236 GLN B 331 ASN B 687 GLN ** B 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 HIS B 954 GLN C 236 GLN C 331 ASN C 687 GLN ** C 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN E 29 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.163036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.115301 restraints weight = 30559.267| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.60 r_work: 0.3055 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31140 Z= 0.205 Angle : 0.547 7.653 42369 Z= 0.295 Chirality : 0.046 0.180 4884 Planarity : 0.004 0.052 5430 Dihedral : 5.413 58.220 4799 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.61 % Allowed : 12.22 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % 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: 0.22 (0.13), residues: 3822 helix: 1.92 (0.20), residues: 705 sheet: 0.34 (0.15), residues: 993 loop : -0.54 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 630 HIS 0.006 0.001 HIS B 951 PHE 0.015 0.001 PHE B 895 TYR 0.020 0.002 TYR B 393 ARG 0.008 0.000 ARG B 992 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11604.64 seconds wall clock time: 204 minutes 52.51 seconds (12292.51 seconds total)