Starting phenix.real_space_refine on Wed Feb 21 18:40:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzi_27799/02_2024/8dzi_27799.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzi_27799/02_2024/8dzi_27799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzi_27799/02_2024/8dzi_27799.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzi_27799/02_2024/8dzi_27799.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzi_27799/02_2024/8dzi_27799.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzi_27799/02_2024/8dzi_27799.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 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 20037 2.51 5 N 5161 2.21 5 O 6134 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 151": "OE1" <-> "OE2" Residue "C GLU 209": "OE1" <-> "OE2" Residue "C GLU 337": "OE1" <-> "OE2" Residue "C GLU 462": "OE1" <-> "OE2" Residue "C GLU 468": "OE1" <-> "OE2" Residue "C GLU 580": "OE1" <-> "OE2" Residue "C GLU 616": "OE1" <-> "OE2" Residue "C GLU 658": "OE1" <-> "OE2" Residue "C GLU 745": "OE1" <-> "OE2" Residue "C GLU 770": "OE1" <-> "OE2" Residue "C GLU 865": "OE1" <-> "OE2" Residue "C GLU 915": "OE1" <-> "OE2" Residue "C GLU 985": "OE1" <-> "OE2" Residue "H GLU 1": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "L GLU 80": "OE1" <-> "OE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A GLU 551": "OE1" <-> "OE2" Residue "A GLU 580": "OE1" <-> "OE2" Residue "A GLU 651": "OE1" <-> "OE2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A GLU 699": "OE1" <-> "OE2" Residue "A GLU 745": "OE1" <-> "OE2" Residue "A GLU 985": "OE1" <-> "OE2" Residue "B GLU 16": "OE1" <-> "OE2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "E GLU 278": "OE1" <-> "OE2" Residue "E GLU 462": "OE1" <-> "OE2" Residue "E GLU 513": "OE1" <-> "OE2" Residue "E GLU 616": "OE1" <-> "OE2" Residue "E GLU 651": "OE1" <-> "OE2" Residue "E GLU 770": "OE1" <-> "OE2" Residue "E GLU 865": "OE1" <-> "OE2" Residue "E GLU 985": "OE1" <-> "OE2" Residue "F GLU 80": "OE1" <-> "OE2" Residue "F GLU 82": "OE1" <-> "OE2" Residue "G GLU 46": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31470 Number of models: 1 Model: "" Number of chains: 32 Chain: "C" Number of atoms: 8496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1083, 8496 Classifications: {'peptide': 1083} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 60, 'TRANS': 1022} Chain breaks: 9 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 823 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 100} Chain: "A" Number of atoms: 8467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1080, 8467 Classifications: {'peptide': 1080} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 59, 'TRANS': 1020} Chain breaks: 8 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "D" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 823 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 100} Chain: "E" Number of atoms: 8420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1074, 8420 Classifications: {'peptide': 1074} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 59, 'TRANS': 1014} Chain breaks: 8 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 823 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 100} Chain: "G" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 16.02, per 1000 atoms: 0.51 Number of scatterers: 31470 At special positions: 0 Unit cell: (177.62, 146.59, 218.28, 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 6134 8.00 N 5161 7.00 C 20037 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 161 " 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=2.04 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.02 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.04 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 H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 161 " 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 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 129 " - pdb=" SG CYS E 161 " distance=2.03 Simple disulfide: pdb=" SG CYS E 288 " - pdb=" SG CYS E 298 " distance=2.02 Simple disulfide: pdb=" SG CYS E 333 " - pdb=" SG CYS E 358 " distance=2.03 Simple disulfide: pdb=" SG CYS E 376 " - pdb=" SG CYS E 429 " distance=2.03 Simple disulfide: pdb=" SG CYS E 388 " - pdb=" SG CYS E 522 " distance=2.03 Simple disulfide: pdb=" SG CYS E 477 " - pdb=" SG CYS E 485 " distance=2.03 Simple disulfide: pdb=" SG CYS E 535 " - pdb=" SG CYS E 587 " distance=2.03 Simple disulfide: pdb=" SG CYS E 614 " - pdb=" SG CYS E 646 " distance=2.03 Simple disulfide: pdb=" SG CYS E 659 " - pdb=" SG CYS E 668 " distance=2.04 Simple disulfide: pdb=" SG CYS E 735 " - pdb=" SG CYS E 757 " distance=2.03 Simple disulfide: pdb=" SG CYS E 740 " - pdb=" SG CYS E 746 " distance=2.03 Simple disulfide: pdb=" SG CYS E 837 " - pdb=" SG CYS E 848 " distance=2.03 Simple disulfide: pdb=" SG CYS E1029 " - pdb=" SG CYS E1040 " distance=2.03 Simple disulfide: pdb=" SG CYS E1079 " - pdb=" SG CYS E1123 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " NAG-ASN " NAG A1301 " - " ASN A 600 " " NAG A1302 " - " ASN A 61 " " NAG A1303 " - " ASN A 613 " " NAG A1304 " - " ASN A 654 " " NAG A1305 " - " ASN A1131 " " NAG A1307 " - " ASN A 231 " " NAG A1308 " - " ASN A 340 " " NAG A1309 " - " ASN A 367 " " NAG C1301 " - " ASN C 600 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 613 " " NAG C1304 " - " ASN C 654 " " NAG E1301 " - " ASN E 231 " " NAG E1302 " - " ASN E 61 " " NAG E1303 " - " ASN E 328 " " NAG E1304 " - " ASN E 613 " " NAG E1305 " - " ASN E 654 " " NAG E1306 " - " ASN E1071 " " NAG E1307 " - " ASN E 340 " " NAG E1308 " - " ASN E 160 " " NAG E1309 " - " ASN E 135 " " NAG I 1 " - " ASN C1095 " " NAG J 1 " - " ASN C1131 " " NAG K 1 " - " ASN C 706 " " NAG M 1 " - " ASN C 714 " " NAG N 1 " - " ASN C 798 " " NAG O 1 " - " ASN C1071 " " NAG P 1 " - " ASN C 279 " " NAG Q 1 " - " ASN A1095 " " NAG R 1 " - " ASN A 706 " " NAG S 1 " - " ASN A 714 " " NAG T 1 " - " ASN A 798 " " NAG U 1 " - " ASN A1071 " " NAG V 1 " - " ASN A 279 " " NAG W 1 " - " ASN E 120 " " NAG X 1 " - " ASN E 279 " " NAG Y 1 " - " ASN E 706 " " NAG Z 1 " - " ASN E1131 " " NAG a 1 " - " ASN E1095 " " NAG b 1 " - " ASN E 714 " " NAG c 1 " - " ASN E 798 " Time building additional restraints: 15.10 Conformation dependent library (CDL) restraints added in 6.0 seconds 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7290 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 59 sheets defined 22.0% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.37 Creating SS restraints... Processing helix chain 'C' and resid 150 through 154 removed outlier: 3.536A pdb=" N VAL C 154 " --> pdb=" O SER C 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 150 through 154' Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 340 Processing helix chain 'C' and resid 362 through 368 removed outlier: 3.754A pdb=" N LEU C 368 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 385 Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 435 through 440 Processing helix chain 'C' and resid 495 through 501 removed outlier: 3.839A pdb=" N VAL C 500 " --> pdb=" O PRO C 496 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY C 501 " --> pdb=" O THR C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 754 removed outlier: 3.737A pdb=" N ASN C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 780 removed outlier: 4.034A pdb=" N GLN C 759 " --> pdb=" O SER C 755 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR C 775 " --> pdb=" O GLN C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 824 Processing helix chain 'C' and resid 847 through 852 Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 888 removed outlier: 3.539A 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: 4.329A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 937 removed outlier: 3.577A pdb=" N GLN C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP C 933 " --> pdb=" O GLY C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 965 removed outlier: 3.504A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER C 964 " --> pdb=" O VAL C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 981 removed outlier: 3.597A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU C 981 " --> pdb=" O ILE C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1029 removed outlier: 3.859A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1142 removed outlier: 3.671A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'A' and resid 150 through 154 Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'A' and resid 362 through 368 removed outlier: 3.801A pdb=" N LEU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 387 removed outlier: 3.533A pdb=" N ASN A 385 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP A 386 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 495 through 500 removed outlier: 4.597A pdb=" N VAL A 500 " --> pdb=" O THR A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 754 removed outlier: 3.614A pdb=" N GLY A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 780 Processing helix chain 'A' and resid 813 through 824 removed outlier: 3.575A pdb=" N VAL A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 853 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 888 Processing helix chain 'A' and resid 894 through 906 Processing helix chain 'A' and resid 909 through 916 removed outlier: 4.301A pdb=" N LEU A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 937 removed outlier: 3.593A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 964 removed outlier: 4.040A pdb=" N SER A 964 " --> pdb=" O VAL A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1030 removed outlier: 4.185A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1142 removed outlier: 3.783A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'E' and resid 150 through 154 removed outlier: 3.589A pdb=" N VAL E 154 " --> pdb=" O SER E 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 150 through 154' Processing helix chain 'E' and resid 291 through 301 Processing helix chain 'E' and resid 334 through 340 Processing helix chain 'E' and resid 361 through 368 removed outlier: 4.112A pdb=" N LEU E 365 " --> pdb=" O ASP E 361 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN E 367 " --> pdb=" O SER E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 386 removed outlier: 3.616A pdb=" N LEU E 384 " --> pdb=" O PRO E 381 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASN E 385 " --> pdb=" O THR E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 408 removed outlier: 3.513A pdb=" N ALA E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 419 Processing helix chain 'E' and resid 498 through 503 removed outlier: 3.948A pdb=" N GLN E 503 " --> pdb=" O GLY E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 734 through 740 removed outlier: 3.623A pdb=" N TYR E 738 " --> pdb=" O ASP E 734 " (cutoff:3.500A) Processing helix chain 'E' and resid 743 through 754 removed outlier: 3.754A pdb=" N GLY E 754 " --> pdb=" O LEU E 750 " (cutoff:3.500A) Processing helix chain 'E' and resid 755 through 780 Processing helix chain 'E' and resid 813 through 824 Processing helix chain 'E' and resid 845 through 852 Processing helix chain 'E' and resid 863 through 881 Processing helix chain 'E' and resid 883 through 888 Processing helix chain 'E' and resid 894 through 907 Processing helix chain 'E' and resid 909 through 916 removed outlier: 4.226A pdb=" N LEU E 913 " --> pdb=" O THR E 909 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR E 914 " --> pdb=" O GLN E 910 " (cutoff:3.500A) Processing helix chain 'E' and resid 916 through 937 removed outlier: 3.681A pdb=" N GLN E 932 " --> pdb=" O ILE E 928 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP E 933 " --> pdb=" O GLY E 929 " (cutoff:3.500A) Processing helix chain 'E' and resid 942 through 965 removed outlier: 3.629A pdb=" N LEU E 963 " --> pdb=" O LEU E 959 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER E 964 " --> pdb=" O VAL E 960 " (cutoff:3.500A) Processing helix chain 'E' and resid 973 through 981 Processing helix chain 'E' and resid 982 through 1029 Processing helix chain 'E' and resid 1137 through 1142 Processing helix chain 'G' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.463A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR C 63 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL C 264 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE C 196 " --> pdb=" O ASP C 225 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASP C 225 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE C 198 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N HIS C 202 " --> pdb=" O ALA C 219 " (cutoff:3.500A) removed outlier: 9.212A pdb=" N ALA C 219 " --> pdb=" O HIS C 202 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL C 36 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 4.802A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE A 323 " --> pdb=" O ASN A 539 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.830A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 82 through 83 Processing sheet with id=AA5, first strand: chain 'C' and resid 82 through 83 removed outlier: 4.376A pdb=" N GLY C 101 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA C 240 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ILE C 99 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE C 163 " --> pdb=" O VAL C 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.595A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER C 313 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 322 through 323 removed outlier: 6.889A pdb=" N ILE C 323 " --> pdb=" O ASN C 539 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA C 572 " --> pdb=" O GLY C 563 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N PHE C 562 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 353 through 355 removed outlier: 4.972A pdb=" N ASN C 391 " --> pdb=" O GLU C 513 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU C 513 " --> pdb=" O ASN C 391 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 353 through 355 removed outlier: 4.972A pdb=" N ASN C 391 " --> pdb=" O GLU C 513 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU C 513 " --> pdb=" O ASN C 391 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.126A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 450 through 451 Processing sheet with id=AB3, first strand: chain 'C' and resid 470 through 471 removed outlier: 3.529A pdb=" N TYR C 486 " --> pdb=" O TYR C 470 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 651 through 652 removed outlier: 5.975A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 698 through 701 removed outlier: 3.581A pdb=" N LYS E 787 " --> pdb=" O ASN C 700 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.690A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 6.154A 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=AB7, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.690A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR C1073 " --> pdb=" O SER C1094 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 730 through 732 removed outlier: 4.494A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 785 through 786 removed outlier: 5.924A pdb=" N ILE C 785 " --> pdb=" O ASN A 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 1117 through 1119 Processing sheet with id=AC2, first strand: chain 'H' and resid 57 through 60 removed outlier: 5.928A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ILE H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE H 34 " --> pdb=" O ILE H 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 72 through 73 removed outlier: 3.508A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'L' and resid 46 through 49 removed outlier: 6.430A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.290A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N SER A 200 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.304A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AC9, first strand: chain 'A' and resid 82 through 83 removed outlier: 4.515A pdb=" N GLY A 101 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA A 240 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE A 99 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N GLU A 130 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N CYS A 161 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLN A 132 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ASN A 159 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.472A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER A 313 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.665A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA A 432 " --> pdb=" O PHE A 372 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.245A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AD5, first strand: chain 'A' and resid 651 through 657 removed outlier: 5.880A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL A 653 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.785A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N GLY A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N SER A1052 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A1058 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU A1060 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER A1048 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 731 through 733 Processing sheet with id=AD8, first strand: chain 'A' and resid 785 through 787 removed outlier: 5.892A pdb=" N ILE A 785 " --> pdb=" O ASN E 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'A' and resid 1117 through 1119 Processing sheet with id=AE1, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AE2, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AE3, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.752A pdb=" N VAL B 114 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE B 34 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ILE B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 72 through 73 Processing sheet with id=AE5, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.713A pdb=" N SER D 22 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 54 through 55 removed outlier: 6.415A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 27 through 30 removed outlier: 3.604A pdb=" N VAL E 88 " --> pdb=" O PHE E 189 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL E 224 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N SER E 200 " --> pdb=" O PRO E 222 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 48 through 55 removed outlier: 4.243A pdb=" N ASP E 284 " --> pdb=" O LYS E 275 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 81 through 83 removed outlier: 4.333A pdb=" N GLY E 101 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 11.320A pdb=" N ILE E 126 " --> pdb=" O THR E 162 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N THR E 162 " --> pdb=" O ILE E 126 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL E 128 " --> pdb=" O ASN E 160 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ASN E 160 " --> pdb=" O VAL E 128 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N GLU E 130 " --> pdb=" O ALA E 158 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA E 158 " --> pdb=" O GLU E 130 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N GLN E 132 " --> pdb=" O SER E 156 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 308 through 316 removed outlier: 5.554A pdb=" N ILE E 309 " --> pdb=" O THR E 596 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N THR E 596 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLN E 311 " --> pdb=" O VAL E 594 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL E 594 " --> pdb=" O GLN E 311 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER E 313 " --> pdb=" O VAL E 592 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLY E 591 " --> pdb=" O GLN E 610 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 321 through 325 removed outlier: 3.908A pdb=" N GLU E 321 " --> pdb=" O CYS E 535 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ASP E 571 " --> pdb=" O ILE E 584 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 351 through 354 removed outlier: 4.834A pdb=" N ASN E 391 " --> pdb=" O GLU E 513 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLU E 513 " --> pdb=" O ASN E 391 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 351 through 354 Processing sheet with id=AF5, first strand: chain 'E' and resid 449 through 451 Processing sheet with id=AF6, first strand: chain 'E' and resid 651 through 653 removed outlier: 4.449A pdb=" N THR E 693 " --> pdb=" O VAL E 653 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE E 667 " --> pdb=" O ILE E 663 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 708 through 725 removed outlier: 6.756A pdb=" N SER E 708 " --> pdb=" O THR E1073 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR E1073 " --> pdb=" O SER E 708 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ALA E 710 " --> pdb=" O ASN E1071 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN E1071 " --> pdb=" O ALA E 710 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU E1069 " --> pdb=" O PRO E 712 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N GLY E1056 " --> pdb=" O SER E1052 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N SER E1052 " --> pdb=" O GLY E1056 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL E1058 " --> pdb=" O PRO E1050 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU E1060 " --> pdb=" O SER E1048 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N SER E1048 " --> pdb=" O LEU E1060 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL E1062 " --> pdb=" O LEU E1046 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 708 through 725 removed outlier: 6.756A pdb=" N SER E 708 " --> pdb=" O THR E1073 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR E1073 " --> pdb=" O SER E 708 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ALA E 710 " --> pdb=" O ASN E1071 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN E1071 " --> pdb=" O ALA E 710 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU E1069 " --> pdb=" O PRO E 712 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA E1075 " --> pdb=" O PHE E1092 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N PHE E1092 " --> pdb=" O ALA E1075 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 730 through 733 removed outlier: 4.389A pdb=" N LYS E 730 " --> pdb=" O LEU E 858 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 1117 through 1122 removed outlier: 4.291A pdb=" N ALA E1084 " --> pdb=" O SER E1120 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AG3, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.230A pdb=" N LEU F 11 " --> pdb=" O GLU F 106 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL F 86 " --> pdb=" O GLN F 39 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TYR F 50 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AG5, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.612A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) 1176 hydrogen bonds defined for protein. 3213 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: 16.20 Time building geometry restraints manager: 15.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9947 1.35 - 1.47: 8137 1.47 - 1.59: 13937 1.59 - 1.71: 2 1.71 - 1.83: 177 Bond restraints: 32200 Sorted by residual: bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.504 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.502 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C1 NAG Q 1 " pdb=" O5 NAG Q 1 " ideal model delta sigma weight residual 1.406 1.496 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C1 NAG U 1 " pdb=" O5 NAG U 1 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C1 NAG E1306 " pdb=" O5 NAG E1306 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.68e+01 ... (remaining 32195 not shown) Histogram of bond angle deviations from ideal: 98.71 - 105.79: 773 105.79 - 112.88: 17224 112.88 - 119.97: 10426 119.97 - 127.05: 15031 127.05 - 134.14: 320 Bond angle restraints: 43774 Sorted by residual: angle pdb=" C GLY A 479 " pdb=" N VAL A 480 " pdb=" CA VAL A 480 " ideal model delta sigma weight residual 121.97 129.57 -7.60 1.80e+00 3.09e-01 1.78e+01 angle pdb=" C ASN E 85 " pdb=" CA ASN E 85 " pdb=" CB ASN E 85 " ideal model delta sigma weight residual 115.89 110.53 5.36 1.32e+00 5.74e-01 1.65e+01 angle pdb=" CA PRO L 96 " pdb=" N PRO L 96 " pdb=" CD PRO L 96 " ideal model delta sigma weight residual 112.00 106.88 5.12 1.40e+00 5.10e-01 1.34e+01 angle pdb=" CA MET C 737 " pdb=" CB MET C 737 " pdb=" CG MET C 737 " ideal model delta sigma weight residual 114.10 121.31 -7.21 2.00e+00 2.50e-01 1.30e+01 angle pdb=" CA LEU C 422 " pdb=" CB LEU C 422 " pdb=" CG LEU C 422 " ideal model delta sigma weight residual 116.30 128.68 -12.38 3.50e+00 8.16e-02 1.25e+01 ... (remaining 43769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.95: 17798 24.95 - 49.89: 1682 49.89 - 74.84: 312 74.84 - 99.78: 131 99.78 - 124.73: 88 Dihedral angle restraints: 20011 sinusoidal: 8653 harmonic: 11358 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 5.88 87.12 1 1.00e+01 1.00e-02 9.12e+01 dihedral pdb=" CB CYS A 837 " pdb=" SG CYS A 837 " pdb=" SG CYS A 848 " pdb=" CB CYS A 848 " ideal model delta sinusoidal sigma weight residual -86.00 -169.27 83.27 1 1.00e+01 1.00e-02 8.48e+01 dihedral pdb=" CA SER L 95 " pdb=" C SER L 95 " pdb=" N PRO L 96 " pdb=" CA PRO L 96 " ideal model delta harmonic sigma weight residual -180.00 -148.96 -31.04 0 5.00e+00 4.00e-02 3.85e+01 ... (remaining 20008 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 5008 0.128 - 0.256: 46 0.256 - 0.384: 12 0.384 - 0.512: 4 0.512 - 0.640: 1 Chirality restraints: 5071 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN C1095 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.48e+00 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 600 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.11e+00 ... (remaining 5068 not shown) Planarity restraints: 5607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER F 95 " 0.084 5.00e-02 4.00e+02 1.27e-01 2.56e+01 pdb=" N PRO F 96 " -0.219 5.00e-02 4.00e+02 pdb=" CA PRO F 96 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO F 96 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 95 " 0.084 5.00e-02 4.00e+02 1.26e-01 2.53e+01 pdb=" N PRO L 96 " -0.218 5.00e-02 4.00e+02 pdb=" CA PRO L 96 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO L 96 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 95 " -0.080 5.00e-02 4.00e+02 1.19e-01 2.27e+01 pdb=" N PRO D 96 " 0.206 5.00e-02 4.00e+02 pdb=" CA PRO D 96 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO D 96 " -0.063 5.00e-02 4.00e+02 ... (remaining 5604 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 777 2.67 - 3.22: 32294 3.22 - 3.78: 55179 3.78 - 4.34: 73829 4.34 - 4.90: 113978 Nonbonded interactions: 276057 Sorted by model distance: nonbonded pdb=" OH TYR E 652 " pdb=" OG1 THR E 693 " model vdw 2.107 2.440 nonbonded pdb=" O ALA E 289 " pdb=" OG1 THR E 629 " model vdw 2.117 2.440 nonbonded pdb=" OG SER C 491 " pdb=" OG SER C 493 " model vdw 2.136 2.440 nonbonded pdb=" OG1 THR A 107 " pdb=" OD2 ASP A 109 " model vdw 2.143 2.440 nonbonded pdb=" OG SER G 17 " pdb=" OE1 GLN G 82 " model vdw 2.147 2.440 ... (remaining 276052 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 69 or resid 74 through 142 or resid 149 through \ 174 or resid 180 through 826 or resid 831 through 833 or (resid 834 and (name N \ or name CA or name C or name O or name CB )) or resid 835 through 837 or resid \ 845 through 1144 or resid 1301 through 1305)) selection = (chain 'C' and (resid 25 through 142 or resid 149 through 174 or resid 180 throu \ gh 244 or resid 254 through 621 or resid 629 through 826 or resid 831 through 83 \ 3 or (resid 834 and (name N or name CA or name C or name O or name CB )) or resi \ d 835 through 837 or resid 845 through 1144 or resid 1301 through 1305)) selection = (chain 'E' and (resid 25 through 174 or resid 180 through 244 or resid 254 throu \ gh 621 or resid 629 through 837 or resid 845 through 1144 or resid 1301 through \ 1305)) } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.590 Check model and map are aligned: 0.460 Set scattering table: 0.300 Process input model: 89.770 Find NCS groups from input model: 2.610 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 32200 Z= 0.255 Angle : 0.697 12.382 43774 Z= 0.364 Chirality : 0.050 0.640 5071 Planarity : 0.006 0.127 5566 Dihedral : 21.878 124.730 12577 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.25 % Favored : 96.57 % Rotamer: Outliers : 0.38 % Allowed : 32.27 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: 0.05 (0.13), residues: 3850 helix: 2.30 (0.19), residues: 706 sheet: -0.01 (0.17), residues: 830 loop : -0.67 (0.12), residues: 2314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 47 HIS 0.003 0.001 HIS E 202 PHE 0.031 0.001 PHE E 562 TYR 0.026 0.001 TYR C 492 ARG 0.007 0.001 ARG C 270 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 42 time to evaluate : 3.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 113 MET cc_start: 0.9696 (tpt) cc_final: 0.9265 (mmm) REVERT: A 897 MET cc_start: 0.8859 (mmm) cc_final: 0.8387 (mmt) REVERT: E 368 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7267 (mt) REVERT: E 866 MET cc_start: 0.9296 (ptp) cc_final: 0.9094 (ptp) outliers start: 13 outliers final: 7 residues processed: 55 average time/residue: 0.5282 time to fit residues: 51.7578 Evaluate side-chains 49 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 3.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 288 CYS Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 883 TRP Chi-restraints excluded: chain E residue 1040 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 325 optimal weight: 10.0000 chunk 292 optimal weight: 30.0000 chunk 162 optimal weight: 20.0000 chunk 99 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 302 optimal weight: 20.0000 chunk 117 optimal weight: 50.0000 chunk 183 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 chunk 350 optimal weight: 9.9990 overall best weight: 9.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 ASN C 202 HIS ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 502 HIS ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 GLN C 604 GLN C 610 GLN C 700 ASN ** C 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 989 GLN C1020 ASN ** C1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 ASN A 357 ASN A 434 ASN A 436 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN A 610 GLN A 638 ASN A 954 GLN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1055 HIS ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 391 ASN E 503 GLN ** E 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 577 GLN ** E 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 687 GLN E 748 ASN E 752 GLN E 759 GLN ** E 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 922 ASN ** E 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1002 GLN E1008 GLN E1033 GLN ** E1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1132 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 32200 Z= 0.402 Angle : 0.752 10.930 43774 Z= 0.379 Chirality : 0.049 0.388 5071 Planarity : 0.006 0.126 5566 Dihedral : 17.199 113.991 5557 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 26.89 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.03 % Favored : 95.79 % Rotamer: Outliers : 5.22 % Allowed : 29.53 % Favored : 65.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: 3850 helix: 2.22 (0.19), residues: 737 sheet: -0.11 (0.17), residues: 864 loop : -0.70 (0.13), residues: 2249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 64 HIS 0.006 0.001 HIS A 516 PHE 0.016 0.002 PHE C 756 TYR 0.023 0.002 TYR A 362 ARG 0.009 0.001 ARG C 270 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 41 time to evaluate : 3.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 86 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.8143 (p0) REVERT: C 127 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8158 (tptp) REVERT: C 263 TYR cc_start: 0.8758 (OUTLIER) cc_final: 0.8351 (m-80) REVERT: A 436 ASN cc_start: 0.8990 (OUTLIER) cc_final: 0.8730 (m-40) REVERT: E 368 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7592 (mt) REVERT: E 453 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.8106 (m-80) REVERT: E 577 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8158 (mp10) REVERT: E 915 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8042 (mt-10) outliers start: 177 outliers final: 88 residues processed: 212 average time/residue: 0.3956 time to fit residues: 142.6360 Evaluate side-chains 136 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 40 time to evaluate : 3.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 393 TYR Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 506 ARG Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 437 LYS Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 516 HIS Chi-restraints excluded: chain A residue 544 LYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 288 CYS Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 405 ARG Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 530 LEU Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 577 GLN Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 596 THR Chi-restraints excluded: chain E residue 600 ASN Chi-restraints excluded: chain E residue 707 ASN Chi-restraints excluded: chain E residue 742 ASP Chi-restraints excluded: chain E residue 759 GLN Chi-restraints excluded: chain E residue 783 LYS Chi-restraints excluded: chain E residue 791 ILE Chi-restraints excluded: chain E residue 836 ASP Chi-restraints excluded: chain E residue 855 LEU Chi-restraints excluded: chain E residue 863 THR Chi-restraints excluded: chain E residue 883 TRP Chi-restraints excluded: chain E residue 915 GLU Chi-restraints excluded: chain E residue 1040 CYS Chi-restraints excluded: chain E residue 1047 MET Chi-restraints excluded: chain E residue 1133 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain G residue 43 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 194 optimal weight: 5.9990 chunk 108 optimal weight: 50.0000 chunk 291 optimal weight: 20.0000 chunk 238 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 351 optimal weight: 10.0000 chunk 379 optimal weight: 5.9990 chunk 312 optimal weight: 3.9990 chunk 348 optimal weight: 6.9990 chunk 119 optimal weight: 20.0000 chunk 281 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 850 GLN C 916 ASN ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1098 HIS ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 989 GLN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 367 ASN ** E 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 577 GLN ** E 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 932 GLN ** E 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 32200 Z= 0.291 Angle : 0.693 11.852 43774 Z= 0.344 Chirality : 0.048 0.464 5071 Planarity : 0.006 0.124 5566 Dihedral : 14.883 108.194 5553 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 23.72 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.16 % Favored : 95.66 % Rotamer: Outliers : 5.04 % Allowed : 29.74 % Favored : 65.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: 3850 helix: 2.20 (0.19), residues: 736 sheet: -0.23 (0.17), residues: 851 loop : -0.73 (0.13), residues: 2263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.005 0.001 HIS E 66 PHE 0.018 0.001 PHE C 181 TYR 0.018 0.001 TYR A 362 ARG 0.012 0.001 ARG C 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 40 time to evaluate : 3.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 127 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8053 (tptp) REVERT: C 836 ASP cc_start: 0.2793 (OUTLIER) cc_final: 0.2536 (m-30) REVERT: A 989 GLN cc_start: 0.9687 (OUTLIER) cc_final: 0.9232 (mm-40) REVERT: A 1110 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8663 (mm-40) REVERT: E 368 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7374 (mt) REVERT: E 453 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.8151 (m-80) outliers start: 171 outliers final: 110 residues processed: 207 average time/residue: 0.4085 time to fit residues: 144.0796 Evaluate side-chains 156 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 40 time to evaluate : 3.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain C residue 393 TYR Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 506 ARG Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 555 LYS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 949 VAL Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 516 HIS Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 621 ILE Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 707 ASN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 989 GLN Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 231 ASN Chi-restraints excluded: chain E residue 235 PHE Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 288 CYS Chi-restraints excluded: chain E residue 325 ARG Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 596 THR Chi-restraints excluded: chain E residue 707 ASN Chi-restraints excluded: chain E residue 716 THR Chi-restraints excluded: chain E residue 721 THR Chi-restraints excluded: chain E residue 742 ASP Chi-restraints excluded: chain E residue 783 LYS Chi-restraints excluded: chain E residue 791 ILE Chi-restraints excluded: chain E residue 823 VAL Chi-restraints excluded: chain E residue 836 ASP Chi-restraints excluded: chain E residue 855 LEU Chi-restraints excluded: chain E residue 883 TRP Chi-restraints excluded: chain E residue 1040 CYS Chi-restraints excluded: chain E residue 1047 MET Chi-restraints excluded: chain E residue 1125 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 69 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 346 optimal weight: 9.9990 chunk 264 optimal weight: 4.9990 chunk 182 optimal weight: 30.0000 chunk 38 optimal weight: 30.0000 chunk 167 optimal weight: 30.0000 chunk 235 optimal weight: 8.9990 chunk 352 optimal weight: 3.9990 chunk 373 optimal weight: 2.9990 chunk 184 optimal weight: 10.0000 chunk 334 optimal weight: 20.0000 chunk 100 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 748 ASN ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 957 ASN ** E1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 32200 Z= 0.271 Angle : 0.660 11.204 43774 Z= 0.329 Chirality : 0.047 0.357 5071 Planarity : 0.006 0.124 5566 Dihedral : 12.817 102.461 5553 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 23.31 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.44 % Favored : 95.38 % Rotamer: Outliers : 6.13 % Allowed : 28.79 % Favored : 65.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: 3850 helix: 2.23 (0.19), residues: 738 sheet: -0.32 (0.17), residues: 866 loop : -0.71 (0.13), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 64 HIS 0.004 0.001 HIS E1045 PHE 0.014 0.001 PHE G 105 TYR 0.016 0.001 TYR C1064 ARG 0.014 0.001 ARG E 405 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 40 time to evaluate : 3.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 86 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.8106 (p0) REVERT: C 127 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8103 (tptp) REVERT: C 531 VAL cc_start: 0.7180 (OUTLIER) cc_final: 0.6942 (p) REVERT: C 836 ASP cc_start: 0.2822 (OUTLIER) cc_final: 0.2557 (m-30) REVERT: A 730 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8806 (mtmm) REVERT: A 866 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8777 (pmm) REVERT: A 989 GLN cc_start: 0.9693 (OUTLIER) cc_final: 0.9262 (mm-40) REVERT: A 1110 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8645 (mm-40) REVERT: E 127 LYS cc_start: 0.9516 (OUTLIER) cc_final: 0.9302 (mmtt) REVERT: E 201 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.7750 (ttpp) REVERT: E 368 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7283 (mt) REVERT: E 453 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.8173 (m-80) REVERT: E 737 MET cc_start: 0.8857 (ptt) cc_final: 0.8480 (ptt) outliers start: 208 outliers final: 152 residues processed: 244 average time/residue: 0.4119 time to fit residues: 166.9427 Evaluate side-chains 204 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 40 time to evaluate : 3.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 393 TYR Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 506 ARG Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 555 LYS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 915 GLU Chi-restraints excluded: chain C residue 949 VAL Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 516 HIS Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 707 ASN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 989 GLN Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 231 ASN Chi-restraints excluded: chain E residue 235 PHE Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 288 CYS Chi-restraints excluded: chain E residue 325 ARG Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 404 VAL Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 503 GLN Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 596 THR Chi-restraints excluded: chain E residue 600 ASN Chi-restraints excluded: chain E residue 615 THR Chi-restraints excluded: chain E residue 631 ARG Chi-restraints excluded: chain E residue 707 ASN Chi-restraints excluded: chain E residue 716 THR Chi-restraints excluded: chain E residue 721 THR Chi-restraints excluded: chain E residue 742 ASP Chi-restraints excluded: chain E residue 783 LYS Chi-restraints excluded: chain E residue 791 ILE Chi-restraints excluded: chain E residue 823 VAL Chi-restraints excluded: chain E residue 836 ASP Chi-restraints excluded: chain E residue 855 LEU Chi-restraints excluded: chain E residue 883 TRP Chi-restraints excluded: chain E residue 913 LEU Chi-restraints excluded: chain E residue 938 THR Chi-restraints excluded: chain E residue 991 ASP Chi-restraints excluded: chain E residue 1040 CYS Chi-restraints excluded: chain E residue 1047 MET Chi-restraints excluded: chain E residue 1125 VAL Chi-restraints excluded: chain E residue 1133 THR Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 115 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 310 optimal weight: 6.9990 chunk 211 optimal weight: 10.0000 chunk 5 optimal weight: 0.3980 chunk 277 optimal weight: 30.0000 chunk 153 optimal weight: 30.0000 chunk 318 optimal weight: 8.9990 chunk 257 optimal weight: 0.5980 chunk 0 optimal weight: 50.0000 chunk 190 optimal weight: 0.9990 chunk 334 optimal weight: 20.0000 chunk 94 optimal weight: 7.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 ASN ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN A 989 GLN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 560 GLN ** E 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 917 GLN ** E 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 32200 Z= 0.212 Angle : 0.626 11.693 43774 Z= 0.311 Chirality : 0.046 0.341 5071 Planarity : 0.005 0.124 5566 Dihedral : 11.433 95.366 5552 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.21 % Favored : 95.61 % Rotamer: Outliers : 5.22 % Allowed : 29.77 % Favored : 65.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: 3850 helix: 2.34 (0.19), residues: 737 sheet: -0.41 (0.17), residues: 873 loop : -0.69 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 36 HIS 0.004 0.001 HIS E 66 PHE 0.014 0.001 PHE G 105 TYR 0.018 0.001 TYR A 199 ARG 0.006 0.000 ARG E 185 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 41 time to evaluate : 3.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 127 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8165 (tptp) REVERT: C 531 VAL cc_start: 0.7154 (OUTLIER) cc_final: 0.6917 (p) REVERT: C 836 ASP cc_start: 0.2939 (OUTLIER) cc_final: 0.2677 (m-30) REVERT: L 90 GLN cc_start: 0.9486 (OUTLIER) cc_final: 0.9171 (pp30) REVERT: A 730 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8786 (mtmm) REVERT: A 866 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8780 (pmm) REVERT: A 989 GLN cc_start: 0.9652 (OUTLIER) cc_final: 0.9108 (mm-40) REVERT: A 1110 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8630 (mm-40) REVERT: E 127 LYS cc_start: 0.9500 (OUTLIER) cc_final: 0.9083 (mmtt) REVERT: E 201 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.7739 (ttpp) REVERT: E 368 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7214 (mt) REVERT: E 453 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.8158 (m-80) REVERT: E 737 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8432 (ptt) outliers start: 177 outliers final: 126 residues processed: 213 average time/residue: 0.4082 time to fit residues: 145.5514 Evaluate side-chains 179 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 40 time to evaluate : 3.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 347 VAL Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 393 TYR Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 477 CYS Chi-restraints excluded: chain C residue 506 ARG Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 555 LYS Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 915 GLU Chi-restraints excluded: chain C residue 949 VAL Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 707 ASN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 989 GLN Chi-restraints excluded: chain A residue 1006 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 235 PHE Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 325 ARG Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 596 THR Chi-restraints excluded: chain E residue 615 THR Chi-restraints excluded: chain E residue 631 ARG Chi-restraints excluded: chain E residue 716 THR Chi-restraints excluded: chain E residue 721 THR Chi-restraints excluded: chain E residue 737 MET Chi-restraints excluded: chain E residue 783 LYS Chi-restraints excluded: chain E residue 823 VAL Chi-restraints excluded: chain E residue 836 ASP Chi-restraints excluded: chain E residue 837 CYS Chi-restraints excluded: chain E residue 855 LEU Chi-restraints excluded: chain E residue 883 TRP Chi-restraints excluded: chain E residue 884 THR Chi-restraints excluded: chain E residue 913 LEU Chi-restraints excluded: chain E residue 938 THR Chi-restraints excluded: chain E residue 991 ASP Chi-restraints excluded: chain E residue 1040 CYS Chi-restraints excluded: chain E residue 1047 MET Chi-restraints excluded: chain E residue 1125 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 115 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 125 optimal weight: 8.9990 chunk 336 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 219 optimal weight: 20.0000 chunk 92 optimal weight: 7.9990 chunk 373 optimal weight: 20.0000 chunk 310 optimal weight: 30.0000 chunk 172 optimal weight: 30.0000 chunk 31 optimal weight: 30.0000 chunk 123 optimal weight: 20.0000 chunk 196 optimal weight: 20.0000 overall best weight: 11.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 ASN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 553 ASN ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1132 ASN A 30 ASN ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 910 GLN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 869 GLN ** E 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 32200 Z= 0.490 Angle : 0.770 11.586 43774 Z= 0.390 Chirality : 0.047 0.383 5071 Planarity : 0.006 0.125 5566 Dihedral : 11.135 99.412 5551 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 32.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.32 % Favored : 94.49 % Rotamer: Outliers : 7.13 % Allowed : 28.50 % Favored : 64.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -0.33 (0.13), residues: 3850 helix: 1.92 (0.19), residues: 750 sheet: -0.45 (0.17), residues: 860 loop : -0.88 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 64 HIS 0.008 0.002 HIS A 516 PHE 0.020 0.002 PHE A 196 TYR 0.018 0.002 TYR A 362 ARG 0.009 0.001 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 40 time to evaluate : 4.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 41 LYS cc_start: 0.9533 (OUTLIER) cc_final: 0.9319 (ptpp) REVERT: C 127 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8112 (tptp) REVERT: C 464 ASP cc_start: 0.7074 (OUTLIER) cc_final: 0.6361 (p0) REVERT: C 468 GLU cc_start: 0.9319 (OUTLIER) cc_final: 0.8994 (mp0) REVERT: C 836 ASP cc_start: 0.3560 (OUTLIER) cc_final: 0.3350 (m-30) REVERT: A 436 ASN cc_start: 0.9196 (OUTLIER) cc_final: 0.8961 (m-40) REVERT: A 730 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8876 (mtmm) REVERT: A 737 MET cc_start: 0.9330 (ppp) cc_final: 0.9109 (ppp) REVERT: A 866 MET cc_start: 0.9143 (pmm) cc_final: 0.8842 (pmm) REVERT: A 1110 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8709 (mm-40) REVERT: E 368 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7466 (mt) REVERT: E 426 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8924 (m-80) REVERT: E 453 PHE cc_start: 0.8719 (OUTLIER) cc_final: 0.8245 (m-80) REVERT: E 737 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8555 (ptt) REVERT: E 915 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8025 (mt-10) REVERT: G 93 MET cc_start: 0.9170 (tpp) cc_final: 0.8934 (tpp) outliers start: 242 outliers final: 182 residues processed: 276 average time/residue: 0.4305 time to fit residues: 194.8655 Evaluate side-chains 235 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 40 time to evaluate : 3.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 291 ASP Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 352 ARG Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 393 TYR Chi-restraints excluded: chain C residue 398 VAL Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 477 CYS Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 495 ARG Chi-restraints excluded: chain C residue 506 ARG Chi-restraints excluded: chain C residue 516 HIS Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 555 LYS Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 718 SER Chi-restraints excluded: chain C residue 720 THR Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 783 LYS Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 836 ASP Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 949 VAL Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain C residue 1062 VAL Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 98 ARG Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 434 ASN Chi-restraints excluded: chain A residue 436 ASN Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain A residue 516 HIS Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 638 ASN Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 707 ASN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 753 TYR Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 1047 MET Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 235 PHE Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 325 ARG Chi-restraints excluded: chain E residue 340 ASN Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 426 PHE Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 484 ASN Chi-restraints excluded: chain E residue 503 GLN Chi-restraints excluded: chain E residue 537 ASN Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 596 THR Chi-restraints excluded: chain E residue 600 ASN Chi-restraints excluded: chain E residue 610 GLN Chi-restraints excluded: chain E residue 615 THR Chi-restraints excluded: chain E residue 631 ARG Chi-restraints excluded: chain E residue 707 ASN Chi-restraints excluded: chain E residue 716 THR Chi-restraints excluded: chain E residue 721 THR Chi-restraints excluded: chain E residue 737 MET Chi-restraints excluded: chain E residue 742 ASP Chi-restraints excluded: chain E residue 783 LYS Chi-restraints excluded: chain E residue 788 THR Chi-restraints excluded: chain E residue 791 ILE Chi-restraints excluded: chain E residue 823 VAL Chi-restraints excluded: chain E residue 836 ASP Chi-restraints excluded: chain E residue 837 CYS Chi-restraints excluded: chain E residue 883 TRP Chi-restraints excluded: chain E residue 884 THR Chi-restraints excluded: chain E residue 915 GLU Chi-restraints excluded: chain E residue 938 THR Chi-restraints excluded: chain E residue 991 ASP Chi-restraints excluded: chain E residue 1040 CYS Chi-restraints excluded: chain E residue 1047 MET Chi-restraints excluded: chain E residue 1125 VAL Chi-restraints excluded: chain E residue 1133 THR Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 115 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 360 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 chunk 272 optimal weight: 10.0000 chunk 211 optimal weight: 4.9990 chunk 314 optimal weight: 6.9990 chunk 208 optimal weight: 6.9990 chunk 372 optimal weight: 40.0000 chunk 232 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 chunk 171 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A 952 ASN A 989 GLN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 946 GLN ** E 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 32200 Z= 0.227 Angle : 0.649 11.675 43774 Z= 0.324 Chirality : 0.047 0.351 5071 Planarity : 0.005 0.125 5566 Dihedral : 10.329 98.784 5551 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 23.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.31 % Favored : 95.51 % Rotamer: Outliers : 5.63 % Allowed : 29.47 % Favored : 64.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.13), residues: 3850 helix: 2.27 (0.19), residues: 737 sheet: -0.44 (0.17), residues: 858 loop : -0.85 (0.13), residues: 2255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 64 HIS 0.005 0.001 HIS C 502 PHE 0.019 0.001 PHE A 152 TYR 0.024 0.001 TYR C 492 ARG 0.007 0.001 ARG C 270 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 40 time to evaluate : 3.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 127 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8179 (tptp) REVERT: C 464 ASP cc_start: 0.7055 (OUTLIER) cc_final: 0.6271 (p0) REVERT: C 468 GLU cc_start: 0.9293 (OUTLIER) cc_final: 0.8986 (mp0) REVERT: C 531 VAL cc_start: 0.7366 (OUTLIER) cc_final: 0.7149 (p) REVERT: A 307 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8806 (ttmm) REVERT: A 730 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8731 (mtmm) REVERT: A 866 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8810 (pmm) REVERT: A 1110 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8672 (mm-40) REVERT: E 127 LYS cc_start: 0.9539 (OUTLIER) cc_final: 0.9152 (mmtt) REVERT: E 201 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7630 (ttpp) REVERT: E 368 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7358 (mt) REVERT: E 453 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.7978 (m-80) REVERT: E 694 MET cc_start: 0.8856 (mmm) cc_final: 0.8443 (tpt) REVERT: E 737 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8528 (ptt) outliers start: 191 outliers final: 145 residues processed: 226 average time/residue: 0.4304 time to fit residues: 160.2829 Evaluate side-chains 198 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 40 time to evaluate : 3.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 393 TYR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 477 CYS Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 506 ARG Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 555 LYS Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 783 LYS Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 949 VAL Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 470 TYR Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 707 ASN Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 753 TYR Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 235 PHE Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 503 GLN Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 610 GLN Chi-restraints excluded: chain E residue 615 THR Chi-restraints excluded: chain E residue 631 ARG Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 705 SER Chi-restraints excluded: chain E residue 707 ASN Chi-restraints excluded: chain E residue 716 THR Chi-restraints excluded: chain E residue 737 MET Chi-restraints excluded: chain E residue 783 LYS Chi-restraints excluded: chain E residue 788 THR Chi-restraints excluded: chain E residue 823 VAL Chi-restraints excluded: chain E residue 836 ASP Chi-restraints excluded: chain E residue 837 CYS Chi-restraints excluded: chain E residue 855 LEU Chi-restraints excluded: chain E residue 883 TRP Chi-restraints excluded: chain E residue 938 THR Chi-restraints excluded: chain E residue 991 ASP Chi-restraints excluded: chain E residue 1040 CYS Chi-restraints excluded: chain E residue 1047 MET Chi-restraints excluded: chain E residue 1125 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 115 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 230 optimal weight: 8.9990 chunk 148 optimal weight: 50.0000 chunk 222 optimal weight: 5.9990 chunk 112 optimal weight: 40.0000 chunk 73 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 236 optimal weight: 9.9990 chunk 253 optimal weight: 30.0000 chunk 183 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 292 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 32200 Z= 0.335 Angle : 0.683 10.669 43774 Z= 0.343 Chirality : 0.046 0.365 5071 Planarity : 0.005 0.123 5566 Dihedral : 9.761 100.237 5551 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 27.74 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.19 % Favored : 94.60 % Rotamer: Outliers : 5.66 % Allowed : 29.30 % Favored : 65.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -0.28 (0.13), residues: 3850 helix: 2.11 (0.19), residues: 744 sheet: -0.50 (0.17), residues: 881 loop : -0.86 (0.13), residues: 2225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 64 HIS 0.005 0.001 HIS A 516 PHE 0.020 0.001 PHE E 562 TYR 0.026 0.002 TYR C 492 ARG 0.006 0.001 ARG E 643 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 40 time to evaluate : 3.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 127 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8143 (tptp) REVERT: C 464 ASP cc_start: 0.7155 (OUTLIER) cc_final: 0.6452 (p0) REVERT: C 468 GLU cc_start: 0.9300 (OUTLIER) cc_final: 0.8969 (mp0) REVERT: C 531 VAL cc_start: 0.7458 (OUTLIER) cc_final: 0.7240 (p) REVERT: A 307 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8784 (ttmm) REVERT: A 866 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8834 (pmm) REVERT: A 1110 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8697 (mm-40) REVERT: E 201 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7685 (ttpp) REVERT: E 368 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7411 (mt) REVERT: E 453 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.8181 (m-80) REVERT: E 694 MET cc_start: 0.8866 (mmm) cc_final: 0.8446 (tpt) REVERT: E 737 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8560 (ptt) outliers start: 192 outliers final: 171 residues processed: 227 average time/residue: 0.4421 time to fit residues: 167.9911 Evaluate side-chains 222 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 40 time to evaluate : 3.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 159 ASN Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 352 ARG Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 393 TYR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 477 CYS Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 506 ARG Chi-restraints excluded: chain C residue 516 HIS Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 550 THR Chi-restraints excluded: chain C residue 552 SER Chi-restraints excluded: chain C residue 555 LYS Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 688 SER Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 783 LYS Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 949 VAL Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 123 ASN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 470 TYR Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 495 ARG Chi-restraints excluded: chain A residue 516 HIS Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 707 ASN Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 753 TYR Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 235 PHE Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 340 ASN Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 503 GLN Chi-restraints excluded: chain E residue 537 ASN Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 596 THR Chi-restraints excluded: chain E residue 600 ASN Chi-restraints excluded: chain E residue 610 GLN Chi-restraints excluded: chain E residue 615 THR Chi-restraints excluded: chain E residue 631 ARG Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 705 SER Chi-restraints excluded: chain E residue 707 ASN Chi-restraints excluded: chain E residue 716 THR Chi-restraints excluded: chain E residue 721 THR Chi-restraints excluded: chain E residue 737 MET Chi-restraints excluded: chain E residue 742 ASP Chi-restraints excluded: chain E residue 783 LYS Chi-restraints excluded: chain E residue 788 THR Chi-restraints excluded: chain E residue 823 VAL Chi-restraints excluded: chain E residue 836 ASP Chi-restraints excluded: chain E residue 837 CYS Chi-restraints excluded: chain E residue 855 LEU Chi-restraints excluded: chain E residue 883 TRP Chi-restraints excluded: chain E residue 884 THR Chi-restraints excluded: chain E residue 916 ASN Chi-restraints excluded: chain E residue 938 THR Chi-restraints excluded: chain E residue 979 SER Chi-restraints excluded: chain E residue 991 ASP Chi-restraints excluded: chain E residue 1040 CYS Chi-restraints excluded: chain E residue 1047 MET Chi-restraints excluded: chain E residue 1062 VAL Chi-restraints excluded: chain E residue 1125 VAL Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 52 TYR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 115 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 338 optimal weight: 8.9990 chunk 356 optimal weight: 8.9990 chunk 325 optimal weight: 7.9990 chunk 346 optimal weight: 6.9990 chunk 208 optimal weight: 0.5980 chunk 151 optimal weight: 20.0000 chunk 272 optimal weight: 3.9990 chunk 106 optimal weight: 0.0870 chunk 313 optimal weight: 0.0000 chunk 327 optimal weight: 6.9990 chunk 345 optimal weight: 3.9990 overall best weight: 1.7366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 445 ASN ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 318 GLN ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 577 GLN ** E 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 917 GLN ** E 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 32200 Z= 0.181 Angle : 0.621 10.933 43774 Z= 0.310 Chirality : 0.046 0.341 5071 Planarity : 0.005 0.124 5566 Dihedral : 9.026 98.644 5551 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 21.06 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.13 % Favored : 95.66 % Rotamer: Outliers : 4.60 % Allowed : 30.18 % Favored : 65.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -0.16 (0.14), residues: 3850 helix: 2.31 (0.19), residues: 735 sheet: -0.42 (0.17), residues: 883 loop : -0.81 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 33 HIS 0.004 0.001 HIS E 66 PHE 0.017 0.001 PHE E 556 TYR 0.028 0.001 TYR C 492 ARG 0.005 0.000 ARG A 902 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 40 time to evaluate : 3.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 31 SER cc_start: 0.7946 (OUTLIER) cc_final: 0.6942 (p) REVERT: C 127 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8193 (tptp) REVERT: C 464 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.6663 (p0) REVERT: C 468 GLU cc_start: 0.9330 (OUTLIER) cc_final: 0.9037 (mp0) REVERT: C 531 VAL cc_start: 0.7298 (OUTLIER) cc_final: 0.7070 (p) REVERT: C 694 MET cc_start: 0.8599 (ptm) cc_final: 0.8282 (mtp) REVERT: A 307 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8763 (ttmm) REVERT: A 866 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8784 (pmm) REVERT: A 1110 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8690 (mm-40) REVERT: E 127 LYS cc_start: 0.9487 (OUTLIER) cc_final: 0.9067 (mmtt) REVERT: E 201 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7615 (ttpp) REVERT: E 368 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.7113 (mt) REVERT: E 453 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.8128 (m-80) REVERT: E 694 MET cc_start: 0.8962 (mmm) cc_final: 0.8639 (tpt) REVERT: E 737 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8510 (ptt) REVERT: E 897 MET cc_start: 0.8555 (mtp) cc_final: 0.8335 (mtt) outliers start: 156 outliers final: 128 residues processed: 189 average time/residue: 0.4060 time to fit residues: 129.3416 Evaluate side-chains 181 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 40 time to evaluate : 3.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain C residue 393 TYR Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 477 CYS Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 506 ARG Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 555 LYS Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 470 TYR Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 707 ASN Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 753 TYR Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 503 GLN Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 615 THR Chi-restraints excluded: chain E residue 631 ARG Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 707 ASN Chi-restraints excluded: chain E residue 721 THR Chi-restraints excluded: chain E residue 737 MET Chi-restraints excluded: chain E residue 783 LYS Chi-restraints excluded: chain E residue 823 VAL Chi-restraints excluded: chain E residue 837 CYS Chi-restraints excluded: chain E residue 855 LEU Chi-restraints excluded: chain E residue 883 TRP Chi-restraints excluded: chain E residue 884 THR Chi-restraints excluded: chain E residue 916 ASN Chi-restraints excluded: chain E residue 938 THR Chi-restraints excluded: chain E residue 991 ASP Chi-restraints excluded: chain E residue 1040 CYS Chi-restraints excluded: chain E residue 1047 MET Chi-restraints excluded: chain E residue 1062 VAL Chi-restraints excluded: chain E residue 1125 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 227 optimal weight: 6.9990 chunk 366 optimal weight: 30.0000 chunk 223 optimal weight: 5.9990 chunk 173 optimal weight: 0.9990 chunk 254 optimal weight: 4.9990 chunk 384 optimal weight: 50.0000 chunk 353 optimal weight: 5.9990 chunk 306 optimal weight: 8.9990 chunk 31 optimal weight: 30.0000 chunk 236 optimal weight: 5.9990 chunk 187 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 952 ASN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 32200 Z= 0.221 Angle : 0.612 10.234 43774 Z= 0.307 Chirality : 0.045 0.340 5071 Planarity : 0.005 0.124 5566 Dihedral : 8.711 99.293 5551 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 22.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.65 % Favored : 95.17 % Rotamer: Outliers : 4.60 % Allowed : 30.09 % Favored : 65.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -0.15 (0.14), residues: 3850 helix: 2.29 (0.19), residues: 744 sheet: -0.37 (0.17), residues: 885 loop : -0.82 (0.13), residues: 2221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 64 HIS 0.003 0.001 HIS E 66 PHE 0.012 0.001 PHE F 84 TYR 0.034 0.001 TYR C 492 ARG 0.005 0.000 ARG C 270 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7700 Ramachandran restraints generated. 3850 Oldfield, 0 Emsley, 3850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 40 time to evaluate : 4.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 127 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8220 (tptp) REVERT: C 464 ASP cc_start: 0.7437 (OUTLIER) cc_final: 0.6726 (p0) REVERT: C 468 GLU cc_start: 0.9329 (OUTLIER) cc_final: 0.9033 (mp0) REVERT: C 531 VAL cc_start: 0.7366 (OUTLIER) cc_final: 0.7146 (p) REVERT: C 694 MET cc_start: 0.8630 (ptm) cc_final: 0.8179 (mtp) REVERT: A 307 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8782 (ttmm) REVERT: A 866 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8790 (pmm) REVERT: A 1110 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8672 (mm-40) REVERT: E 201 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.7616 (ttpp) REVERT: E 368 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7159 (mt) REVERT: E 453 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.8175 (m-80) REVERT: E 694 MET cc_start: 0.8982 (mmm) cc_final: 0.8695 (tpt) REVERT: E 737 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8511 (ptt) outliers start: 156 outliers final: 135 residues processed: 190 average time/residue: 0.4636 time to fit residues: 150.8673 Evaluate side-chains 186 residues out of total 3406 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 40 time to evaluate : 3.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 127 LYS Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 393 TYR Chi-restraints excluded: chain C residue 464 ASP Chi-restraints excluded: chain C residue 468 GLU Chi-restraints excluded: chain C residue 477 CYS Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 506 ARG Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 555 LYS Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 643 ARG Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 971 SER Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1040 CYS Chi-restraints excluded: chain C residue 1133 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 20 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 307 LYS Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 470 TYR Chi-restraints excluded: chain A residue 477 CYS Chi-restraints excluded: chain A residue 526 LYS Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 707 ASN Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 731 THR Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 753 TYR Chi-restraints excluded: chain A residue 756 PHE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 864 ASP Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 87 LYS Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 89 CYS Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 HIS Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 123 ASN Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 458 LEU Chi-restraints excluded: chain E residue 503 GLN Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 585 THR Chi-restraints excluded: chain E residue 615 THR Chi-restraints excluded: chain E residue 631 ARG Chi-restraints excluded: chain E residue 642 THR Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 707 ASN Chi-restraints excluded: chain E residue 721 THR Chi-restraints excluded: chain E residue 737 MET Chi-restraints excluded: chain E residue 783 LYS Chi-restraints excluded: chain E residue 823 VAL Chi-restraints excluded: chain E residue 836 ASP Chi-restraints excluded: chain E residue 837 CYS Chi-restraints excluded: chain E residue 855 LEU Chi-restraints excluded: chain E residue 883 TRP Chi-restraints excluded: chain E residue 884 THR Chi-restraints excluded: chain E residue 913 LEU Chi-restraints excluded: chain E residue 938 THR Chi-restraints excluded: chain E residue 991 ASP Chi-restraints excluded: chain E residue 1040 CYS Chi-restraints excluded: chain E residue 1047 MET Chi-restraints excluded: chain E residue 1062 VAL Chi-restraints excluded: chain E residue 1125 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 32 SER Chi-restraints excluded: chain F residue 91 GLN Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 386 random chunks: chunk 243 optimal weight: 5.9990 chunk 326 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 282 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 85 optimal weight: 0.0570 chunk 306 optimal weight: 8.9990 chunk 128 optimal weight: 8.9990 chunk 314 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 overall best weight: 5.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 951 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.024454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.018244 restraints weight = 555375.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.018707 restraints weight = 331886.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.018993 restraints weight = 229235.364| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 32200 Z= 0.275 Angle : 0.625 10.095 43774 Z= 0.317 Chirality : 0.045 0.361 5071 Planarity : 0.005 0.122 5566 Dihedral : 8.586 99.826 5551 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 25.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.94 % Favored : 94.88 % Rotamer: Outliers : 4.77 % Allowed : 29.80 % Favored : 65.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -0.16 (0.14), residues: 3850 helix: 2.27 (0.19), residues: 746 sheet: -0.39 (0.17), residues: 882 loop : -0.83 (0.13), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 64 HIS 0.004 0.001 HIS A 516 PHE 0.013 0.001 PHE A 32 TYR 0.027 0.001 TYR C 492 ARG 0.006 0.001 ARG C 270 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5117.00 seconds wall clock time: 97 minutes 2.94 seconds (5822.94 seconds total)