Starting phenix.real_space_refine on Fri Feb 23 23:09:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7q_12753/02_2024/7o7q_12753.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7q_12753/02_2024/7o7q_12753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7q_12753/02_2024/7o7q_12753.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7q_12753/02_2024/7o7q_12753.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7q_12753/02_2024/7o7q_12753.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7q_12753/02_2024/7o7q_12753.pdb" } resolution = 3.6 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 ------------------------------------------------------------------------------- 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= -0.000 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 172 5.16 5 C 25734 2.51 5 N 6746 2.21 5 O 7878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 82": "OD1" <-> "OD2" Residue "A PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 184": "OE1" <-> "OE2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A ASP 282": "OD1" <-> "OD2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 519": "OD1" <-> "OD2" Residue "A ASP 533": "OD1" <-> "OD2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 636": "OD1" <-> "OD2" Residue "A ARG 645": "NH1" <-> "NH2" Residue "A TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 672": "OD1" <-> "OD2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 737": "OE1" <-> "OE2" Residue "A GLU 753": "OE1" <-> "OE2" Residue "A PHE 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 795": "OE1" <-> "OE2" Residue "A TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 842": "OE1" <-> "OE2" Residue "A GLU 878": "OE1" <-> "OE2" Residue "A GLU 908": "OE1" <-> "OE2" Residue "A ASP 953": "OD1" <-> "OD2" Residue "A ASP 988": "OD1" <-> "OD2" Residue "A GLU 999": "OE1" <-> "OE2" Residue "A TYR 1025": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1030": "OE1" <-> "OE2" Residue "A TYR 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1137": "OE1" <-> "OE2" Residue "A TYR 1197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1198": "OE1" <-> "OE2" Residue "A TYR 1216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1227": "OD1" <-> "OD2" Residue "A TYR 1264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1311": "OE1" <-> "OE2" Residue "A TYR 1312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1337": "OE1" <-> "OE2" Residue "A PHE 1339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 56": "OE1" <-> "OE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 160": "OE1" <-> "OE2" Residue "B ASP 169": "OD1" <-> "OD2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "B GLU 244": "OE1" <-> "OE2" Residue "B TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 274": "OD1" <-> "OD2" Residue "B TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "B TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 323": "OE1" <-> "OE2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "B PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 533": "OD1" <-> "OD2" Residue "B ASP 554": "OD1" <-> "OD2" Residue "B ASP 601": "OD1" <-> "OD2" Residue "B GLU 612": "OE1" <-> "OE2" Residue "B PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 636": "OD1" <-> "OD2" Residue "B ARG 645": "NH1" <-> "NH2" Residue "B TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 753": "OE1" <-> "OE2" Residue "B ASP 760": "OD1" <-> "OD2" Residue "B PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 795": "OE1" <-> "OE2" Residue "B TYR 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 842": "OE1" <-> "OE2" Residue "B PHE 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 886": "OE1" <-> "OE2" Residue "B GLU 911": "OE1" <-> "OE2" Residue "B GLU 930": "OE1" <-> "OE2" Residue "B GLU 941": "OE1" <-> "OE2" Residue "B ASP 953": "OD1" <-> "OD2" Residue "B GLU 992": "OE1" <-> "OE2" Residue "B TYR 1025": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1030": "OE1" <-> "OE2" Residue "B TYR 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1097": "OD1" <-> "OD2" Residue "B GLU 1137": "OE1" <-> "OE2" Residue "B TYR 1197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1227": "OD1" <-> "OD2" Residue "B TYR 1264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 82": "OD1" <-> "OD2" Residue "C PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 184": "OE1" <-> "OE2" Residue "C PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 216": "OE1" <-> "OE2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C ASP 282": "OD1" <-> "OD2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 323": "OE1" <-> "OE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "C PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 519": "OD1" <-> "OD2" Residue "C ASP 533": "OD1" <-> "OD2" Residue "C GLU 612": "OE1" <-> "OE2" Residue "C PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 636": "OD1" <-> "OD2" Residue "C ARG 645": "NH1" <-> "NH2" Residue "C TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 672": "OD1" <-> "OD2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 737": "OE1" <-> "OE2" Residue "C GLU 753": "OE1" <-> "OE2" Residue "C PHE 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 795": "OE1" <-> "OE2" Residue "C TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 842": "OE1" <-> "OE2" Residue "C GLU 878": "OE1" <-> "OE2" Residue "C GLU 908": "OE1" <-> "OE2" Residue "C ASP 953": "OD1" <-> "OD2" Residue "C ASP 988": "OD1" <-> "OD2" Residue "C GLU 999": "OE1" <-> "OE2" Residue "C TYR 1025": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1030": "OE1" <-> "OE2" Residue "C TYR 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1137": "OE1" <-> "OE2" Residue "C TYR 1197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1198": "OE1" <-> "OE2" Residue "C TYR 1216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1227": "OD1" <-> "OD2" Residue "C TYR 1264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1311": "OE1" <-> "OE2" Residue "C TYR 1312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1337": "OE1" <-> "OE2" Residue "C PHE 1339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "D PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D ASP 169": "OD1" <-> "OD2" Residue "D PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D GLU 244": "OE1" <-> "OE2" Residue "D TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 274": "OD1" <-> "OD2" Residue "D TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 313": "NH1" <-> "NH2" Residue "D TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 323": "OE1" <-> "OE2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "D PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 533": "OD1" <-> "OD2" Residue "D ASP 554": "OD1" <-> "OD2" Residue "D ASP 601": "OD1" <-> "OD2" Residue "D GLU 612": "OE1" <-> "OE2" Residue "D PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 636": "OD1" <-> "OD2" Residue "D ARG 645": "NH1" <-> "NH2" Residue "D TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 753": "OE1" <-> "OE2" Residue "D ASP 760": "OD1" <-> "OD2" Residue "D PHE 792": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 795": "OE1" <-> "OE2" Residue "D TYR 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 842": "OE1" <-> "OE2" Residue "D PHE 870": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 886": "OE1" <-> "OE2" Residue "D GLU 908": "OE1" <-> "OE2" Residue "D GLU 911": "OE1" <-> "OE2" Residue "D GLU 930": "OE1" <-> "OE2" Residue "D GLU 941": "OE1" <-> "OE2" Residue "D ASP 953": "OD1" <-> "OD2" Residue "D GLU 992": "OE1" <-> "OE2" Residue "D TYR 1025": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1030": "OE1" <-> "OE2" Residue "D TYR 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1097": "OD1" <-> "OD2" Residue "D GLU 1137": "OE1" <-> "OE2" Residue "D TYR 1197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1227": "OD1" <-> "OD2" Residue "D TYR 1264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1312": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 40530 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 10023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1285, 10023 Classifications: {'peptide': 1285} Link IDs: {'PTRANS': 67, 'TRANS': 1217} Chain breaks: 1 Chain: "B" Number of atoms: 9968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1278, 9968 Classifications: {'peptide': 1278} Link IDs: {'PTRANS': 66, 'TRANS': 1211} Chain breaks: 1 Chain: "C" Number of atoms: 10023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1285, 10023 Classifications: {'peptide': 1285} Link IDs: {'PTRANS': 67, 'TRANS': 1217} Chain breaks: 1 Chain: "D" Number of atoms: 9968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1278, 9968 Classifications: {'peptide': 1278} Link IDs: {'PTRANS': 66, 'TRANS': 1211} Chain breaks: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" 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: "B" 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: "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: "D" 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 Time building chain proxies: 19.86, per 1000 atoms: 0.49 Number of scatterers: 40530 At special positions: 0 Unit cell: (214.635, 149.721, 158.097, 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 172 16.00 O 7878 8.00 N 6746 7.00 C 25734 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 86 " distance=2.03 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 299 " distance=2.02 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS B 431 " distance=2.02 Simple disulfide: pdb=" SG CYS A 431 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 563 " distance=2.03 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS A 771 " distance=2.03 Simple disulfide: pdb=" SG CYS A 642 " - pdb=" SG CYS A 689 " distance=2.03 Simple disulfide: pdb=" SG CYS A 821 " - pdb=" SG CYS A 849 " distance=2.03 Simple disulfide: pdb=" SG CYS A 847 " - pdb=" SG CYS A 883 " distance=2.03 Simple disulfide: pdb=" SG CYS A 921 " - pdb=" SG CYS A1321 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1127 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 86 " distance=2.03 Simple disulfide: pdb=" SG CYS B 251 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 269 " - pdb=" SG CYS B 287 " distance=2.03 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 563 " distance=2.03 Simple disulfide: pdb=" SG CYS B 595 " - pdb=" SG CYS B 771 " distance=2.03 Simple disulfide: pdb=" SG CYS B 642 " - pdb=" SG CYS B 689 " distance=2.03 Simple disulfide: pdb=" SG CYS B 821 " - pdb=" SG CYS B 849 " distance=2.04 Simple disulfide: pdb=" SG CYS B 847 " - pdb=" SG CYS B 883 " distance=2.03 Simple disulfide: pdb=" SG CYS B 921 " - pdb=" SG CYS B1321 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 86 " distance=2.03 Simple disulfide: pdb=" SG CYS C 251 " - pdb=" SG CYS C 299 " distance=2.02 Simple disulfide: pdb=" SG CYS C 269 " - pdb=" SG CYS C 287 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS D 431 " distance=2.02 Simple disulfide: pdb=" SG CYS C 431 " - pdb=" SG CYS D 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 470 " - pdb=" SG CYS C 563 " distance=2.03 Simple disulfide: pdb=" SG CYS C 595 " - pdb=" SG CYS C 771 " distance=2.03 Simple disulfide: pdb=" SG CYS C 642 " - pdb=" SG CYS C 689 " distance=2.03 Simple disulfide: pdb=" SG CYS C 821 " - pdb=" SG CYS C 849 " distance=2.03 Simple disulfide: pdb=" SG CYS C 847 " - pdb=" SG CYS C 883 " distance=2.03 Simple disulfide: pdb=" SG CYS C 921 " - pdb=" SG CYS C1321 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1127 " distance=2.03 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 86 " distance=2.03 Simple disulfide: pdb=" SG CYS D 251 " - pdb=" SG CYS D 299 " distance=2.03 Simple disulfide: pdb=" SG CYS D 269 " - pdb=" SG CYS D 287 " distance=2.03 Simple disulfide: pdb=" SG CYS D 470 " - pdb=" SG CYS D 563 " distance=2.03 Simple disulfide: pdb=" SG CYS D 595 " - pdb=" SG CYS D 771 " distance=2.03 Simple disulfide: pdb=" SG CYS D 642 " - pdb=" SG CYS D 689 " distance=2.03 Simple disulfide: pdb=" SG CYS D 821 " - pdb=" SG CYS D 849 " distance=2.04 Simple disulfide: pdb=" SG CYS D 847 " - pdb=" SG CYS D 883 " distance=2.03 Simple disulfide: pdb=" SG CYS D 921 " - pdb=" SG CYS D1321 " distance=2.03 Simple disulfide: pdb=" SG CYS D1079 " - pdb=" SG CYS D1127 " 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG A2001 " - " ASN A 55 " " NAG A2002 " - " ASN A 70 " " NAG A2003 " - " ASN A 247 " " NAG A2004 " - " ASN A 396 " " NAG A2005 " - " ASN A 410 " " NAG B2001 " - " ASN B 55 " " NAG B2002 " - " ASN B 70 " " NAG B2003 " - " ASN B 247 " " NAG B2004 " - " ASN B 396 " " NAG B2005 " - " ASN B 410 " " NAG C2001 " - " ASN C 55 " " NAG C2002 " - " ASN C 70 " " NAG C2003 " - " ASN C 247 " " NAG C2004 " - " ASN C 396 " " NAG C2005 " - " ASN C 410 " " NAG D2001 " - " ASN D 55 " " NAG D2002 " - " ASN D 70 " " NAG D2003 " - " ASN D 247 " " NAG D2004 " - " ASN D 396 " " NAG D2005 " - " ASN D 410 " " NAG E 1 " - " ASN A 869 " " NAG F 1 " - " ASN A 991 " " NAG G 1 " - " ASN B 869 " " NAG H 1 " - " ASN B 991 " " NAG I 1 " - " ASN C 869 " " NAG J 1 " - " ASN C 991 " " NAG K 1 " - " ASN D 869 " " NAG L 1 " - " ASN D 991 " Time building additional restraints: 15.41 Conformation dependent library (CDL) restraints added in 7.1 seconds 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9600 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 0 sheets defined 16.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.65 Creating SS restraints... Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 602 through 607 Processing helix chain 'A' and resid 615 through 621 Processing helix chain 'A' and resid 666 through 673 Processing helix chain 'A' and resid 953 through 965 removed outlier: 5.227A pdb=" N SER A 957 " --> pdb=" O ASP A 953 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA A 958 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N MET A 959 " --> pdb=" O LEU A 955 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLN A 960 " --> pdb=" O GLY A 956 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN A 961 " --> pdb=" O SER A 957 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 993 Proline residue: A 982 - end of helix removed outlier: 3.806A pdb=" N TYR A 985 " --> pdb=" O ALA A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1017 Processing helix chain 'A' and resid 1039 through 1055 Processing helix chain 'A' and resid 1060 through 1073 Processing helix chain 'A' and resid 1098 through 1111 Processing helix chain 'A' and resid 1119 through 1137 Processing helix chain 'A' and resid 1144 through 1157 Processing helix chain 'A' and resid 1160 through 1172 Processing helix chain 'A' and resid 1225 through 1241 Processing helix chain 'A' and resid 1251 through 1268 Processing helix chain 'A' and resid 1294 through 1297 No H-bonds generated for 'chain 'A' and resid 1294 through 1297' Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 602 through 607 Processing helix chain 'B' and resid 615 through 621 Processing helix chain 'B' and resid 666 through 673 Processing helix chain 'B' and resid 953 through 965 removed outlier: 5.227A pdb=" N SER B 957 " --> pdb=" O ASP B 953 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA B 958 " --> pdb=" O ILE B 954 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N MET B 959 " --> pdb=" O LEU B 955 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLN B 960 " --> pdb=" O GLY B 956 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN B 961 " --> pdb=" O SER B 957 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 993 Proline residue: B 982 - end of helix removed outlier: 3.811A pdb=" N TYR B 985 " --> pdb=" O ALA B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1017 Processing helix chain 'B' and resid 1039 through 1055 Processing helix chain 'B' and resid 1060 through 1073 Processing helix chain 'B' and resid 1098 through 1111 Processing helix chain 'B' and resid 1119 through 1137 Processing helix chain 'B' and resid 1144 through 1157 Processing helix chain 'B' and resid 1160 through 1172 Processing helix chain 'B' and resid 1225 through 1241 Processing helix chain 'B' and resid 1251 through 1268 Processing helix chain 'B' and resid 1294 through 1297 No H-bonds generated for 'chain 'B' and resid 1294 through 1297' Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 602 through 607 Processing helix chain 'C' and resid 615 through 621 Processing helix chain 'C' and resid 666 through 673 Processing helix chain 'C' and resid 953 through 965 removed outlier: 5.227A pdb=" N SER C 957 " --> pdb=" O ASP C 953 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA C 958 " --> pdb=" O ILE C 954 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N MET C 959 " --> pdb=" O LEU C 955 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLN C 960 " --> pdb=" O GLY C 956 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN C 961 " --> pdb=" O SER C 957 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 993 Proline residue: C 982 - end of helix removed outlier: 3.806A pdb=" N TYR C 985 " --> pdb=" O ALA C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 998 through 1017 Processing helix chain 'C' and resid 1039 through 1055 Processing helix chain 'C' and resid 1060 through 1073 Processing helix chain 'C' and resid 1098 through 1111 Processing helix chain 'C' and resid 1119 through 1137 Processing helix chain 'C' and resid 1144 through 1157 Processing helix chain 'C' and resid 1160 through 1172 Processing helix chain 'C' and resid 1225 through 1241 Processing helix chain 'C' and resid 1251 through 1268 Processing helix chain 'C' and resid 1294 through 1297 No H-bonds generated for 'chain 'C' and resid 1294 through 1297' Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 602 through 607 Processing helix chain 'D' and resid 615 through 621 Processing helix chain 'D' and resid 666 through 673 Processing helix chain 'D' and resid 953 through 965 removed outlier: 5.228A pdb=" N SER D 957 " --> pdb=" O ASP D 953 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA D 958 " --> pdb=" O ILE D 954 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N MET D 959 " --> pdb=" O LEU D 955 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLN D 960 " --> pdb=" O GLY D 956 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN D 961 " --> pdb=" O SER D 957 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR D 962 " --> pdb=" O ALA D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 973 through 993 Proline residue: D 982 - end of helix removed outlier: 3.811A pdb=" N TYR D 985 " --> pdb=" O ALA D 981 " (cutoff:3.500A) Processing helix chain 'D' and resid 998 through 1017 Processing helix chain 'D' and resid 1039 through 1055 Processing helix chain 'D' and resid 1060 through 1073 Processing helix chain 'D' and resid 1098 through 1111 Processing helix chain 'D' and resid 1119 through 1137 Processing helix chain 'D' and resid 1144 through 1157 Processing helix chain 'D' and resid 1160 through 1172 Processing helix chain 'D' and resid 1225 through 1241 Processing helix chain 'D' and resid 1251 through 1268 Processing helix chain 'D' and resid 1294 through 1297 No H-bonds generated for 'chain 'D' and resid 1294 through 1297' 540 hydrogen bonds defined for protein. 1620 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: 8.07 Time building geometry restraints manager: 16.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 6721 1.26 - 1.41: 9881 1.41 - 1.55: 24495 1.55 - 1.70: 71 1.70 - 1.84: 252 Bond restraints: 41420 Sorted by residual: bond pdb=" C SER D 949 " pdb=" N VAL D 950 " ideal model delta sigma weight residual 1.330 1.117 0.213 1.42e-02 4.96e+03 2.25e+02 bond pdb=" C SER C 949 " pdb=" N VAL C 950 " ideal model delta sigma weight residual 1.330 1.172 0.159 1.97e-02 2.58e+03 6.48e+01 bond pdb=" C GLN C 168 " pdb=" N ASP C 169 " ideal model delta sigma weight residual 1.329 1.466 -0.138 1.86e-02 2.89e+03 5.47e+01 bond pdb=" C GLN A 168 " pdb=" N ASP A 169 " ideal model delta sigma weight residual 1.329 1.466 -0.137 1.86e-02 2.89e+03 5.44e+01 bond pdb=" C GLY B 629 " pdb=" N PHE B 630 " ideal model delta sigma weight residual 1.331 1.241 0.089 1.48e-02 4.57e+03 3.64e+01 ... (remaining 41415 not shown) Histogram of bond angle deviations from ideal: 97.32 - 105.39: 1204 105.39 - 113.47: 22591 113.47 - 121.54: 21611 121.54 - 129.62: 10486 129.62 - 137.69: 378 Bond angle restraints: 56270 Sorted by residual: angle pdb=" N MET A 464 " pdb=" CA MET A 464 " pdb=" C MET A 464 " ideal model delta sigma weight residual 110.65 99.13 11.52 1.26e+00 6.30e-01 8.35e+01 angle pdb=" N MET C 464 " pdb=" CA MET C 464 " pdb=" C MET C 464 " ideal model delta sigma weight residual 110.65 99.13 11.52 1.26e+00 6.30e-01 8.35e+01 angle pdb=" N ASN B 154 " pdb=" CA ASN B 154 " pdb=" C ASN B 154 " ideal model delta sigma weight residual 110.48 97.32 13.16 1.48e+00 4.57e-01 7.91e+01 angle pdb=" N ASN D 154 " pdb=" CA ASN D 154 " pdb=" C ASN D 154 " ideal model delta sigma weight residual 110.48 97.37 13.11 1.48e+00 4.57e-01 7.84e+01 angle pdb=" N MET D 464 " pdb=" CA MET D 464 " pdb=" C MET D 464 " ideal model delta sigma weight residual 110.65 99.92 10.73 1.26e+00 6.30e-01 7.25e+01 ... (remaining 56265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.51: 23483 21.51 - 43.01: 1676 43.01 - 64.52: 313 64.52 - 86.02: 66 86.02 - 107.53: 24 Dihedral angle restraints: 25562 sinusoidal: 10648 harmonic: 14914 Sorted by residual: dihedral pdb=" CB CYS D1079 " pdb=" SG CYS D1079 " pdb=" SG CYS D1127 " pdb=" CB CYS D1127 " ideal model delta sinusoidal sigma weight residual 93.00 175.59 -82.59 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS B1079 " pdb=" SG CYS B1079 " pdb=" SG CYS B1127 " pdb=" CB CYS B1127 " ideal model delta sinusoidal sigma weight residual 93.00 175.59 -82.59 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS A 431 " pdb=" SG CYS A 431 " pdb=" SG CYS B 278 " pdb=" CB CYS B 278 " ideal model delta sinusoidal sigma weight residual 93.00 152.91 -59.91 1 1.00e+01 1.00e-02 4.79e+01 ... (remaining 25559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.308: 6479 0.308 - 0.617: 31 0.617 - 0.925: 0 0.925 - 1.234: 0 1.234 - 1.542: 4 Chirality restraints: 6514 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.76 0.36 2.00e-02 2.50e+03 3.16e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.42e+02 chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.32e+02 ... (remaining 6511 not shown) Planarity restraints: 7230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " -0.175 2.00e-02 2.50e+03 1.48e-01 2.74e+02 pdb=" C7 NAG L 1 " 0.037 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " 0.040 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " 0.238 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " -0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " -0.162 2.00e-02 2.50e+03 1.37e-01 2.34e+02 pdb=" C7 NAG H 1 " 0.034 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " 0.039 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " 0.219 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " -0.129 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.163 2.00e-02 2.50e+03 1.35e-01 2.28e+02 pdb=" C7 NAG E 2 " 0.045 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.120 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.218 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " 0.021 2.00e-02 2.50e+03 ... (remaining 7227 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 245 2.39 - 3.02: 26835 3.02 - 3.65: 62657 3.65 - 4.27: 89987 4.27 - 4.90: 143593 Nonbonded interactions: 323317 Sorted by model distance: nonbonded pdb=" O GLY C 952 " pdb=" NH1 ARG C1297 " model vdw 1.769 2.520 nonbonded pdb=" SD MET C 959 " pdb=" NE2 GLN C 995 " model vdw 1.802 2.880 nonbonded pdb=" OG1 THR A 656 " pdb=" O PRO D 657 " model vdw 1.867 2.440 nonbonded pdb=" SD MET A 959 " pdb=" NE2 GLN A 995 " model vdw 1.874 2.880 nonbonded pdb=" O PRO B 657 " pdb=" OG1 THR C 656 " model vdw 1.878 2.440 ... (remaining 323312 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 26 through 1337 or resid 2001 through 2005)) selection = chain 'B' selection = (chain 'C' and (resid 26 through 1337 or resid 2001 through 2005)) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 7.790 Check model and map are aligned: 0.540 Set scattering table: 0.340 Process input model: 89.840 Find NCS groups from input model: 3.100 Set up NCS constraints: 0.350 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 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 : 0.010 0.297 41420 Z= 0.640 Angle : 1.538 17.084 56270 Z= 0.891 Chirality : 0.081 1.542 6514 Planarity : 0.009 0.148 7202 Dihedral : 15.204 107.530 15830 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 1.45 % Allowed : 14.50 % Favored : 84.05 % Rotamer: Outliers : 0.63 % Allowed : 4.85 % Favored : 94.52 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.10), residues: 5110 helix: -0.89 (0.15), residues: 856 sheet: -2.05 (0.10), residues: 1858 loop : -4.12 (0.10), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP D 765 HIS 0.015 0.002 HIS A1195 PHE 0.030 0.003 PHE B 155 TYR 0.041 0.003 TYR C 166 ARG 0.016 0.001 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 851 time to evaluate : 4.442 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.8152 (tt) cc_final: 0.7838 (tt) REVERT: A 203 TYR cc_start: 0.6196 (m-10) cc_final: 0.5830 (m-80) REVERT: A 208 GLN cc_start: 0.7860 (tt0) cc_final: 0.7534 (tp40) REVERT: A 384 ILE cc_start: 0.9459 (pt) cc_final: 0.9127 (mm) REVERT: A 456 LYS cc_start: 0.9008 (mmmt) cc_final: 0.8602 (mmmt) REVERT: A 458 PHE cc_start: 0.7986 (p90) cc_final: 0.7757 (p90) REVERT: A 567 LYS cc_start: 0.8319 (tppt) cc_final: 0.8072 (tppt) REVERT: A 672 ASP cc_start: 0.8422 (t0) cc_final: 0.8200 (t0) REVERT: A 766 LYS cc_start: 0.6956 (mmtp) cc_final: 0.6713 (mptt) REVERT: A 828 LEU cc_start: 0.7951 (pt) cc_final: 0.6938 (pp) REVERT: A 931 LEU cc_start: 0.9160 (tp) cc_final: 0.8949 (tp) REVERT: A 988 ASP cc_start: 0.9012 (m-30) cc_final: 0.8329 (m-30) REVERT: A 1015 GLN cc_start: 0.8202 (tp40) cc_final: 0.7743 (tp40) REVERT: A 1035 ASN cc_start: 0.6454 (m110) cc_final: 0.6095 (m110) REVERT: A 1161 ASP cc_start: 0.9030 (p0) cc_final: 0.8784 (p0) REVERT: A 1165 GLU cc_start: 0.9133 (tt0) cc_final: 0.8843 (tt0) REVERT: A 1217 LEU cc_start: 0.9586 (mm) cc_final: 0.9339 (mm) REVERT: A 1314 MET cc_start: 0.8748 (mpp) cc_final: 0.8284 (mpp) REVERT: A 1323 TYR cc_start: 0.7304 (t80) cc_final: 0.6954 (t80) REVERT: B 134 ASP cc_start: 0.8351 (t0) cc_final: 0.7543 (t70) REVERT: B 183 LEU cc_start: 0.7730 (mt) cc_final: 0.7479 (mt) REVERT: B 208 GLN cc_start: 0.7935 (tt0) cc_final: 0.7698 (tp-100) REVERT: B 532 SER cc_start: 0.7150 (t) cc_final: 0.6944 (m) REVERT: B 561 GLU cc_start: 0.7418 (pt0) cc_final: 0.6839 (pt0) REVERT: B 605 LEU cc_start: 0.8613 (tp) cc_final: 0.8305 (tp) REVERT: B 688 MET cc_start: 0.8262 (ppp) cc_final: 0.7905 (ppp) REVERT: B 741 TRP cc_start: 0.8007 (t-100) cc_final: 0.7388 (t-100) REVERT: B 787 ARG cc_start: 0.8136 (mtt180) cc_final: 0.7380 (mtm180) REVERT: B 858 TRP cc_start: 0.7775 (m-90) cc_final: 0.7296 (m-90) REVERT: B 1105 ILE cc_start: 0.8878 (mt) cc_final: 0.8653 (mt) REVERT: B 1147 LYS cc_start: 0.8985 (mttp) cc_final: 0.8553 (mttp) REVERT: B 1149 LEU cc_start: 0.9611 (tp) cc_final: 0.9408 (tt) REVERT: B 1161 ASP cc_start: 0.8914 (p0) cc_final: 0.8521 (p0) REVERT: B 1172 GLU cc_start: 0.9031 (tt0) cc_final: 0.8318 (tm-30) REVERT: B 1229 THR cc_start: 0.9058 (p) cc_final: 0.8843 (p) REVERT: B 1241 GLN cc_start: 0.8945 (mm-40) cc_final: 0.8532 (tm-30) REVERT: B 1330 TYR cc_start: 0.8312 (p90) cc_final: 0.8081 (p90) REVERT: C 50 LEU cc_start: 0.8134 (tt) cc_final: 0.7805 (tt) REVERT: C 203 TYR cc_start: 0.6209 (m-10) cc_final: 0.5844 (m-80) REVERT: C 208 GLN cc_start: 0.7781 (tt0) cc_final: 0.7456 (tp40) REVERT: C 260 VAL cc_start: 0.4773 (p) cc_final: 0.4528 (p) REVERT: C 384 ILE cc_start: 0.9458 (pt) cc_final: 0.9135 (mm) REVERT: C 456 LYS cc_start: 0.9010 (mmmt) cc_final: 0.8593 (mmmt) REVERT: C 458 PHE cc_start: 0.7960 (p90) cc_final: 0.7752 (p90) REVERT: C 567 LYS cc_start: 0.8336 (tppt) cc_final: 0.8089 (tppt) REVERT: C 672 ASP cc_start: 0.8415 (t0) cc_final: 0.8202 (t0) REVERT: C 828 LEU cc_start: 0.7962 (pt) cc_final: 0.6926 (pp) REVERT: C 931 LEU cc_start: 0.9158 (tp) cc_final: 0.8946 (tp) REVERT: C 977 MET cc_start: 0.9145 (mmm) cc_final: 0.8887 (mmm) REVERT: C 988 ASP cc_start: 0.8988 (m-30) cc_final: 0.8301 (m-30) REVERT: C 1015 GLN cc_start: 0.8201 (tp40) cc_final: 0.7571 (tp40) REVERT: C 1035 ASN cc_start: 0.6623 (m110) cc_final: 0.6163 (m110) REVERT: C 1161 ASP cc_start: 0.8997 (p0) cc_final: 0.8735 (p0) REVERT: C 1165 GLU cc_start: 0.9148 (tt0) cc_final: 0.8848 (tt0) REVERT: C 1217 LEU cc_start: 0.9576 (mm) cc_final: 0.9328 (mm) REVERT: C 1314 MET cc_start: 0.8858 (mpp) cc_final: 0.8403 (mpp) REVERT: C 1323 TYR cc_start: 0.7190 (t80) cc_final: 0.6788 (t80) REVERT: D 134 ASP cc_start: 0.8285 (t0) cc_final: 0.7524 (t70) REVERT: D 183 LEU cc_start: 0.7778 (mt) cc_final: 0.7497 (mt) REVERT: D 561 GLU cc_start: 0.7324 (pt0) cc_final: 0.6744 (pt0) REVERT: D 605 LEU cc_start: 0.8679 (tp) cc_final: 0.8375 (tp) REVERT: D 673 MET cc_start: 0.8245 (tpp) cc_final: 0.7974 (tpp) REVERT: D 688 MET cc_start: 0.8328 (ppp) cc_final: 0.7952 (ppp) REVERT: D 741 TRP cc_start: 0.8021 (t-100) cc_final: 0.7379 (t-100) REVERT: D 787 ARG cc_start: 0.8140 (mtt180) cc_final: 0.7299 (mtm180) REVERT: D 858 TRP cc_start: 0.7641 (m-90) cc_final: 0.7209 (m-90) REVERT: D 1105 ILE cc_start: 0.8833 (mt) cc_final: 0.8605 (mt) REVERT: D 1161 ASP cc_start: 0.8897 (p0) cc_final: 0.8482 (p0) REVERT: D 1229 THR cc_start: 0.9050 (p) cc_final: 0.8839 (p) REVERT: D 1241 GLN cc_start: 0.8958 (mm-40) cc_final: 0.8533 (tm-30) outliers start: 28 outliers final: 20 residues processed: 869 average time/residue: 0.5119 time to fit residues: 737.7042 Evaluate side-chains 593 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 573 time to evaluate : 4.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 960 GLN Chi-restraints excluded: chain A residue 963 GLN Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 954 ILE Chi-restraints excluded: chain B residue 960 GLN Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 954 ILE Chi-restraints excluded: chain C residue 960 GLN Chi-restraints excluded: chain C residue 963 GLN Chi-restraints excluded: chain D residue 396 ASN Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 954 ILE Chi-restraints excluded: chain D residue 960 GLN Chi-restraints excluded: chain D residue 965 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 430 optimal weight: 0.9980 chunk 386 optimal weight: 9.9990 chunk 214 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 260 optimal weight: 8.9990 chunk 206 optimal weight: 30.0000 chunk 399 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 243 optimal weight: 0.5980 chunk 297 optimal weight: 2.9990 chunk 463 optimal weight: 0.0770 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 GLN A 217 HIS A 646 HIS A 851 ASN A 854 GLN ** A 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 963 GLN A 983 ASN A1325 GLN B 30 GLN B 132 GLN B 424 ASN B 479 HIS B 511 HIS ** B 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 GLN ** B 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1020 HIS ** B1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1038 ASN B1089 ASN C 132 GLN C 217 HIS C 646 HIS C 851 ASN C 854 GLN ** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 963 GLN ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN D 132 GLN D 424 ASN D 479 HIS D 582 HIS D 693 GLN ** D 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1020 HIS ** D1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1038 ASN D1089 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 41420 Z= 0.236 Angle : 0.866 13.278 56270 Z= 0.424 Chirality : 0.051 0.645 6514 Planarity : 0.006 0.068 7202 Dihedral : 9.227 67.422 6348 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.00 % Favored : 89.73 % Rotamer: Outliers : 2.62 % Allowed : 14.00 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.11), residues: 5110 helix: 0.24 (0.17), residues: 882 sheet: -1.60 (0.11), residues: 1864 loop : -3.46 (0.11), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B1237 HIS 0.012 0.001 HIS A1195 PHE 0.022 0.002 PHE D 74 TYR 0.040 0.002 TYR A 649 ARG 0.008 0.001 ARG D 370 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 688 time to evaluate : 4.657 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 TYR cc_start: 0.7149 (p90) cc_final: 0.6939 (p90) REVERT: A 101 MET cc_start: 0.8411 (mtp) cc_final: 0.7484 (mmm) REVERT: A 192 PHE cc_start: 0.7901 (t80) cc_final: 0.7685 (t80) REVERT: A 208 GLN cc_start: 0.7736 (tt0) cc_final: 0.7487 (tp-100) REVERT: A 384 ILE cc_start: 0.9472 (pt) cc_final: 0.9243 (mm) REVERT: A 456 LYS cc_start: 0.9003 (mmmt) cc_final: 0.8605 (mmmt) REVERT: A 672 ASP cc_start: 0.8366 (t0) cc_final: 0.8138 (t0) REVERT: A 766 LYS cc_start: 0.7064 (mmtp) cc_final: 0.6848 (mptt) REVERT: A 787 ARG cc_start: 0.8610 (ptt-90) cc_final: 0.8333 (ptt-90) REVERT: A 934 LYS cc_start: 0.8184 (tppt) cc_final: 0.7936 (mmmt) REVERT: A 977 MET cc_start: 0.9233 (mmm) cc_final: 0.8771 (mmm) REVERT: A 988 ASP cc_start: 0.8935 (m-30) cc_final: 0.8619 (m-30) REVERT: A 1015 GLN cc_start: 0.8261 (tp40) cc_final: 0.7930 (tp-100) REVERT: A 1161 ASP cc_start: 0.8984 (p0) cc_final: 0.8673 (p0) REVERT: A 1165 GLU cc_start: 0.9098 (tt0) cc_final: 0.8821 (tt0) REVERT: A 1208 MET cc_start: 0.9081 (ppp) cc_final: 0.8870 (ppp) REVERT: A 1217 LEU cc_start: 0.9608 (mm) cc_final: 0.9294 (mp) REVERT: A 1314 MET cc_start: 0.8710 (mpp) cc_final: 0.8253 (mpp) REVERT: A 1323 TYR cc_start: 0.7120 (t80) cc_final: 0.6822 (t80) REVERT: B 67 VAL cc_start: 0.7581 (OUTLIER) cc_final: 0.7319 (p) REVERT: B 134 ASP cc_start: 0.8120 (t0) cc_final: 0.7538 (t70) REVERT: B 183 LEU cc_start: 0.7758 (mt) cc_final: 0.7550 (mt) REVERT: B 222 GLU cc_start: 0.8347 (pt0) cc_final: 0.8100 (pp20) REVERT: B 318 MET cc_start: 0.5043 (mmm) cc_final: 0.4831 (mmm) REVERT: B 372 VAL cc_start: 0.8614 (OUTLIER) cc_final: 0.8302 (p) REVERT: B 387 ARG cc_start: 0.7937 (mtt180) cc_final: 0.7488 (ttm-80) REVERT: B 500 MET cc_start: 0.6913 (ttt) cc_final: 0.6671 (ttt) REVERT: B 519 ASP cc_start: 0.6695 (m-30) cc_final: 0.6431 (m-30) REVERT: B 561 GLU cc_start: 0.7235 (pt0) cc_final: 0.6685 (pt0) REVERT: B 605 LEU cc_start: 0.8382 (tp) cc_final: 0.7988 (tp) REVERT: B 627 LEU cc_start: 0.9020 (tp) cc_final: 0.8769 (tt) REVERT: B 673 MET cc_start: 0.8505 (tpp) cc_final: 0.8186 (tpp) REVERT: B 688 MET cc_start: 0.8340 (ppp) cc_final: 0.8003 (ppp) REVERT: B 741 TRP cc_start: 0.8042 (t-100) cc_final: 0.7361 (t-100) REVERT: B 787 ARG cc_start: 0.8355 (mtt180) cc_final: 0.8139 (mpt-90) REVERT: B 858 TRP cc_start: 0.7530 (m-90) cc_final: 0.6997 (m-90) REVERT: B 965 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7295 (mm) REVERT: B 977 MET cc_start: 0.9119 (mmm) cc_final: 0.8686 (mmm) REVERT: B 992 GLU cc_start: 0.8167 (tp30) cc_final: 0.7730 (tp30) REVERT: B 1018 TYR cc_start: 0.7861 (m-80) cc_final: 0.7501 (m-80) REVERT: B 1161 ASP cc_start: 0.8822 (p0) cc_final: 0.8417 (p0) REVERT: B 1168 LYS cc_start: 0.9005 (ttmt) cc_final: 0.8777 (pttp) REVERT: B 1172 GLU cc_start: 0.8973 (tt0) cc_final: 0.8261 (tm-30) REVERT: C 31 TYR cc_start: 0.7156 (p90) cc_final: 0.6921 (p90) REVERT: C 101 MET cc_start: 0.8426 (mtp) cc_final: 0.7585 (mtp) REVERT: C 121 MET cc_start: 0.7357 (ttt) cc_final: 0.7089 (ttt) REVERT: C 192 PHE cc_start: 0.7891 (t80) cc_final: 0.7671 (t80) REVERT: C 208 GLN cc_start: 0.7724 (tt0) cc_final: 0.7488 (tp-100) REVERT: C 373 ASP cc_start: 0.8203 (t0) cc_final: 0.7921 (t0) REVERT: C 384 ILE cc_start: 0.9476 (pt) cc_final: 0.9195 (mm) REVERT: C 456 LYS cc_start: 0.9005 (mmmt) cc_final: 0.8610 (mmmt) REVERT: C 672 ASP cc_start: 0.8367 (t0) cc_final: 0.8141 (t0) REVERT: C 787 ARG cc_start: 0.8603 (ptt-90) cc_final: 0.8322 (ptt-90) REVERT: C 934 LYS cc_start: 0.8169 (tppt) cc_final: 0.7909 (mmmt) REVERT: C 988 ASP cc_start: 0.8946 (m-30) cc_final: 0.8607 (m-30) REVERT: C 1015 GLN cc_start: 0.8362 (tp40) cc_final: 0.7916 (tp40) REVERT: C 1161 ASP cc_start: 0.8945 (p0) cc_final: 0.8614 (p0) REVERT: C 1165 GLU cc_start: 0.9118 (tt0) cc_final: 0.8835 (tt0) REVERT: C 1208 MET cc_start: 0.9072 (ppp) cc_final: 0.8852 (ppp) REVERT: C 1217 LEU cc_start: 0.9601 (mm) cc_final: 0.9281 (mp) REVERT: C 1314 MET cc_start: 0.8704 (mpp) cc_final: 0.8253 (mpp) REVERT: C 1323 TYR cc_start: 0.7074 (t80) cc_final: 0.6715 (t80) REVERT: D 31 TYR cc_start: 0.6603 (p90) cc_final: 0.6369 (p90) REVERT: D 67 VAL cc_start: 0.7647 (OUTLIER) cc_final: 0.7392 (p) REVERT: D 114 PHE cc_start: 0.7100 (t80) cc_final: 0.6837 (t80) REVERT: D 134 ASP cc_start: 0.8059 (t0) cc_final: 0.7527 (t70) REVERT: D 222 GLU cc_start: 0.8318 (pt0) cc_final: 0.8071 (pp20) REVERT: D 318 MET cc_start: 0.5184 (mmm) cc_final: 0.4959 (mmm) REVERT: D 372 VAL cc_start: 0.8614 (OUTLIER) cc_final: 0.8302 (p) REVERT: D 500 MET cc_start: 0.6946 (ttt) cc_final: 0.6533 (ttt) REVERT: D 605 LEU cc_start: 0.8501 (tp) cc_final: 0.8110 (tp) REVERT: D 673 MET cc_start: 0.8530 (tpp) cc_final: 0.8126 (tpp) REVERT: D 688 MET cc_start: 0.8373 (ppp) cc_final: 0.8058 (ppp) REVERT: D 741 TRP cc_start: 0.8069 (t-100) cc_final: 0.7389 (t-100) REVERT: D 765 TRP cc_start: 0.7554 (m100) cc_final: 0.6999 (m100) REVERT: D 787 ARG cc_start: 0.8334 (mtt180) cc_final: 0.8091 (mpt-90) REVERT: D 858 TRP cc_start: 0.7478 (m-90) cc_final: 0.6969 (m-90) REVERT: D 912 LYS cc_start: 0.8659 (ptmm) cc_final: 0.8237 (ptmm) REVERT: D 977 MET cc_start: 0.9084 (mmm) cc_final: 0.8676 (mmm) REVERT: D 990 LEU cc_start: 0.8378 (mt) cc_final: 0.8136 (mp) REVERT: D 992 GLU cc_start: 0.8261 (tp30) cc_final: 0.7772 (tp30) REVERT: D 1018 TYR cc_start: 0.7838 (m-80) cc_final: 0.7507 (m-80) REVERT: D 1149 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9206 (tt) REVERT: D 1161 ASP cc_start: 0.8794 (p0) cc_final: 0.8388 (p0) REVERT: D 1168 LYS cc_start: 0.9027 (ttmt) cc_final: 0.8782 (pttp) REVERT: D 1258 LEU cc_start: 0.8866 (mt) cc_final: 0.8652 (mp) REVERT: D 1330 TYR cc_start: 0.8319 (p90) cc_final: 0.7336 (p90) outliers start: 117 outliers final: 58 residues processed: 757 average time/residue: 0.4917 time to fit residues: 634.4102 Evaluate side-chains 655 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 591 time to evaluate : 4.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 523 HIS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 569 ASP Chi-restraints excluded: chain A residue 635 ASN Chi-restraints excluded: chain A residue 646 HIS Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 960 GLN Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1253 ASP Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 965 LEU Chi-restraints excluded: chain B residue 1125 LEU Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain B residue 1315 LYS Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 523 HIS Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 635 ASN Chi-restraints excluded: chain C residue 646 HIS Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 960 GLN Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1253 ASP Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 786 LEU Chi-restraints excluded: chain D residue 949 SER Chi-restraints excluded: chain D residue 1149 LEU Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1305 LEU Chi-restraints excluded: chain D residue 1315 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 257 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 385 optimal weight: 0.9980 chunk 315 optimal weight: 7.9990 chunk 127 optimal weight: 7.9990 chunk 463 optimal weight: 0.9990 chunk 501 optimal weight: 6.9990 chunk 413 optimal weight: 10.0000 chunk 460 optimal weight: 7.9990 chunk 158 optimal weight: 10.0000 chunk 372 optimal weight: 9.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN A 460 HIS A 851 ASN A 938 ASN ** A 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 964 ASN A1009 ASN A1020 HIS ** A1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN B 445 HIS B 691 GLN B 994 GLN B1035 ASN ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 GLN C 460 HIS C 851 ASN C 938 ASN ** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1009 ASN C1020 HIS ** C1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 GLN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 ASN D 445 HIS D 511 HIS D 691 GLN ** D1035 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 41420 Z= 0.431 Angle : 0.892 19.912 56270 Z= 0.450 Chirality : 0.051 0.413 6514 Planarity : 0.006 0.072 7202 Dihedral : 8.284 64.966 6312 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.57 % Favored : 88.20 % Rotamer: Outliers : 4.30 % Allowed : 17.36 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.11), residues: 5110 helix: 0.57 (0.17), residues: 860 sheet: -1.37 (0.11), residues: 1808 loop : -3.29 (0.11), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP C 741 HIS 0.032 0.002 HIS A 646 PHE 0.033 0.003 PHE B 114 TYR 0.025 0.003 TYR C 254 ARG 0.007 0.001 ARG B 370 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 592 time to evaluate : 4.504 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: A 114 PHE cc_start: 0.7029 (t80) cc_final: 0.6730 (t80) REVERT: A 216 GLU cc_start: 0.8005 (mp0) cc_final: 0.7794 (mp0) REVERT: A 224 PHE cc_start: 0.7431 (p90) cc_final: 0.7091 (p90) REVERT: A 373 ASP cc_start: 0.8416 (t0) cc_final: 0.8127 (t0) REVERT: A 384 ILE cc_start: 0.9548 (pt) cc_final: 0.9294 (mm) REVERT: A 415 MET cc_start: 0.6687 (ppp) cc_final: 0.6215 (ppp) REVERT: A 456 LYS cc_start: 0.9255 (mmmt) cc_final: 0.8763 (mmmt) REVERT: A 567 LYS cc_start: 0.8412 (tppt) cc_final: 0.8127 (tppt) REVERT: A 672 ASP cc_start: 0.8633 (t0) cc_final: 0.8418 (t0) REVERT: A 766 LYS cc_start: 0.7343 (mmtp) cc_final: 0.7104 (mptt) REVERT: A 787 ARG cc_start: 0.8627 (ptt-90) cc_final: 0.8314 (ptt-90) REVERT: A 988 ASP cc_start: 0.9069 (m-30) cc_final: 0.8745 (m-30) REVERT: A 1015 GLN cc_start: 0.8312 (tp40) cc_final: 0.8085 (tp40) REVERT: A 1109 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9110 (mm) REVERT: A 1161 ASP cc_start: 0.9077 (p0) cc_final: 0.8774 (p0) REVERT: A 1165 GLU cc_start: 0.9181 (tt0) cc_final: 0.8900 (tt0) REVERT: A 1217 LEU cc_start: 0.9662 (mm) cc_final: 0.9435 (mm) REVERT: A 1314 MET cc_start: 0.8765 (mpp) cc_final: 0.8100 (mpp) REVERT: B 134 ASP cc_start: 0.8783 (t0) cc_final: 0.8067 (t70) REVERT: B 181 PHE cc_start: 0.7539 (p90) cc_final: 0.7302 (p90) REVERT: B 222 GLU cc_start: 0.8318 (pt0) cc_final: 0.8018 (pp20) REVERT: B 318 MET cc_start: 0.5808 (mmm) cc_final: 0.5383 (tpt) REVERT: B 373 ASP cc_start: 0.8459 (p0) cc_final: 0.7886 (t0) REVERT: B 387 ARG cc_start: 0.8147 (mtt180) cc_final: 0.7795 (ttm-80) REVERT: B 500 MET cc_start: 0.7121 (ttt) cc_final: 0.6623 (ttt) REVERT: B 561 GLU cc_start: 0.7500 (pt0) cc_final: 0.7018 (pt0) REVERT: B 578 LEU cc_start: 0.8619 (mt) cc_final: 0.8029 (pp) REVERT: B 605 LEU cc_start: 0.8627 (tp) cc_final: 0.8278 (tp) REVERT: B 627 LEU cc_start: 0.9277 (tp) cc_final: 0.8995 (tt) REVERT: B 669 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8727 (t80) REVERT: B 673 MET cc_start: 0.8806 (tpp) cc_final: 0.8314 (tpp) REVERT: B 741 TRP cc_start: 0.8725 (t-100) cc_final: 0.7918 (t-100) REVERT: B 786 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7379 (mp) REVERT: B 787 ARG cc_start: 0.8570 (mtt180) cc_final: 0.8308 (mpt-90) REVERT: B 858 TRP cc_start: 0.7623 (m-90) cc_final: 0.6956 (m-90) REVERT: B 934 LYS cc_start: 0.8019 (tppt) cc_final: 0.7814 (tppt) REVERT: B 977 MET cc_start: 0.9246 (mmm) cc_final: 0.8787 (mmm) REVERT: B 987 LEU cc_start: 0.9584 (tt) cc_final: 0.9329 (pp) REVERT: B 1147 LYS cc_start: 0.9116 (mttp) cc_final: 0.8702 (mttp) REVERT: B 1161 ASP cc_start: 0.8937 (p0) cc_final: 0.8541 (p0) REVERT: B 1172 GLU cc_start: 0.9070 (tt0) cc_final: 0.8261 (tm-30) REVERT: B 1208 MET cc_start: 0.9011 (ppp) cc_final: 0.8768 (ppp) REVERT: B 1217 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9190 (mm) REVERT: C 114 PHE cc_start: 0.6985 (t80) cc_final: 0.6676 (t80) REVERT: C 169 ASP cc_start: 0.6649 (m-30) cc_final: 0.5957 (m-30) REVERT: C 224 PHE cc_start: 0.7395 (p90) cc_final: 0.7056 (p90) REVERT: C 384 ILE cc_start: 0.9557 (pt) cc_final: 0.9336 (mm) REVERT: C 415 MET cc_start: 0.6693 (ppp) cc_final: 0.6212 (ppp) REVERT: C 456 LYS cc_start: 0.9258 (mmmt) cc_final: 0.8758 (mmmt) REVERT: C 567 LYS cc_start: 0.8421 (tppt) cc_final: 0.8136 (tppt) REVERT: C 672 ASP cc_start: 0.8628 (t0) cc_final: 0.8406 (t0) REVERT: C 787 ARG cc_start: 0.8628 (ptt-90) cc_final: 0.8312 (ptt-90) REVERT: C 988 ASP cc_start: 0.9073 (m-30) cc_final: 0.8764 (m-30) REVERT: C 1109 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9108 (mm) REVERT: C 1161 ASP cc_start: 0.9070 (p0) cc_final: 0.8767 (p0) REVERT: C 1165 GLU cc_start: 0.9187 (tt0) cc_final: 0.8901 (tt0) REVERT: C 1217 LEU cc_start: 0.9656 (mm) cc_final: 0.9422 (mm) REVERT: C 1314 MET cc_start: 0.8738 (mpp) cc_final: 0.8058 (mpp) REVERT: D 134 ASP cc_start: 0.8777 (t0) cc_final: 0.8083 (t70) REVERT: D 222 GLU cc_start: 0.8301 (pt0) cc_final: 0.8010 (pp20) REVERT: D 318 MET cc_start: 0.5701 (mmm) cc_final: 0.5252 (tpt) REVERT: D 373 ASP cc_start: 0.8448 (p0) cc_final: 0.7852 (t0) REVERT: D 387 ARG cc_start: 0.8126 (mtt180) cc_final: 0.7796 (ttm-80) REVERT: D 500 MET cc_start: 0.7152 (OUTLIER) cc_final: 0.6512 (ttt) REVERT: D 541 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.6026 (pt) REVERT: D 561 GLU cc_start: 0.7465 (pt0) cc_final: 0.6984 (pt0) REVERT: D 578 LEU cc_start: 0.8625 (mt) cc_final: 0.8031 (pp) REVERT: D 605 LEU cc_start: 0.8637 (tp) cc_final: 0.8297 (tp) REVERT: D 669 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.8759 (t80) REVERT: D 673 MET cc_start: 0.8848 (tpp) cc_final: 0.8278 (tpp) REVERT: D 741 TRP cc_start: 0.8764 (t-100) cc_final: 0.7864 (t-100) REVERT: D 786 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7405 (mp) REVERT: D 787 ARG cc_start: 0.8583 (mtt180) cc_final: 0.8331 (mpt-90) REVERT: D 858 TRP cc_start: 0.7659 (m-90) cc_final: 0.7014 (m-90) REVERT: D 977 MET cc_start: 0.9247 (mmm) cc_final: 0.8806 (mmm) REVERT: D 987 LEU cc_start: 0.9558 (tt) cc_final: 0.9268 (pp) REVERT: D 990 LEU cc_start: 0.8673 (mt) cc_final: 0.8451 (mp) REVERT: D 1147 LYS cc_start: 0.9068 (mttp) cc_final: 0.8665 (mttp) REVERT: D 1149 LEU cc_start: 0.9649 (OUTLIER) cc_final: 0.9364 (tt) REVERT: D 1161 ASP cc_start: 0.8944 (p0) cc_final: 0.8561 (p0) REVERT: D 1208 MET cc_start: 0.8967 (ppp) cc_final: 0.8725 (ppp) REVERT: D 1217 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9195 (mm) outliers start: 192 outliers final: 107 residues processed: 740 average time/residue: 0.4566 time to fit residues: 579.9537 Evaluate side-chains 650 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 532 time to evaluate : 4.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 389 ASN Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 523 HIS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 635 ASN Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 917 ASN Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 960 GLN Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1127 CYS Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1206 VAL Chi-restraints excluded: chain A residue 1253 ASP Chi-restraints excluded: chain A residue 1270 THR Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 757 THR Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 947 SER Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 1110 LEU Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain B residue 1305 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 389 ASN Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 523 HIS Chi-restraints excluded: chain C residue 559 ASP Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 917 ASN Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 960 GLN Chi-restraints excluded: chain C residue 983 ASN Chi-restraints excluded: chain C residue 1041 LEU Chi-restraints excluded: chain C residue 1087 LEU Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1127 CYS Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1206 VAL Chi-restraints excluded: chain C residue 1218 THR Chi-restraints excluded: chain C residue 1253 ASP Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 182 GLN Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 500 MET Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 645 ARG Chi-restraints excluded: chain D residue 669 PHE Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 786 LEU Chi-restraints excluded: chain D residue 861 THR Chi-restraints excluded: chain D residue 947 SER Chi-restraints excluded: chain D residue 949 SER Chi-restraints excluded: chain D residue 1110 LEU Chi-restraints excluded: chain D residue 1144 VAL Chi-restraints excluded: chain D residue 1149 LEU Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1217 LEU Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1305 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 458 optimal weight: 6.9990 chunk 348 optimal weight: 5.9990 chunk 240 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 221 optimal weight: 0.3980 chunk 311 optimal weight: 4.9990 chunk 465 optimal weight: 0.0010 chunk 492 optimal weight: 3.9990 chunk 243 optimal weight: 0.0970 chunk 441 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 HIS A 466 HIS A 851 ASN ** A 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN ** A1301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 HIS B 310 GLN B 790 GLN B 976 ASN ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 HIS C 466 HIS C 851 ASN ** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 HIS D 310 GLN D 790 GLN D1035 ASN ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 41420 Z= 0.226 Angle : 0.780 15.798 56270 Z= 0.377 Chirality : 0.049 0.344 6514 Planarity : 0.005 0.066 7202 Dihedral : 7.666 68.586 6308 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.53 % Favored : 90.23 % Rotamer: Outliers : 4.21 % Allowed : 19.49 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.11), residues: 5110 helix: 0.88 (0.18), residues: 858 sheet: -1.23 (0.12), residues: 1796 loop : -3.05 (0.11), residues: 2456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 436 HIS 0.008 0.001 HIS A1195 PHE 0.022 0.002 PHE B 808 TYR 0.031 0.002 TYR B1007 ARG 0.004 0.000 ARG D 360 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 596 time to evaluate : 4.662 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: A 114 PHE cc_start: 0.6916 (t80) cc_final: 0.6705 (t80) REVERT: A 192 PHE cc_start: 0.8063 (t80) cc_final: 0.7814 (t80) REVERT: A 373 ASP cc_start: 0.8299 (t0) cc_final: 0.7973 (t0) REVERT: A 384 ILE cc_start: 0.9536 (pt) cc_final: 0.9249 (mm) REVERT: A 387 ARG cc_start: 0.8507 (mtt180) cc_final: 0.7715 (mtt90) REVERT: A 456 LYS cc_start: 0.9200 (mmmt) cc_final: 0.8789 (mmmt) REVERT: A 567 LYS cc_start: 0.8364 (tppt) cc_final: 0.8115 (tppt) REVERT: A 672 ASP cc_start: 0.8606 (t0) cc_final: 0.8346 (t0) REVERT: A 766 LYS cc_start: 0.7504 (mmtp) cc_final: 0.7183 (mptt) REVERT: A 968 MET cc_start: 0.8619 (tpp) cc_final: 0.8401 (tpp) REVERT: A 977 MET cc_start: 0.9195 (mmm) cc_final: 0.8944 (mmm) REVERT: A 988 ASP cc_start: 0.8948 (m-30) cc_final: 0.8581 (m-30) REVERT: A 1015 GLN cc_start: 0.8337 (tp40) cc_final: 0.8077 (tp40) REVERT: A 1109 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9042 (mm) REVERT: A 1149 LEU cc_start: 0.9692 (OUTLIER) cc_final: 0.9408 (tt) REVERT: A 1161 ASP cc_start: 0.9016 (p0) cc_final: 0.8697 (p0) REVERT: A 1165 GLU cc_start: 0.9152 (tt0) cc_final: 0.8867 (tt0) REVERT: A 1208 MET cc_start: 0.9136 (ppp) cc_final: 0.8900 (ppp) REVERT: A 1217 LEU cc_start: 0.9637 (mm) cc_final: 0.9297 (mp) REVERT: A 1314 MET cc_start: 0.8770 (mpp) cc_final: 0.8058 (mpp) REVERT: B 181 PHE cc_start: 0.7571 (p90) cc_final: 0.7331 (p90) REVERT: B 222 GLU cc_start: 0.8344 (pt0) cc_final: 0.8091 (pp20) REVERT: B 318 MET cc_start: 0.5514 (mmm) cc_final: 0.5135 (tpt) REVERT: B 373 ASP cc_start: 0.8291 (p0) cc_final: 0.7829 (t0) REVERT: B 387 ARG cc_start: 0.8127 (mtt180) cc_final: 0.7543 (ttm-80) REVERT: B 500 MET cc_start: 0.6489 (ttt) cc_final: 0.6269 (ttt) REVERT: B 561 GLU cc_start: 0.7486 (pt0) cc_final: 0.6999 (pt0) REVERT: B 605 LEU cc_start: 0.8506 (tp) cc_final: 0.8135 (tp) REVERT: B 673 MET cc_start: 0.8648 (tpp) cc_final: 0.8088 (tpp) REVERT: B 786 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7210 (tt) REVERT: B 787 ARG cc_start: 0.8593 (mtt180) cc_final: 0.8205 (mpt-90) REVERT: B 811 LYS cc_start: 0.8229 (mmtp) cc_final: 0.7922 (mmtm) REVERT: B 858 TRP cc_start: 0.7630 (m-90) cc_final: 0.6957 (m-90) REVERT: B 965 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7397 (mm) REVERT: B 977 MET cc_start: 0.9161 (mmm) cc_final: 0.8617 (mmm) REVERT: B 987 LEU cc_start: 0.9505 (tt) cc_final: 0.9242 (pp) REVERT: B 1018 TYR cc_start: 0.7842 (m-80) cc_final: 0.7618 (m-80) REVERT: B 1161 ASP cc_start: 0.8885 (p0) cc_final: 0.8480 (p0) REVERT: B 1168 LYS cc_start: 0.9039 (ttmt) cc_final: 0.8838 (ptmm) REVERT: B 1172 GLU cc_start: 0.9028 (tt0) cc_final: 0.8211 (tm-30) REVERT: B 1208 MET cc_start: 0.8902 (ppp) cc_final: 0.8637 (ppp) REVERT: B 1217 LEU cc_start: 0.9394 (mm) cc_final: 0.9177 (mm) REVERT: C 114 PHE cc_start: 0.6900 (t80) cc_final: 0.6679 (t80) REVERT: C 192 PHE cc_start: 0.8084 (t80) cc_final: 0.7838 (t80) REVERT: C 373 ASP cc_start: 0.8413 (t0) cc_final: 0.8188 (t0) REVERT: C 384 ILE cc_start: 0.9578 (pt) cc_final: 0.9311 (mm) REVERT: C 456 LYS cc_start: 0.9187 (mmmt) cc_final: 0.8780 (mmmt) REVERT: C 567 LYS cc_start: 0.8367 (tppt) cc_final: 0.8119 (tppt) REVERT: C 672 ASP cc_start: 0.8578 (t0) cc_final: 0.8324 (t0) REVERT: C 988 ASP cc_start: 0.8960 (m-30) cc_final: 0.8618 (m-30) REVERT: C 1109 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9033 (mm) REVERT: C 1149 LEU cc_start: 0.9666 (OUTLIER) cc_final: 0.9354 (tt) REVERT: C 1161 ASP cc_start: 0.9012 (p0) cc_final: 0.8670 (p0) REVERT: C 1165 GLU cc_start: 0.9158 (tt0) cc_final: 0.8867 (tt0) REVERT: C 1208 MET cc_start: 0.9135 (ppp) cc_final: 0.8887 (ppp) REVERT: C 1217 LEU cc_start: 0.9631 (mm) cc_final: 0.9314 (mp) REVERT: C 1314 MET cc_start: 0.8779 (mpp) cc_final: 0.8096 (mpp) REVERT: D 74 PHE cc_start: 0.8412 (t80) cc_final: 0.8206 (t80) REVERT: D 222 GLU cc_start: 0.8330 (pt0) cc_final: 0.8080 (pp20) REVERT: D 318 MET cc_start: 0.5744 (mmm) cc_final: 0.5346 (tpt) REVERT: D 372 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.7913 (p) REVERT: D 373 ASP cc_start: 0.8302 (p0) cc_final: 0.7802 (t0) REVERT: D 387 ARG cc_start: 0.8115 (mtt180) cc_final: 0.7555 (ttm-80) REVERT: D 500 MET cc_start: 0.6415 (OUTLIER) cc_final: 0.6195 (ttt) REVERT: D 561 GLU cc_start: 0.7468 (pt0) cc_final: 0.6958 (pt0) REVERT: D 605 LEU cc_start: 0.8525 (tp) cc_final: 0.8148 (tp) REVERT: D 673 MET cc_start: 0.8641 (tpp) cc_final: 0.8149 (tpp) REVERT: D 786 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7201 (tt) REVERT: D 787 ARG cc_start: 0.8603 (mtt180) cc_final: 0.8242 (mpt-90) REVERT: D 858 TRP cc_start: 0.7619 (m-90) cc_final: 0.6994 (m-90) REVERT: D 977 MET cc_start: 0.9124 (mmm) cc_final: 0.8612 (mmm) REVERT: D 987 LEU cc_start: 0.9486 (tt) cc_final: 0.9242 (pp) REVERT: D 1018 TYR cc_start: 0.7831 (m-80) cc_final: 0.7610 (m-80) REVERT: D 1149 LEU cc_start: 0.9636 (OUTLIER) cc_final: 0.9322 (tt) REVERT: D 1161 ASP cc_start: 0.8905 (p0) cc_final: 0.8474 (p0) REVERT: D 1168 LYS cc_start: 0.9054 (ttmt) cc_final: 0.8841 (ptmm) REVERT: D 1208 MET cc_start: 0.8916 (ppp) cc_final: 0.8654 (ppp) REVERT: D 1217 LEU cc_start: 0.9391 (mm) cc_final: 0.9163 (mm) outliers start: 188 outliers final: 99 residues processed: 743 average time/residue: 0.4723 time to fit residues: 602.8991 Evaluate side-chains 666 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 557 time to evaluate : 4.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 523 HIS Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 635 ASN Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 917 ASN Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 960 GLN Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1218 THR Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 965 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1080 PHE Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain B residue 1305 LEU Chi-restraints excluded: chain B residue 1333 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 121 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 396 ASN Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 523 HIS Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 849 CYS Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 917 ASN Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 960 GLN Chi-restraints excluded: chain C residue 983 ASN Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1091 ILE Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1149 LEU Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 173 ASN Chi-restraints excluded: chain D residue 182 GLN Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 500 MET Chi-restraints excluded: chain D residue 645 ARG Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 654 THR Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 786 LEU Chi-restraints excluded: chain D residue 935 LEU Chi-restraints excluded: chain D residue 947 SER Chi-restraints excluded: chain D residue 949 SER Chi-restraints excluded: chain D residue 1063 ILE Chi-restraints excluded: chain D residue 1080 PHE Chi-restraints excluded: chain D residue 1144 VAL Chi-restraints excluded: chain D residue 1149 LEU Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1305 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 410 optimal weight: 10.0000 chunk 279 optimal weight: 0.0050 chunk 7 optimal weight: 10.0000 chunk 367 optimal weight: 0.6980 chunk 203 optimal weight: 9.9990 chunk 420 optimal weight: 6.9990 chunk 340 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 251 optimal weight: 8.9990 chunk 442 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 overall best weight: 3.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 HIS ** A 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 ASN ** A 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1072 GLN ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 HIS C 851 ASN ** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 964 ASN ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1179 ASN ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 964 ASN D1072 GLN ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 41420 Z= 0.368 Angle : 0.826 16.641 56270 Z= 0.410 Chirality : 0.049 0.343 6514 Planarity : 0.005 0.060 7202 Dihedral : 7.732 71.112 6308 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.55 % Favored : 88.26 % Rotamer: Outliers : 5.37 % Allowed : 20.16 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.11), residues: 5110 helix: 0.65 (0.17), residues: 856 sheet: -1.18 (0.12), residues: 1758 loop : -3.05 (0.11), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 436 HIS 0.009 0.001 HIS A1195 PHE 0.024 0.002 PHE D 735 TYR 0.038 0.002 TYR D1007 ARG 0.007 0.001 ARG D 598 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 571 time to evaluate : 4.746 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: A 114 PHE cc_start: 0.7283 (t80) cc_final: 0.7043 (t80) REVERT: A 192 PHE cc_start: 0.8182 (t80) cc_final: 0.7887 (t80) REVERT: A 456 LYS cc_start: 0.9268 (mmmt) cc_final: 0.8807 (mmmt) REVERT: A 498 LEU cc_start: 0.5344 (OUTLIER) cc_final: 0.5054 (mt) REVERT: A 567 LYS cc_start: 0.8445 (tppt) cc_final: 0.8197 (tppt) REVERT: A 672 ASP cc_start: 0.8695 (t0) cc_final: 0.8455 (t0) REVERT: A 766 LYS cc_start: 0.7586 (mmtp) cc_final: 0.7183 (mptt) REVERT: A 787 ARG cc_start: 0.8644 (ptt-90) cc_final: 0.8161 (mtm180) REVERT: A 965 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7484 (mm) REVERT: A 988 ASP cc_start: 0.8958 (m-30) cc_final: 0.8588 (m-30) REVERT: A 1109 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9075 (mm) REVERT: A 1149 LEU cc_start: 0.9716 (OUTLIER) cc_final: 0.9463 (tt) REVERT: A 1161 ASP cc_start: 0.9085 (p0) cc_final: 0.8770 (p0) REVERT: A 1165 GLU cc_start: 0.9197 (tt0) cc_final: 0.8909 (tt0) REVERT: A 1208 MET cc_start: 0.9181 (ppp) cc_final: 0.8833 (ppp) REVERT: A 1217 LEU cc_start: 0.9661 (mm) cc_final: 0.9435 (mm) REVERT: A 1314 MET cc_start: 0.8717 (mpp) cc_final: 0.7936 (mpp) REVERT: B 181 PHE cc_start: 0.7600 (p90) cc_final: 0.7388 (p90) REVERT: B 182 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.7301 (tp-100) REVERT: B 246 MET cc_start: 0.8136 (mtm) cc_final: 0.7926 (mtp) REVERT: B 318 MET cc_start: 0.5577 (mmm) cc_final: 0.5137 (tpt) REVERT: B 373 ASP cc_start: 0.8402 (p0) cc_final: 0.7907 (t0) REVERT: B 387 ARG cc_start: 0.8089 (mtt180) cc_final: 0.7500 (ttm-80) REVERT: B 500 MET cc_start: 0.7108 (ttt) cc_final: 0.6752 (ttt) REVERT: B 520 MET cc_start: 0.7606 (tmm) cc_final: 0.7210 (tmm) REVERT: B 532 SER cc_start: 0.7994 (t) cc_final: 0.7692 (m) REVERT: B 561 GLU cc_start: 0.7505 (pt0) cc_final: 0.7032 (pt0) REVERT: B 605 LEU cc_start: 0.8567 (tp) cc_final: 0.8172 (tp) REVERT: B 627 LEU cc_start: 0.9293 (tp) cc_final: 0.9039 (tt) REVERT: B 669 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8758 (t80) REVERT: B 673 MET cc_start: 0.8841 (tpp) cc_final: 0.8235 (tpp) REVERT: B 688 MET cc_start: 0.8285 (ppp) cc_final: 0.7849 (ppp) REVERT: B 786 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7294 (tt) REVERT: B 787 ARG cc_start: 0.8730 (mtt180) cc_final: 0.8330 (mpt-90) REVERT: B 858 TRP cc_start: 0.7688 (m-90) cc_final: 0.7016 (m-90) REVERT: B 965 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7525 (mm) REVERT: B 977 MET cc_start: 0.9155 (mmm) cc_final: 0.8653 (mmm) REVERT: B 1147 LYS cc_start: 0.9104 (mttp) cc_final: 0.8727 (mttp) REVERT: B 1161 ASP cc_start: 0.9007 (p0) cc_final: 0.8582 (p0) REVERT: B 1172 GLU cc_start: 0.9113 (tt0) cc_final: 0.8269 (tm-30) REVERT: B 1208 MET cc_start: 0.8850 (ppp) cc_final: 0.8502 (ppp) REVERT: B 1217 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9214 (mm) REVERT: C 66 SER cc_start: 0.8970 (t) cc_final: 0.8663 (p) REVERT: C 114 PHE cc_start: 0.7362 (t80) cc_final: 0.7082 (t80) REVERT: C 192 PHE cc_start: 0.8184 (t80) cc_final: 0.7887 (t80) REVERT: C 456 LYS cc_start: 0.9258 (mmmt) cc_final: 0.8790 (mmmt) REVERT: C 567 LYS cc_start: 0.8478 (tppt) cc_final: 0.8225 (tppt) REVERT: C 646 HIS cc_start: 0.5940 (OUTLIER) cc_final: 0.4772 (t70) REVERT: C 656 THR cc_start: -0.1531 (OUTLIER) cc_final: -0.2410 (p) REVERT: C 672 ASP cc_start: 0.8646 (t0) cc_final: 0.8352 (t0) REVERT: C 673 MET cc_start: 0.9182 (tpp) cc_final: 0.8918 (tpp) REVERT: C 687 LYS cc_start: 0.9283 (tttt) cc_final: 0.8796 (tptp) REVERT: C 787 ARG cc_start: 0.8606 (ptt-90) cc_final: 0.7927 (mtm180) REVERT: C 968 MET cc_start: 0.8539 (tpt) cc_final: 0.7551 (pmm) REVERT: C 1073 ARG cc_start: 0.8889 (mmt-90) cc_final: 0.8676 (mmt-90) REVERT: C 1109 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9089 (mm) REVERT: C 1149 LEU cc_start: 0.9701 (OUTLIER) cc_final: 0.9453 (tt) REVERT: C 1161 ASP cc_start: 0.9071 (p0) cc_final: 0.8762 (p0) REVERT: C 1165 GLU cc_start: 0.9170 (tt0) cc_final: 0.8887 (tt0) REVERT: C 1208 MET cc_start: 0.9184 (ppp) cc_final: 0.8833 (ppp) REVERT: C 1217 LEU cc_start: 0.9660 (mm) cc_final: 0.9415 (mm) REVERT: C 1314 MET cc_start: 0.8704 (mpp) cc_final: 0.7916 (mpp) REVERT: D 74 PHE cc_start: 0.8421 (t80) cc_final: 0.8200 (t80) REVERT: D 182 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7402 (tp-100) REVERT: D 183 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6490 (mp) REVERT: D 318 MET cc_start: 0.5541 (mmm) cc_final: 0.5100 (tpt) REVERT: D 373 ASP cc_start: 0.8400 (p0) cc_final: 0.7912 (t0) REVERT: D 500 MET cc_start: 0.6929 (OUTLIER) cc_final: 0.6579 (ttt) REVERT: D 520 MET cc_start: 0.7596 (tmm) cc_final: 0.7218 (tmm) REVERT: D 541 LEU cc_start: 0.6586 (OUTLIER) cc_final: 0.6161 (pt) REVERT: D 561 GLU cc_start: 0.7506 (pt0) cc_final: 0.7015 (pt0) REVERT: D 605 LEU cc_start: 0.8553 (tp) cc_final: 0.8223 (tp) REVERT: D 669 PHE cc_start: 0.9024 (OUTLIER) cc_final: 0.8750 (t80) REVERT: D 673 MET cc_start: 0.8887 (tpp) cc_final: 0.8406 (tpp) REVERT: D 688 MET cc_start: 0.8306 (ppp) cc_final: 0.7866 (ppp) REVERT: D 786 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7283 (tt) REVERT: D 787 ARG cc_start: 0.8744 (mtt180) cc_final: 0.8359 (mpt-90) REVERT: D 858 TRP cc_start: 0.7663 (m-90) cc_final: 0.7032 (m-90) REVERT: D 911 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7308 (mm-30) REVERT: D 965 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7287 (mm) REVERT: D 977 MET cc_start: 0.9176 (mmm) cc_final: 0.8642 (mmm) REVERT: D 1147 LYS cc_start: 0.9061 (mttp) cc_final: 0.8713 (mttp) REVERT: D 1149 LEU cc_start: 0.9662 (OUTLIER) cc_final: 0.9384 (tt) REVERT: D 1161 ASP cc_start: 0.9018 (p0) cc_final: 0.8616 (p0) REVERT: D 1208 MET cc_start: 0.8845 (ppp) cc_final: 0.8573 (ppp) REVERT: D 1217 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9215 (mm) outliers start: 240 outliers final: 149 residues processed: 756 average time/residue: 0.4497 time to fit residues: 587.0181 Evaluate side-chains 692 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 521 time to evaluate : 4.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 917 ASN Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 960 GLN Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1091 ILE Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1127 CYS Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1218 THR Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1253 ASP Chi-restraints excluded: chain A residue 1270 THR Chi-restraints excluded: chain A residue 1323 TYR Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 182 GLN Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 506 VAL Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 669 PHE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 947 SER Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 965 LEU Chi-restraints excluded: chain B residue 1042 THR Chi-restraints excluded: chain B residue 1080 PHE Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1110 LEU Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1149 LEU Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain B residue 1305 LEU Chi-restraints excluded: chain B residue 1333 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 396 ASN Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 506 VAL Chi-restraints excluded: chain C residue 559 ASP Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 646 HIS Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 849 CYS Chi-restraints excluded: chain C residue 861 THR Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 917 ASN Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 960 GLN Chi-restraints excluded: chain C residue 983 ASN Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1087 LEU Chi-restraints excluded: chain C residue 1091 ILE Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1127 CYS Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1149 LEU Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1253 ASP Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain C residue 1323 TYR Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 173 ASN Chi-restraints excluded: chain D residue 182 GLN Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 500 MET Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 607 MET Chi-restraints excluded: chain D residue 645 ARG Chi-restraints excluded: chain D residue 654 THR Chi-restraints excluded: chain D residue 669 PHE Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 786 LEU Chi-restraints excluded: chain D residue 935 LEU Chi-restraints excluded: chain D residue 947 SER Chi-restraints excluded: chain D residue 949 SER Chi-restraints excluded: chain D residue 965 LEU Chi-restraints excluded: chain D residue 1042 THR Chi-restraints excluded: chain D residue 1080 PHE Chi-restraints excluded: chain D residue 1110 LEU Chi-restraints excluded: chain D residue 1144 VAL Chi-restraints excluded: chain D residue 1149 LEU Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1217 LEU Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1253 ASP Chi-restraints excluded: chain D residue 1299 LEU Chi-restraints excluded: chain D residue 1305 LEU Chi-restraints excluded: chain D residue 1333 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 165 optimal weight: 20.0000 chunk 443 optimal weight: 0.7980 chunk 97 optimal weight: 9.9990 chunk 289 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 493 optimal weight: 5.9990 chunk 409 optimal weight: 7.9990 chunk 228 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 163 optimal weight: 0.9990 chunk 259 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 ASN ** A 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 ASN ** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 964 ASN ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN ** D 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 964 ASN ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 41420 Z= 0.261 Angle : 0.775 13.923 56270 Z= 0.377 Chirality : 0.049 0.404 6514 Planarity : 0.005 0.059 7202 Dihedral : 7.510 71.461 6308 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.80 % Favored : 89.96 % Rotamer: Outliers : 4.54 % Allowed : 22.33 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.11), residues: 5110 helix: 0.82 (0.18), residues: 870 sheet: -1.11 (0.12), residues: 1766 loop : -2.97 (0.12), residues: 2474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 436 HIS 0.007 0.001 HIS A1195 PHE 0.026 0.002 PHE A 669 TYR 0.031 0.002 TYR D1007 ARG 0.005 0.000 ARG B 338 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 578 time to evaluate : 4.905 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: A 114 PHE cc_start: 0.7299 (t80) cc_final: 0.6962 (t80) REVERT: A 161 LEU cc_start: 0.9524 (pt) cc_final: 0.9301 (mt) REVERT: A 192 PHE cc_start: 0.8192 (t80) cc_final: 0.7895 (t80) REVERT: A 246 MET cc_start: 0.6752 (mmt) cc_final: 0.6537 (mmt) REVERT: A 387 ARG cc_start: 0.8557 (mtt180) cc_final: 0.7728 (mtt90) REVERT: A 456 LYS cc_start: 0.9253 (mmmt) cc_final: 0.8937 (mmmm) REVERT: A 567 LYS cc_start: 0.8448 (tppt) cc_final: 0.8206 (tppt) REVERT: A 646 HIS cc_start: 0.5928 (OUTLIER) cc_final: 0.4754 (t70) REVERT: A 672 ASP cc_start: 0.8653 (t0) cc_final: 0.8359 (t0) REVERT: A 766 LYS cc_start: 0.7540 (mmtp) cc_final: 0.7115 (mptt) REVERT: A 787 ARG cc_start: 0.8578 (ptt-90) cc_final: 0.8110 (mtm180) REVERT: A 977 MET cc_start: 0.9138 (mmm) cc_final: 0.8877 (mmm) REVERT: A 988 ASP cc_start: 0.8924 (m-30) cc_final: 0.8586 (m-30) REVERT: A 1016 LEU cc_start: 0.9110 (mp) cc_final: 0.8872 (mp) REVERT: A 1109 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9073 (mm) REVERT: A 1121 VAL cc_start: 0.8952 (m) cc_final: 0.8737 (p) REVERT: A 1149 LEU cc_start: 0.9711 (OUTLIER) cc_final: 0.9456 (tt) REVERT: A 1161 ASP cc_start: 0.9075 (p0) cc_final: 0.8758 (p0) REVERT: A 1165 GLU cc_start: 0.9188 (tt0) cc_final: 0.8904 (tt0) REVERT: A 1217 LEU cc_start: 0.9618 (mm) cc_final: 0.9302 (mp) REVERT: A 1314 MET cc_start: 0.8719 (mpp) cc_final: 0.7973 (mpp) REVERT: B 65 GLU cc_start: 0.7747 (mp0) cc_final: 0.7451 (mp0) REVERT: B 173 ASN cc_start: 0.7790 (OUTLIER) cc_final: 0.7421 (p0) REVERT: B 181 PHE cc_start: 0.7630 (p90) cc_final: 0.7404 (p90) REVERT: B 222 GLU cc_start: 0.8273 (pt0) cc_final: 0.8002 (pp20) REVERT: B 246 MET cc_start: 0.8099 (mtm) cc_final: 0.7883 (mtp) REVERT: B 318 MET cc_start: 0.5621 (mmm) cc_final: 0.5280 (tpt) REVERT: B 373 ASP cc_start: 0.8313 (p0) cc_final: 0.7906 (t0) REVERT: B 500 MET cc_start: 0.6958 (ttt) cc_final: 0.6629 (ttt) REVERT: B 520 MET cc_start: 0.7348 (tmm) cc_final: 0.7018 (tmm) REVERT: B 561 GLU cc_start: 0.7572 (pt0) cc_final: 0.7091 (pt0) REVERT: B 602 GLN cc_start: 0.7595 (tm-30) cc_final: 0.7380 (tm-30) REVERT: B 605 LEU cc_start: 0.8496 (tp) cc_final: 0.8280 (tp) REVERT: B 627 LEU cc_start: 0.9235 (tp) cc_final: 0.8934 (tt) REVERT: B 673 MET cc_start: 0.8780 (tpp) cc_final: 0.8146 (tpp) REVERT: B 688 MET cc_start: 0.8330 (ppp) cc_final: 0.8000 (ppp) REVERT: B 786 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7310 (tt) REVERT: B 787 ARG cc_start: 0.8715 (mtt180) cc_final: 0.8280 (mpt-90) REVERT: B 858 TRP cc_start: 0.7699 (m-90) cc_final: 0.7011 (m-90) REVERT: B 965 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7489 (mm) REVERT: B 977 MET cc_start: 0.9079 (mmm) cc_final: 0.8569 (mmm) REVERT: B 987 LEU cc_start: 0.9509 (tt) cc_final: 0.9290 (pp) REVERT: B 1147 LYS cc_start: 0.9115 (mttp) cc_final: 0.8681 (mttp) REVERT: B 1161 ASP cc_start: 0.9002 (p0) cc_final: 0.8626 (p0) REVERT: B 1172 GLU cc_start: 0.9080 (tt0) cc_final: 0.8193 (tm-30) REVERT: C 114 PHE cc_start: 0.7296 (t80) cc_final: 0.6977 (t80) REVERT: C 192 PHE cc_start: 0.8195 (t80) cc_final: 0.7895 (t80) REVERT: C 310 GLN cc_start: 0.8584 (mp-120) cc_final: 0.8381 (mp-120) REVERT: C 456 LYS cc_start: 0.9245 (mmmt) cc_final: 0.8930 (mmmm) REVERT: C 567 LYS cc_start: 0.8456 (tppt) cc_final: 0.8215 (tppt) REVERT: C 656 THR cc_start: -0.1632 (OUTLIER) cc_final: -0.2109 (p) REVERT: C 672 ASP cc_start: 0.8610 (t0) cc_final: 0.8277 (t0) REVERT: C 673 MET cc_start: 0.9008 (tpp) cc_final: 0.8798 (tpp) REVERT: C 687 LYS cc_start: 0.9279 (tttt) cc_final: 0.8820 (tptt) REVERT: C 787 ARG cc_start: 0.8546 (ptt-90) cc_final: 0.8082 (mtm180) REVERT: C 968 MET cc_start: 0.8489 (tpt) cc_final: 0.7245 (pmm) REVERT: C 988 ASP cc_start: 0.8946 (m-30) cc_final: 0.8477 (m-30) REVERT: C 1109 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9071 (mm) REVERT: C 1121 VAL cc_start: 0.8953 (m) cc_final: 0.8740 (p) REVERT: C 1149 LEU cc_start: 0.9686 (OUTLIER) cc_final: 0.9406 (tp) REVERT: C 1161 ASP cc_start: 0.9045 (p0) cc_final: 0.8718 (p0) REVERT: C 1165 GLU cc_start: 0.9199 (tt0) cc_final: 0.8901 (tt0) REVERT: C 1208 MET cc_start: 0.9131 (ppp) cc_final: 0.8817 (ppp) REVERT: C 1314 MET cc_start: 0.8708 (mpp) cc_final: 0.7944 (mpp) REVERT: D 173 ASN cc_start: 0.7636 (OUTLIER) cc_final: 0.7403 (p0) REVERT: D 183 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6269 (mp) REVERT: D 222 GLU cc_start: 0.8264 (pt0) cc_final: 0.7995 (pp20) REVERT: D 318 MET cc_start: 0.5625 (mmm) cc_final: 0.5259 (tpt) REVERT: D 373 ASP cc_start: 0.8294 (p0) cc_final: 0.7922 (t0) REVERT: D 500 MET cc_start: 0.6617 (ttt) cc_final: 0.6308 (mtp) REVERT: D 520 MET cc_start: 0.7433 (tmm) cc_final: 0.7108 (tmm) REVERT: D 541 LEU cc_start: 0.6558 (OUTLIER) cc_final: 0.6199 (pt) REVERT: D 561 GLU cc_start: 0.7497 (pt0) cc_final: 0.6799 (pt0) REVERT: D 605 LEU cc_start: 0.8491 (tp) cc_final: 0.8129 (tp) REVERT: D 673 MET cc_start: 0.8736 (tpp) cc_final: 0.8264 (tpp) REVERT: D 688 MET cc_start: 0.8396 (ppp) cc_final: 0.8068 (ppp) REVERT: D 786 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7588 (mp) REVERT: D 787 ARG cc_start: 0.8717 (mtt180) cc_final: 0.8280 (mpt-90) REVERT: D 858 TRP cc_start: 0.7713 (m-90) cc_final: 0.7106 (m-90) REVERT: D 911 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7335 (mm-30) REVERT: D 965 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7200 (mm) REVERT: D 977 MET cc_start: 0.9137 (mmm) cc_final: 0.8599 (mmm) REVERT: D 987 LEU cc_start: 0.9529 (tt) cc_final: 0.9308 (pp) REVERT: D 1147 LYS cc_start: 0.9087 (mttp) cc_final: 0.8679 (mttp) REVERT: D 1149 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9352 (tt) REVERT: D 1161 ASP cc_start: 0.9001 (p0) cc_final: 0.8613 (p0) outliers start: 203 outliers final: 146 residues processed: 735 average time/residue: 0.4630 time to fit residues: 591.1724 Evaluate side-chains 701 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 540 time to evaluate : 4.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 646 HIS Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 917 ASN Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 960 GLN Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1091 ILE Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1218 THR Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1253 ASP Chi-restraints excluded: chain A residue 1270 THR Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 947 SER Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 965 LEU Chi-restraints excluded: chain B residue 1042 THR Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1080 PHE Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1110 LEU Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain B residue 1270 THR Chi-restraints excluded: chain B residue 1305 LEU Chi-restraints excluded: chain B residue 1333 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 849 CYS Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 917 ASN Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 960 GLN Chi-restraints excluded: chain C residue 983 ASN Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1091 ILE Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1149 LEU Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1253 ASP Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain C residue 1298 LEU Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 173 ASN Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 366 PHE Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 607 MET Chi-restraints excluded: chain D residue 645 ARG Chi-restraints excluded: chain D residue 654 THR Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 786 LEU Chi-restraints excluded: chain D residue 935 LEU Chi-restraints excluded: chain D residue 947 SER Chi-restraints excluded: chain D residue 949 SER Chi-restraints excluded: chain D residue 965 LEU Chi-restraints excluded: chain D residue 1042 THR Chi-restraints excluded: chain D residue 1063 ILE Chi-restraints excluded: chain D residue 1080 PHE Chi-restraints excluded: chain D residue 1097 ASP Chi-restraints excluded: chain D residue 1110 LEU Chi-restraints excluded: chain D residue 1127 CYS Chi-restraints excluded: chain D residue 1144 VAL Chi-restraints excluded: chain D residue 1149 LEU Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1253 ASP Chi-restraints excluded: chain D residue 1305 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 475 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 281 optimal weight: 10.0000 chunk 360 optimal weight: 1.9990 chunk 279 optimal weight: 3.9990 chunk 415 optimal weight: 8.9990 chunk 275 optimal weight: 5.9990 chunk 491 optimal weight: 0.9990 chunk 307 optimal weight: 4.9990 chunk 299 optimal weight: 0.9980 chunk 226 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 GLN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 ASN ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 GLN B 132 GLN ** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN B1072 GLN ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 ASN ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 ASN D1072 GLN ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 41420 Z= 0.221 Angle : 0.757 14.603 56270 Z= 0.364 Chirality : 0.048 0.357 6514 Planarity : 0.005 0.059 7202 Dihedral : 7.326 71.253 6308 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.70 % Favored : 89.10 % Rotamer: Outliers : 4.56 % Allowed : 22.95 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.11), residues: 5110 helix: 0.91 (0.18), residues: 866 sheet: -1.00 (0.12), residues: 1726 loop : -2.86 (0.12), residues: 2518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 436 HIS 0.006 0.001 HIS A1195 PHE 0.025 0.002 PHE C 669 TYR 0.042 0.002 TYR B1007 ARG 0.004 0.000 ARG D 598 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 579 time to evaluate : 4.034 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: A 114 PHE cc_start: 0.7260 (t80) cc_final: 0.6930 (t80) REVERT: A 161 LEU cc_start: 0.9503 (pt) cc_final: 0.9291 (mt) REVERT: A 192 PHE cc_start: 0.8178 (t80) cc_final: 0.7854 (t80) REVERT: A 246 MET cc_start: 0.6808 (mmt) cc_final: 0.6544 (mmt) REVERT: A 310 GLN cc_start: 0.8409 (mp10) cc_final: 0.8125 (pm20) REVERT: A 387 ARG cc_start: 0.8449 (mtt180) cc_final: 0.7668 (mtt90) REVERT: A 456 LYS cc_start: 0.9214 (mmmt) cc_final: 0.8886 (mmmm) REVERT: A 567 LYS cc_start: 0.8432 (tppt) cc_final: 0.8193 (tppt) REVERT: A 582 HIS cc_start: 0.7303 (t70) cc_final: 0.6972 (t70) REVERT: A 646 HIS cc_start: 0.5953 (OUTLIER) cc_final: 0.4748 (t70) REVERT: A 672 ASP cc_start: 0.8620 (t0) cc_final: 0.8320 (t0) REVERT: A 687 LYS cc_start: 0.9242 (tttt) cc_final: 0.8682 (tptt) REVERT: A 766 LYS cc_start: 0.7597 (mmtp) cc_final: 0.7160 (mptt) REVERT: A 787 ARG cc_start: 0.8637 (ptt-90) cc_final: 0.8182 (mtm180) REVERT: A 965 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7689 (mm) REVERT: A 988 ASP cc_start: 0.8874 (m-30) cc_final: 0.8477 (m-30) REVERT: A 1016 LEU cc_start: 0.9102 (mp) cc_final: 0.8865 (mp) REVERT: A 1109 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9038 (mm) REVERT: A 1121 VAL cc_start: 0.8940 (m) cc_final: 0.8725 (p) REVERT: A 1149 LEU cc_start: 0.9707 (OUTLIER) cc_final: 0.9454 (tt) REVERT: A 1161 ASP cc_start: 0.9044 (p0) cc_final: 0.8710 (p0) REVERT: A 1165 GLU cc_start: 0.9191 (tt0) cc_final: 0.8910 (tt0) REVERT: A 1217 LEU cc_start: 0.9607 (mm) cc_final: 0.9312 (mp) REVERT: A 1314 MET cc_start: 0.8709 (mpp) cc_final: 0.7987 (mpp) REVERT: B 65 GLU cc_start: 0.7754 (mp0) cc_final: 0.7409 (mp0) REVERT: B 114 PHE cc_start: 0.7355 (t80) cc_final: 0.6834 (t80) REVERT: B 222 GLU cc_start: 0.8240 (pt0) cc_final: 0.7983 (pp20) REVERT: B 246 MET cc_start: 0.8082 (mtm) cc_final: 0.7852 (mtp) REVERT: B 318 MET cc_start: 0.5794 (mmm) cc_final: 0.5191 (tpt) REVERT: B 373 ASP cc_start: 0.8224 (p0) cc_final: 0.7919 (t0) REVERT: B 387 ARG cc_start: 0.8049 (mtt180) cc_final: 0.7466 (ttm-80) REVERT: B 499 ILE cc_start: 0.8131 (mt) cc_final: 0.7682 (tp) REVERT: B 500 MET cc_start: 0.7140 (ttt) cc_final: 0.6874 (ttt) REVERT: B 520 MET cc_start: 0.7303 (tmm) cc_final: 0.7026 (tmm) REVERT: B 561 GLU cc_start: 0.7533 (pt0) cc_final: 0.6722 (pt0) REVERT: B 602 GLN cc_start: 0.7475 (tm-30) cc_final: 0.7201 (tm-30) REVERT: B 627 LEU cc_start: 0.9208 (tp) cc_final: 0.8912 (tt) REVERT: B 673 MET cc_start: 0.8756 (tpp) cc_final: 0.8124 (tpp) REVERT: B 688 MET cc_start: 0.8333 (ppp) cc_final: 0.8072 (ppp) REVERT: B 787 ARG cc_start: 0.8696 (mtt180) cc_final: 0.8236 (mpt-90) REVERT: B 977 MET cc_start: 0.9085 (mmm) cc_final: 0.8509 (mmm) REVERT: B 1147 LYS cc_start: 0.9109 (mttp) cc_final: 0.8679 (mttp) REVERT: B 1161 ASP cc_start: 0.9005 (p0) cc_final: 0.8656 (p0) REVERT: B 1172 GLU cc_start: 0.9077 (tt0) cc_final: 0.8205 (tm-30) REVERT: C 114 PHE cc_start: 0.7192 (t80) cc_final: 0.6887 (t80) REVERT: C 192 PHE cc_start: 0.8185 (t80) cc_final: 0.7859 (t80) REVERT: C 456 LYS cc_start: 0.9199 (mmmt) cc_final: 0.8867 (mmmm) REVERT: C 567 LYS cc_start: 0.8438 (tppt) cc_final: 0.8196 (tppt) REVERT: C 582 HIS cc_start: 0.7144 (t70) cc_final: 0.6826 (t70) REVERT: C 646 HIS cc_start: 0.5838 (OUTLIER) cc_final: 0.4634 (t70) REVERT: C 654 THR cc_start: 0.7175 (OUTLIER) cc_final: 0.6928 (t) REVERT: C 656 THR cc_start: -0.1785 (OUTLIER) cc_final: -0.2941 (p) REVERT: C 672 ASP cc_start: 0.8567 (t0) cc_final: 0.8281 (t0) REVERT: C 687 LYS cc_start: 0.9261 (tttt) cc_final: 0.8775 (tptt) REVERT: C 764 GLU cc_start: 0.5544 (mp0) cc_final: 0.5083 (mt-10) REVERT: C 787 ARG cc_start: 0.8536 (ptt-90) cc_final: 0.8100 (mtm180) REVERT: C 968 MET cc_start: 0.8400 (tpt) cc_final: 0.7106 (pmm) REVERT: C 988 ASP cc_start: 0.8846 (m-30) cc_final: 0.8341 (m-30) REVERT: C 1109 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9058 (mm) REVERT: C 1121 VAL cc_start: 0.8929 (m) cc_final: 0.8711 (p) REVERT: C 1149 LEU cc_start: 0.9692 (OUTLIER) cc_final: 0.9410 (tt) REVERT: C 1161 ASP cc_start: 0.9042 (p0) cc_final: 0.8702 (p0) REVERT: C 1165 GLU cc_start: 0.9178 (tt0) cc_final: 0.8921 (tt0) REVERT: C 1314 MET cc_start: 0.8678 (mpp) cc_final: 0.7916 (mpp) REVERT: D 222 GLU cc_start: 0.8256 (pt0) cc_final: 0.7999 (pp20) REVERT: D 244 GLU cc_start: 0.8327 (pm20) cc_final: 0.8014 (tm-30) REVERT: D 318 MET cc_start: 0.5810 (mmm) cc_final: 0.5195 (tpt) REVERT: D 373 ASP cc_start: 0.8222 (p0) cc_final: 0.7982 (t0) REVERT: D 499 ILE cc_start: 0.8171 (mt) cc_final: 0.7711 (tp) REVERT: D 520 MET cc_start: 0.7275 (tmm) cc_final: 0.6979 (tmm) REVERT: D 541 LEU cc_start: 0.6488 (OUTLIER) cc_final: 0.6152 (pt) REVERT: D 561 GLU cc_start: 0.7393 (pt0) cc_final: 0.7100 (pt0) REVERT: D 673 MET cc_start: 0.8710 (tpp) cc_final: 0.8218 (tpp) REVERT: D 688 MET cc_start: 0.8364 (ppp) cc_final: 0.8142 (ppp) REVERT: D 787 ARG cc_start: 0.8698 (mtt180) cc_final: 0.8247 (mpt-90) REVERT: D 811 LYS cc_start: 0.8326 (mmtp) cc_final: 0.7921 (mmtp) REVERT: D 965 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7213 (mm) REVERT: D 977 MET cc_start: 0.9114 (mmm) cc_final: 0.8586 (mmm) REVERT: D 987 LEU cc_start: 0.9495 (tt) cc_final: 0.9290 (pp) REVERT: D 1147 LYS cc_start: 0.9038 (mttp) cc_final: 0.8633 (mttp) REVERT: D 1149 LEU cc_start: 0.9625 (OUTLIER) cc_final: 0.9327 (tt) REVERT: D 1161 ASP cc_start: 0.9014 (p0) cc_final: 0.8667 (p0) outliers start: 204 outliers final: 155 residues processed: 735 average time/residue: 0.4540 time to fit residues: 576.9769 Evaluate side-chains 721 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 554 time to evaluate : 5.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 523 HIS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 646 HIS Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 821 CYS Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 917 ASN Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 960 GLN Chi-restraints excluded: chain A residue 965 LEU Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1091 ILE Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1127 CYS Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1218 THR Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1253 ASP Chi-restraints excluded: chain A residue 1270 THR Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 635 ASN Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 947 SER Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 1042 THR Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1080 PHE Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1110 LEU Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1227 ASP Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain B residue 1305 LEU Chi-restraints excluded: chain B residue 1333 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 646 HIS Chi-restraints excluded: chain C residue 654 THR Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 821 CYS Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 849 CYS Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 917 ASN Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 960 GLN Chi-restraints excluded: chain C residue 983 ASN Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1091 ILE Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1127 CYS Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1149 LEU Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1253 ASP Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 366 PHE Chi-restraints excluded: chain D residue 445 HIS Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 607 MET Chi-restraints excluded: chain D residue 635 ASN Chi-restraints excluded: chain D residue 645 ARG Chi-restraints excluded: chain D residue 654 THR Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 947 SER Chi-restraints excluded: chain D residue 949 SER Chi-restraints excluded: chain D residue 965 LEU Chi-restraints excluded: chain D residue 1042 THR Chi-restraints excluded: chain D residue 1063 ILE Chi-restraints excluded: chain D residue 1080 PHE Chi-restraints excluded: chain D residue 1097 ASP Chi-restraints excluded: chain D residue 1110 LEU Chi-restraints excluded: chain D residue 1144 VAL Chi-restraints excluded: chain D residue 1149 LEU Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1227 ASP Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1253 ASP Chi-restraints excluded: chain D residue 1305 LEU Chi-restraints excluded: chain D residue 1333 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 304 optimal weight: 7.9990 chunk 196 optimal weight: 7.9990 chunk 293 optimal weight: 0.9980 chunk 148 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 312 optimal weight: 0.9990 chunk 334 optimal weight: 10.0000 chunk 243 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 386 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 ASN ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 GLN ** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 976 ASN ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 41420 Z= 0.227 Angle : 0.767 16.529 56270 Z= 0.367 Chirality : 0.048 0.340 6514 Planarity : 0.005 0.059 7202 Dihedral : 7.254 72.775 6308 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.69 % Favored : 90.12 % Rotamer: Outliers : 4.30 % Allowed : 23.47 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.12), residues: 5110 helix: 0.89 (0.18), residues: 872 sheet: -0.96 (0.12), residues: 1722 loop : -2.81 (0.12), residues: 2516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 436 HIS 0.005 0.001 HIS A1195 PHE 0.024 0.002 PHE C 669 TYR 0.023 0.002 TYR B 31 ARG 0.004 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 582 time to evaluate : 4.482 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: symmetry clash REVERT: A 114 PHE cc_start: 0.7214 (t80) cc_final: 0.6865 (t80) REVERT: A 192 PHE cc_start: 0.8157 (t80) cc_final: 0.7840 (t80) REVERT: A 310 GLN cc_start: 0.8332 (mp10) cc_final: 0.8104 (pm20) REVERT: A 456 LYS cc_start: 0.9221 (mmmt) cc_final: 0.8883 (mmmm) REVERT: A 567 LYS cc_start: 0.8423 (tppt) cc_final: 0.8181 (tppt) REVERT: A 582 HIS cc_start: 0.7161 (t70) cc_final: 0.6885 (t70) REVERT: A 672 ASP cc_start: 0.8603 (t0) cc_final: 0.8277 (t0) REVERT: A 687 LYS cc_start: 0.9247 (tttt) cc_final: 0.8712 (tptt) REVERT: A 787 ARG cc_start: 0.8624 (ptt-90) cc_final: 0.8153 (mtm180) REVERT: A 988 ASP cc_start: 0.8969 (m-30) cc_final: 0.8573 (m-30) REVERT: A 1015 GLN cc_start: 0.8068 (tp40) cc_final: 0.7793 (tp40) REVERT: A 1016 LEU cc_start: 0.9150 (mp) cc_final: 0.8913 (mp) REVERT: A 1018 TYR cc_start: 0.8162 (m-80) cc_final: 0.7830 (t80) REVERT: A 1109 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9016 (mm) REVERT: A 1121 VAL cc_start: 0.8940 (m) cc_final: 0.8727 (p) REVERT: A 1149 LEU cc_start: 0.9705 (OUTLIER) cc_final: 0.9445 (tt) REVERT: A 1161 ASP cc_start: 0.9037 (p0) cc_final: 0.8684 (p0) REVERT: A 1165 GLU cc_start: 0.9194 (tt0) cc_final: 0.8904 (tt0) REVERT: A 1314 MET cc_start: 0.8691 (mpp) cc_final: 0.7948 (mpp) REVERT: B 65 GLU cc_start: 0.7789 (mp0) cc_final: 0.7436 (mp0) REVERT: B 114 PHE cc_start: 0.7014 (t80) cc_final: 0.6673 (t80) REVERT: B 222 GLU cc_start: 0.8249 (pt0) cc_final: 0.7991 (pp20) REVERT: B 246 MET cc_start: 0.8069 (mtm) cc_final: 0.7854 (mtp) REVERT: B 318 MET cc_start: 0.5768 (mmm) cc_final: 0.5120 (tpt) REVERT: B 373 ASP cc_start: 0.8212 (p0) cc_final: 0.7973 (t0) REVERT: B 387 ARG cc_start: 0.8043 (mtt180) cc_final: 0.7456 (ttm-80) REVERT: B 499 ILE cc_start: 0.8139 (mt) cc_final: 0.7679 (tp) REVERT: B 500 MET cc_start: 0.7184 (ttt) cc_final: 0.6939 (ttt) REVERT: B 520 MET cc_start: 0.7485 (tmm) cc_final: 0.7191 (tmm) REVERT: B 602 GLN cc_start: 0.7542 (tm-30) cc_final: 0.7330 (tm-30) REVERT: B 627 LEU cc_start: 0.9212 (tp) cc_final: 0.8907 (tt) REVERT: B 673 MET cc_start: 0.8826 (tpp) cc_final: 0.8226 (tpp) REVERT: B 688 MET cc_start: 0.8369 (ppp) cc_final: 0.8166 (ppp) REVERT: B 787 ARG cc_start: 0.8666 (mtt180) cc_final: 0.8209 (mpt-90) REVERT: B 870 PHE cc_start: 0.8508 (t80) cc_final: 0.8287 (t80) REVERT: B 977 MET cc_start: 0.9065 (mmm) cc_final: 0.8503 (mmm) REVERT: B 1147 LYS cc_start: 0.9109 (mttp) cc_final: 0.8687 (mttp) REVERT: B 1161 ASP cc_start: 0.9009 (p0) cc_final: 0.8667 (p0) REVERT: B 1172 GLU cc_start: 0.9060 (tt0) cc_final: 0.8204 (tm-30) REVERT: C 114 PHE cc_start: 0.7084 (t80) cc_final: 0.6770 (t80) REVERT: C 192 PHE cc_start: 0.8180 (t80) cc_final: 0.7857 (t80) REVERT: C 310 GLN cc_start: 0.8439 (mp-120) cc_final: 0.8181 (pt0) REVERT: C 456 LYS cc_start: 0.9207 (mmmt) cc_final: 0.8872 (mmmm) REVERT: C 567 LYS cc_start: 0.8425 (tppt) cc_final: 0.8183 (tppt) REVERT: C 582 HIS cc_start: 0.7147 (t70) cc_final: 0.6872 (t70) REVERT: C 656 THR cc_start: -0.2251 (OUTLIER) cc_final: -0.2797 (p) REVERT: C 672 ASP cc_start: 0.8577 (t0) cc_final: 0.8222 (t0) REVERT: C 687 LYS cc_start: 0.9243 (tttt) cc_final: 0.8654 (tptt) REVERT: C 764 GLU cc_start: 0.5811 (mp0) cc_final: 0.5502 (mt-10) REVERT: C 787 ARG cc_start: 0.8543 (ptt-90) cc_final: 0.8113 (mtm180) REVERT: C 851 ASN cc_start: 0.8981 (m-40) cc_final: 0.8287 (m110) REVERT: C 965 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7216 (mm) REVERT: C 968 MET cc_start: 0.8310 (tpt) cc_final: 0.7479 (pmm) REVERT: C 988 ASP cc_start: 0.8839 (m-30) cc_final: 0.8321 (m-30) REVERT: C 1016 LEU cc_start: 0.9144 (mp) cc_final: 0.8929 (mp) REVERT: C 1109 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9016 (mm) REVERT: C 1121 VAL cc_start: 0.8928 (m) cc_final: 0.8712 (p) REVERT: C 1149 LEU cc_start: 0.9707 (OUTLIER) cc_final: 0.9437 (tt) REVERT: C 1161 ASP cc_start: 0.9053 (p0) cc_final: 0.8701 (p0) REVERT: C 1165 GLU cc_start: 0.9179 (tt0) cc_final: 0.8921 (tt0) REVERT: C 1314 MET cc_start: 0.8687 (mpp) cc_final: 0.7921 (mpp) REVERT: D 32 MET cc_start: 0.7940 (ttp) cc_final: 0.7525 (ttp) REVERT: D 222 GLU cc_start: 0.8252 (pt0) cc_final: 0.7999 (pp20) REVERT: D 244 GLU cc_start: 0.8317 (pm20) cc_final: 0.8031 (tm-30) REVERT: D 318 MET cc_start: 0.5851 (mmm) cc_final: 0.5215 (tpt) REVERT: D 373 ASP cc_start: 0.8202 (p0) cc_final: 0.7987 (t0) REVERT: D 387 ARG cc_start: 0.8063 (mtt180) cc_final: 0.7525 (ttm-80) REVERT: D 499 ILE cc_start: 0.8083 (mt) cc_final: 0.7626 (tp) REVERT: D 520 MET cc_start: 0.7503 (tmm) cc_final: 0.7225 (tmm) REVERT: D 561 GLU cc_start: 0.7536 (pt0) cc_final: 0.6734 (pt0) REVERT: D 602 GLN cc_start: 0.7467 (tm-30) cc_final: 0.7208 (tm-30) REVERT: D 673 MET cc_start: 0.8746 (tpp) cc_final: 0.8277 (tpp) REVERT: D 688 MET cc_start: 0.8378 (ppp) cc_final: 0.8156 (ppp) REVERT: D 787 ARG cc_start: 0.8672 (mtt180) cc_final: 0.8221 (mpt-90) REVERT: D 811 LYS cc_start: 0.8256 (mmtp) cc_final: 0.7857 (mmtp) REVERT: D 965 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.6561 (mm) REVERT: D 977 MET cc_start: 0.9110 (mmm) cc_final: 0.8602 (mmm) REVERT: D 987 LEU cc_start: 0.9485 (tt) cc_final: 0.9284 (pp) REVERT: D 1015 GLN cc_start: 0.8757 (tp40) cc_final: 0.8252 (tp40) REVERT: D 1147 LYS cc_start: 0.9034 (mttp) cc_final: 0.8642 (mttp) REVERT: D 1149 LEU cc_start: 0.9611 (OUTLIER) cc_final: 0.9311 (tt) REVERT: D 1161 ASP cc_start: 0.9015 (p0) cc_final: 0.8678 (p0) outliers start: 192 outliers final: 167 residues processed: 732 average time/residue: 0.4539 time to fit residues: 572.0028 Evaluate side-chains 724 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 549 time to evaluate : 4.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 523 HIS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 635 ASN Chi-restraints excluded: chain A residue 646 HIS Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 821 CYS Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 917 ASN Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 960 GLN Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1091 ILE Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1127 CYS Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1218 THR Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1253 ASP Chi-restraints excluded: chain A residue 1270 THR Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 947 SER Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 1042 THR Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1080 PHE Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1227 ASP Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain B residue 1253 ASP Chi-restraints excluded: chain B residue 1270 THR Chi-restraints excluded: chain B residue 1305 LEU Chi-restraints excluded: chain B residue 1333 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 500 MET Chi-restraints excluded: chain C residue 523 HIS Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 821 CYS Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 849 CYS Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 917 ASN Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 960 GLN Chi-restraints excluded: chain C residue 965 LEU Chi-restraints excluded: chain C residue 983 ASN Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1091 ILE Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1127 CYS Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1149 LEU Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1253 ASP Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain C residue 1298 LEU Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 445 HIS Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 607 MET Chi-restraints excluded: chain D residue 645 ARG Chi-restraints excluded: chain D residue 654 THR Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 762 ILE Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 794 VAL Chi-restraints excluded: chain D residue 947 SER Chi-restraints excluded: chain D residue 949 SER Chi-restraints excluded: chain D residue 965 LEU Chi-restraints excluded: chain D residue 1042 THR Chi-restraints excluded: chain D residue 1080 PHE Chi-restraints excluded: chain D residue 1097 ASP Chi-restraints excluded: chain D residue 1101 LEU Chi-restraints excluded: chain D residue 1127 CYS Chi-restraints excluded: chain D residue 1144 VAL Chi-restraints excluded: chain D residue 1149 LEU Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1227 ASP Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1253 ASP Chi-restraints excluded: chain D residue 1305 LEU Chi-restraints excluded: chain D residue 1333 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 447 optimal weight: 6.9990 chunk 470 optimal weight: 0.0470 chunk 429 optimal weight: 10.0000 chunk 458 optimal weight: 6.9990 chunk 275 optimal weight: 7.9990 chunk 199 optimal weight: 0.9980 chunk 359 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 413 optimal weight: 3.9990 chunk 433 optimal weight: 0.0040 chunk 456 optimal weight: 5.9990 overall best weight: 1.8094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 GLN ** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1252 GLN ** D 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 41420 Z= 0.226 Angle : 0.768 14.838 56270 Z= 0.368 Chirality : 0.048 0.334 6514 Planarity : 0.005 0.059 7202 Dihedral : 7.212 73.119 6308 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.16 % Favored : 89.65 % Rotamer: Outliers : 4.21 % Allowed : 23.94 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.12), residues: 5110 helix: 0.94 (0.18), residues: 878 sheet: -0.95 (0.12), residues: 1712 loop : -2.79 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 436 HIS 0.005 0.001 HIS B 263 PHE 0.023 0.002 PHE C 458 TYR 0.027 0.002 TYR D1007 ARG 0.004 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 573 time to evaluate : 4.603 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: A 114 PHE cc_start: 0.7138 (t80) cc_final: 0.6793 (t80) REVERT: A 192 PHE cc_start: 0.8206 (t80) cc_final: 0.7888 (t80) REVERT: A 310 GLN cc_start: 0.8311 (mp10) cc_final: 0.7933 (mp10) REVERT: A 452 PHE cc_start: 0.9236 (t80) cc_final: 0.9028 (t80) REVERT: A 456 LYS cc_start: 0.9131 (mmmt) cc_final: 0.8798 (mmmm) REVERT: A 567 LYS cc_start: 0.8402 (tppt) cc_final: 0.8196 (tppt) REVERT: A 582 HIS cc_start: 0.7144 (t70) cc_final: 0.6904 (t70) REVERT: A 672 ASP cc_start: 0.8590 (t0) cc_final: 0.8254 (t0) REVERT: A 687 LYS cc_start: 0.9277 (tttt) cc_final: 0.8733 (tptt) REVERT: A 787 ARG cc_start: 0.8615 (ptt-90) cc_final: 0.8165 (mtm180) REVERT: A 851 ASN cc_start: 0.8837 (t0) cc_final: 0.8419 (m-40) REVERT: A 988 ASP cc_start: 0.8973 (m-30) cc_final: 0.8579 (m-30) REVERT: A 1015 GLN cc_start: 0.8123 (tp40) cc_final: 0.7853 (tp40) REVERT: A 1016 LEU cc_start: 0.9143 (mp) cc_final: 0.8897 (mp) REVERT: A 1018 TYR cc_start: 0.8145 (m-80) cc_final: 0.7823 (t80) REVERT: A 1109 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.8998 (mm) REVERT: A 1121 VAL cc_start: 0.8935 (m) cc_final: 0.8724 (p) REVERT: A 1149 LEU cc_start: 0.9705 (OUTLIER) cc_final: 0.9453 (tt) REVERT: A 1161 ASP cc_start: 0.9056 (p0) cc_final: 0.8694 (p0) REVERT: A 1165 GLU cc_start: 0.9207 (tt0) cc_final: 0.8912 (tt0) REVERT: A 1314 MET cc_start: 0.8693 (mpp) cc_final: 0.7947 (mpp) REVERT: B 65 GLU cc_start: 0.7807 (mp0) cc_final: 0.7443 (mp0) REVERT: B 169 ASP cc_start: 0.6785 (t0) cc_final: 0.6569 (t0) REVERT: B 222 GLU cc_start: 0.8249 (pt0) cc_final: 0.7990 (pp20) REVERT: B 246 MET cc_start: 0.8092 (mtm) cc_final: 0.7869 (mtp) REVERT: B 318 MET cc_start: 0.5793 (mmm) cc_final: 0.5445 (tpt) REVERT: B 373 ASP cc_start: 0.8198 (p0) cc_final: 0.7975 (t0) REVERT: B 387 ARG cc_start: 0.8031 (mtt180) cc_final: 0.7818 (ttm-80) REVERT: B 499 ILE cc_start: 0.8097 (mt) cc_final: 0.7646 (tp) REVERT: B 500 MET cc_start: 0.7288 (ttt) cc_final: 0.7055 (ttt) REVERT: B 520 MET cc_start: 0.7490 (tmm) cc_final: 0.7202 (tmm) REVERT: B 602 GLN cc_start: 0.7602 (tm-30) cc_final: 0.7368 (tm-30) REVERT: B 627 LEU cc_start: 0.9216 (tp) cc_final: 0.8898 (tt) REVERT: B 673 MET cc_start: 0.8895 (tpp) cc_final: 0.8334 (tpp) REVERT: B 688 MET cc_start: 0.8376 (ppp) cc_final: 0.8172 (ppp) REVERT: B 787 ARG cc_start: 0.8679 (mtt180) cc_final: 0.8207 (mpt-90) REVERT: B 977 MET cc_start: 0.9054 (mmm) cc_final: 0.8499 (mmm) REVERT: B 1147 LYS cc_start: 0.9102 (mttp) cc_final: 0.8679 (mttp) REVERT: B 1161 ASP cc_start: 0.9005 (p0) cc_final: 0.8719 (p0) REVERT: B 1172 GLU cc_start: 0.9057 (tt0) cc_final: 0.8227 (tm-30) REVERT: C 114 PHE cc_start: 0.7173 (t80) cc_final: 0.6820 (t80) REVERT: C 192 PHE cc_start: 0.8179 (t80) cc_final: 0.7861 (t80) REVERT: C 452 PHE cc_start: 0.9224 (t80) cc_final: 0.9011 (t80) REVERT: C 456 LYS cc_start: 0.9117 (mmmt) cc_final: 0.8779 (mmmm) REVERT: C 567 LYS cc_start: 0.8410 (tppt) cc_final: 0.8199 (tppt) REVERT: C 582 HIS cc_start: 0.7111 (t70) cc_final: 0.6874 (t70) REVERT: C 656 THR cc_start: -0.2090 (OUTLIER) cc_final: -0.2666 (p) REVERT: C 672 ASP cc_start: 0.8558 (t0) cc_final: 0.8286 (t0) REVERT: C 687 LYS cc_start: 0.9244 (tttt) cc_final: 0.8716 (tptt) REVERT: C 764 GLU cc_start: 0.5789 (mp0) cc_final: 0.5513 (mt-10) REVERT: C 787 ARG cc_start: 0.8573 (ptt-90) cc_final: 0.8127 (mtm180) REVERT: C 851 ASN cc_start: 0.8938 (m-40) cc_final: 0.8282 (m110) REVERT: C 968 MET cc_start: 0.8397 (tpt) cc_final: 0.8173 (tpp) REVERT: C 988 ASP cc_start: 0.8839 (m-30) cc_final: 0.8317 (m-30) REVERT: C 1016 LEU cc_start: 0.9132 (mp) cc_final: 0.8913 (mp) REVERT: C 1109 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9005 (mm) REVERT: C 1121 VAL cc_start: 0.8925 (m) cc_final: 0.8710 (p) REVERT: C 1149 LEU cc_start: 0.9718 (OUTLIER) cc_final: 0.9461 (tt) REVERT: C 1161 ASP cc_start: 0.9055 (p0) cc_final: 0.8700 (p0) REVERT: C 1165 GLU cc_start: 0.9181 (tt0) cc_final: 0.8915 (tt0) REVERT: C 1314 MET cc_start: 0.8684 (mpp) cc_final: 0.7944 (mpp) REVERT: D 222 GLU cc_start: 0.8254 (pt0) cc_final: 0.8001 (pp20) REVERT: D 318 MET cc_start: 0.5905 (mmm) cc_final: 0.5551 (tpt) REVERT: D 387 ARG cc_start: 0.7985 (mtt180) cc_final: 0.7474 (ttm-80) REVERT: D 499 ILE cc_start: 0.8065 (mt) cc_final: 0.7613 (tp) REVERT: D 520 MET cc_start: 0.7476 (tmm) cc_final: 0.7204 (tmm) REVERT: D 602 GLN cc_start: 0.7374 (tm-30) cc_final: 0.7153 (tm-30) REVERT: D 673 MET cc_start: 0.8881 (tpp) cc_final: 0.8432 (tpp) REVERT: D 688 MET cc_start: 0.8391 (ppp) cc_final: 0.8160 (ppp) REVERT: D 787 ARG cc_start: 0.8680 (mtt180) cc_final: 0.8212 (mpt-90) REVERT: D 811 LYS cc_start: 0.8288 (mmtp) cc_final: 0.7874 (mmtp) REVERT: D 977 MET cc_start: 0.9111 (mmm) cc_final: 0.8619 (mmm) REVERT: D 987 LEU cc_start: 0.9475 (tt) cc_final: 0.9273 (pp) REVERT: D 1015 GLN cc_start: 0.8664 (tp40) cc_final: 0.8139 (tp40) REVERT: D 1147 LYS cc_start: 0.9029 (mttp) cc_final: 0.8636 (mttp) REVERT: D 1149 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9294 (tt) REVERT: D 1161 ASP cc_start: 0.9009 (p0) cc_final: 0.8696 (p0) outliers start: 188 outliers final: 166 residues processed: 715 average time/residue: 0.4605 time to fit residues: 568.5960 Evaluate side-chains 716 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 544 time to evaluate : 4.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 523 HIS Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 635 ASN Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 821 CYS Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 960 GLN Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1091 ILE Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1127 CYS Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1220 GLN Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1253 ASP Chi-restraints excluded: chain A residue 1270 THR Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 366 PHE Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 947 SER Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 1042 THR Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1080 PHE Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1149 LEU Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1227 ASP Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain B residue 1253 ASP Chi-restraints excluded: chain B residue 1270 THR Chi-restraints excluded: chain B residue 1305 LEU Chi-restraints excluded: chain B residue 1333 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 500 MET Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 821 CYS Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 849 CYS Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 917 ASN Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 983 ASN Chi-restraints excluded: chain C residue 1007 TYR Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1091 ILE Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1127 CYS Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1149 LEU Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1253 ASP Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain C residue 1298 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 348 THR Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 366 PHE Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 445 HIS Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 607 MET Chi-restraints excluded: chain D residue 645 ARG Chi-restraints excluded: chain D residue 654 THR Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 762 ILE Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 794 VAL Chi-restraints excluded: chain D residue 947 SER Chi-restraints excluded: chain D residue 949 SER Chi-restraints excluded: chain D residue 1042 THR Chi-restraints excluded: chain D residue 1080 PHE Chi-restraints excluded: chain D residue 1097 ASP Chi-restraints excluded: chain D residue 1101 LEU Chi-restraints excluded: chain D residue 1127 CYS Chi-restraints excluded: chain D residue 1144 VAL Chi-restraints excluded: chain D residue 1149 LEU Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1227 ASP Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1253 ASP Chi-restraints excluded: chain D residue 1305 LEU Chi-restraints excluded: chain D residue 1333 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 300 optimal weight: 9.9990 chunk 484 optimal weight: 7.9990 chunk 295 optimal weight: 8.9990 chunk 229 optimal weight: 1.9990 chunk 336 optimal weight: 4.9990 chunk 508 optimal weight: 8.9990 chunk 467 optimal weight: 6.9990 chunk 404 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 312 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 ASN ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1187 GLN ** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 GLN ** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1072 GLN ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN ** C 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1179 ASN C1187 GLN ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1009 ASN D1072 GLN D1159 ASN ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 41420 Z= 0.387 Angle : 0.850 15.320 56270 Z= 0.419 Chirality : 0.050 0.330 6514 Planarity : 0.005 0.061 7202 Dihedral : 7.481 77.503 6305 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 23.02 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.74 % Favored : 88.06 % Rotamer: Outliers : 4.21 % Allowed : 24.43 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.11), residues: 5110 helix: 0.61 (0.17), residues: 864 sheet: -1.22 (0.12), residues: 1728 loop : -2.91 (0.11), residues: 2518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 765 HIS 0.007 0.001 HIS C 511 PHE 0.037 0.003 PHE B 114 TYR 0.039 0.002 TYR D 31 ARG 0.010 0.001 ARG D 598 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 527 time to evaluate : 4.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 PHE cc_start: 0.7328 (t80) cc_final: 0.6998 (t80) REVERT: A 192 PHE cc_start: 0.8365 (t80) cc_final: 0.8064 (t80) REVERT: A 246 MET cc_start: 0.6603 (mmt) cc_final: 0.6250 (mmt) REVERT: A 387 ARG cc_start: 0.8480 (mtt180) cc_final: 0.7721 (mtt90) REVERT: A 456 LYS cc_start: 0.9256 (mmmt) cc_final: 0.8726 (mmmm) REVERT: A 567 LYS cc_start: 0.8483 (tppt) cc_final: 0.8260 (tppt) REVERT: A 672 ASP cc_start: 0.8629 (t0) cc_final: 0.8334 (t0) REVERT: A 687 LYS cc_start: 0.9308 (tttt) cc_final: 0.8781 (tptt) REVERT: A 1016 LEU cc_start: 0.9187 (mp) cc_final: 0.8955 (mp) REVERT: A 1109 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9065 (mm) REVERT: A 1121 VAL cc_start: 0.8998 (m) cc_final: 0.8788 (p) REVERT: A 1149 LEU cc_start: 0.9722 (OUTLIER) cc_final: 0.9480 (tt) REVERT: A 1161 ASP cc_start: 0.9106 (p0) cc_final: 0.8772 (p0) REVERT: A 1165 GLU cc_start: 0.9193 (tt0) cc_final: 0.8934 (tt0) REVERT: A 1314 MET cc_start: 0.8717 (mpp) cc_final: 0.7973 (mpp) REVERT: B 65 GLU cc_start: 0.7855 (mp0) cc_final: 0.7615 (mp0) REVERT: B 169 ASP cc_start: 0.6949 (t0) cc_final: 0.6736 (t0) REVERT: B 222 GLU cc_start: 0.8271 (pt0) cc_final: 0.8027 (pp20) REVERT: B 318 MET cc_start: 0.6011 (mmm) cc_final: 0.5518 (tpt) REVERT: B 373 ASP cc_start: 0.8338 (p0) cc_final: 0.7920 (t0) REVERT: B 500 MET cc_start: 0.7513 (ttt) cc_final: 0.7231 (ttt) REVERT: B 520 MET cc_start: 0.7559 (tmm) cc_final: 0.7317 (tmm) REVERT: B 602 GLN cc_start: 0.7499 (tm-30) cc_final: 0.7254 (tm-30) REVERT: B 627 LEU cc_start: 0.9319 (tp) cc_final: 0.9104 (tt) REVERT: B 673 MET cc_start: 0.9067 (tpp) cc_final: 0.8506 (tpp) REVERT: B 786 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7783 (mp) REVERT: B 787 ARG cc_start: 0.8742 (mtt180) cc_final: 0.8257 (mpt-90) REVERT: B 977 MET cc_start: 0.9090 (mmm) cc_final: 0.8511 (mmm) REVERT: B 1147 LYS cc_start: 0.9143 (mttp) cc_final: 0.8431 (mttp) REVERT: B 1161 ASP cc_start: 0.9040 (p0) cc_final: 0.8755 (p0) REVERT: B 1172 GLU cc_start: 0.9112 (tt0) cc_final: 0.8192 (tm-30) REVERT: B 1311 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7879 (mp0) REVERT: C 114 PHE cc_start: 0.7389 (t80) cc_final: 0.7068 (t80) REVERT: C 192 PHE cc_start: 0.8340 (t80) cc_final: 0.8034 (t80) REVERT: C 456 LYS cc_start: 0.9240 (mmmt) cc_final: 0.8697 (mmmm) REVERT: C 567 LYS cc_start: 0.8494 (tppt) cc_final: 0.8273 (tppt) REVERT: C 607 MET cc_start: 0.7580 (tmm) cc_final: 0.7291 (ppp) REVERT: C 672 ASP cc_start: 0.8615 (t0) cc_final: 0.8371 (t0) REVERT: C 687 LYS cc_start: 0.9322 (tttt) cc_final: 0.8810 (tptt) REVERT: C 764 GLU cc_start: 0.6029 (mp0) cc_final: 0.5829 (mt-10) REVERT: C 851 ASN cc_start: 0.9001 (m-40) cc_final: 0.8384 (m110) REVERT: C 968 MET cc_start: 0.8581 (tpt) cc_final: 0.8284 (tpp) REVERT: C 988 ASP cc_start: 0.8881 (m-30) cc_final: 0.8424 (m-30) REVERT: C 1109 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9064 (mm) REVERT: C 1121 VAL cc_start: 0.8994 (m) cc_final: 0.8782 (p) REVERT: C 1149 LEU cc_start: 0.9736 (OUTLIER) cc_final: 0.9497 (tt) REVERT: C 1161 ASP cc_start: 0.9085 (p0) cc_final: 0.8749 (p0) REVERT: C 1165 GLU cc_start: 0.9203 (tt0) cc_final: 0.8937 (tt0) REVERT: C 1208 MET cc_start: 0.9294 (ppp) cc_final: 0.8910 (ppp) REVERT: C 1314 MET cc_start: 0.8699 (mpp) cc_final: 0.7935 (mpp) REVERT: D 169 ASP cc_start: 0.6877 (t0) cc_final: 0.6666 (t0) REVERT: D 222 GLU cc_start: 0.8254 (pt0) cc_final: 0.8011 (pp20) REVERT: D 318 MET cc_start: 0.6120 (mmm) cc_final: 0.5629 (tpt) REVERT: D 500 MET cc_start: 0.6966 (ttm) cc_final: 0.6642 (ttm) REVERT: D 520 MET cc_start: 0.7531 (tmm) cc_final: 0.7306 (tmm) REVERT: D 673 MET cc_start: 0.9127 (tpp) cc_final: 0.8553 (tpp) REVERT: D 786 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7808 (mp) REVERT: D 787 ARG cc_start: 0.8742 (mtt180) cc_final: 0.8262 (mpt-90) REVERT: D 811 LYS cc_start: 0.8351 (mmtp) cc_final: 0.8019 (mmtm) REVERT: D 987 LEU cc_start: 0.9542 (tt) cc_final: 0.9307 (pp) REVERT: D 1015 GLN cc_start: 0.8653 (tp40) cc_final: 0.8420 (tp40) REVERT: D 1147 LYS cc_start: 0.9105 (mttp) cc_final: 0.8593 (mttp) REVERT: D 1149 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9367 (tt) REVERT: D 1161 ASP cc_start: 0.9040 (p0) cc_final: 0.8741 (p0) REVERT: D 1311 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7811 (mp0) outliers start: 188 outliers final: 162 residues processed: 677 average time/residue: 0.4570 time to fit residues: 538.4925 Evaluate side-chains 678 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 507 time to evaluate : 4.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 396 ASN Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 500 MET Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 635 ASN Chi-restraints excluded: chain A residue 651 ASN Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 758 VAL Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 849 CYS Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 917 ASN Chi-restraints excluded: chain A residue 949 SER Chi-restraints excluded: chain A residue 960 GLN Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1109 LEU Chi-restraints excluded: chain A residue 1127 CYS Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1220 GLN Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1270 THR Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 445 HIS Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 519 ASP Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 645 ARG Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 783 THR Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 947 SER Chi-restraints excluded: chain B residue 949 SER Chi-restraints excluded: chain B residue 1042 THR Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1080 PHE Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1101 LEU Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1149 LEU Chi-restraints excluded: chain B residue 1156 LEU Chi-restraints excluded: chain B residue 1227 ASP Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain B residue 1253 ASP Chi-restraints excluded: chain B residue 1270 THR Chi-restraints excluded: chain B residue 1305 LEU Chi-restraints excluded: chain B residue 1311 GLU Chi-restraints excluded: chain B residue 1333 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 408 SER Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 486 THR Chi-restraints excluded: chain C residue 500 MET Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 821 CYS Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 849 CYS Chi-restraints excluded: chain C residue 861 THR Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 917 ASN Chi-restraints excluded: chain C residue 949 SER Chi-restraints excluded: chain C residue 983 ASN Chi-restraints excluded: chain C residue 1007 TYR Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1091 ILE Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1127 CYS Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1149 LEU Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 420 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 551 VAL Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 607 MET Chi-restraints excluded: chain D residue 645 ARG Chi-restraints excluded: chain D residue 654 THR Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 786 LEU Chi-restraints excluded: chain D residue 794 VAL Chi-restraints excluded: chain D residue 947 SER Chi-restraints excluded: chain D residue 949 SER Chi-restraints excluded: chain D residue 1042 THR Chi-restraints excluded: chain D residue 1080 PHE Chi-restraints excluded: chain D residue 1097 ASP Chi-restraints excluded: chain D residue 1101 LEU Chi-restraints excluded: chain D residue 1110 LEU Chi-restraints excluded: chain D residue 1127 CYS Chi-restraints excluded: chain D residue 1144 VAL Chi-restraints excluded: chain D residue 1149 LEU Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1227 ASP Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1253 ASP Chi-restraints excluded: chain D residue 1305 LEU Chi-restraints excluded: chain D residue 1311 GLU Chi-restraints excluded: chain D residue 1333 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 321 optimal weight: 2.9990 chunk 430 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 373 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 405 optimal weight: 1.9990 chunk 169 optimal weight: 0.2980 chunk 416 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 74 optimal weight: 20.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 GLN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 GLN ** A1325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 GLN B 691 GLN ** B 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 964 ASN B1072 GLN ** B1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 GLN ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 983 ASN ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1252 GLN D 691 GLN ** D 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1072 GLN ** D1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.105957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.084473 restraints weight = 116700.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.087546 restraints weight = 62436.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.089640 restraints weight = 40446.051| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 41420 Z= 0.204 Angle : 0.796 15.514 56270 Z= 0.377 Chirality : 0.049 0.340 6514 Planarity : 0.005 0.060 7202 Dihedral : 7.125 77.697 6305 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.35 % Favored : 90.45 % Rotamer: Outliers : 3.20 % Allowed : 26.09 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.12), residues: 5110 helix: 0.96 (0.18), residues: 868 sheet: -1.09 (0.12), residues: 1712 loop : -2.70 (0.12), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 436 HIS 0.006 0.001 HIS D 263 PHE 0.027 0.002 PHE B 114 TYR 0.038 0.002 TYR A 800 ARG 0.004 0.000 ARG C 270 =============================================================================== Job complete usr+sys time: 9966.34 seconds wall clock time: 183 minutes 3.21 seconds (10983.21 seconds total)