Starting phenix.real_space_refine on Wed Jul 24 12:08:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoe_33346/07_2024/7xoe_33346.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoe_33346/07_2024/7xoe_33346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoe_33346/07_2024/7xoe_33346.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoe_33346/07_2024/7xoe_33346.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoe_33346/07_2024/7xoe_33346.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoe_33346/07_2024/7xoe_33346.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.039 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 111 5.16 5 C 16298 2.51 5 N 4202 2.21 5 O 4976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 195": "OD1" <-> "OD2" Residue "A TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A ASP 250": "OD1" <-> "OD2" Residue "A PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 361": "OD1" <-> "OD2" Residue "A TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 386": "OD1" <-> "OD2" Residue "A PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A ASP 424": "OD1" <-> "OD2" Residue "A ASP 425": "OD1" <-> "OD2" Residue "A GLU 551": "OE1" <-> "OE2" Residue "A ASP 565": "OD1" <-> "OD2" Residue "A ASP 568": "OD1" <-> "OD2" Residue "A PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 651": "OE1" <-> "OE2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A ASP 660": "OD1" <-> "OD2" Residue "A TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 699": "OE1" <-> "OE2" Residue "A PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 734": "OD1" <-> "OD2" Residue "A GLU 745": "OE1" <-> "OE2" Residue "A PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 770": "OE1" <-> "OE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 845": "OD1" <-> "OD2" Residue "A PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 915": "OE1" <-> "OE2" Residue "A GLU 985": "OE1" <-> "OE2" Residue "A GLU 987": "OE1" <-> "OE2" Residue "A ASP 991": "OD1" <-> "OD2" Residue "A GLU 1028": "OE1" <-> "OE2" Residue "A ASP 1038": "OD1" <-> "OD2" Residue "A GLU 1069": "OE1" <-> "OE2" Residue "A PHE 1086": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1089": "OE1" <-> "OE2" Residue "A GLU 1108": "OE1" <-> "OE2" Residue "A PHE 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1136": "OD1" <-> "OD2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B ASP 86": "OD1" <-> "OD2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 153": "OE1" <-> "OE2" Residue "B TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 221": "OE1" <-> "OE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B GLU 337": "OE1" <-> "OE2" Residue "B TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 403": "OE1" <-> "OE2" Residue "B TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 425": "OD1" <-> "OD2" Residue "B TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 568": "OD1" <-> "OD2" Residue "B ASP 583": "OD1" <-> "OD2" Residue "B TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 651": "OE1" <-> "OE2" Residue "B PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 734": "OD1" <-> "OD2" Residue "B GLU 777": "OE1" <-> "OE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 805": "OD1" <-> "OD2" Residue "B ASP 864": "OD1" <-> "OD2" Residue "B PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 915": "OE1" <-> "OE2" Residue "B ASP 976": "OD1" <-> "OD2" Residue "B GLU 985": "OE1" <-> "OE2" Residue "B GLU 987": "OE1" <-> "OE2" Residue "B ASP 991": "OD1" <-> "OD2" Residue "B GLU 1028": "OE1" <-> "OE2" Residue "B GLU 1108": "OE1" <-> "OE2" Residue "B PHE 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1124": "OD1" <-> "OD2" Residue "B ASP 1136": "OD1" <-> "OD2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 40": "OD1" <-> "OD2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 136": "OD1" <-> "OD2" Residue "C TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 177": "OE1" <-> "OE2" Residue "C ASP 195": "OD1" <-> "OD2" Residue "C PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 212": "OD1" <-> "OD2" Residue "C TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 402": "OD1" <-> "OD2" Residue "C TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 513": "OE1" <-> "OE2" Residue "C PHE 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 568": "OD1" <-> "OD2" Residue "C GLU 658": "OE1" <-> "OE2" Residue "C ASP 660": "OD1" <-> "OD2" Residue "C ASP 742": "OD1" <-> "OD2" Residue "C GLU 770": "OE1" <-> "OE2" Residue "C ASP 772": "OD1" <-> "OD2" Residue "C GLU 777": "OE1" <-> "OE2" Residue "C ASP 805": "OD1" <-> "OD2" Residue "C ASP 991": "OD1" <-> "OD2" Residue "C GLU 1028": "OE1" <-> "OE2" Residue "C GLU 1069": "OE1" <-> "OE2" Residue "C PHE 1086": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 25587 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8137 Classifications: {'peptide': 1053} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 50, 'TRANS': 1002} Chain breaks: 6 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 70 Chain: "B" Number of atoms: 8420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 8420 Classifications: {'peptide': 1079} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 52, 'TRANS': 1026} Chain breaks: 5 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 8400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1078, 8400 Classifications: {'peptide': 1078} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 52, 'TRANS': 1025} Chain breaks: 5 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 14.20, per 1000 atoms: 0.55 Number of scatterers: 25587 At special positions: 0 Unit cell: (143, 160.6, 187, 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 111 16.00 O 4976 8.00 N 4202 7.00 C 16298 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 163 " distance=1.98 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.02 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.04 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.04 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.00 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.09 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.02 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.02 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.04 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 163 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.04 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.07 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.02 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.01 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.02 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.04 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 163 " distance=1.96 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.04 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.05 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.02 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.05 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.04 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.06 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.04 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.04 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " 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 Atom "HETATM25557 O5 NAG C1304 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1301 " - " ASN A 162 " " NAG A1302 " - " ASN A 231 " " NAG A1303 " - " ASN A 613 " " NAG A1304 " - " ASN A 279 " " NAG A1305 " - " ASN A 654 " " NAG A1306 " - " ASN A 706 " " NAG A1307 " - " ASN A1071 " " NAG A1308 " - " ASN A 61 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 613 " " NAG B1303 " - " ASN B 279 " " NAG B1304 " - " ASN B 328 " " NAG B1305 " - " ASN B 654 " " NAG B1306 " - " ASN B 706 " " NAG B1307 " - " ASN B1071 " " NAG C1301 " - " ASN C 613 " " NAG C1302 " - " ASN C 714 " " NAG C1304 " - " ASN C 279 " " NAG C1305 " - " ASN C 706 " " NAG C1306 " - " ASN C1071 " Time building additional restraints: 10.94 Conformation dependent library (CDL) restraints added in 4.6 seconds 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6014 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 46 sheets defined 23.9% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.45 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 400 through 408 Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 735 through 740 Processing helix chain 'A' and resid 743 through 753 removed outlier: 4.118A pdb=" N TYR A 753 " --> pdb=" O LEU A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 780 removed outlier: 3.505A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 847 through 852 Processing helix chain 'A' and resid 863 through 879 Processing helix chain 'A' and resid 894 through 907 Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.772A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 Processing helix chain 'A' and resid 942 through 963 removed outlier: 3.725A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 979 Processing helix chain 'A' and resid 982 through 1030 Processing helix chain 'A' and resid 1113 through 1117 removed outlier: 3.606A pdb=" N THR A1117 " --> pdb=" O THR A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1143 Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 364 through 369 Processing helix chain 'B' and resid 380 through 386 Processing helix chain 'B' and resid 402 through 407 Processing helix chain 'B' and resid 734 through 741 Processing helix chain 'B' and resid 743 through 753 removed outlier: 3.938A pdb=" N TYR B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 780 removed outlier: 3.577A pdb=" N THR B 775 " --> pdb=" O GLN B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 863 through 876 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.542A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 907 Processing helix chain 'B' and resid 910 through 916 Processing helix chain 'B' and resid 916 through 937 Processing helix chain 'B' and resid 943 through 963 removed outlier: 3.740A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 979 Processing helix chain 'B' and resid 982 through 1030 removed outlier: 3.511A pdb=" N VAL B 988 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1113 through 1115 No H-bonds generated for 'chain 'B' and resid 1113 through 1115' Processing helix chain 'B' and resid 1138 through 1143 Processing helix chain 'C' and resid 193 through 197 Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 340 Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 362 through 368 Processing helix chain 'C' and resid 380 through 387 removed outlier: 3.590A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 435 through 440 removed outlier: 3.739A pdb=" N ASP C 439 " --> pdb=" O SER C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 754 removed outlier: 3.530A pdb=" N SER C 747 " --> pdb=" O SER C 743 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU C 749 " --> pdb=" O GLU C 745 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR C 753 " --> pdb=" O LEU C 749 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY C 754 " --> pdb=" O LEU C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 780 Processing helix chain 'C' and resid 799 through 803 Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 846 through 852 Processing helix chain 'C' and resid 863 through 879 Processing helix chain 'C' and resid 894 through 907 Processing helix chain 'C' and resid 910 through 916 Processing helix chain 'C' and resid 916 through 937 removed outlier: 3.622A pdb=" N ILE C 920 " --> pdb=" O ASN C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 963 removed outlier: 3.764A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 979 Processing helix chain 'C' and resid 982 through 1029 removed outlier: 3.525A pdb=" N GLU C1014 " --> pdb=" O ILE C1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 1113 through 1115 No H-bonds generated for 'chain 'C' and resid 1113 through 1115' Processing helix chain 'C' and resid 1138 through 1143 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 7.722A pdb=" N THR A 271 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASP A 287 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A 273 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA A 285 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS A 275 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 93 Processing sheet with id=AA5, first strand: chain 'A' and resid 102 through 104 Processing sheet with id=AA6, first strand: chain 'A' and resid 102 through 104 removed outlier: 4.674A pdb=" N PHE A 131 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N THR A 112 " --> pdb=" O CYS A 129 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N CYS A 129 " --> pdb=" O THR A 112 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 190 through 191 Processing sheet with id=AA8, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.262A pdb=" N GLU A 306 " --> pdb=" O GLY A 598 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY A 598 " --> pdb=" O GLU A 306 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AB1, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.927A pdb=" N LEU A 510 " --> pdb=" O CYS A 429 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N CYS A 429 " --> pdb=" O LEU A 510 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 449 through 450 Processing sheet with id=AB3, first strand: chain 'A' and resid 661 through 664 removed outlier: 6.676A pdb=" N ILE A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 700 through 701 removed outlier: 7.487A pdb=" N ASN A 700 " --> pdb=" O LYS B 787 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 715 through 725 removed outlier: 3.855A pdb=" N ALA A1053 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET A1047 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 732 through 733 removed outlier: 3.725A pdb=" N SER A 732 " --> pdb=" O THR A 856 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 785 through 787 removed outlier: 6.330A pdb=" N ILE A 785 " --> pdb=" O ASN C 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1073 through 1074 Processing sheet with id=AB9, first strand: chain 'A' and resid 1077 through 1079 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 6.555A pdb=" N LEU B 273 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA B 285 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS B 275 " --> pdb=" O THR B 283 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 124 through 129 Processing sheet with id=AC4, first strand: chain 'B' and resid 308 through 315 removed outlier: 4.958A pdb=" N ASN B 314 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLY B 590 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL B 607 " --> pdb=" O ILE B 648 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 351 through 355 removed outlier: 3.677A pdb=" N VAL B 392 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL B 430 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS B 375 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC7, first strand: chain 'B' and resid 536 through 540 removed outlier: 3.708A pdb=" N GLY B 545 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 661 through 664 removed outlier: 6.637A pdb=" N ILE B 667 " --> pdb=" O ILE B 663 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 708 through 709 removed outlier: 3.562A pdb=" N THR B1073 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR B1102 " --> pdb=" O VAL B1091 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 715 through 719 Processing sheet with id=AD2, first strand: chain 'B' and resid 715 through 719 removed outlier: 3.646A pdb=" N MET B1047 " --> pdb=" O VAL B1062 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 731 through 732 Processing sheet with id=AD4, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.141A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AD6, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.062A pdb=" N VAL C 36 " --> pdb=" O LEU C 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.685A pdb=" N GLN C 268 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N THR C 271 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ASP C 287 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU C 273 " --> pdb=" O ALA C 285 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA C 285 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LYS C 275 " --> pdb=" O THR C 283 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 82 through 83 Processing sheet with id=AD9, first strand: chain 'C' and resid 154 through 155 removed outlier: 7.370A pdb=" N LEU C 139 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ARG C 243 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL C 141 " --> pdb=" O ARG C 243 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 308 through 315 removed outlier: 5.579A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASN C 314 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLY C 590 " --> pdb=" O ASN C 314 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 353 through 355 Processing sheet with id=AE3, first strand: chain 'C' and resid 358 through 359 removed outlier: 7.569A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AE5, first strand: chain 'C' and resid 536 through 540 Processing sheet with id=AE6, first strand: chain 'C' and resid 661 through 664 removed outlier: 6.910A pdb=" N ILE C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C 692 " --> pdb=" O CYS C 668 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 709 through 712 removed outlier: 3.657A pdb=" N THR C1102 " --> pdb=" O VAL C1091 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 715 through 725 removed outlier: 3.695A pdb=" N VAL C1065 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET C1047 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 731 through 733 Processing sheet with id=AF1, first strand: chain 'C' and resid 1078 through 1079 881 hydrogen bonds defined for protein. 2343 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: 10.57 Time building geometry restraints manager: 11.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 7990 1.34 - 1.48: 5503 1.48 - 1.62: 12522 1.62 - 1.76: 0 1.76 - 1.90: 140 Bond restraints: 26155 Sorted by residual: bond pdb=" N LYS A 525 " pdb=" CA LYS A 525 " ideal model delta sigma weight residual 1.458 1.491 -0.033 6.30e-03 2.52e+04 2.69e+01 bond pdb=" N THR A 19 " pdb=" CA THR A 19 " ideal model delta sigma weight residual 1.457 1.489 -0.032 6.40e-03 2.44e+04 2.57e+01 bond pdb=" N VAL C1065 " pdb=" CA VAL C1065 " ideal model delta sigma weight residual 1.454 1.493 -0.039 7.70e-03 1.69e+04 2.54e+01 bond pdb=" N VAL B1065 " pdb=" CA VAL B1065 " ideal model delta sigma weight residual 1.454 1.492 -0.038 7.70e-03 1.69e+04 2.42e+01 bond pdb=" N GLY A 697 " pdb=" CA GLY A 697 " ideal model delta sigma weight residual 1.445 1.482 -0.037 8.30e-03 1.45e+04 2.01e+01 ... (remaining 26150 not shown) Histogram of bond angle deviations from ideal: 85.46 - 95.27: 2 95.27 - 105.08: 548 105.08 - 114.89: 15678 114.89 - 124.69: 18762 124.69 - 134.50: 616 Bond angle restraints: 35606 Sorted by residual: angle pdb=" C CYS C 129 " pdb=" CA CYS C 129 " pdb=" CB CYS C 129 " ideal model delta sigma weight residual 111.11 85.46 25.65 2.10e+00 2.27e-01 1.49e+02 angle pdb=" C CYS A 129 " pdb=" CA CYS A 129 " pdb=" CB CYS A 129 " ideal model delta sigma weight residual 109.66 93.30 16.36 1.94e+00 2.66e-01 7.11e+01 angle pdb=" CA ASN A 61 " pdb=" CB ASN A 61 " pdb=" CG ASN A 61 " ideal model delta sigma weight residual 112.60 120.65 -8.05 1.00e+00 1.00e+00 6.48e+01 angle pdb=" N MET C 150 " pdb=" CA MET C 150 " pdb=" C MET C 150 " ideal model delta sigma weight residual 108.38 119.12 -10.74 1.35e+00 5.49e-01 6.32e+01 angle pdb=" CA PHE A 183 " pdb=" C PHE A 183 " pdb=" O PHE A 183 " ideal model delta sigma weight residual 120.36 113.25 7.11 1.07e+00 8.73e-01 4.41e+01 ... (remaining 35601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.82: 14479 25.82 - 51.65: 1198 51.65 - 77.47: 369 77.47 - 103.30: 75 103.30 - 129.12: 23 Dihedral angle restraints: 16144 sinusoidal: 6800 harmonic: 9344 Sorted by residual: dihedral pdb=" C CYS C 129 " pdb=" N CYS C 129 " pdb=" CA CYS C 129 " pdb=" CB CYS C 129 " ideal model delta harmonic sigma weight residual -122.60 -94.52 -28.08 0 2.50e+00 1.60e-01 1.26e+02 dihedral pdb=" CB CYS A 659 " pdb=" SG CYS A 659 " pdb=" SG CYS A 668 " pdb=" CB CYS A 668 " ideal model delta sinusoidal sigma weight residual 93.00 12.05 80.95 1 1.00e+01 1.00e-02 8.09e+01 dihedral pdb=" CB CYS A 735 " pdb=" SG CYS A 735 " pdb=" SG CYS A 757 " pdb=" CB CYS A 757 " ideal model delta sinusoidal sigma weight residual 93.00 162.75 -69.75 1 1.00e+01 1.00e-02 6.28e+01 ... (remaining 16141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.242: 4129 0.242 - 0.484: 44 0.484 - 0.726: 6 0.726 - 0.967: 0 0.967 - 1.209: 3 Chirality restraints: 4182 Sorted by residual: chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 613 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -3.61 1.21 2.00e-01 2.50e+01 3.66e+01 chirality pdb=" C1 NAG C1306 " pdb=" ND2 ASN C1071 " pdb=" C2 NAG C1306 " pdb=" O5 NAG C1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.35 -1.05 2.00e-01 2.50e+01 2.78e+01 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 162 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.37 -1.03 2.00e-01 2.50e+01 2.64e+01 ... (remaining 4179 not shown) Planarity restraints: 4570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1302 " -0.332 2.00e-02 2.50e+03 2.87e-01 1.03e+03 pdb=" C7 NAG B1302 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG B1302 " -0.034 2.00e-02 2.50e+03 pdb=" N2 NAG B1302 " 0.502 2.00e-02 2.50e+03 pdb=" O7 NAG B1302 " -0.210 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1308 " 0.282 2.00e-02 2.50e+03 2.41e-01 7.28e+02 pdb=" C7 NAG A1308 " -0.068 2.00e-02 2.50e+03 pdb=" C8 NAG A1308 " 0.167 2.00e-02 2.50e+03 pdb=" N2 NAG A1308 " -0.421 2.00e-02 2.50e+03 pdb=" O7 NAG A1308 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1303 " 0.224 2.00e-02 2.50e+03 1.87e-01 4.37e+02 pdb=" C7 NAG B1303 " -0.060 2.00e-02 2.50e+03 pdb=" C8 NAG B1303 " 0.159 2.00e-02 2.50e+03 pdb=" N2 NAG B1303 " -0.309 2.00e-02 2.50e+03 pdb=" O7 NAG B1303 " -0.013 2.00e-02 2.50e+03 ... (remaining 4567 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 22 2.26 - 2.92: 11638 2.92 - 3.58: 35765 3.58 - 4.24: 58918 4.24 - 4.90: 93625 Nonbonded interactions: 199968 Sorted by model distance: nonbonded pdb=" OG1 THR B 615 " pdb=" C1 NAG B1302 " model vdw 1.596 3.470 nonbonded pdb=" OD1 ASP B 212 " pdb=" OH TYR B 263 " model vdw 1.990 2.440 nonbonded pdb=" O THR B 390 " pdb=" O GLU B 513 " model vdw 2.027 2.432 nonbonded pdb=" O ASP C 291 " pdb=" OG SER C 294 " model vdw 2.074 2.440 nonbonded pdb=" OD1 ASP B 291 " pdb=" OG SER B 294 " model vdw 2.085 2.440 ... (remaining 199963 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 16 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 101 or (resid 102 and (name N or n \ ame CA or name C or name O or name CB )) or resid 103 through 174 or resid 183 t \ hrough 210 or (resid 211 and (name N or name CA or name C or name O or name CB ) \ ) or resid 212 through 615 or (resid 616 and (name N or name CA or name C or nam \ e O or name CB )) or resid 617 through 618 or resid 637 through 1143 or resid 13 \ 01 through 1306)) selection = (chain 'B' and (resid 16 through 81 or (resid 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 through 99 or (resid 100 and (name N or na \ me CA or name C or name O or name CB )) or resid 101 or (resid 102 and (name N o \ r name CA or name C or name O or name CB )) or resid 103 through 123 or (resid 1 \ 24 and (name N or name CA or name C or name O or name CB )) or resid 125 through \ 127 or (resid 128 and (name N or name CA or name C or name O or name CB )) or r \ esid 129 through 130 or (resid 131 through 132 and (name N or name CA or name C \ or name O or name CB )) or resid 133 through 140 or (resid 141 through 147 and ( \ name N or name CA or name C or name O or name CB )) or resid 148 or (resid 149 t \ hrough 151 and (name N or name CA or name C or name O or name CB )) or resid 152 \ or (resid 153 and (name N or name CA or name C or name O or name CB )) or resid \ 154 or (resid 155 and (name N or name CA or name C or name O or name CB )) or r \ esid 156 through 210 or (resid 211 and (name N or name CA or name C or name O or \ name CB )) or resid 212 through 314 or (resid 315 through 316 and (name N or na \ me CA or name C or name O or name CB )) or resid 317 or (resid 318 and (name N o \ r name CA or name C or name O or name CB )) or resid 319 through 464 or resid 48 \ 9 through 524 or (resid 525 through 526 and (name N or name CA or name C or name \ O or name CB )) or resid 527 through 618 or resid 634 or resid 638 through 1143 \ or resid 1301 through 1306)) selection = (chain 'C' and (resid 16 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 81 or (resid 82 and (name N or nam \ e CA or name C or name O or name CB )) or resid 83 through 99 or (resid 100 and \ (name N or name CA or name C or name O or name CB )) or resid 101 through 123 or \ (resid 124 and (name N or name CA or name C or name O or name CB )) or resid 12 \ 5 through 127 or (resid 128 and (name N or name CA or name C or name O or name C \ B )) or resid 129 through 130 or (resid 131 through 132 and (name N or name CA o \ r name C or name O or name CB )) or resid 133 through 140 or (resid 141 through \ 147 and (name N or name CA or name C or name O or name CB )) or resid 148 or (re \ sid 149 through 151 and (name N or name CA or name C or name O or name CB )) or \ resid 152 or (resid 153 and (name N or name CA or name C or name O or name CB )) \ or resid 154 or (resid 155 and (name N or name CA or name C or name O or name C \ B )) or resid 156 through 174 or resid 183 through 314 or (resid 315 through 316 \ and (name N or name CA or name C or name O or name CB )) or resid 317 or (resid \ 318 and (name N or name CA or name C or name O or name CB )) or resid 319 throu \ gh 464 or resid 489 through 524 or (resid 525 through 526 and (name N or name CA \ or name C or name O or name CB )) or resid 527 through 615 or (resid 616 and (n \ ame N or name CA or name C or name O or name CB )) or resid 617 through 618 or r \ esid 637 through 1143 or resid 1301 through 1306)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 8.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 1.060 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 71.540 Find NCS groups from input model: 3.240 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 : 0.011 0.089 26155 Z= 0.741 Angle : 1.495 25.645 35606 Z= 1.039 Chirality : 0.097 1.209 4182 Planarity : 0.009 0.287 4550 Dihedral : 21.159 129.123 10019 Min Nonbonded Distance : 1.596 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 1.10 % Allowed : 13.62 % Favored : 85.28 % Rotamer: Outliers : 15.63 % Allowed : 11.76 % Favored : 72.61 % Cbeta Deviations : 0.20 % 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: -4.45 (0.12), residues: 3172 helix: -2.32 (0.15), residues: 663 sheet: -1.94 (0.22), residues: 521 loop : -3.70 (0.11), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 433 HIS 0.009 0.002 HIS C 242 PHE 0.044 0.003 PHE C 90 TYR 0.060 0.003 TYR A 450 ARG 0.009 0.001 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 433 poor density : 270 time to evaluate : 2.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASN cc_start: 0.1092 (OUTLIER) cc_final: 0.0667 (m-40) REVERT: A 223 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.7061 (tp) REVERT: A 399 ILE cc_start: 0.4624 (OUTLIER) cc_final: 0.4093 (pt) REVERT: A 584 ILE cc_start: 0.6996 (OUTLIER) cc_final: 0.6420 (pt) REVERT: A 655 ASN cc_start: 0.8612 (OUTLIER) cc_final: 0.8343 (p0) REVERT: A 657 TYR cc_start: 0.7484 (OUTLIER) cc_final: 0.6736 (m-80) REVERT: A 660 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.7456 (p0) REVERT: A 976 ASP cc_start: 0.8815 (t70) cc_final: 0.8423 (t0) REVERT: A 1033 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8699 (tt0) REVERT: A 1142 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7758 (mm) REVERT: B 86 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7844 (p0) REVERT: B 92 SER cc_start: 0.6819 (OUTLIER) cc_final: 0.6386 (p) REVERT: B 187 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7550 (mmm160) REVERT: B 189 PHE cc_start: 0.7738 (m-80) cc_final: 0.7439 (m-80) REVERT: B 202 SER cc_start: 0.6362 (OUTLIER) cc_final: 0.5062 (p) REVERT: B 690 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8850 (pp) REVERT: B 777 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7946 (mp0) REVERT: B 807 SER cc_start: 0.9048 (OUTLIER) cc_final: 0.8824 (p) REVERT: B 820 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.8399 (m-80) REVERT: B 850 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.7155 (pt0) REVERT: B 944 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8226 (mttp) REVERT: B 959 LEU cc_start: 0.9357 (tp) cc_final: 0.9068 (tp) REVERT: B 980 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7848 (ptp90) REVERT: C 164 THR cc_start: 0.7887 (OUTLIER) cc_final: 0.7507 (p) REVERT: C 199 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8457 (mptt) REVERT: C 502 TYR cc_start: 0.8223 (m-80) cc_final: 0.7941 (t80) REVERT: C 525 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8653 (mmtm) REVERT: C 743 SER cc_start: 0.8068 (OUTLIER) cc_final: 0.7696 (t) REVERT: C 988 VAL cc_start: 0.9488 (OUTLIER) cc_final: 0.9111 (p) REVERT: C 997 ARG cc_start: 0.9459 (OUTLIER) cc_final: 0.9258 (mtt180) outliers start: 433 outliers final: 53 residues processed: 626 average time/residue: 0.3884 time to fit residues: 375.4901 Evaluate side-chains 206 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 127 time to evaluate : 2.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 614 CYS Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 657 TYR Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 668 CYS Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 893 ILE Chi-restraints excluded: chain A residue 983 LYS Chi-restraints excluded: chain A residue 1033 GLN Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 187 ARG Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 618 PRO Chi-restraints excluded: chain B residue 652 HIS Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 772 ASP Chi-restraints excluded: chain B residue 777 GLU Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 827 ASP Chi-restraints excluded: chain B residue 850 GLN Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 884 THR Chi-restraints excluded: chain B residue 944 LYS Chi-restraints excluded: chain B residue 980 ARG Chi-restraints excluded: chain B residue 1081 ASP Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 525 LYS Chi-restraints excluded: chain C residue 647 LEU Chi-restraints excluded: chain C residue 657 TYR Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 743 SER Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 916 ASN Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 985 GLU Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 997 ARG Chi-restraints excluded: chain C residue 1014 GLU Chi-restraints excluded: chain C residue 1081 ASP Chi-restraints excluded: chain C residue 1129 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 269 optimal weight: 3.9990 chunk 241 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 163 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 250 optimal weight: 8.9990 chunk 96 optimal weight: 0.6980 chunk 152 optimal weight: 8.9990 chunk 186 optimal weight: 0.5980 chunk 289 optimal weight: 6.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 85 ASN A 185 ASN ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 357 ASN A 434 ASN A 457 ASN A 490 GLN A 781 GLN A 869 GLN A 922 ASN A 950 ASN A 952 ASN A 962 GLN A 989 GLN ** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1110 GLN B 97 ASN B 236 GLN B 414 ASN B 478 ASN B 761 ASN B 801 GLN B 850 GLN B 923 GLN B 962 GLN ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1095 ASN B1110 GLN ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 119 ASN C 145 ASN C 162 ASN ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN C 391 ASN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 553 ASN C 922 ASN C 950 ASN C 951 GLN C1085 HIS Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 26155 Z= 0.308 Angle : 0.850 14.801 35606 Z= 0.426 Chirality : 0.050 0.487 4182 Planarity : 0.005 0.068 4550 Dihedral : 13.632 105.031 4542 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.24 % Favored : 90.61 % Rotamer: Outliers : 5.74 % Allowed : 19.74 % Favored : 74.52 % 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: -2.99 (0.13), residues: 3172 helix: 0.27 (0.18), residues: 667 sheet: -1.77 (0.20), residues: 590 loop : -3.08 (0.12), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 149 HIS 0.005 0.001 HIS A1085 PHE 0.038 0.002 PHE C 339 TYR 0.022 0.002 TYR A 450 ARG 0.009 0.001 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 133 time to evaluate : 2.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.9193 (t) cc_final: 0.8967 (m) REVERT: A 197 TYR cc_start: 0.8933 (OUTLIER) cc_final: 0.8471 (p90) REVERT: A 209 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8657 (tt) REVERT: A 284 ASP cc_start: 0.9210 (t0) cc_final: 0.8983 (t0) REVERT: A 286 VAL cc_start: 0.8950 (OUTLIER) cc_final: 0.8526 (m) REVERT: A 655 ASN cc_start: 0.8673 (OUTLIER) cc_final: 0.8271 (p0) REVERT: A 660 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.7767 (p0) REVERT: A 976 ASP cc_start: 0.8674 (t70) cc_final: 0.8333 (t0) REVERT: A 977 ILE cc_start: 0.8780 (mm) cc_final: 0.8134 (mm) REVERT: A 1142 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7728 (mt) REVERT: B 61 ASN cc_start: 0.5212 (OUTLIER) cc_final: 0.4989 (t0) REVERT: B 92 SER cc_start: 0.6429 (OUTLIER) cc_final: 0.6052 (t) REVERT: B 385 ASN cc_start: 0.7793 (t0) cc_final: 0.7186 (m-40) REVERT: B 690 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8651 (pp) REVERT: B 846 LEU cc_start: 0.8451 (tt) cc_final: 0.7571 (mm) REVERT: B 959 LEU cc_start: 0.9590 (tp) cc_final: 0.9307 (tp) REVERT: C 199 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8399 (mptt) REVERT: C 502 TYR cc_start: 0.8359 (m-80) cc_final: 0.7922 (t80) outliers start: 159 outliers final: 79 residues processed: 275 average time/residue: 0.3469 time to fit residues: 154.9216 Evaluate side-chains 191 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 102 time to evaluate : 2.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 614 CYS Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 657 TYR Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain B residue 61 ASN Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 827 ASP Chi-restraints excluded: chain B residue 853 ASN Chi-restraints excluded: chain B residue 867 ILE Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 883 TRP Chi-restraints excluded: chain B residue 906 ILE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 949 VAL Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1068 GLN Chi-restraints excluded: chain B residue 1095 ASN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 657 TYR Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 783 LYS Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 964 SER Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 1018 SER Chi-restraints excluded: chain C residue 1047 MET Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1113 THR Chi-restraints excluded: chain C residue 1129 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 160 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 197 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 290 optimal weight: 1.9990 chunk 313 optimal weight: 2.9990 chunk 258 optimal weight: 10.0000 chunk 287 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 232 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 748 ASN ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 761 ASN ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1033 GLN B 30 ASN B 85 ASN ** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 GLN B 952 ASN B 954 GLN ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1095 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 HIS ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 GLN C 478 ASN ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 26155 Z= 0.318 Angle : 0.746 11.202 35606 Z= 0.377 Chirality : 0.046 0.257 4182 Planarity : 0.005 0.069 4550 Dihedral : 10.718 97.419 4444 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.87 % Favored : 90.04 % Rotamer: Outliers : 5.99 % Allowed : 19.88 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.14), residues: 3172 helix: 1.23 (0.20), residues: 666 sheet: -1.56 (0.20), residues: 570 loop : -2.83 (0.12), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 149 HIS 0.006 0.001 HIS A1061 PHE 0.040 0.002 PHE B 339 TYR 0.017 0.002 TYR B1064 ARG 0.014 0.001 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 105 time to evaluate : 2.836 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: A 54 LEU cc_start: 0.9174 (mt) cc_final: 0.8600 (pp) REVERT: A 77 PHE cc_start: 0.7166 (m-10) cc_final: 0.5837 (m-10) REVERT: A 88 VAL cc_start: 0.9221 (m) cc_final: 0.8951 (t) REVERT: A 197 TYR cc_start: 0.8973 (OUTLIER) cc_final: 0.8531 (p90) REVERT: A 655 ASN cc_start: 0.8639 (OUTLIER) cc_final: 0.7963 (p0) REVERT: A 932 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8749 (tm-30) REVERT: A 976 ASP cc_start: 0.8617 (t70) cc_final: 0.8274 (t0) REVERT: B 174 MET cc_start: 0.7416 (mtt) cc_final: 0.7018 (mtt) REVERT: B 385 ASN cc_start: 0.7901 (t0) cc_final: 0.7232 (m-40) REVERT: B 813 SER cc_start: 0.8583 (OUTLIER) cc_final: 0.8264 (m) REVERT: C 199 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8277 (mppt) REVERT: C 268 GLN cc_start: 0.9279 (OUTLIER) cc_final: 0.9073 (pt0) REVERT: C 339 PHE cc_start: 0.7697 (OUTLIER) cc_final: 0.6932 (p90) REVERT: C 502 TYR cc_start: 0.8469 (m-80) cc_final: 0.7994 (t80) REVERT: C 770 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7881 (tm-30) outliers start: 166 outliers final: 101 residues processed: 254 average time/residue: 0.3275 time to fit residues: 139.7208 Evaluate side-chains 201 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 92 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 657 TYR Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 932 GLN Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 813 SER Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 827 ASP Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 870 TYR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 883 TRP Chi-restraints excluded: chain B residue 906 ILE Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1025 LYS Chi-restraints excluded: chain B residue 1068 GLN Chi-restraints excluded: chain B residue 1111 ILE Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 657 TYR Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 770 GLU Chi-restraints excluded: chain C residue 783 LYS Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 906 ILE Chi-restraints excluded: chain C residue 910 GLN Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 964 SER Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1018 SER Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1081 ASP Chi-restraints excluded: chain C residue 1113 THR Chi-restraints excluded: chain C residue 1116 ASN Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1125 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 286 optimal weight: 0.6980 chunk 218 optimal weight: 0.7980 chunk 150 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 chunk 194 optimal weight: 2.9990 chunk 291 optimal weight: 0.8980 chunk 308 optimal weight: 3.9990 chunk 152 optimal weight: 8.9990 chunk 276 optimal weight: 0.0470 chunk 83 optimal weight: 0.5980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1007 GLN A1116 ASN ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN B 700 ASN ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 GLN C 784 GLN C1080 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26155 Z= 0.174 Angle : 0.647 13.877 35606 Z= 0.323 Chirality : 0.044 0.248 4182 Planarity : 0.004 0.050 4550 Dihedral : 9.537 92.561 4425 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.38 % Favored : 92.53 % Rotamer: Outliers : 4.51 % Allowed : 21.51 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.14), residues: 3172 helix: 1.70 (0.20), residues: 685 sheet: -1.22 (0.21), residues: 539 loop : -2.67 (0.12), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 433 HIS 0.004 0.001 HIS C 204 PHE 0.026 0.001 PHE C 339 TYR 0.015 0.001 TYR A 450 ARG 0.010 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 109 time to evaluate : 2.756 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: A 88 VAL cc_start: 0.9214 (m) cc_final: 0.8924 (t) REVERT: A 187 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7575 (mmp-170) REVERT: A 197 TYR cc_start: 0.8947 (OUTLIER) cc_final: 0.8526 (p90) REVERT: A 286 VAL cc_start: 0.8571 (OUTLIER) cc_final: 0.8304 (m) REVERT: A 655 ASN cc_start: 0.8660 (OUTLIER) cc_final: 0.7997 (p0) REVERT: A 976 ASP cc_start: 0.8540 (t70) cc_final: 0.8187 (t0) REVERT: B 174 MET cc_start: 0.7360 (mtt) cc_final: 0.6983 (mtt) REVERT: B 385 ASN cc_start: 0.7848 (t0) cc_final: 0.7212 (m-40) REVERT: B 1047 MET cc_start: 0.7759 (ptp) cc_final: 0.7167 (mtm) REVERT: C 150 MET cc_start: 0.8174 (pmm) cc_final: 0.7451 (pmm) REVERT: C 175 ASP cc_start: 0.3684 (OUTLIER) cc_final: 0.3393 (t70) REVERT: C 199 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8276 (mppt) REVERT: C 268 GLN cc_start: 0.9273 (OUTLIER) cc_final: 0.9060 (pt0) REVERT: C 339 PHE cc_start: 0.7640 (OUTLIER) cc_final: 0.6856 (p90) REVERT: C 481 LYS cc_start: 0.4446 (OUTLIER) cc_final: 0.4087 (tppt) outliers start: 125 outliers final: 72 residues processed: 224 average time/residue: 0.3340 time to fit residues: 123.1866 Evaluate side-chains 177 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 96 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 657 TYR Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 668 CYS Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1131 ASN Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 827 ASP Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 870 TYR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 883 TRP Chi-restraints excluded: chain B residue 906 ILE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 1068 GLN Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 481 LYS Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 783 LYS Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1081 ASP Chi-restraints excluded: chain C residue 1113 THR Chi-restraints excluded: chain C residue 1116 ASN Chi-restraints excluded: chain C residue 1125 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 256 optimal weight: 20.0000 chunk 175 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 229 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 263 optimal weight: 6.9990 chunk 213 optimal weight: 0.0020 chunk 0 optimal weight: 20.0000 chunk 157 optimal weight: 3.9990 chunk 276 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 2.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 GLN A1110 GLN B 236 GLN B 391 ASN B 414 ASN ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1105 ASN B1139 GLN ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 26155 Z= 0.371 Angle : 0.724 10.242 35606 Z= 0.363 Chirality : 0.045 0.250 4182 Planarity : 0.004 0.056 4550 Dihedral : 9.282 88.036 4415 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.09 % Favored : 89.82 % Rotamer: Outliers : 6.17 % Allowed : 20.43 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.14), residues: 3172 helix: 1.44 (0.20), residues: 679 sheet: -1.33 (0.20), residues: 598 loop : -2.64 (0.13), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 64 HIS 0.007 0.001 HIS C 204 PHE 0.025 0.002 PHE C 165 TYR 0.017 0.002 TYR B 266 ARG 0.012 0.001 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 81 time to evaluate : 2.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 VAL cc_start: 0.9254 (m) cc_final: 0.8935 (t) REVERT: A 197 TYR cc_start: 0.8965 (OUTLIER) cc_final: 0.8545 (p90) REVERT: A 655 ASN cc_start: 0.8569 (OUTLIER) cc_final: 0.8009 (p0) REVERT: A 976 ASP cc_start: 0.8605 (t70) cc_final: 0.8358 (t0) REVERT: C 54 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8438 (tm) REVERT: C 175 ASP cc_start: 0.3958 (OUTLIER) cc_final: 0.3550 (t70) REVERT: C 199 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8222 (mppt) REVERT: C 339 PHE cc_start: 0.7647 (OUTLIER) cc_final: 0.6831 (p90) REVERT: C 481 LYS cc_start: 0.4845 (OUTLIER) cc_final: 0.4416 (tppt) outliers start: 171 outliers final: 116 residues processed: 243 average time/residue: 0.3264 time to fit residues: 131.9556 Evaluate side-chains 194 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 71 time to evaluate : 2.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 655 ASN Chi-restraints excluded: chain A residue 657 TYR Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 668 CYS Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1131 ASN Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 827 ASP Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 853 ASN Chi-restraints excluded: chain B residue 867 ILE Chi-restraints excluded: chain B residue 870 TYR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 883 TRP Chi-restraints excluded: chain B residue 906 ILE Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 944 LYS Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1025 LYS Chi-restraints excluded: chain B residue 1040 CYS Chi-restraints excluded: chain B residue 1068 GLN Chi-restraints excluded: chain B residue 1111 ILE Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 481 LYS Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain C residue 783 LYS Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 906 ILE Chi-restraints excluded: chain C residue 910 GLN Chi-restraints excluded: chain C residue 964 SER Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1081 ASP Chi-restraints excluded: chain C residue 1116 ASN Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1125 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 103 optimal weight: 6.9990 chunk 277 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 308 optimal weight: 2.9990 chunk 256 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 821 ASN B 892 GLN ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN C 411 GLN C 801 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.5682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 26155 Z= 0.363 Angle : 0.726 10.603 35606 Z= 0.366 Chirality : 0.046 0.264 4182 Planarity : 0.005 0.065 4550 Dihedral : 9.089 82.361 4412 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.98 % Favored : 90.92 % Rotamer: Outliers : 5.77 % Allowed : 21.47 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.14), residues: 3172 helix: 1.21 (0.20), residues: 686 sheet: -1.02 (0.22), residues: 557 loop : -2.66 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 64 HIS 0.008 0.001 HIS A1045 PHE 0.035 0.002 PHE C 165 TYR 0.020 0.002 TYR A 28 ARG 0.013 0.001 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 82 time to evaluate : 2.623 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: A 17 ASN cc_start: 0.0072 (OUTLIER) cc_final: -0.0405 (m-40) REVERT: A 197 TYR cc_start: 0.8954 (OUTLIER) cc_final: 0.8643 (p90) REVERT: A 430 VAL cc_start: 0.5886 (OUTLIER) cc_final: 0.5519 (p) REVERT: A 1142 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7576 (mm) REVERT: B 174 MET cc_start: 0.7364 (mtt) cc_final: 0.6973 (mtt) REVERT: B 1047 MET cc_start: 0.7983 (ptp) cc_final: 0.7746 (mtm) REVERT: C 150 MET cc_start: 0.8373 (pmm) cc_final: 0.7620 (pmm) REVERT: C 175 ASP cc_start: 0.4121 (OUTLIER) cc_final: 0.3533 (t70) REVERT: C 199 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8259 (mppt) REVERT: C 339 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.6884 (p90) REVERT: C 481 LYS cc_start: 0.4779 (OUTLIER) cc_final: 0.3910 (tptp) REVERT: C 963 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9392 (mp) outliers start: 160 outliers final: 116 residues processed: 233 average time/residue: 0.3432 time to fit residues: 131.4135 Evaluate side-chains 195 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 70 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 614 CYS Chi-restraints excluded: chain A residue 657 TYR Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1131 ASN Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 827 ASP Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 853 ASN Chi-restraints excluded: chain B residue 870 TYR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 883 TRP Chi-restraints excluded: chain B residue 906 ILE Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 944 LYS Chi-restraints excluded: chain B residue 949 VAL Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1025 LYS Chi-restraints excluded: chain B residue 1040 CYS Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 481 LYS Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain C residue 783 LYS Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 906 ILE Chi-restraints excluded: chain C residue 910 GLN Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 964 SER Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1081 ASP Chi-restraints excluded: chain C residue 1116 ASN Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain C residue 1125 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 297 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 175 optimal weight: 1.9990 chunk 225 optimal weight: 9.9990 chunk 174 optimal weight: 3.9990 chunk 259 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 307 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 748 ASN ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.5996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 26155 Z= 0.304 Angle : 0.677 10.903 35606 Z= 0.339 Chirality : 0.044 0.247 4182 Planarity : 0.004 0.051 4550 Dihedral : 8.666 77.495 4408 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.86 % Favored : 91.05 % Rotamer: Outliers : 5.27 % Allowed : 22.12 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.14), residues: 3172 helix: 1.37 (0.20), residues: 691 sheet: -0.99 (0.21), residues: 571 loop : -2.62 (0.13), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 64 HIS 0.007 0.001 HIS A1045 PHE 0.023 0.001 PHE C 339 TYR 0.018 0.001 TYR B1064 ARG 0.012 0.001 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 76 time to evaluate : 2.887 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: A 197 TYR cc_start: 0.8935 (p90) cc_final: 0.8649 (p90) REVERT: A 430 VAL cc_start: 0.6103 (OUTLIER) cc_final: 0.5780 (p) REVERT: A 1026 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8608 (tpp) REVERT: B 174 MET cc_start: 0.7400 (mtt) cc_final: 0.6978 (mtt) REVERT: C 150 MET cc_start: 0.8486 (pmm) cc_final: 0.7771 (pmm) REVERT: C 175 ASP cc_start: 0.4444 (OUTLIER) cc_final: 0.3874 (t70) REVERT: C 212 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7766 (t70) REVERT: C 339 PHE cc_start: 0.7744 (OUTLIER) cc_final: 0.6850 (p90) REVERT: C 481 LYS cc_start: 0.4735 (OUTLIER) cc_final: 0.3757 (tptp) outliers start: 146 outliers final: 115 residues processed: 209 average time/residue: 0.3444 time to fit residues: 118.0367 Evaluate side-chains 189 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 68 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 657 TYR Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 668 CYS Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 748 ASN Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1131 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 827 ASP Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 867 ILE Chi-restraints excluded: chain B residue 870 TYR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 883 TRP Chi-restraints excluded: chain B residue 906 ILE Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 944 LYS Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1025 LYS Chi-restraints excluded: chain B residue 1040 CYS Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain B residue 1111 ILE Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 481 LYS Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain C residue 783 LYS Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 906 ILE Chi-restraints excluded: chain C residue 964 SER Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1081 ASP Chi-restraints excluded: chain C residue 1116 ASN Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain C residue 1125 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 190 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 chunk 92 optimal weight: 0.6980 chunk 60 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 209 optimal weight: 0.6980 chunk 152 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 241 optimal weight: 8.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.6178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26155 Z= 0.227 Angle : 0.636 10.290 35606 Z= 0.318 Chirality : 0.043 0.248 4182 Planarity : 0.004 0.052 4550 Dihedral : 8.243 73.875 4402 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.60 % Favored : 92.31 % Rotamer: Outliers : 4.19 % Allowed : 22.88 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.15), residues: 3172 helix: 1.66 (0.21), residues: 679 sheet: -0.93 (0.21), residues: 592 loop : -2.51 (0.13), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 64 HIS 0.007 0.001 HIS A1045 PHE 0.023 0.001 PHE C 339 TYR 0.015 0.001 TYR B1064 ARG 0.011 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 79 time to evaluate : 2.805 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: A 17 ASN cc_start: -0.0108 (OUTLIER) cc_final: -0.0538 (m-40) REVERT: A 197 TYR cc_start: 0.8932 (p90) cc_final: 0.8657 (p90) REVERT: A 430 VAL cc_start: 0.6071 (OUTLIER) cc_final: 0.5749 (p) REVERT: B 174 MET cc_start: 0.7346 (mtt) cc_final: 0.6951 (mtt) REVERT: C 150 MET cc_start: 0.8589 (pmm) cc_final: 0.7915 (pmm) REVERT: C 175 ASP cc_start: 0.4243 (OUTLIER) cc_final: 0.3663 (t70) REVERT: C 339 PHE cc_start: 0.7787 (OUTLIER) cc_final: 0.6898 (p90) REVERT: C 481 LYS cc_start: 0.4653 (OUTLIER) cc_final: 0.4277 (tppt) outliers start: 116 outliers final: 94 residues processed: 187 average time/residue: 0.3425 time to fit residues: 105.5483 Evaluate side-chains 170 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 71 time to evaluate : 2.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 657 TYR Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 668 CYS Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1131 ASN Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 846 LEU Chi-restraints excluded: chain B residue 870 TYR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 883 TRP Chi-restraints excluded: chain B residue 906 ILE Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 944 LYS Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 481 LYS Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 964 SER Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1081 ASP Chi-restraints excluded: chain C residue 1116 ASN Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain C residue 1125 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 279 optimal weight: 2.9990 chunk 294 optimal weight: 4.9990 chunk 268 optimal weight: 0.8980 chunk 286 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 224 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 258 optimal weight: 10.0000 chunk 270 optimal weight: 0.9980 chunk 285 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 ASN ** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 GLN ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.6458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 26155 Z= 0.278 Angle : 0.657 9.908 35606 Z= 0.329 Chirality : 0.044 0.253 4182 Planarity : 0.004 0.061 4550 Dihedral : 7.945 68.191 4400 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.17 % Favored : 90.73 % Rotamer: Outliers : 4.19 % Allowed : 23.06 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.14), residues: 3172 helix: 1.62 (0.20), residues: 680 sheet: -1.02 (0.21), residues: 559 loop : -2.50 (0.13), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 64 HIS 0.006 0.001 HIS C 204 PHE 0.023 0.001 PHE C 339 TYR 0.016 0.001 TYR B1064 ARG 0.004 0.000 ARG C 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 75 time to evaluate : 2.788 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: A 17 ASN cc_start: -0.0113 (OUTLIER) cc_final: -0.0545 (m-40) REVERT: A 174 MET cc_start: 0.5358 (ptp) cc_final: 0.4567 (pmm) REVERT: A 197 TYR cc_start: 0.8931 (p90) cc_final: 0.8649 (p90) REVERT: A 430 VAL cc_start: 0.6065 (OUTLIER) cc_final: 0.5744 (p) REVERT: C 33 THR cc_start: 0.8795 (OUTLIER) cc_final: 0.8552 (t) REVERT: C 175 ASP cc_start: 0.4627 (OUTLIER) cc_final: 0.3897 (t70) REVERT: C 339 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.6935 (p90) REVERT: C 481 LYS cc_start: 0.4661 (OUTLIER) cc_final: 0.4289 (tppt) outliers start: 116 outliers final: 101 residues processed: 184 average time/residue: 0.3322 time to fit residues: 102.9149 Evaluate side-chains 178 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 71 time to evaluate : 2.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 657 TYR Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 668 CYS Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain A residue 1131 ASN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 867 ILE Chi-restraints excluded: chain B residue 870 TYR Chi-restraints excluded: chain B residue 883 TRP Chi-restraints excluded: chain B residue 906 ILE Chi-restraints excluded: chain B residue 908 VAL Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain B residue 944 LYS Chi-restraints excluded: chain B residue 949 VAL Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain B residue 1111 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 481 LYS Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 964 SER Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1081 ASP Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain C residue 1125 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 188 optimal weight: 0.6980 chunk 302 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 210 optimal weight: 2.9990 chunk 317 optimal weight: 0.8980 chunk 292 optimal weight: 2.9990 chunk 253 optimal weight: 0.0270 chunk 26 optimal weight: 0.9990 chunk 195 optimal weight: 0.9980 chunk 155 optimal weight: 8.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 GLN ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1007 GLN ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.6544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26155 Z= 0.172 Angle : 0.611 10.880 35606 Z= 0.304 Chirality : 0.043 0.241 4182 Planarity : 0.004 0.054 4550 Dihedral : 7.487 63.912 4396 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.28 % Favored : 92.62 % Rotamer: Outliers : 3.54 % Allowed : 23.64 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.15), residues: 3172 helix: 2.06 (0.21), residues: 668 sheet: -0.86 (0.21), residues: 585 loop : -2.38 (0.13), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 149 HIS 0.006 0.001 HIS A1045 PHE 0.023 0.001 PHE C 339 TYR 0.015 0.001 TYR B 263 ARG 0.005 0.000 ARG C 354 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6344 Ramachandran restraints generated. 3172 Oldfield, 0 Emsley, 3172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 79 time to evaluate : 2.838 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: A 17 ASN cc_start: -0.0133 (OUTLIER) cc_final: -0.0557 (m-40) REVERT: A 174 MET cc_start: 0.5082 (ptp) cc_final: 0.4503 (pmm) REVERT: A 197 TYR cc_start: 0.8967 (p90) cc_final: 0.8682 (p90) REVERT: A 430 VAL cc_start: 0.6008 (OUTLIER) cc_final: 0.5691 (p) REVERT: B 174 MET cc_start: 0.7387 (mtt) cc_final: 0.7024 (mtt) REVERT: B 1047 MET cc_start: 0.7749 (ptp) cc_final: 0.7187 (mtm) REVERT: C 33 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8526 (t) REVERT: C 175 ASP cc_start: 0.4303 (OUTLIER) cc_final: 0.3645 (t70) REVERT: C 212 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7755 (t70) REVERT: C 339 PHE cc_start: 0.7778 (OUTLIER) cc_final: 0.6884 (p90) REVERT: C 481 LYS cc_start: 0.4366 (OUTLIER) cc_final: 0.3970 (tppt) outliers start: 98 outliers final: 79 residues processed: 171 average time/residue: 0.3361 time to fit residues: 95.0566 Evaluate side-chains 157 residues out of total 2803 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 71 time to evaluate : 2.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 657 TYR Chi-restraints excluded: chain A residue 659 CYS Chi-restraints excluded: chain A residue 668 CYS Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 726 VAL Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 971 SER Chi-restraints excluded: chain A residue 1015 ILE Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1114 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 221 GLU Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 498 TYR Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 820 PHE Chi-restraints excluded: chain B residue 870 TYR Chi-restraints excluded: chain B residue 883 TRP Chi-restraints excluded: chain B residue 906 ILE Chi-restraints excluded: chain B residue 944 LYS Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 1111 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 317 VAL Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 339 PHE Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 481 LYS Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 706 ASN Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 817 ASP Chi-restraints excluded: chain C residue 863 THR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 964 SER Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1081 ASP Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain C residue 1125 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 319 random chunks: chunk 201 optimal weight: 1.9990 chunk 269 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 233 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 253 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 260 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.068785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.046679 restraints weight = 153441.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.048015 restraints weight = 84405.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.048866 restraints weight = 57785.722| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.6686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 26155 Z= 0.238 Angle : 0.631 10.170 35606 Z= 0.315 Chirality : 0.043 0.253 4182 Planarity : 0.004 0.055 4550 Dihedral : 7.434 59.573 4396 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.61 % Favored : 91.30 % Rotamer: Outliers : 3.83 % Allowed : 23.31 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.15), residues: 3172 helix: 1.93 (0.21), residues: 674 sheet: -0.93 (0.21), residues: 573 loop : -2.36 (0.13), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 64 HIS 0.006 0.001 HIS A1045 PHE 0.023 0.001 PHE C 339 TYR 0.014 0.001 TYR B1064 ARG 0.005 0.000 ARG C 100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4725.05 seconds wall clock time: 87 minutes 10.77 seconds (5230.77 seconds total)