Starting phenix.real_space_refine on Wed Mar 20 21:26:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wly_32594/03_2024/7wly_32594.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wly_32594/03_2024/7wly_32594.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wly_32594/03_2024/7wly_32594.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wly_32594/03_2024/7wly_32594.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wly_32594/03_2024/7wly_32594.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wly_32594/03_2024/7wly_32594.pdb" } resolution = 3.4 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= 0.022 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 129 5.16 5 C 18219 2.51 5 N 4722 2.21 5 O 5480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 34": "NH1" <-> "NH2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 745": "OD1" <-> "OD2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B ASP 339": "OD1" <-> "OD2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 568": "OD1" <-> "OD2" Residue "B ASP 586": "OD1" <-> "OD2" Residue "B TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 819": "OE1" <-> "OE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 983": "NH1" <-> "NH2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 290": "OD1" <-> "OD2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C ASP 467": "OD1" <-> "OD2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C ARG 498": "NH1" <-> "NH2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 847": "NH1" <-> "NH2" Residue "C PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 19": "NH1" <-> "NH2" Residue "P PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 30": "OD1" <-> "OD2" Residue "P TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 1": "OD1" <-> "OD2" Residue "O TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 39": "OD1" <-> "OD2" Residue "O PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 86": "OE1" <-> "OE2" Residue "O TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 19": "NH1" <-> "NH2" Residue "Y PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 1": "OD1" <-> "OD2" Residue "X TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 39": "OD1" <-> "OD2" Residue "X TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 86": "OE1" <-> "OE2" Residue "X TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28550 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8196 Classifications: {'peptide': 1051} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 57, 'TRANS': 993} Chain breaks: 7 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 8090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 8090 Classifications: {'peptide': 1042} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 56, 'TRANS': 985} Chain breaks: 8 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 8225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8225 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 56, 'TRANS': 1001} Chain breaks: 7 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 24 Chain: "P" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 962 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 838 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain breaks: 1 Chain: "X" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 838 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 101} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 14.36, per 1000 atoms: 0.50 Number of scatterers: 28550 At special positions: 0 Unit cell: (132.834, 170.352, 202.8, 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 129 16.00 O 5480 8.00 N 4722 7.00 C 18219 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.02 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.02 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 93 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 22 " - pdb=" SG CYS Y 96 " distance=2.04 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 93 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A1074 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 717 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A1098 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 616 " " NAG B1303 " - " ASN B 709 " " NAG B1304 " - " ASN B 717 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B1098 " " NAG B1309 " - " ASN B 331 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C 717 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1098 " " NAG C1309 " - " ASN C1134 " " NAG D 1 " - " ASN C 165 " " NAG E 1 " - " ASN C 234 " Time building additional restraints: 10.80 Conformation dependent library (CDL) restraints added in 4.9 seconds 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6770 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 64 sheets defined 22.8% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.75 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.807A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 542 through 546 removed outlier: 3.640A pdb=" N LEU A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 removed outlier: 3.803A pdb=" N VAL A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 639 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.762A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.298A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.426A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1034 removed outlier: 3.843A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.106A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.130A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 633 through 639 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 4.079A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.524A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.531A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.936A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B1001 " --> pdb=" O ILE B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.667A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.231A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 Processing helix chain 'C' and resid 404 through 410 removed outlier: 4.176A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 836 through 841 removed outlier: 3.622A pdb=" N CYS C 840 " --> pdb=" O GLN C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 857 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 885 through 891 removed outlier: 3.951A pdb=" N PHE C 888 " --> pdb=" O GLY C 885 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.766A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'Y' and resid 28 through 32 removed outlier: 3.712A pdb=" N ASP Y 31 " --> pdb=" O THR Y 28 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N TYR Y 32 " --> pdb=" O PHE Y 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 28 through 32' Processing helix chain 'Y' and resid 87 through 91 removed outlier: 3.893A pdb=" N THR Y 91 " --> pdb=" O ALA Y 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.627A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.627A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.524A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.963A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.568A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 313 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.773A pdb=" N THR A 645 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.235A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 538 through 540 removed outlier: 3.586A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.564A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.925A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 719 removed outlier: 6.604A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 722 through 728 Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.532A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.664A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.902A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.631A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 52 through 55 removed outlier: 3.901A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.583A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE B 106 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 312 Processing sheet with id=AC4, first strand: chain 'B' and resid 318 through 319 Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.528A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.184A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.844A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 713 Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD4, first strand: chain 'B' and resid 725 through 728 Processing sheet with id=AD5, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.605A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B 735 " --> pdb=" O THR B 859 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.886A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.818A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 3.657A pdb=" N VAL B1094 " --> pdb=" O THR B1105 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AE1, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.707A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 65 through 66 removed outlier: 3.531A pdb=" N GLY C 268 " --> pdb=" O TYR C 91 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.506A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER C 116 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 134 through 135 Processing sheet with id=AE5, first strand: chain 'C' and resid 187 through 190 Processing sheet with id=AE6, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.676A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 318 through 319 removed outlier: 4.265A pdb=" N PHE C 318 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 324 through 328 removed outlier: 3.967A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.541A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.586A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 565 through 567 removed outlier: 6.169A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.735A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 712 through 713 removed outlier: 3.918A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL C1094 " --> pdb=" O THR C1105 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 721 through 728 removed outlier: 6.682A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 721 through 728 Processing sheet with id=AF8, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.442A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AG1, first strand: chain 'C' and resid 1089 through 1090 Processing sheet with id=AG2, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AG3, first strand: chain 'P' and resid 45 through 51 removed outlier: 5.631A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 5 through 7 removed outlier: 3.598A pdb=" N ALA O 19 " --> pdb=" O ILE O 80 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 10 through 12 removed outlier: 3.506A pdb=" N LEU O 11 " --> pdb=" O LYS O 108 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP O 110 " --> pdb=" O LEU O 11 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP O 40 " --> pdb=" O LEU O 52 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 3 through 7 Processing sheet with id=AG7, first strand: chain 'Y' and resid 11 through 12 Processing sheet with id=AG8, first strand: chain 'Y' and resid 45 through 51 removed outlier: 5.640A pdb=" N TRP Y 47 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ARG Y 38 " --> pdb=" O TRP Y 47 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'X' and resid 5 through 7 Processing sheet with id=AH1, first strand: chain 'X' and resid 10 through 12 removed outlier: 3.572A pdb=" N LEU X 11 " --> pdb=" O LYS X 108 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP X 110 " --> pdb=" O LEU X 11 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP X 40 " --> pdb=" O LEU X 52 " (cutoff:3.500A) 1052 hydrogen bonds defined for protein. 2811 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.85 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: 1.21 - 1.33: 7373 1.33 - 1.45: 6212 1.45 - 1.58: 15464 1.58 - 1.70: 0 1.70 - 1.82: 165 Bond restraints: 29214 Sorted by residual: bond pdb=" N ILE A 805 " pdb=" CA ILE A 805 " ideal model delta sigma weight residual 1.452 1.495 -0.043 1.18e-02 7.18e+03 1.33e+01 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" N VAL Y 100 " pdb=" CA VAL Y 100 " ideal model delta sigma weight residual 1.454 1.494 -0.040 1.19e-02 7.06e+03 1.14e+01 bond pdb=" N VAL B 445 " pdb=" CA VAL B 445 " ideal model delta sigma weight residual 1.460 1.499 -0.040 1.21e-02 6.83e+03 1.07e+01 bond pdb=" N ARG B 237 " pdb=" CA ARG B 237 " ideal model delta sigma weight residual 1.457 1.497 -0.041 1.24e-02 6.50e+03 1.07e+01 ... (remaining 29209 not shown) Histogram of bond angle deviations from ideal: 99.08 - 106.12: 791 106.12 - 113.16: 15829 113.16 - 120.20: 10474 120.20 - 127.24: 12411 127.24 - 134.27: 254 Bond angle restraints: 39759 Sorted by residual: angle pdb=" N TYR C 449 " pdb=" CA TYR C 449 " pdb=" C TYR C 449 " ideal model delta sigma weight residual 113.61 105.41 8.20 1.50e+00 4.44e-01 2.99e+01 angle pdb=" N ASN A 907 " pdb=" CA ASN A 907 " pdb=" C ASN A 907 " ideal model delta sigma weight residual 112.89 106.42 6.47 1.24e+00 6.50e-01 2.72e+01 angle pdb=" C GLU B 702 " pdb=" CA GLU B 702 " pdb=" CB GLU B 702 " ideal model delta sigma weight residual 110.06 117.19 -7.13 1.39e+00 5.18e-01 2.63e+01 angle pdb=" N ALA A 163 " pdb=" CA ALA A 163 " pdb=" CB ALA A 163 " ideal model delta sigma weight residual 110.77 102.42 8.35 1.63e+00 3.76e-01 2.62e+01 angle pdb=" N LEU B 753 " pdb=" CA LEU B 753 " pdb=" C LEU B 753 " ideal model delta sigma weight residual 112.89 106.81 6.08 1.24e+00 6.50e-01 2.40e+01 ... (remaining 39754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.04: 16943 23.04 - 46.08: 680 46.08 - 69.13: 106 69.13 - 92.17: 39 92.17 - 115.21: 11 Dihedral angle restraints: 17779 sinusoidal: 7247 harmonic: 10532 Sorted by residual: dihedral pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual -86.00 -158.82 72.82 1 1.00e+01 1.00e-02 6.76e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 162.17 -69.17 1 1.00e+01 1.00e-02 6.19e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -42.47 -43.53 1 1.00e+01 1.00e-02 2.64e+01 ... (remaining 17776 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 4282 0.111 - 0.221: 280 0.221 - 0.332: 9 0.332 - 0.442: 3 0.442 - 0.553: 2 Chirality restraints: 4576 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.41e+01 chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.64e+00 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.07e+00 ... (remaining 4573 not shown) Planarity restraints: 5137 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1305 " -0.342 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG A1305 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG A1305 " -0.090 2.00e-02 2.50e+03 pdb=" N2 NAG A1305 " 0.527 2.00e-02 2.50e+03 pdb=" O7 NAG A1305 " -0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1301 " -0.342 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG C1301 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG C1301 " -0.094 2.00e-02 2.50e+03 pdb=" N2 NAG C1301 " 0.527 2.00e-02 2.50e+03 pdb=" O7 NAG C1301 " -0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1308 " -0.342 2.00e-02 2.50e+03 2.95e-01 1.08e+03 pdb=" C7 NAG B1308 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG B1308 " -0.147 2.00e-02 2.50e+03 pdb=" N2 NAG B1308 " 0.524 2.00e-02 2.50e+03 pdb=" O7 NAG B1308 " -0.119 2.00e-02 2.50e+03 ... (remaining 5134 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3196 2.75 - 3.28: 29340 3.28 - 3.82: 45696 3.82 - 4.36: 54866 4.36 - 4.90: 94100 Nonbonded interactions: 227198 Sorted by model distance: nonbonded pdb=" O GLU B 309 " pdb=" OH TYR B 313 " model vdw 2.207 2.440 nonbonded pdb=" OG SER C 112 " pdb=" O PHE C 133 " model vdw 2.225 2.440 nonbonded pdb=" O TYR A 313 " pdb=" OG SER A 596 " model vdw 2.237 2.440 nonbonded pdb=" O THR C 676 " pdb=" OG1 THR C 676 " model vdw 2.264 2.440 nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.269 2.440 ... (remaining 227193 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 27 through 66 or (resid 67 and (name N or name CA or name \ C or name O or name CB )) or resid 77 through 109 or (resid 110 through 111 and \ (name N or name CA or name C or name O or name CB )) or resid 112 or (resid 113 \ through 114 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 5 through 119 or (resid 120 through 121 and (name N or name CA or name C or name \ O or name CB )) or resid 122 through 136 or (resid 137 and (name N or name CA o \ r name C or name O or name CB )) or resid 138 through 158 or (resid 159 and (nam \ e N or name CA or name C or name O or name CB )) or resid 160 through 172 or (re \ sid 173 and (name N or name CA or name C or name O or name CB )) or resid 174 th \ rough 176 or (resid 177 through 178 and (name N or name CA or name C or name O o \ r name CB )) or resid 185 through 227 or (resid 228 through 229 and (name N or n \ ame CA or name C or name O or name CB )) or resid 230 through 269 or (resid 270 \ through 271 and (name N or name CA or name C or name O or name CB )) or resid 27 \ 2 through 334 or (resid 335 and (name N or name CA or name C or name O or name C \ B )) or resid 336 through 392 or (resid 393 through 394 and (name N or name CA o \ r name C or name O or name CB )) or resid 395 through 402 or (resid 403 and (nam \ e N or name CA or name C or name O or name CB )) or resid 404 through 461 or (re \ sid 462 and (name N or name CA or name C or name O or name CB )) or resid 463 th \ rough 502 or (resid 503 and (name N or name CA or name C or name O or name CB )) \ or resid 504 through 516 or (resid 517 through 518 and (name N or name CA or na \ me C or name O or name CB )) or resid 519 through 522 or (resid 523 and (name N \ or name CA or name C or name O or name CB )) or resid 524 through 527 or (resid \ 528 through 529 and (name N or name CA or name C or name O or name CB )) or resi \ d 530 through 532 or (resid 533 and (name N or name CA or name C or name O or na \ me CB )) or resid 534 through 550 or (resid 551 and (name N or name CA or name C \ or name O or name CB )) or resid 552 through 581 or (resid 582 through 583 and \ (name N or name CA or name C or name O or name CB )) or resid 584 through 622 or \ resid 632 through 827 or (resid 828 through 829 and (name N or name CA or name \ C or name O or name CB )) or resid 830 through 978 or (resid 979 and (name N or \ name CA or name C or name O or name CB )) or resid 980 through 984 or (resid 985 \ and (name N or name CA or name C or name O or name CB )) or resid 986 through 9 \ 87 or (resid 988 through 990 and (name N or name CA or name C or name O or name \ CB )) or resid 991 through 993 or (resid 994 and (name N or name CA or name C or \ name O or name CB )) or resid 995 through 1147 or resid 1301 through 1309)) selection = (chain 'B' and (resid 27 through 66 or (resid 67 and (name N or name CA or name \ C or name O or name CB )) or resid 77 through 109 or (resid 110 through 111 and \ (name N or name CA or name C or name O or name CB )) or resid 112 through 113 or \ (resid 114 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 5 through 119 or (resid 120 through 121 and (name N or name CA or name C or name \ O or name CB )) or resid 122 through 128 or (resid 129 and (name N or name CA o \ r name C or name O or name CB )) or resid 130 through 158 or (resid 159 and (nam \ e N or name CA or name C or name O or name CB )) or resid 160 through 205 or (re \ sid 206 and (name N or name CA or name C or name O or name CB )) or resid 207 th \ rough 270 or (resid 271 and (name N or name CA or name C or name O or name CB )) \ or resid 272 through 334 or (resid 335 and (name N or name CA or name C or name \ O or name CB )) or resid 336 through 345 or (resid 346 and (name N or name CA o \ r name C or name O or name CB )) or resid 347 through 356 or (resid 357 and (nam \ e N or name CA or name C or name O or name CB )) or resid 358 through 370 or (re \ sid 371 through 372 and (name N or name CA or name C or name O or name CB )) or \ resid 373 through 402 or (resid 403 and (name N or name CA or name C or name O o \ r name CB )) or resid 404 through 408 or (resid 409 and (name N or name CA or na \ me C or name O or name CB )) or resid 410 through 426 or (resid 427 and (name N \ or name CA or name C or name O or name CB )) or resid 428 through 454 or (resid \ 455 and (name N or name CA or name C or name O or name CB )) or resid 456 throug \ h 516 or (resid 517 through 518 and (name N or name CA or name C or name O or na \ me CB )) or resid 519 through 827 or (resid 828 through 829 and (name N or name \ CA or name C or name O or name CB )) or resid 830 through 984 or (resid 985 and \ (name N or name CA or name C or name O or name CB )) or resid 986 through 1126 o \ r (resid 1127 and (name N or name CA or name C or name O or name CB )) or resid \ 1128 through 1147 or resid 1301 through 1309)) selection = (chain 'C' and (resid 27 through 112 or (resid 113 through 114 and (name N or na \ me CA or name C or name O or name CB )) or resid 115 through 120 or (resid 121 a \ nd (name N or name CA or name C or name O or name CB )) or resid 122 through 136 \ or (resid 137 and (name N or name CA or name C or name O or name CB )) or resid \ 138 through 142 or (resid 158 through 159 and (name N or name CA or name C or n \ ame O or name CB )) or resid 160 through 172 or (resid 173 and (name N or name C \ A or name C or name O or name CB )) or resid 174 through 176 or (resid 177 throu \ gh 178 and (name N or name CA or name C or name O or name CB )) or resid 185 thr \ ough 205 or (resid 206 and (name N or name CA or name C or name O or name CB )) \ or resid 207 through 227 or (resid 228 through 229 and (name N or name CA or nam \ e C or name O or name CB )) or resid 230 through 269 or (resid 270 through 271 a \ nd (name N or name CA or name C or name O or name CB )) or resid 272 through 345 \ or (resid 346 and (name N or name CA or name C or name O or name CB )) or resid \ 347 through 356 or (resid 357 and (name N or name CA or name C or name O or nam \ e CB )) or resid 358 through 370 or (resid 371 through 372 and (name N or name C \ A or name C or name O or name CB )) or resid 373 through 408 or (resid 409 and ( \ name N or name CA or name C or name O or name CB )) or resid 410 through 426 or \ (resid 427 and (name N or name CA or name C or name O or name CB )) or resid 428 \ through 454 or (resid 455 and (name N or name CA or name C or name O or name CB \ )) or resid 456 through 517 or (resid 518 and (name N or name CA or name C or n \ ame O or name CB )) or resid 519 through 522 or (resid 523 and (name N or name C \ A or name C or name O or name CB )) or resid 524 through 532 or (resid 533 and ( \ name N or name CA or name C or name O or name CB )) or resid 534 through 550 or \ (resid 551 and (name N or name CA or name C or name O or name CB )) or resid 552 \ through 581 or (resid 582 through 583 and (name N or name CA or name C or name \ O or name CB )) or resid 584 through 622 or resid 632 through 836 or resid 848 t \ hrough 987 or (resid 988 through 990 and (name N or name CA or name C or name O \ or name CB )) or resid 991 through 993 or (resid 994 and (name N or name CA or n \ ame C or name O or name CB )) or resid 995 through 1147 or resid 1301 through 13 \ 09)) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'O' selection = chain 'X' } ncs_group { reference = chain 'P' selection = (chain 'Y' and (resid 1 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 127 or (resid 128 and (name N or na \ me CA or name C or name O or name CB )) or resid 129 through 130)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 13.480 Check model and map are aligned: 0.410 Set scattering table: 0.260 Process input model: 77.680 Find NCS groups from input model: 2.300 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 : 0.007 0.086 29214 Z= 0.461 Angle : 0.859 12.650 39759 Z= 0.549 Chirality : 0.058 0.553 4576 Planarity : 0.012 0.297 5108 Dihedral : 13.273 115.210 10880 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.97 % Allowed : 8.78 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % 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: -2.55 (0.13), residues: 3565 helix: -0.05 (0.19), residues: 730 sheet: -1.76 (0.18), residues: 856 loop : -2.37 (0.12), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 886 HIS 0.004 0.001 HIS B1064 PHE 0.036 0.002 PHE C 592 TYR 0.020 0.002 TYR C1067 ARG 0.003 0.001 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 283 time to evaluate : 3.376 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: A 44 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.6817 (pmm-80) REVERT: A 49 HIS cc_start: 0.7629 (t70) cc_final: 0.7203 (t70) REVERT: A 464 PHE cc_start: 0.8663 (m-80) cc_final: 0.8275 (m-80) REVERT: A 498 ARG cc_start: 0.7991 (mtt-85) cc_final: 0.7629 (mmm-85) REVERT: A 934 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.7689 (mm) REVERT: B 981 PHE cc_start: 0.7665 (m-10) cc_final: 0.6934 (m-80) REVERT: C 54 LEU cc_start: 0.9069 (mp) cc_final: 0.8717 (mt) REVERT: C 198 ASP cc_start: 0.7899 (p0) cc_final: 0.7665 (p0) REVERT: C 342 PHE cc_start: 0.5887 (m-80) cc_final: 0.5117 (m-10) REVERT: C 508 TYR cc_start: 0.4255 (OUTLIER) cc_final: 0.2869 (t80) REVERT: C 547 LYS cc_start: 0.7226 (ptmt) cc_final: 0.6993 (ptmm) REVERT: P 36 TRP cc_start: 0.3059 (m100) cc_final: 0.2495 (m100) REVERT: X 29 LEU cc_start: -0.2832 (mt) cc_final: -0.3060 (tt) outliers start: 30 outliers final: 9 residues processed: 310 average time/residue: 0.3891 time to fit residues: 197.5621 Evaluate side-chains 183 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 171 time to evaluate : 3.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 0.5980 chunk 272 optimal weight: 0.9980 chunk 151 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 184 optimal weight: 0.5980 chunk 145 optimal weight: 3.9990 chunk 282 optimal weight: 0.0980 chunk 109 optimal weight: 40.0000 chunk 171 optimal weight: 4.9990 chunk 210 optimal weight: 2.9990 chunk 326 optimal weight: 9.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 87 ASN A 321 GLN A 370 ASN A 448 ASN ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A 804 GLN ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A 953 ASN A1058 HIS A1106 GLN A1135 ASN B 218 GLN B 239 GLN B 314 GLN B 580 GLN B 751 ASN B 779 GLN B 804 GLN B 955 ASN B1101 HIS C 360 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 690 GLN C 751 ASN C 960 ASN C 965 GLN C1113 GLN C1135 ASN O 98 GLN Y 13 GLN Y 39 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 29214 Z= 0.175 Angle : 0.616 11.381 39759 Z= 0.310 Chirality : 0.046 0.282 4576 Planarity : 0.004 0.055 5108 Dihedral : 8.564 99.030 4559 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.91 % Allowed : 11.86 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % 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: -1.85 (0.14), residues: 3565 helix: 0.89 (0.20), residues: 725 sheet: -1.44 (0.17), residues: 890 loop : -2.01 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 353 HIS 0.004 0.001 HIS P 35 PHE 0.024 0.001 PHE A 168 TYR 0.021 0.001 TYR B 796 ARG 0.004 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 210 time to evaluate : 3.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7703 (t80) cc_final: 0.7482 (t80) REVERT: A 189 LEU cc_start: 0.8645 (mm) cc_final: 0.8269 (mm) REVERT: A 448 ASN cc_start: 0.3607 (OUTLIER) cc_final: 0.3259 (t0) REVERT: B 29 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.8041 (p) REVERT: C 177 MET cc_start: 0.8901 (ttt) cc_final: 0.7852 (mmp) REVERT: C 508 TYR cc_start: 0.4211 (OUTLIER) cc_final: 0.2927 (t80) REVERT: O 54 TYR cc_start: 0.6504 (p90) cc_final: 0.6079 (p90) REVERT: Y 32 TYR cc_start: 0.7106 (m-80) cc_final: 0.6724 (m-80) REVERT: Y 98 LYS cc_start: 0.5705 (OUTLIER) cc_final: 0.5052 (tppt) outliers start: 59 outliers final: 25 residues processed: 261 average time/residue: 0.3657 time to fit residues: 160.0530 Evaluate side-chains 193 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 164 time to evaluate : 3.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain Y residue 98 LYS Chi-restraints excluded: chain X residue 30 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 272 optimal weight: 1.9990 chunk 222 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 327 optimal weight: 5.9990 chunk 353 optimal weight: 7.9990 chunk 291 optimal weight: 0.6980 chunk 324 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 262 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 836 GLN A 949 GLN A 953 ASN B 437 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 935 GLN P 35 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 29214 Z= 0.254 Angle : 0.600 12.710 39759 Z= 0.301 Chirality : 0.045 0.304 4576 Planarity : 0.004 0.054 5108 Dihedral : 7.386 94.260 4549 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.36 % Allowed : 13.38 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % 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: -1.70 (0.14), residues: 3565 helix: 0.89 (0.20), residues: 735 sheet: -1.34 (0.17), residues: 871 loop : -1.87 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 353 HIS 0.011 0.001 HIS P 35 PHE 0.020 0.001 PHE C1121 TYR 0.019 0.001 TYR C1067 ARG 0.004 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 183 time to evaluate : 3.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.5914 (pmm-80) REVERT: C 177 MET cc_start: 0.8862 (ttt) cc_final: 0.7770 (mmp) REVERT: Y 64 VAL cc_start: 0.0086 (OUTLIER) cc_final: -0.0312 (m) REVERT: Y 117 MET cc_start: 0.1012 (mpp) cc_final: -0.0243 (mtm) REVERT: X 4 MET cc_start: 0.2633 (mtm) cc_final: 0.2399 (mtp) outliers start: 73 outliers final: 39 residues processed: 246 average time/residue: 0.3651 time to fit residues: 150.7847 Evaluate side-chains 201 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 160 time to evaluate : 3.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain Y residue 37 VAL Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain X residue 30 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 7.9990 chunk 246 optimal weight: 7.9990 chunk 169 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 chunk 219 optimal weight: 9.9990 chunk 328 optimal weight: 20.0000 chunk 347 optimal weight: 6.9990 chunk 171 optimal weight: 2.9990 chunk 311 optimal weight: 0.4980 chunk 93 optimal weight: 2.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN B 317 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 901 GLN C 955 ASN Y 35 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 29214 Z= 0.376 Angle : 0.638 12.611 39759 Z= 0.323 Chirality : 0.047 0.307 4576 Planarity : 0.004 0.054 5108 Dihedral : 6.930 90.713 4546 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.11 % Allowed : 14.09 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % 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: -1.73 (0.14), residues: 3565 helix: 0.76 (0.19), residues: 734 sheet: -1.30 (0.17), residues: 861 loop : -1.87 (0.13), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 353 HIS 0.005 0.001 HIS C1064 PHE 0.026 0.002 PHE C1121 TYR 0.022 0.002 TYR C1067 ARG 0.005 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 168 time to evaluate : 2.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 ARG cc_start: 0.7693 (mtt-85) cc_final: 0.7466 (mmm-85) REVERT: A 983 ARG cc_start: 0.8210 (tmm-80) cc_final: 0.8004 (tmm-80) REVERT: B 353 TRP cc_start: 0.2949 (p-90) cc_final: 0.0475 (p-90) REVERT: C 660 TYR cc_start: 0.8209 (OUTLIER) cc_final: 0.6229 (m-80) REVERT: P 86 LEU cc_start: 0.1672 (OUTLIER) cc_final: 0.1442 (pp) REVERT: Y 35 HIS cc_start: 0.2334 (m90) cc_final: 0.1951 (m-70) REVERT: Y 98 LYS cc_start: 0.5814 (OUTLIER) cc_final: 0.4705 (tppt) REVERT: Y 117 MET cc_start: 0.1094 (mpp) cc_final: -0.0160 (mtm) REVERT: X 37 TYR cc_start: 0.5245 (m-10) cc_final: 0.5025 (m-10) outliers start: 96 outliers final: 67 residues processed: 253 average time/residue: 0.3594 time to fit residues: 152.9819 Evaluate side-chains 229 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 159 time to evaluate : 3.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain P residue 4 LEU Chi-restraints excluded: chain P residue 12 VAL Chi-restraints excluded: chain P residue 37 VAL Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 95 GLN Chi-restraints excluded: chain Y residue 37 VAL Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 98 LYS Chi-restraints excluded: chain Y residue 130 SER Chi-restraints excluded: chain X residue 30 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 0.7980 chunk 197 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 259 optimal weight: 8.9990 chunk 143 optimal weight: 7.9990 chunk 296 optimal weight: 2.9990 chunk 240 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 chunk 312 optimal weight: 1.9990 chunk 87 optimal weight: 0.2980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN B 218 GLN B1088 HIS ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29214 Z= 0.213 Angle : 0.570 12.563 39759 Z= 0.286 Chirality : 0.045 0.290 4576 Planarity : 0.004 0.056 5108 Dihedral : 6.500 87.096 4546 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.11 % Allowed : 14.48 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % 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: -1.43 (0.14), residues: 3565 helix: 1.12 (0.20), residues: 727 sheet: -1.13 (0.18), residues: 859 loop : -1.70 (0.13), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP O 40 HIS 0.006 0.001 HIS P 35 PHE 0.026 0.001 PHE B 175 TYR 0.018 0.001 TYR C1067 ARG 0.004 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 171 time to evaluate : 2.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.6027 (pmm-80) REVERT: A 170 TYR cc_start: 0.7575 (t80) cc_final: 0.7367 (t80) REVERT: A 498 ARG cc_start: 0.7687 (mtt-85) cc_final: 0.7469 (mmm-85) REVERT: B 267 VAL cc_start: 0.8058 (OUTLIER) cc_final: 0.7820 (p) REVERT: B 353 TRP cc_start: 0.2879 (p-90) cc_final: 0.0471 (p-90) REVERT: C 1037 SER cc_start: 0.8717 (OUTLIER) cc_final: 0.8476 (p) REVERT: P 83 MET cc_start: 0.3133 (OUTLIER) cc_final: 0.2083 (tmm) REVERT: Y 98 LYS cc_start: 0.5780 (OUTLIER) cc_final: 0.4784 (tppt) REVERT: Y 114 GLU cc_start: 0.2330 (tt0) cc_final: 0.1166 (pp20) REVERT: X 101 PHE cc_start: 0.6034 (m-10) cc_final: 0.4500 (m-10) outliers start: 96 outliers final: 62 residues processed: 255 average time/residue: 0.3459 time to fit residues: 150.7035 Evaluate side-chains 227 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 160 time to evaluate : 3.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain P residue 83 MET Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain Y residue 37 VAL Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 98 LYS Chi-restraints excluded: chain Y residue 130 SER Chi-restraints excluded: chain X residue 3 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 9.9990 chunk 313 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 204 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 348 optimal weight: 0.0570 chunk 289 optimal weight: 0.5980 chunk 161 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 182 optimal weight: 0.5980 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 185 ASN C 239 GLN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 35 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29214 Z= 0.183 Angle : 0.555 11.571 39759 Z= 0.277 Chirality : 0.044 0.282 4576 Planarity : 0.004 0.053 5108 Dihedral : 6.190 80.844 4546 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.75 % Allowed : 15.42 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.23 (0.14), residues: 3565 helix: 1.27 (0.20), residues: 736 sheet: -0.97 (0.18), residues: 878 loop : -1.59 (0.14), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP O 40 HIS 0.006 0.001 HIS P 35 PHE 0.023 0.001 PHE B 175 TYR 0.020 0.001 TYR C 508 ARG 0.003 0.000 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 175 time to evaluate : 2.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.5944 (pmm-80) REVERT: A 130 VAL cc_start: 0.8642 (t) cc_final: 0.8419 (t) REVERT: A 170 TYR cc_start: 0.7616 (t80) cc_final: 0.7356 (t80) REVERT: A 498 ARG cc_start: 0.7687 (mtt-85) cc_final: 0.7451 (mmm-85) REVERT: B 353 TRP cc_start: 0.2848 (p-90) cc_final: 0.0496 (p-90) REVERT: C 177 MET cc_start: 0.8638 (ttt) cc_final: 0.7544 (mmp) REVERT: C 353 TRP cc_start: 0.1278 (p-90) cc_final: -0.0658 (p-90) REVERT: C 660 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.6191 (m-80) REVERT: Y 32 TYR cc_start: 0.6436 (m-80) cc_final: 0.6109 (m-80) REVERT: Y 35 HIS cc_start: 0.2190 (m90) cc_final: 0.1659 (m-70) REVERT: Y 98 LYS cc_start: 0.5894 (OUTLIER) cc_final: 0.4914 (tppt) REVERT: Y 114 GLU cc_start: 0.1946 (tt0) cc_final: 0.1128 (pp20) REVERT: Y 117 MET cc_start: 0.0892 (mpp) cc_final: -0.0180 (mtm) REVERT: X 98 GLN cc_start: 0.6740 (mp10) cc_final: 0.6462 (mm-40) REVERT: X 101 PHE cc_start: 0.5927 (m-10) cc_final: 0.4399 (m-10) outliers start: 85 outliers final: 59 residues processed: 253 average time/residue: 0.3512 time to fit residues: 151.6339 Evaluate side-chains 223 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 161 time to evaluate : 2.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 95 GLN Chi-restraints excluded: chain Y residue 37 VAL Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain Y residue 98 LYS Chi-restraints excluded: chain X residue 3 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 198 optimal weight: 0.9980 chunk 254 optimal weight: 20.0000 chunk 197 optimal weight: 0.7980 chunk 293 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 346 optimal weight: 50.0000 chunk 217 optimal weight: 5.9990 chunk 211 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN B 218 GLN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 29214 Z= 0.310 Angle : 0.602 11.052 39759 Z= 0.303 Chirality : 0.045 0.306 4576 Planarity : 0.004 0.053 5108 Dihedral : 6.273 75.154 4546 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.92 % Allowed : 15.81 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.30 (0.14), residues: 3565 helix: 1.09 (0.20), residues: 733 sheet: -0.84 (0.18), residues: 860 loop : -1.68 (0.13), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP P 36 HIS 0.004 0.001 HIS P 35 PHE 0.025 0.002 PHE C1121 TYR 0.021 0.001 TYR C1067 ARG 0.004 0.000 ARG P 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 160 time to evaluate : 3.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.5971 (pmm-80) REVERT: A 170 TYR cc_start: 0.7611 (t80) cc_final: 0.7352 (t80) REVERT: A 498 ARG cc_start: 0.7728 (mtt-85) cc_final: 0.7478 (mmm-85) REVERT: B 377 PHE cc_start: 0.5611 (OUTLIER) cc_final: 0.4235 (t80) REVERT: C 134 GLN cc_start: 0.8045 (tp40) cc_final: 0.7820 (tp40) REVERT: C 177 MET cc_start: 0.8633 (ttt) cc_final: 0.7526 (mmp) REVERT: C 231 ILE cc_start: 0.9130 (pt) cc_final: 0.8915 (mp) REVERT: C 551 VAL cc_start: 0.8448 (OUTLIER) cc_final: 0.8203 (m) REVERT: C 660 TYR cc_start: 0.8181 (OUTLIER) cc_final: 0.6317 (m-80) REVERT: C 697 MET cc_start: 0.6927 (mtp) cc_final: 0.6675 (mtp) REVERT: P 64 VAL cc_start: 0.1582 (p) cc_final: 0.1302 (t) REVERT: P 117 MET cc_start: 0.4674 (tpt) cc_final: 0.4258 (tpp) REVERT: Y 114 GLU cc_start: 0.2020 (tt0) cc_final: 0.0972 (pp20) REVERT: X 98 GLN cc_start: 0.6932 (mp10) cc_final: 0.6702 (mm-40) REVERT: X 101 PHE cc_start: 0.5997 (m-10) cc_final: 0.4769 (m-10) outliers start: 90 outliers final: 71 residues processed: 241 average time/residue: 0.3353 time to fit residues: 140.0096 Evaluate side-chains 227 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 152 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 803 SER Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 95 GLN Chi-restraints excluded: chain Y residue 37 VAL Chi-restraints excluded: chain Y residue 51 VAL Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain X residue 3 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 8.9990 chunk 138 optimal weight: 0.1980 chunk 207 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 220 optimal weight: 10.0000 chunk 236 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 chunk 32 optimal weight: 20.0000 chunk 272 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29214 Z= 0.178 Angle : 0.555 11.171 39759 Z= 0.277 Chirality : 0.044 0.285 4576 Planarity : 0.004 0.051 5108 Dihedral : 5.928 64.080 4546 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.62 % Allowed : 16.33 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.11 (0.14), residues: 3565 helix: 1.34 (0.20), residues: 730 sheet: -0.74 (0.18), residues: 850 loop : -1.57 (0.13), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP P 36 HIS 0.004 0.001 HIS Y 35 PHE 0.018 0.001 PHE B 175 TYR 0.018 0.001 TYR C 508 ARG 0.003 0.000 ARG A 905 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 167 time to evaluate : 3.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.5948 (pmm-80) REVERT: A 170 TYR cc_start: 0.7623 (t80) cc_final: 0.7367 (t80) REVERT: A 498 ARG cc_start: 0.7742 (mtt-85) cc_final: 0.7506 (mmm-85) REVERT: B 377 PHE cc_start: 0.5394 (OUTLIER) cc_final: 0.4141 (t80) REVERT: C 134 GLN cc_start: 0.8017 (tp40) cc_final: 0.7751 (tp40) REVERT: C 177 MET cc_start: 0.8586 (ttt) cc_final: 0.7474 (mmp) REVERT: C 353 TRP cc_start: 0.1421 (p-90) cc_final: -0.0517 (p-90) REVERT: C 495 TYR cc_start: 0.0850 (OUTLIER) cc_final: 0.0040 (m-10) REVERT: C 559 PHE cc_start: 0.6885 (OUTLIER) cc_final: 0.6244 (t80) REVERT: C 660 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.6349 (m-80) REVERT: P 64 VAL cc_start: 0.1621 (p) cc_final: 0.1403 (t) REVERT: P 117 MET cc_start: 0.4452 (tpt) cc_final: 0.4134 (tpp) REVERT: Y 114 GLU cc_start: 0.1805 (tt0) cc_final: 0.0967 (pp20) REVERT: X 98 GLN cc_start: 0.6993 (mp10) cc_final: 0.6411 (mp10) REVERT: X 101 PHE cc_start: 0.5899 (m-10) cc_final: 0.4347 (m-10) outliers start: 81 outliers final: 60 residues processed: 238 average time/residue: 0.3239 time to fit residues: 133.5001 Evaluate side-chains 221 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 156 time to evaluate : 2.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 95 GLN Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 37 VAL Chi-restraints excluded: chain Y residue 51 VAL Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain X residue 3 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 0.0470 chunk 332 optimal weight: 0.9990 chunk 303 optimal weight: 0.6980 chunk 323 optimal weight: 20.0000 chunk 194 optimal weight: 1.9990 chunk 140 optimal weight: 0.2980 chunk 253 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 292 optimal weight: 0.9980 chunk 305 optimal weight: 1.9990 chunk 322 optimal weight: 5.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 185 ASN B 437 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 29214 Z= 0.143 Angle : 0.541 10.412 39759 Z= 0.269 Chirality : 0.043 0.267 4576 Planarity : 0.004 0.049 5108 Dihedral : 5.498 55.192 4546 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.11 % Allowed : 17.23 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.14), residues: 3565 helix: 1.52 (0.20), residues: 734 sheet: -0.62 (0.18), residues: 859 loop : -1.47 (0.14), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP P 36 HIS 0.004 0.001 HIS Y 35 PHE 0.025 0.001 PHE C 565 TYR 0.018 0.001 TYR O 37 ARG 0.005 0.000 ARG P 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 173 time to evaluate : 3.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.5997 (pmm-80) REVERT: A 498 ARG cc_start: 0.7837 (mtt-85) cc_final: 0.7577 (mmm-85) REVERT: B 377 PHE cc_start: 0.5347 (OUTLIER) cc_final: 0.4250 (t80) REVERT: B 436 TRP cc_start: 0.1628 (p90) cc_final: 0.1327 (p90) REVERT: C 134 GLN cc_start: 0.7901 (tp40) cc_final: 0.7620 (tp40) REVERT: C 177 MET cc_start: 0.8610 (ttt) cc_final: 0.7509 (mmp) REVERT: C 495 TYR cc_start: 0.0965 (OUTLIER) cc_final: 0.0211 (m-10) REVERT: C 559 PHE cc_start: 0.6756 (OUTLIER) cc_final: 0.6203 (t80) REVERT: P 46 GLU cc_start: 0.7612 (pm20) cc_final: 0.7149 (mm-30) REVERT: P 64 VAL cc_start: 0.1621 (p) cc_final: 0.1362 (t) REVERT: P 117 MET cc_start: 0.4382 (tpt) cc_final: 0.4137 (tpp) REVERT: Y 114 GLU cc_start: 0.1374 (tt0) cc_final: 0.0665 (pp20) REVERT: X 101 PHE cc_start: 0.5815 (m-10) cc_final: 0.4510 (m-10) outliers start: 65 outliers final: 49 residues processed: 230 average time/residue: 0.3545 time to fit residues: 139.9890 Evaluate side-chains 208 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 155 time to evaluate : 3.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain O residue 95 GLN Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 37 VAL Chi-restraints excluded: chain Y residue 57 THR Chi-restraints excluded: chain X residue 3 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 8.9990 chunk 341 optimal weight: 20.0000 chunk 208 optimal weight: 6.9990 chunk 162 optimal weight: 0.5980 chunk 237 optimal weight: 0.1980 chunk 358 optimal weight: 5.9990 chunk 330 optimal weight: 20.0000 chunk 285 optimal weight: 0.0070 chunk 29 optimal weight: 9.9990 chunk 220 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 overall best weight: 1.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 394 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 185 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 29214 Z= 0.268 Angle : 0.578 10.709 39759 Z= 0.290 Chirality : 0.045 0.299 4576 Planarity : 0.004 0.049 5108 Dihedral : 5.596 56.065 4546 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.33 % Allowed : 17.14 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.00 (0.14), residues: 3565 helix: 1.32 (0.20), residues: 731 sheet: -0.63 (0.18), residues: 858 loop : -1.48 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP P 36 HIS 0.003 0.001 HIS A 49 PHE 0.023 0.001 PHE C 565 TYR 0.019 0.001 TYR C1067 ARG 0.005 0.000 ARG A 905 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7130 Ramachandran restraints generated. 3565 Oldfield, 0 Emsley, 3565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 155 time to evaluate : 3.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.5978 (pmm-80) REVERT: A 52 GLN cc_start: 0.7766 (tm-30) cc_final: 0.7536 (tm-30) REVERT: A 402 ILE cc_start: 0.7736 (tp) cc_final: 0.7431 (pt) REVERT: A 434 ILE cc_start: 0.8612 (mp) cc_final: 0.8339 (mm) REVERT: A 498 ARG cc_start: 0.7814 (mtt-85) cc_final: 0.7561 (mmm-85) REVERT: B 377 PHE cc_start: 0.5398 (OUTLIER) cc_final: 0.4207 (t80) REVERT: B 436 TRP cc_start: 0.1505 (p90) cc_final: 0.1229 (p90) REVERT: C 134 GLN cc_start: 0.7706 (tp40) cc_final: 0.7455 (tp40) REVERT: C 177 MET cc_start: 0.8636 (ttt) cc_final: 0.7539 (mmp) REVERT: C 353 TRP cc_start: 0.1554 (p-90) cc_final: -0.0569 (p-90) REVERT: C 495 TYR cc_start: 0.0926 (OUTLIER) cc_final: 0.0141 (m-10) REVERT: C 660 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.6359 (m-80) REVERT: P 46 GLU cc_start: 0.7698 (pm20) cc_final: 0.6967 (mm-30) REVERT: P 64 VAL cc_start: 0.1717 (p) cc_final: 0.1479 (t) REVERT: Y 114 GLU cc_start: 0.1608 (tt0) cc_final: 0.0883 (pp20) REVERT: X 101 PHE cc_start: 0.5817 (m-10) cc_final: 0.4469 (m-10) outliers start: 72 outliers final: 60 residues processed: 220 average time/residue: 0.3366 time to fit residues: 129.1162 Evaluate side-chains 215 residues out of total 3154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 151 time to evaluate : 3.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ARG Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 377 PHE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 501 TYR Chi-restraints excluded: chain C residue 532 ASN Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 660 TYR Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 692 ILE Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 749 CYS Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1037 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain O residue 77 THR Chi-restraints excluded: chain O residue 95 GLN Chi-restraints excluded: chain Y residue 12 VAL Chi-restraints excluded: chain Y residue 37 VAL Chi-restraints excluded: chain Y residue 51 VAL Chi-restraints excluded: chain Y residue 57 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 0.1980 chunk 304 optimal weight: 1.9990 chunk 87 optimal weight: 0.1980 chunk 263 optimal weight: 3.9990 chunk 42 optimal weight: 20.0000 chunk 79 optimal weight: 4.9990 chunk 286 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 chunk 293 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 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 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 625 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN B 218 GLN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.147409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.100708 restraints weight = 76747.424| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 3.70 r_work: 0.3223 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29214 Z= 0.214 Angle : 0.558 10.981 39759 Z= 0.279 Chirality : 0.044 0.289 4576 Planarity : 0.004 0.050 5108 Dihedral : 5.552 56.801 4546 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.20 % Allowed : 17.10 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.07 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.14), residues: 3565 helix: 1.33 (0.20), residues: 732 sheet: -0.55 (0.18), residues: 850 loop : -1.46 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP P 36 HIS 0.003 0.001 HIS B1088 PHE 0.024 0.001 PHE C 565 TYR 0.018 0.001 TYR C1067 ARG 0.005 0.000 ARG A 905 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5611.48 seconds wall clock time: 102 minutes 34.50 seconds (6154.50 seconds total)