Starting phenix.real_space_refine on Sat Mar 16 02:30:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtz_27712/03_2024/8dtz_27712.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtz_27712/03_2024/8dtz_27712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtz_27712/03_2024/8dtz_27712.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtz_27712/03_2024/8dtz_27712.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtz_27712/03_2024/8dtz_27712.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtz_27712/03_2024/8dtz_27712.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.005 sd= 0.077 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: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 804 5.16 5 C 82240 2.51 5 N 22136 2.21 5 O 24340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 17": "OD1" <-> "OD2" Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 458": "OD1" <-> "OD2" Residue "A ASP 474": "OD1" <-> "OD2" Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 591": "OE1" <-> "OE2" Residue "A TYR 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1196": "OD1" <-> "OD2" Residue "A TYR 1226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2113": "OE1" <-> "OE2" Residue "A TYR 2155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2172": "OE1" <-> "OE2" Residue "A PHE 2202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2222": "OE1" <-> "OE2" Residue "A GLU 2635": "OE1" <-> "OE2" Residue "A ASP 2678": "OD1" <-> "OD2" Residue "A GLU 2681": "OE1" <-> "OE2" Residue "A TYR 3623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3832": "OD1" <-> "OD2" Residue "A PHE 4016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4153": "OE1" <-> "OE2" Residue "A TYR 4566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4836": "OD1" <-> "OD2" Residue "A GLU 4905": "OE1" <-> "OE2" Residue "B ASP 17": "OD1" <-> "OD2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 458": "OD1" <-> "OD2" Residue "B ASP 474": "OD1" <-> "OD2" Residue "B PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 591": "OE1" <-> "OE2" Residue "B TYR 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1196": "OD1" <-> "OD2" Residue "B TYR 1226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2113": "OE1" <-> "OE2" Residue "B TYR 2155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2172": "OE1" <-> "OE2" Residue "B PHE 2202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2222": "OE1" <-> "OE2" Residue "B GLU 2635": "OE1" <-> "OE2" Residue "B ASP 2678": "OD1" <-> "OD2" Residue "B GLU 2681": "OE1" <-> "OE2" Residue "B TYR 3623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 3832": "OD1" <-> "OD2" Residue "B PHE 4016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4153": "OE1" <-> "OE2" Residue "B TYR 4566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 4836": "OD1" <-> "OD2" Residue "B GLU 4905": "OE1" <-> "OE2" Residue "C ASP 17": "OD1" <-> "OD2" Residue "C PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 458": "OD1" <-> "OD2" Residue "C ASP 474": "OD1" <-> "OD2" Residue "C PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 591": "OE1" <-> "OE2" Residue "C TYR 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1196": "OD1" <-> "OD2" Residue "C TYR 1226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2113": "OE1" <-> "OE2" Residue "C TYR 2155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2172": "OE1" <-> "OE2" Residue "C PHE 2202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2222": "OE1" <-> "OE2" Residue "C GLU 2635": "OE1" <-> "OE2" Residue "C ASP 2678": "OD1" <-> "OD2" Residue "C GLU 2681": "OE1" <-> "OE2" Residue "C TYR 3623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 3713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 3832": "OD1" <-> "OD2" Residue "C PHE 4016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4153": "OE1" <-> "OE2" Residue "C TYR 4566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 4836": "OD1" <-> "OD2" Residue "C GLU 4905": "OE1" <-> "OE2" Residue "D ASP 17": "OD1" <-> "OD2" Residue "D PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 458": "OD1" <-> "OD2" Residue "D ASP 474": "OD1" <-> "OD2" Residue "D PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 591": "OE1" <-> "OE2" Residue "D TYR 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1196": "OD1" <-> "OD2" Residue "D TYR 1226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2113": "OE1" <-> "OE2" Residue "D TYR 2155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2172": "OE1" <-> "OE2" Residue "D PHE 2202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2222": "OE1" <-> "OE2" Residue "D GLU 2635": "OE1" <-> "OE2" Residue "D ASP 2678": "OD1" <-> "OD2" Residue "D GLU 2681": "OE1" <-> "OE2" Residue "D TYR 3623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 3713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 3832": "OD1" <-> "OD2" Residue "D PHE 4016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4153": "OE1" <-> "OE2" Residue "D TYR 4566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 4836": "OD1" <-> "OD2" Residue "D GLU 4905": "OE1" <-> "OE2" Residue "E PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.36s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 129524 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 31562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4061, 31562 Classifications: {'peptide': 4061} Incomplete info: {'truncation_to_alanine': 237} Link IDs: {'PTRANS': 145, 'TRANS': 3915} Chain breaks: 24 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 919 Unresolved non-hydrogen angles: 1122 Unresolved non-hydrogen dihedrals: 776 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 14, 'PHE:plan': 7, 'GLU:plan': 29, 'ARG:plan': 30} Unresolved non-hydrogen planarities: 508 Chain: "B" Number of atoms: 31562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4061, 31562 Classifications: {'peptide': 4061} Incomplete info: {'truncation_to_alanine': 237} Link IDs: {'PTRANS': 145, 'TRANS': 3915} Chain breaks: 24 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 919 Unresolved non-hydrogen angles: 1122 Unresolved non-hydrogen dihedrals: 776 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 14, 'PHE:plan': 7, 'GLU:plan': 29, 'ARG:plan': 30} Unresolved non-hydrogen planarities: 508 Chain: "C" Number of atoms: 31562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4061, 31562 Classifications: {'peptide': 4061} Incomplete info: {'truncation_to_alanine': 237} Link IDs: {'PTRANS': 145, 'TRANS': 3915} Chain breaks: 24 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 919 Unresolved non-hydrogen angles: 1122 Unresolved non-hydrogen dihedrals: 776 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 14, 'PHE:plan': 7, 'GLU:plan': 29, 'ARG:plan': 30} Unresolved non-hydrogen planarities: 508 Chain: "D" Number of atoms: 31562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4061, 31562 Classifications: {'peptide': 4061} Incomplete info: {'truncation_to_alanine': 237} Link IDs: {'PTRANS': 145, 'TRANS': 3915} Chain breaks: 24 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 919 Unresolved non-hydrogen angles: 1122 Unresolved non-hydrogen dihedrals: 776 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 11, 'TRP:plan': 2, 'ASP:plan': 14, 'PHE:plan': 7, 'GLU:plan': 29, 'ARG:plan': 30} Unresolved non-hydrogen planarities: 508 Chain: "E" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "H" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 30883 SG CYS A4887 203.965 192.301 126.193 1.00 15.09 S ATOM 30908 SG CYS A4890 202.509 193.842 122.974 1.00 12.83 S ATOM 62445 SG CYS B4887 192.302 169.681 126.193 1.00 15.09 S ATOM 62470 SG CYS B4890 193.843 171.137 122.974 1.00 12.83 S ATOM 94007 SG CYS C4887 169.682 181.344 126.193 1.00 15.09 S ATOM 94032 SG CYS C4890 171.138 179.803 122.974 1.00 12.83 S ATOM A0JQ9 SG CYS D4887 181.345 203.964 126.193 1.00 15.09 S ATOM A0JQY SG CYS D4890 179.804 202.508 122.974 1.00 12.83 S Residues with excluded nonbonded symmetry interactions: 28 residue: pdb=" N VAL A 663 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL A 663 " occ=0.50 residue: pdb=" N MET A 678 " occ=0.99 ... (6 atoms not shown) pdb=" CE MET A 678 " occ=0.99 residue: pdb=" N CYS A 736 " occ=0.00 ... (4 atoms not shown) pdb=" SG CYS A 736 " occ=0.00 residue: pdb=" N ARG A 739 " occ=0.83 ... (9 atoms not shown) pdb=" NH2 ARG A 739 " occ=0.83 residue: pdb=" N SER A 742 " occ=0.47 ... (4 atoms not shown) pdb=" OG SER A 742 " occ=0.47 residue: pdb=" N HIS A 808 " occ=0.94 ... (8 atoms not shown) pdb=" NE2 HIS A 808 " occ=0.94 residue: pdb=" N LYS A 812 " occ=0.69 ... (7 atoms not shown) pdb=" NZ LYS A 812 " occ=0.69 residue: pdb=" N VAL B 663 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL B 663 " occ=0.50 residue: pdb=" N MET B 678 " occ=0.99 ... (6 atoms not shown) pdb=" CE MET B 678 " occ=0.99 residue: pdb=" N CYS B 736 " occ=0.00 ... (4 atoms not shown) pdb=" SG CYS B 736 " occ=0.00 residue: pdb=" N ARG B 739 " occ=0.83 ... (9 atoms not shown) pdb=" NH2 ARG B 739 " occ=0.83 residue: pdb=" N SER B 742 " occ=0.47 ... (4 atoms not shown) pdb=" OG SER B 742 " occ=0.47 ... (remaining 16 not shown) Time building chain proxies: 48.76, per 1000 atoms: 0.38 Number of scatterers: 129524 At special positions: 0 Unit cell: (374.76, 374.76, 217.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 804 16.00 O 24340 8.00 N 22136 7.00 C 82240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 37.57 Conformation dependent library (CDL) restraints added in 17.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A6000 " pdb="ZN ZN A6000 " - pdb=" NE2 HIS A4907 " pdb="ZN ZN A6000 " - pdb=" ND1 HIS A4912 " pdb="ZN ZN A6000 " - pdb=" SG CYS A4890 " pdb="ZN ZN A6000 " - pdb=" SG CYS A4887 " pdb=" ZN B6000 " pdb="ZN ZN B6000 " - pdb=" NE2 HIS B4907 " pdb="ZN ZN B6000 " - pdb=" ND1 HIS B4912 " pdb="ZN ZN B6000 " - pdb=" SG CYS B4890 " pdb="ZN ZN B6000 " - pdb=" SG CYS B4887 " pdb=" ZN C6000 " pdb="ZN ZN C6000 " - pdb=" NE2 HIS C4907 " pdb="ZN ZN C6000 " - pdb=" ND1 HIS C4912 " pdb="ZN ZN C6000 " - pdb=" SG CYS C4890 " pdb="ZN ZN C6000 " - pdb=" SG CYS C4887 " pdb=" ZN D6000 " pdb="ZN ZN D6000 " - pdb=" NE2 HIS D4907 " pdb="ZN ZN D6000 " - pdb=" ND1 HIS D4912 " pdb="ZN ZN D6000 " - pdb=" SG CYS D4890 " pdb="ZN ZN D6000 " - pdb=" SG CYS D4887 " Number of angles added : 4 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 31224 Finding SS restraints... Secondary structure from input PDB file: 592 helices and 84 sheets defined 48.3% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.83 Creating SS restraints... Processing helix chain 'A' and resid 255 through 259 removed outlier: 4.034A pdb=" N THR A 259 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 438 removed outlier: 4.162A pdb=" N LYS A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 471 through 494 removed outlier: 3.699A pdb=" N MET A 494 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 506 Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 525 through 543 Processing helix chain 'A' and resid 554 through 563 Processing helix chain 'A' and resid 568 through 582 Processing helix chain 'A' and resid 584 through 588 removed outlier: 3.529A pdb=" N ASN A 587 " --> pdb=" O GLU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 604 Processing helix chain 'A' and resid 609 through 617 removed outlier: 3.917A pdb=" N VAL A 613 " --> pdb=" O LYS A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 636 Processing helix chain 'A' and resid 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 878 through 901 removed outlier: 3.996A pdb=" N GLY A 901 " --> pdb=" O LYS A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 912 Processing helix chain 'A' and resid 925 through 945 Processing helix chain 'A' and resid 965 through 969 removed outlier: 3.672A pdb=" N ASN A 969 " --> pdb=" O LEU A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1015 Processing helix chain 'A' and resid 1043 through 1061 Processing helix chain 'A' and resid 1092 through 1095 Processing helix chain 'A' and resid 1230 through 1235 Processing helix chain 'A' and resid 1633 through 1637 removed outlier: 4.432A pdb=" N ASN A1637 " --> pdb=" O PRO A1634 " (cutoff:3.500A) Processing helix chain 'A' and resid 1648 through 1666 Processing helix chain 'A' and resid 1672 through 1681 removed outlier: 3.554A pdb=" N SER A1679 " --> pdb=" O HIS A1675 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS A1680 " --> pdb=" O ALA A1676 " (cutoff:3.500A) Processing helix chain 'A' and resid 1682 through 1692 Processing helix chain 'A' and resid 1696 through 1712 Processing helix chain 'A' and resid 1713 through 1723 Processing helix chain 'A' and resid 1784 through 1806 removed outlier: 3.653A pdb=" N LEU A1805 " --> pdb=" O LYS A1801 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS A1806 " --> pdb=" O GLU A1802 " (cutoff:3.500A) Processing helix chain 'A' and resid 1814 through 1831 Proline residue: A1821 - end of helix Processing helix chain 'A' and resid 1836 through 1845 removed outlier: 3.629A pdb=" N GLN A1845 " --> pdb=" O LYS A1841 " (cutoff:3.500A) Processing helix chain 'A' and resid 1898 through 1939 removed outlier: 4.304A pdb=" N GLN A1904 " --> pdb=" O PRO A1900 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N MET A1905 " --> pdb=" O VAL A1901 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS A1906 " --> pdb=" O LYS A1902 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU A1907 " --> pdb=" O LEU A1903 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP A1929 " --> pdb=" O VAL A1925 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP A1930 " --> pdb=" O ALA A1926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1952 through 1958 removed outlier: 3.868A pdb=" N LEU A1956 " --> pdb=" O MET A1952 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A1958 " --> pdb=" O ALA A1954 " (cutoff:3.500A) Processing helix chain 'A' and resid 1999 through 2006 removed outlier: 3.890A pdb=" N MET A2003 " --> pdb=" O HIS A1999 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N CYS A2006 " --> pdb=" O LEU A2002 " (cutoff:3.500A) Processing helix chain 'A' and resid 2010 through 2016 Processing helix chain 'A' and resid 2023 through 2036 removed outlier: 4.524A pdb=" N ARG A2027 " --> pdb=" O THR A2023 " (cutoff:3.500A) Processing helix chain 'A' and resid 2056 through 2072 removed outlier: 3.899A pdb=" N SER A2072 " --> pdb=" O TRP A2068 " (cutoff:3.500A) Processing helix chain 'A' and resid 2076 through 2092 removed outlier: 3.745A pdb=" N VAL A2080 " --> pdb=" O ASP A2076 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A2090 " --> pdb=" O LEU A2086 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR A2091 " --> pdb=" O LEU A2087 " (cutoff:3.500A) Processing helix chain 'A' and resid 2092 through 2104 Proline residue: A2102 - end of helix Processing helix chain 'A' and resid 2111 through 2127 removed outlier: 4.231A pdb=" N ASN A2117 " --> pdb=" O GLU A2113 " (cutoff:3.500A) Processing helix chain 'A' and resid 2136 through 2150 removed outlier: 4.411A pdb=" N LEU A2140 " --> pdb=" O GLU A2136 " (cutoff:3.500A) Processing helix chain 'A' and resid 2152 through 2157 Processing helix chain 'A' and resid 2158 through 2165 removed outlier: 4.157A pdb=" N ARG A2162 " --> pdb=" O PRO A2158 " (cutoff:3.500A) Processing helix chain 'A' and resid 2165 through 2179 Processing helix chain 'A' and resid 2189 through 2202 removed outlier: 3.998A pdb=" N ALA A2193 " --> pdb=" O PRO A2189 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASN A2194 " --> pdb=" O LYS A2190 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A2198 " --> pdb=" O ASN A2194 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU A2199 " --> pdb=" O CYS A2195 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS A2200 " --> pdb=" O CYS A2196 " (cutoff:3.500A) Processing helix chain 'A' and resid 2208 through 2215 Processing helix chain 'A' and resid 2216 through 2223 Processing helix chain 'A' and resid 2238 through 2246 removed outlier: 3.817A pdb=" N ALA A2242 " --> pdb=" O PRO A2238 " (cutoff:3.500A) Processing helix chain 'A' and resid 2249 through 2256 removed outlier: 3.551A pdb=" N ALA A2253 " --> pdb=" O ASN A2249 " (cutoff:3.500A) Processing helix chain 'A' and resid 2257 through 2260 removed outlier: 3.565A pdb=" N ASP A2260 " --> pdb=" O ARG A2257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2257 through 2260' Processing helix chain 'A' and resid 2261 through 2271 removed outlier: 3.809A pdb=" N VAL A2265 " --> pdb=" O LEU A2261 " (cutoff:3.500A) Processing helix chain 'A' and resid 2294 through 2305 removed outlier: 3.686A pdb=" N LEU A2298 " --> pdb=" O GLY A2294 " (cutoff:3.500A) Processing helix chain 'A' and resid 2312 through 2326 removed outlier: 3.768A pdb=" N ALA A2316 " --> pdb=" O VAL A2312 " (cutoff:3.500A) Processing helix chain 'A' and resid 2341 through 2354 removed outlier: 4.649A pdb=" N GLU A2347 " --> pdb=" O LEU A2343 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS A2351 " --> pdb=" O GLU A2347 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE A2352 " --> pdb=" O GLU A2348 " (cutoff:3.500A) Processing helix chain 'A' and resid 2386 through 2402 Processing helix chain 'A' and resid 2415 through 2425 removed outlier: 3.765A pdb=" N ARG A2419 " --> pdb=" O ALA A2415 " (cutoff:3.500A) Processing helix chain 'A' and resid 2430 through 2432 No H-bonds generated for 'chain 'A' and resid 2430 through 2432' Processing helix chain 'A' and resid 2433 through 2440 removed outlier: 3.742A pdb=" N GLN A2440 " --> pdb=" O SER A2436 " (cutoff:3.500A) Processing helix chain 'A' and resid 2461 through 2475 removed outlier: 3.999A pdb=" N ALA A2465 " --> pdb=" O PRO A2461 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A2466 " --> pdb=" O ASP A2462 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A2471 " --> pdb=" O MET A2467 " (cutoff:3.500A) Processing helix chain 'A' and resid 2479 through 2487 removed outlier: 3.929A pdb=" N LEU A2483 " --> pdb=" O VAL A2479 " (cutoff:3.500A) Processing helix chain 'A' and resid 2490 through 2500 removed outlier: 3.566A pdb=" N ALA A2498 " --> pdb=" O ASP A2494 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA A2499 " --> pdb=" O LEU A2495 " (cutoff:3.500A) Processing helix chain 'A' and resid 2511 through 2522 Processing helix chain 'A' and resid 2582 through 2591 removed outlier: 3.959A pdb=" N HIS A2586 " --> pdb=" O SER A2582 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A2589 " --> pdb=" O GLN A2585 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG A2590 " --> pdb=" O HIS A2586 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A2591 " --> pdb=" O LEU A2587 " (cutoff:3.500A) Processing helix chain 'A' and resid 2599 through 2614 removed outlier: 3.783A pdb=" N LYS A2603 " --> pdb=" O ASN A2599 " (cutoff:3.500A) Proline residue: A2605 - end of helix removed outlier: 3.783A pdb=" N THR A2610 " --> pdb=" O LEU A2606 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASN A2611 " --> pdb=" O LYS A2607 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N HIS A2612 " --> pdb=" O LEU A2608 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR A2613 " --> pdb=" O LEU A2609 " (cutoff:3.500A) Processing helix chain 'A' and resid 2621 through 2633 Processing helix chain 'A' and resid 2639 through 2650 removed outlier: 4.037A pdb=" N LEU A2643 " --> pdb=" O LEU A2639 " (cutoff:3.500A) Processing helix chain 'A' and resid 2660 through 2675 removed outlier: 3.656A pdb=" N LEU A2665 " --> pdb=" O PHE A2661 " (cutoff:3.500A) Proline residue: A2666 - end of helix removed outlier: 3.903A pdb=" N SER A2669 " --> pdb=" O LEU A2665 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A2675 " --> pdb=" O VAL A2671 " (cutoff:3.500A) Processing helix chain 'A' and resid 2718 through 2739 Processing helix chain 'A' and resid 2763 through 2785 Proline residue: A2773 - end of helix Processing helix chain 'A' and resid 2816 through 2820 removed outlier: 3.691A pdb=" N GLY A2819 " --> pdb=" O ALA A2816 " (cutoff:3.500A) Processing helix chain 'A' and resid 2833 through 2863 Processing helix chain 'A' and resid 2877 through 2896 removed outlier: 3.935A pdb=" N LYS A2883 " --> pdb=" O LYS A2879 " (cutoff:3.500A) Processing helix chain 'A' and resid 2990 through 3012 removed outlier: 4.295A pdb=" N SER A2996 " --> pdb=" O GLY A2992 " (cutoff:3.500A) Processing helix chain 'A' and resid 3037 through 3050 removed outlier: 3.796A pdb=" N ARG A3042 " --> pdb=" O THR A3038 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS A3046 " --> pdb=" O ARG A3042 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR A3047 " --> pdb=" O THR A3043 " (cutoff:3.500A) Processing helix chain 'A' and resid 3054 through 3063 removed outlier: 3.530A pdb=" N LEU A3060 " --> pdb=" O LEU A3056 " (cutoff:3.500A) Processing helix chain 'A' and resid 3066 through 3083 Processing helix chain 'A' and resid 3090 through 3099 Processing helix chain 'A' and resid 3183 through 3192 Processing helix chain 'A' and resid 3214 through 3225 removed outlier: 4.140A pdb=" N ILE A3218 " --> pdb=" O MET A3214 " (cutoff:3.500A) Processing helix chain 'A' and resid 3238 through 3252 removed outlier: 4.369A pdb=" N TYR A3244 " --> pdb=" O MET A3240 " (cutoff:3.500A) Processing helix chain 'A' and resid 3263 through 3268 removed outlier: 3.700A pdb=" N ALA A3266 " --> pdb=" O CYS A3263 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN A3268 " --> pdb=" O THR A3265 " (cutoff:3.500A) Processing helix chain 'A' and resid 3286 through 3292 Processing helix chain 'A' and resid 3308 through 3324 removed outlier: 4.258A pdb=" N GLN A3312 " --> pdb=" O LYS A3308 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A3319 " --> pdb=" O LYS A3315 " (cutoff:3.500A) Proline residue: A3320 - end of helix Processing helix chain 'A' and resid 3330 through 3344 Processing helix chain 'A' and resid 3355 through 3374 removed outlier: 4.280A pdb=" N THR A3359 " --> pdb=" O LEU A3355 " (cutoff:3.500A) Proline residue: A3370 - end of helix Processing helix chain 'A' and resid 3405 through 3431 removed outlier: 3.896A pdb=" N VAL A3420 " --> pdb=" O GLN A3416 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN A3421 " --> pdb=" O ASN A3417 " (cutoff:3.500A) Processing helix chain 'A' and resid 3436 through 3473 removed outlier: 4.115A pdb=" N ASP A3456 " --> pdb=" O LYS A3452 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG A3457 " --> pdb=" O ARG A3453 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A3467 " --> pdb=" O SER A3463 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ARG A3471 " --> pdb=" O ALA A3467 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A3472 " --> pdb=" O ALA A3468 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU A3473 " --> pdb=" O LEU A3469 " (cutoff:3.500A) Processing helix chain 'A' and resid 3473 through 3491 removed outlier: 3.713A pdb=" N LEU A3477 " --> pdb=" O LEU A3473 " (cutoff:3.500A) Proline residue: A3482 - end of helix removed outlier: 3.502A pdb=" N GLN A3485 " --> pdb=" O ALA A3481 " (cutoff:3.500A) Processing helix chain 'A' and resid 3494 through 3508 removed outlier: 4.288A pdb=" N THR A3500 " --> pdb=" O SER A3496 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A3508 " --> pdb=" O VAL A3504 " (cutoff:3.500A) Processing helix chain 'A' and resid 3513 through 3518 removed outlier: 3.542A pdb=" N LYS A3517 " --> pdb=" O HIS A3513 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU A3518 " --> pdb=" O LEU A3514 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3513 through 3518' Processing helix chain 'A' and resid 3557 through 3566 Processing helix chain 'A' and resid 3615 through 3628 removed outlier: 4.229A pdb=" N SER A3626 " --> pdb=" O GLY A3622 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE A3628 " --> pdb=" O GLU A3624 " (cutoff:3.500A) Processing helix chain 'A' and resid 3628 through 3645 removed outlier: 3.765A pdb=" N HIS A3633 " --> pdb=" O GLU A3629 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR A3634 " --> pdb=" O THR A3630 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE A3635 " --> pdb=" O GLU A3631 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU A3639 " --> pdb=" O PHE A3635 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU A3641 " --> pdb=" O ASP A3637 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP A3642 " --> pdb=" O LYS A3638 " (cutoff:3.500A) Processing helix chain 'A' and resid 3661 through 3676 removed outlier: 3.748A pdb=" N GLN A3665 " --> pdb=" O ASP A3661 " (cutoff:3.500A) Processing helix chain 'A' and resid 3684 through 3698 removed outlier: 3.539A pdb=" N CYS A3698 " --> pdb=" O MET A3694 " (cutoff:3.500A) Processing helix chain 'A' and resid 3715 through 3732 Processing helix chain 'A' and resid 3734 through 3746 Processing helix chain 'A' and resid 3751 through 3766 removed outlier: 3.736A pdb=" N ALA A3756 " --> pdb=" O PRO A3752 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR A3757 " --> pdb=" O MET A3753 " (cutoff:3.500A) Processing helix chain 'A' and resid 3769 through 3784 Processing helix chain 'A' and resid 3786 through 3799 Processing helix chain 'A' and resid 3803 through 3812 removed outlier: 3.566A pdb=" N ARG A3809 " --> pdb=" O ASN A3805 " (cutoff:3.500A) Processing helix chain 'A' and resid 3832 through 3845 Processing helix chain 'A' and resid 3850 through 3857 Processing helix chain 'A' and resid 3868 through 3887 removed outlier: 3.946A pdb=" N SER A3872 " --> pdb=" O ASN A3868 " (cutoff:3.500A) Processing helix chain 'A' and resid 3888 through 3893 removed outlier: 4.038A pdb=" N GLY A3893 " --> pdb=" O TRP A3889 " (cutoff:3.500A) Processing helix chain 'A' and resid 3898 through 3924 removed outlier: 3.537A pdb=" N ARG A3903 " --> pdb=" O GLU A3899 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE A3923 " --> pdb=" O LEU A3919 " (cutoff:3.500A) Processing helix chain 'A' and resid 3927 through 3936 Processing helix chain 'A' and resid 3938 through 3959 removed outlier: 3.783A pdb=" N GLN A3954 " --> pdb=" O PHE A3950 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N MET A3955 " --> pdb=" O ALA A3951 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS A3956 " --> pdb=" O HIS A3952 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN A3959 " --> pdb=" O MET A3955 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3985 removed outlier: 3.808A pdb=" N LEU A3985 " --> pdb=" O LEU A3981 " (cutoff:3.500A) Processing helix chain 'A' and resid 3992 through 4005 removed outlier: 4.464A pdb=" N GLU A4004 " --> pdb=" O ASP A4000 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER A4005 " --> pdb=" O MET A4001 " (cutoff:3.500A) Processing helix chain 'A' and resid 4005 through 4014 Processing helix chain 'A' and resid 4027 through 4032 removed outlier: 4.361A pdb=" N PHE A4031 " --> pdb=" O SER A4027 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A4032 " --> pdb=" O SER A4028 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4027 through 4032' Processing helix chain 'A' and resid 4043 through 4051 removed outlier: 3.542A pdb=" N MET A4051 " --> pdb=" O PHE A4047 " (cutoff:3.500A) Processing helix chain 'A' and resid 4062 through 4069 removed outlier: 3.643A pdb=" N LEU A4066 " --> pdb=" O THR A4062 " (cutoff:3.500A) Processing helix chain 'A' and resid 4079 through 4085 removed outlier: 3.696A pdb=" N VAL A4083 " --> pdb=" O TYR A4079 " (cutoff:3.500A) Processing helix chain 'A' and resid 4087 through 4108 removed outlier: 4.339A pdb=" N LYS A4091 " --> pdb=" O HIS A4087 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN A4096 " --> pdb=" O ASP A4092 " (cutoff:3.500A) Processing helix chain 'A' and resid 4111 through 4121 removed outlier: 3.762A pdb=" N GLN A4115 " --> pdb=" O ASP A4111 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR A4116 " --> pdb=" O THR A4112 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE A4117 " --> pdb=" O ARG A4113 " (cutoff:3.500A) Processing helix chain 'A' and resid 4121 through 4129 Processing helix chain 'A' and resid 4152 through 4160 removed outlier: 3.712A pdb=" N GLU A4160 " --> pdb=" O ARG A4156 " (cutoff:3.500A) Processing helix chain 'A' and resid 4161 through 4179 removed outlier: 3.722A pdb=" N ASN A4177 " --> pdb=" O PHE A4173 " (cutoff:3.500A) Processing helix chain 'A' and resid 4182 through 4204 removed outlier: 3.850A pdb=" N GLU A4186 " --> pdb=" O LYS A4182 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN A4204 " --> pdb=" O GLN A4200 " (cutoff:3.500A) Processing helix chain 'A' and resid 4484 through 4496 removed outlier: 3.598A pdb=" N ASN A4496 " --> pdb=" O TYR A4492 " (cutoff:3.500A) Processing helix chain 'A' and resid 4496 through 4515 Processing helix chain 'A' and resid 4516 through 4518 No H-bonds generated for 'chain 'A' and resid 4516 through 4518' Processing helix chain 'A' and resid 4566 through 4593 Processing helix chain 'A' and resid 4593 through 4612 removed outlier: 3.557A pdb=" N VAL A4597 " --> pdb=" O LYS A4593 " (cutoff:3.500A) Processing helix chain 'A' and resid 4624 through 4630 Processing helix chain 'A' and resid 4631 through 4634 Processing helix chain 'A' and resid 4647 through 4661 removed outlier: 4.028A pdb=" N MET A4653 " --> pdb=" O LYS A4649 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP A4654 " --> pdb=" O ARG A4650 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS A4655 " --> pdb=" O LYS A4651 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N GLU A4658 " --> pdb=" O ASP A4654 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N PHE A4659 " --> pdb=" O LYS A4655 " (cutoff:3.500A) Processing helix chain 'A' and resid 4661 through 4670 removed outlier: 3.870A pdb=" N ILE A4665 " --> pdb=" O GLY A4661 " (cutoff:3.500A) Processing helix chain 'A' and resid 4701 through 4715 Processing helix chain 'A' and resid 4715 through 4734 removed outlier: 3.931A pdb=" N HIS A4732 " --> pdb=" O SER A4728 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYR A4733 " --> pdb=" O VAL A4729 " (cutoff:3.500A) Processing helix chain 'A' and resid 4735 through 4743 removed outlier: 3.761A pdb=" N LEU A4743 " --> pdb=" O ALA A4740 " (cutoff:3.500A) Processing helix chain 'A' and resid 4744 through 4749 removed outlier: 3.568A pdb=" N PHE A4749 " --> pdb=" O ILE A4745 " (cutoff:3.500A) Processing helix chain 'A' and resid 4749 through 4762 removed outlier: 3.823A pdb=" N SER A4758 " --> pdb=" O THR A4754 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL A4759 " --> pdb=" O ILE A4755 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASN A4762 " --> pdb=" O SER A4758 " (cutoff:3.500A) Processing helix chain 'A' and resid 4762 through 4787 removed outlier: 3.640A pdb=" N VAL A4767 " --> pdb=" O GLY A4763 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU A4768 " --> pdb=" O LYS A4764 " (cutoff:3.500A) Processing helix chain 'A' and resid 4788 through 4792 Processing helix chain 'A' and resid 4808 through 4818 Processing helix chain 'A' and resid 4825 through 4830 removed outlier: 3.790A pdb=" N ASP A4828 " --> pdb=" O GLY A4825 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE A4830 " --> pdb=" O GLY A4827 " (cutoff:3.500A) Processing helix chain 'A' and resid 4838 through 4853 Processing helix chain 'A' and resid 4855 through 4886 removed outlier: 4.085A pdb=" N ILE A4865 " --> pdb=" O ILE A4861 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE A4866 " --> pdb=" O GLN A4862 " (cutoff:3.500A) Processing helix chain 'A' and resid 4893 through 4898 removed outlier: 3.872A pdb=" N PHE A4897 " --> pdb=" O GLY A4893 " (cutoff:3.500A) Processing helix chain 'A' and resid 4902 through 4910 Processing helix chain 'A' and resid 4913 through 4926 removed outlier: 3.706A pdb=" N LEU A4921 " --> pdb=" O TYR A4917 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET A4922 " --> pdb=" O LEU A4918 " (cutoff:3.500A) Processing helix chain 'A' and resid 4928 through 4932 removed outlier: 3.561A pdb=" N HIS A4932 " --> pdb=" O GLU A4929 " (cutoff:3.500A) Processing helix chain 'A' and resid 4933 through 4946 removed outlier: 3.590A pdb=" N MET A4942 " --> pdb=" O TYR A4938 " (cutoff:3.500A) Processing helix chain 'A' and resid 4956 through 4961 Processing helix chain 'B' and resid 255 through 259 removed outlier: 4.034A pdb=" N THR B 259 " --> pdb=" O GLN B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 438 removed outlier: 4.162A pdb=" N LYS B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 464 Processing helix chain 'B' and resid 471 through 494 removed outlier: 3.699A pdb=" N MET B 494 " --> pdb=" O GLN B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 506 Processing helix chain 'B' and resid 512 through 518 Processing helix chain 'B' and resid 525 through 543 Processing helix chain 'B' and resid 554 through 563 Processing helix chain 'B' and resid 568 through 582 Processing helix chain 'B' and resid 584 through 588 removed outlier: 3.529A pdb=" N ASN B 587 " --> pdb=" O GLU B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 604 Processing helix chain 'B' and resid 609 through 617 removed outlier: 3.917A pdb=" N VAL B 613 " --> pdb=" O LYS B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 636 Processing helix chain 'B' and resid 875 through 877 No H-bonds generated for 'chain 'B' and resid 875 through 877' Processing helix chain 'B' and resid 878 through 901 removed outlier: 3.996A pdb=" N GLY B 901 " --> pdb=" O LYS B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 912 Processing helix chain 'B' and resid 925 through 945 Processing helix chain 'B' and resid 965 through 969 removed outlier: 3.672A pdb=" N ASN B 969 " --> pdb=" O LEU B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1015 Processing helix chain 'B' and resid 1043 through 1061 Processing helix chain 'B' and resid 1092 through 1095 Processing helix chain 'B' and resid 1230 through 1235 Processing helix chain 'B' and resid 1633 through 1637 removed outlier: 4.432A pdb=" N ASN B1637 " --> pdb=" O PRO B1634 " (cutoff:3.500A) Processing helix chain 'B' and resid 1648 through 1666 Processing helix chain 'B' and resid 1672 through 1681 removed outlier: 3.554A pdb=" N SER B1679 " --> pdb=" O HIS B1675 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS B1680 " --> pdb=" O ALA B1676 " (cutoff:3.500A) Processing helix chain 'B' and resid 1682 through 1692 Processing helix chain 'B' and resid 1696 through 1712 Processing helix chain 'B' and resid 1713 through 1723 Processing helix chain 'B' and resid 1784 through 1806 removed outlier: 3.653A pdb=" N LEU B1805 " --> pdb=" O LYS B1801 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS B1806 " --> pdb=" O GLU B1802 " (cutoff:3.500A) Processing helix chain 'B' and resid 1814 through 1831 Proline residue: B1821 - end of helix Processing helix chain 'B' and resid 1836 through 1845 removed outlier: 3.629A pdb=" N GLN B1845 " --> pdb=" O LYS B1841 " (cutoff:3.500A) Processing helix chain 'B' and resid 1898 through 1939 removed outlier: 4.304A pdb=" N GLN B1904 " --> pdb=" O PRO B1900 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N MET B1905 " --> pdb=" O VAL B1901 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS B1906 " --> pdb=" O LYS B1902 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU B1907 " --> pdb=" O LEU B1903 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP B1929 " --> pdb=" O VAL B1925 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP B1930 " --> pdb=" O ALA B1926 " (cutoff:3.500A) Processing helix chain 'B' and resid 1952 through 1958 removed outlier: 3.868A pdb=" N LEU B1956 " --> pdb=" O MET B1952 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B1958 " --> pdb=" O ALA B1954 " (cutoff:3.500A) Processing helix chain 'B' and resid 1999 through 2006 removed outlier: 3.890A pdb=" N MET B2003 " --> pdb=" O HIS B1999 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N CYS B2006 " --> pdb=" O LEU B2002 " (cutoff:3.500A) Processing helix chain 'B' and resid 2010 through 2016 Processing helix chain 'B' and resid 2023 through 2036 removed outlier: 4.524A pdb=" N ARG B2027 " --> pdb=" O THR B2023 " (cutoff:3.500A) Processing helix chain 'B' and resid 2056 through 2072 removed outlier: 3.899A pdb=" N SER B2072 " --> pdb=" O TRP B2068 " (cutoff:3.500A) Processing helix chain 'B' and resid 2076 through 2092 removed outlier: 3.745A pdb=" N VAL B2080 " --> pdb=" O ASP B2076 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN B2090 " --> pdb=" O LEU B2086 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR B2091 " --> pdb=" O LEU B2087 " (cutoff:3.500A) Processing helix chain 'B' and resid 2092 through 2104 Proline residue: B2102 - end of helix Processing helix chain 'B' and resid 2111 through 2127 removed outlier: 4.231A pdb=" N ASN B2117 " --> pdb=" O GLU B2113 " (cutoff:3.500A) Processing helix chain 'B' and resid 2136 through 2150 removed outlier: 4.411A pdb=" N LEU B2140 " --> pdb=" O GLU B2136 " (cutoff:3.500A) Processing helix chain 'B' and resid 2152 through 2157 Processing helix chain 'B' and resid 2158 through 2165 removed outlier: 4.157A pdb=" N ARG B2162 " --> pdb=" O PRO B2158 " (cutoff:3.500A) Processing helix chain 'B' and resid 2165 through 2179 Processing helix chain 'B' and resid 2189 through 2202 removed outlier: 3.998A pdb=" N ALA B2193 " --> pdb=" O PRO B2189 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASN B2194 " --> pdb=" O LYS B2190 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE B2198 " --> pdb=" O ASN B2194 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU B2199 " --> pdb=" O CYS B2195 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS B2200 " --> pdb=" O CYS B2196 " (cutoff:3.500A) Processing helix chain 'B' and resid 2208 through 2215 Processing helix chain 'B' and resid 2216 through 2223 Processing helix chain 'B' and resid 2238 through 2246 removed outlier: 3.817A pdb=" N ALA B2242 " --> pdb=" O PRO B2238 " (cutoff:3.500A) Processing helix chain 'B' and resid 2249 through 2256 removed outlier: 3.551A pdb=" N ALA B2253 " --> pdb=" O ASN B2249 " (cutoff:3.500A) Processing helix chain 'B' and resid 2257 through 2260 removed outlier: 3.565A pdb=" N ASP B2260 " --> pdb=" O ARG B2257 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2257 through 2260' Processing helix chain 'B' and resid 2261 through 2271 removed outlier: 3.809A pdb=" N VAL B2265 " --> pdb=" O LEU B2261 " (cutoff:3.500A) Processing helix chain 'B' and resid 2294 through 2305 removed outlier: 3.686A pdb=" N LEU B2298 " --> pdb=" O GLY B2294 " (cutoff:3.500A) Processing helix chain 'B' and resid 2312 through 2326 removed outlier: 3.768A pdb=" N ALA B2316 " --> pdb=" O VAL B2312 " (cutoff:3.500A) Processing helix chain 'B' and resid 2341 through 2354 removed outlier: 4.649A pdb=" N GLU B2347 " --> pdb=" O LEU B2343 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS B2351 " --> pdb=" O GLU B2347 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE B2352 " --> pdb=" O GLU B2348 " (cutoff:3.500A) Processing helix chain 'B' and resid 2386 through 2402 Processing helix chain 'B' and resid 2415 through 2425 removed outlier: 3.765A pdb=" N ARG B2419 " --> pdb=" O ALA B2415 " (cutoff:3.500A) Processing helix chain 'B' and resid 2430 through 2432 No H-bonds generated for 'chain 'B' and resid 2430 through 2432' Processing helix chain 'B' and resid 2433 through 2440 removed outlier: 3.742A pdb=" N GLN B2440 " --> pdb=" O SER B2436 " (cutoff:3.500A) Processing helix chain 'B' and resid 2461 through 2475 removed outlier: 3.999A pdb=" N ALA B2465 " --> pdb=" O PRO B2461 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA B2466 " --> pdb=" O ASP B2462 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B2471 " --> pdb=" O MET B2467 " (cutoff:3.500A) Processing helix chain 'B' and resid 2479 through 2487 removed outlier: 3.929A pdb=" N LEU B2483 " --> pdb=" O VAL B2479 " (cutoff:3.500A) Processing helix chain 'B' and resid 2490 through 2500 removed outlier: 3.566A pdb=" N ALA B2498 " --> pdb=" O ASP B2494 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B2499 " --> pdb=" O LEU B2495 " (cutoff:3.500A) Processing helix chain 'B' and resid 2511 through 2522 Processing helix chain 'B' and resid 2582 through 2591 removed outlier: 3.959A pdb=" N HIS B2586 " --> pdb=" O SER B2582 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG B2589 " --> pdb=" O GLN B2585 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG B2590 " --> pdb=" O HIS B2586 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B2591 " --> pdb=" O LEU B2587 " (cutoff:3.500A) Processing helix chain 'B' and resid 2599 through 2614 removed outlier: 3.783A pdb=" N LYS B2603 " --> pdb=" O ASN B2599 " (cutoff:3.500A) Proline residue: B2605 - end of helix removed outlier: 3.783A pdb=" N THR B2610 " --> pdb=" O LEU B2606 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASN B2611 " --> pdb=" O LYS B2607 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N HIS B2612 " --> pdb=" O LEU B2608 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR B2613 " --> pdb=" O LEU B2609 " (cutoff:3.500A) Processing helix chain 'B' and resid 2621 through 2633 Processing helix chain 'B' and resid 2639 through 2650 removed outlier: 4.037A pdb=" N LEU B2643 " --> pdb=" O LEU B2639 " (cutoff:3.500A) Processing helix chain 'B' and resid 2660 through 2675 removed outlier: 3.656A pdb=" N LEU B2665 " --> pdb=" O PHE B2661 " (cutoff:3.500A) Proline residue: B2666 - end of helix removed outlier: 3.903A pdb=" N SER B2669 " --> pdb=" O LEU B2665 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B2675 " --> pdb=" O VAL B2671 " (cutoff:3.500A) Processing helix chain 'B' and resid 2718 through 2739 Processing helix chain 'B' and resid 2763 through 2785 Proline residue: B2773 - end of helix Processing helix chain 'B' and resid 2816 through 2820 removed outlier: 3.691A pdb=" N GLY B2819 " --> pdb=" O ALA B2816 " (cutoff:3.500A) Processing helix chain 'B' and resid 2833 through 2863 Processing helix chain 'B' and resid 2877 through 2896 removed outlier: 3.935A pdb=" N LYS B2883 " --> pdb=" O LYS B2879 " (cutoff:3.500A) Processing helix chain 'B' and resid 2990 through 3012 removed outlier: 4.295A pdb=" N SER B2996 " --> pdb=" O GLY B2992 " (cutoff:3.500A) Processing helix chain 'B' and resid 3037 through 3050 removed outlier: 3.796A pdb=" N ARG B3042 " --> pdb=" O THR B3038 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS B3046 " --> pdb=" O ARG B3042 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR B3047 " --> pdb=" O THR B3043 " (cutoff:3.500A) Processing helix chain 'B' and resid 3054 through 3063 removed outlier: 3.530A pdb=" N LEU B3060 " --> pdb=" O LEU B3056 " (cutoff:3.500A) Processing helix chain 'B' and resid 3066 through 3083 Processing helix chain 'B' and resid 3090 through 3099 Processing helix chain 'B' and resid 3183 through 3192 Processing helix chain 'B' and resid 3214 through 3225 removed outlier: 4.140A pdb=" N ILE B3218 " --> pdb=" O MET B3214 " (cutoff:3.500A) Processing helix chain 'B' and resid 3238 through 3252 removed outlier: 4.369A pdb=" N TYR B3244 " --> pdb=" O MET B3240 " (cutoff:3.500A) Processing helix chain 'B' and resid 3263 through 3268 removed outlier: 3.700A pdb=" N ALA B3266 " --> pdb=" O CYS B3263 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN B3268 " --> pdb=" O THR B3265 " (cutoff:3.500A) Processing helix chain 'B' and resid 3286 through 3292 Processing helix chain 'B' and resid 3308 through 3324 removed outlier: 4.258A pdb=" N GLN B3312 " --> pdb=" O LYS B3308 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU B3319 " --> pdb=" O LYS B3315 " (cutoff:3.500A) Proline residue: B3320 - end of helix Processing helix chain 'B' and resid 3330 through 3344 Processing helix chain 'B' and resid 3355 through 3374 removed outlier: 4.280A pdb=" N THR B3359 " --> pdb=" O LEU B3355 " (cutoff:3.500A) Proline residue: B3370 - end of helix Processing helix chain 'B' and resid 3405 through 3431 removed outlier: 3.896A pdb=" N VAL B3420 " --> pdb=" O GLN B3416 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN B3421 " --> pdb=" O ASN B3417 " (cutoff:3.500A) Processing helix chain 'B' and resid 3436 through 3473 removed outlier: 4.115A pdb=" N ASP B3456 " --> pdb=" O LYS B3452 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG B3457 " --> pdb=" O ARG B3453 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B3467 " --> pdb=" O SER B3463 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ARG B3471 " --> pdb=" O ALA B3467 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU B3472 " --> pdb=" O ALA B3468 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU B3473 " --> pdb=" O LEU B3469 " (cutoff:3.500A) Processing helix chain 'B' and resid 3473 through 3491 removed outlier: 3.713A pdb=" N LEU B3477 " --> pdb=" O LEU B3473 " (cutoff:3.500A) Proline residue: B3482 - end of helix removed outlier: 3.502A pdb=" N GLN B3485 " --> pdb=" O ALA B3481 " (cutoff:3.500A) Processing helix chain 'B' and resid 3494 through 3508 removed outlier: 4.288A pdb=" N THR B3500 " --> pdb=" O SER B3496 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B3508 " --> pdb=" O VAL B3504 " (cutoff:3.500A) Processing helix chain 'B' and resid 3513 through 3518 removed outlier: 3.542A pdb=" N LYS B3517 " --> pdb=" O HIS B3513 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU B3518 " --> pdb=" O LEU B3514 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3513 through 3518' Processing helix chain 'B' and resid 3557 through 3566 Processing helix chain 'B' and resid 3615 through 3628 removed outlier: 4.229A pdb=" N SER B3626 " --> pdb=" O GLY B3622 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE B3628 " --> pdb=" O GLU B3624 " (cutoff:3.500A) Processing helix chain 'B' and resid 3628 through 3645 removed outlier: 3.765A pdb=" N HIS B3633 " --> pdb=" O GLU B3629 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR B3634 " --> pdb=" O THR B3630 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE B3635 " --> pdb=" O GLU B3631 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU B3639 " --> pdb=" O PHE B3635 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU B3641 " --> pdb=" O ASP B3637 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP B3642 " --> pdb=" O LYS B3638 " (cutoff:3.500A) Processing helix chain 'B' and resid 3661 through 3676 removed outlier: 3.748A pdb=" N GLN B3665 " --> pdb=" O ASP B3661 " (cutoff:3.500A) Processing helix chain 'B' and resid 3684 through 3698 removed outlier: 3.539A pdb=" N CYS B3698 " --> pdb=" O MET B3694 " (cutoff:3.500A) Processing helix chain 'B' and resid 3715 through 3732 Processing helix chain 'B' and resid 3734 through 3746 Processing helix chain 'B' and resid 3751 through 3766 removed outlier: 3.736A pdb=" N ALA B3756 " --> pdb=" O PRO B3752 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR B3757 " --> pdb=" O MET B3753 " (cutoff:3.500A) Processing helix chain 'B' and resid 3769 through 3784 Processing helix chain 'B' and resid 3786 through 3799 Processing helix chain 'B' and resid 3803 through 3812 removed outlier: 3.566A pdb=" N ARG B3809 " --> pdb=" O ASN B3805 " (cutoff:3.500A) Processing helix chain 'B' and resid 3832 through 3845 Processing helix chain 'B' and resid 3850 through 3857 Processing helix chain 'B' and resid 3868 through 3887 removed outlier: 3.946A pdb=" N SER B3872 " --> pdb=" O ASN B3868 " (cutoff:3.500A) Processing helix chain 'B' and resid 3888 through 3893 removed outlier: 4.038A pdb=" N GLY B3893 " --> pdb=" O TRP B3889 " (cutoff:3.500A) Processing helix chain 'B' and resid 3898 through 3924 removed outlier: 3.537A pdb=" N ARG B3903 " --> pdb=" O GLU B3899 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE B3923 " --> pdb=" O LEU B3919 " (cutoff:3.500A) Processing helix chain 'B' and resid 3927 through 3936 Processing helix chain 'B' and resid 3938 through 3959 removed outlier: 3.783A pdb=" N GLN B3954 " --> pdb=" O PHE B3950 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N MET B3955 " --> pdb=" O ALA B3951 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS B3956 " --> pdb=" O HIS B3952 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN B3959 " --> pdb=" O MET B3955 " (cutoff:3.500A) Processing helix chain 'B' and resid 3964 through 3985 removed outlier: 3.808A pdb=" N LEU B3985 " --> pdb=" O LEU B3981 " (cutoff:3.500A) Processing helix chain 'B' and resid 3992 through 4005 removed outlier: 4.464A pdb=" N GLU B4004 " --> pdb=" O ASP B4000 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B4005 " --> pdb=" O MET B4001 " (cutoff:3.500A) Processing helix chain 'B' and resid 4005 through 4014 Processing helix chain 'B' and resid 4027 through 4032 removed outlier: 4.361A pdb=" N PHE B4031 " --> pdb=" O SER B4027 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS B4032 " --> pdb=" O SER B4028 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4027 through 4032' Processing helix chain 'B' and resid 4043 through 4051 removed outlier: 3.542A pdb=" N MET B4051 " --> pdb=" O PHE B4047 " (cutoff:3.500A) Processing helix chain 'B' and resid 4062 through 4069 removed outlier: 3.643A pdb=" N LEU B4066 " --> pdb=" O THR B4062 " (cutoff:3.500A) Processing helix chain 'B' and resid 4079 through 4085 removed outlier: 3.696A pdb=" N VAL B4083 " --> pdb=" O TYR B4079 " (cutoff:3.500A) Processing helix chain 'B' and resid 4087 through 4108 removed outlier: 4.339A pdb=" N LYS B4091 " --> pdb=" O HIS B4087 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN B4096 " --> pdb=" O ASP B4092 " (cutoff:3.500A) Processing helix chain 'B' and resid 4111 through 4121 removed outlier: 3.762A pdb=" N GLN B4115 " --> pdb=" O ASP B4111 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR B4116 " --> pdb=" O THR B4112 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE B4117 " --> pdb=" O ARG B4113 " (cutoff:3.500A) Processing helix chain 'B' and resid 4121 through 4129 Processing helix chain 'B' and resid 4152 through 4160 removed outlier: 3.712A pdb=" N GLU B4160 " --> pdb=" O ARG B4156 " (cutoff:3.500A) Processing helix chain 'B' and resid 4161 through 4179 removed outlier: 3.722A pdb=" N ASN B4177 " --> pdb=" O PHE B4173 " (cutoff:3.500A) Processing helix chain 'B' and resid 4182 through 4204 removed outlier: 3.850A pdb=" N GLU B4186 " --> pdb=" O LYS B4182 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN B4204 " --> pdb=" O GLN B4200 " (cutoff:3.500A) Processing helix chain 'B' and resid 4484 through 4496 removed outlier: 3.598A pdb=" N ASN B4496 " --> pdb=" O TYR B4492 " (cutoff:3.500A) Processing helix chain 'B' and resid 4496 through 4515 Processing helix chain 'B' and resid 4516 through 4518 No H-bonds generated for 'chain 'B' and resid 4516 through 4518' Processing helix chain 'B' and resid 4566 through 4593 Processing helix chain 'B' and resid 4593 through 4612 removed outlier: 3.557A pdb=" N VAL B4597 " --> pdb=" O LYS B4593 " (cutoff:3.500A) Processing helix chain 'B' and resid 4624 through 4630 Processing helix chain 'B' and resid 4631 through 4634 Processing helix chain 'B' and resid 4647 through 4661 removed outlier: 4.028A pdb=" N MET B4653 " --> pdb=" O LYS B4649 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP B4654 " --> pdb=" O ARG B4650 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS B4655 " --> pdb=" O LYS B4651 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N GLU B4658 " --> pdb=" O ASP B4654 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N PHE B4659 " --> pdb=" O LYS B4655 " (cutoff:3.500A) Processing helix chain 'B' and resid 4661 through 4670 removed outlier: 3.870A pdb=" N ILE B4665 " --> pdb=" O GLY B4661 " (cutoff:3.500A) Processing helix chain 'B' and resid 4701 through 4715 Processing helix chain 'B' and resid 4715 through 4734 removed outlier: 3.931A pdb=" N HIS B4732 " --> pdb=" O SER B4728 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYR B4733 " --> pdb=" O VAL B4729 " (cutoff:3.500A) Processing helix chain 'B' and resid 4735 through 4743 removed outlier: 3.761A pdb=" N LEU B4743 " --> pdb=" O ALA B4740 " (cutoff:3.500A) Processing helix chain 'B' and resid 4744 through 4749 removed outlier: 3.568A pdb=" N PHE B4749 " --> pdb=" O ILE B4745 " (cutoff:3.500A) Processing helix chain 'B' and resid 4749 through 4762 removed outlier: 3.823A pdb=" N SER B4758 " --> pdb=" O THR B4754 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL B4759 " --> pdb=" O ILE B4755 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASN B4762 " --> pdb=" O SER B4758 " (cutoff:3.500A) Processing helix chain 'B' and resid 4762 through 4787 removed outlier: 3.640A pdb=" N VAL B4767 " --> pdb=" O GLY B4763 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU B4768 " --> pdb=" O LYS B4764 " (cutoff:3.500A) Processing helix chain 'B' and resid 4788 through 4792 Processing helix chain 'B' and resid 4808 through 4818 Processing helix chain 'B' and resid 4825 through 4830 removed outlier: 3.790A pdb=" N ASP B4828 " --> pdb=" O GLY B4825 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE B4830 " --> pdb=" O GLY B4827 " (cutoff:3.500A) Processing helix chain 'B' and resid 4838 through 4853 Processing helix chain 'B' and resid 4855 through 4886 removed outlier: 4.085A pdb=" N ILE B4865 " --> pdb=" O ILE B4861 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE B4866 " --> pdb=" O GLN B4862 " (cutoff:3.500A) Processing helix chain 'B' and resid 4893 through 4898 removed outlier: 3.872A pdb=" N PHE B4897 " --> pdb=" O GLY B4893 " (cutoff:3.500A) Processing helix chain 'B' and resid 4902 through 4910 Processing helix chain 'B' and resid 4913 through 4926 removed outlier: 3.706A pdb=" N LEU B4921 " --> pdb=" O TYR B4917 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET B4922 " --> pdb=" O LEU B4918 " (cutoff:3.500A) Processing helix chain 'B' and resid 4928 through 4932 removed outlier: 3.561A pdb=" N HIS B4932 " --> pdb=" O GLU B4929 " (cutoff:3.500A) Processing helix chain 'B' and resid 4933 through 4946 removed outlier: 3.590A pdb=" N MET B4942 " --> pdb=" O TYR B4938 " (cutoff:3.500A) Processing helix chain 'B' and resid 4956 through 4961 Processing helix chain 'C' and resid 255 through 259 removed outlier: 4.034A pdb=" N THR C 259 " --> pdb=" O GLN C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 438 removed outlier: 4.162A pdb=" N LYS C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 464 Processing helix chain 'C' and resid 471 through 494 removed outlier: 3.699A pdb=" N MET C 494 " --> pdb=" O GLN C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 506 Processing helix chain 'C' and resid 512 through 518 Processing helix chain 'C' and resid 525 through 543 Processing helix chain 'C' and resid 554 through 563 Processing helix chain 'C' and resid 568 through 582 Processing helix chain 'C' and resid 584 through 588 removed outlier: 3.529A pdb=" N ASN C 587 " --> pdb=" O GLU C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 604 Processing helix chain 'C' and resid 609 through 617 removed outlier: 3.917A pdb=" N VAL C 613 " --> pdb=" O LYS C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 636 Processing helix chain 'C' and resid 875 through 877 No H-bonds generated for 'chain 'C' and resid 875 through 877' Processing helix chain 'C' and resid 878 through 901 removed outlier: 3.996A pdb=" N GLY C 901 " --> pdb=" O LYS C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 912 Processing helix chain 'C' and resid 925 through 945 Processing helix chain 'C' and resid 965 through 969 removed outlier: 3.672A pdb=" N ASN C 969 " --> pdb=" O LEU C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 1015 Processing helix chain 'C' and resid 1043 through 1061 Processing helix chain 'C' and resid 1092 through 1095 Processing helix chain 'C' and resid 1230 through 1235 Processing helix chain 'C' and resid 1633 through 1637 removed outlier: 4.432A pdb=" N ASN C1637 " --> pdb=" O PRO C1634 " (cutoff:3.500A) Processing helix chain 'C' and resid 1648 through 1666 Processing helix chain 'C' and resid 1672 through 1681 removed outlier: 3.554A pdb=" N SER C1679 " --> pdb=" O HIS C1675 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS C1680 " --> pdb=" O ALA C1676 " (cutoff:3.500A) Processing helix chain 'C' and resid 1682 through 1692 Processing helix chain 'C' and resid 1696 through 1712 Processing helix chain 'C' and resid 1713 through 1723 Processing helix chain 'C' and resid 1784 through 1806 removed outlier: 3.653A pdb=" N LEU C1805 " --> pdb=" O LYS C1801 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS C1806 " --> pdb=" O GLU C1802 " (cutoff:3.500A) Processing helix chain 'C' and resid 1814 through 1831 Proline residue: C1821 - end of helix Processing helix chain 'C' and resid 1836 through 1845 removed outlier: 3.629A pdb=" N GLN C1845 " --> pdb=" O LYS C1841 " (cutoff:3.500A) Processing helix chain 'C' and resid 1898 through 1939 removed outlier: 4.304A pdb=" N GLN C1904 " --> pdb=" O PRO C1900 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N MET C1905 " --> pdb=" O VAL C1901 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS C1906 " --> pdb=" O LYS C1902 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU C1907 " --> pdb=" O LEU C1903 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP C1929 " --> pdb=" O VAL C1925 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP C1930 " --> pdb=" O ALA C1926 " (cutoff:3.500A) Processing helix chain 'C' and resid 1952 through 1958 removed outlier: 3.868A pdb=" N LEU C1956 " --> pdb=" O MET C1952 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA C1958 " --> pdb=" O ALA C1954 " (cutoff:3.500A) Processing helix chain 'C' and resid 1999 through 2006 removed outlier: 3.890A pdb=" N MET C2003 " --> pdb=" O HIS C1999 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N CYS C2006 " --> pdb=" O LEU C2002 " (cutoff:3.500A) Processing helix chain 'C' and resid 2010 through 2016 Processing helix chain 'C' and resid 2023 through 2036 removed outlier: 4.524A pdb=" N ARG C2027 " --> pdb=" O THR C2023 " (cutoff:3.500A) Processing helix chain 'C' and resid 2056 through 2072 removed outlier: 3.899A pdb=" N SER C2072 " --> pdb=" O TRP C2068 " (cutoff:3.500A) Processing helix chain 'C' and resid 2076 through 2092 removed outlier: 3.745A pdb=" N VAL C2080 " --> pdb=" O ASP C2076 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN C2090 " --> pdb=" O LEU C2086 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR C2091 " --> pdb=" O LEU C2087 " (cutoff:3.500A) Processing helix chain 'C' and resid 2092 through 2104 Proline residue: C2102 - end of helix Processing helix chain 'C' and resid 2111 through 2127 removed outlier: 4.231A pdb=" N ASN C2117 " --> pdb=" O GLU C2113 " (cutoff:3.500A) Processing helix chain 'C' and resid 2136 through 2150 removed outlier: 4.411A pdb=" N LEU C2140 " --> pdb=" O GLU C2136 " (cutoff:3.500A) Processing helix chain 'C' and resid 2152 through 2157 Processing helix chain 'C' and resid 2158 through 2165 removed outlier: 4.157A pdb=" N ARG C2162 " --> pdb=" O PRO C2158 " (cutoff:3.500A) Processing helix chain 'C' and resid 2165 through 2179 Processing helix chain 'C' and resid 2189 through 2202 removed outlier: 3.998A pdb=" N ALA C2193 " --> pdb=" O PRO C2189 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASN C2194 " --> pdb=" O LYS C2190 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE C2198 " --> pdb=" O ASN C2194 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU C2199 " --> pdb=" O CYS C2195 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS C2200 " --> pdb=" O CYS C2196 " (cutoff:3.500A) Processing helix chain 'C' and resid 2208 through 2215 Processing helix chain 'C' and resid 2216 through 2223 Processing helix chain 'C' and resid 2238 through 2246 removed outlier: 3.817A pdb=" N ALA C2242 " --> pdb=" O PRO C2238 " (cutoff:3.500A) Processing helix chain 'C' and resid 2249 through 2256 removed outlier: 3.551A pdb=" N ALA C2253 " --> pdb=" O ASN C2249 " (cutoff:3.500A) Processing helix chain 'C' and resid 2257 through 2260 removed outlier: 3.565A pdb=" N ASP C2260 " --> pdb=" O ARG C2257 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2257 through 2260' Processing helix chain 'C' and resid 2261 through 2271 removed outlier: 3.809A pdb=" N VAL C2265 " --> pdb=" O LEU C2261 " (cutoff:3.500A) Processing helix chain 'C' and resid 2294 through 2305 removed outlier: 3.686A pdb=" N LEU C2298 " --> pdb=" O GLY C2294 " (cutoff:3.500A) Processing helix chain 'C' and resid 2312 through 2326 removed outlier: 3.768A pdb=" N ALA C2316 " --> pdb=" O VAL C2312 " (cutoff:3.500A) Processing helix chain 'C' and resid 2341 through 2354 removed outlier: 4.649A pdb=" N GLU C2347 " --> pdb=" O LEU C2343 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS C2351 " --> pdb=" O GLU C2347 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE C2352 " --> pdb=" O GLU C2348 " (cutoff:3.500A) Processing helix chain 'C' and resid 2386 through 2402 Processing helix chain 'C' and resid 2415 through 2425 removed outlier: 3.765A pdb=" N ARG C2419 " --> pdb=" O ALA C2415 " (cutoff:3.500A) Processing helix chain 'C' and resid 2430 through 2432 No H-bonds generated for 'chain 'C' and resid 2430 through 2432' Processing helix chain 'C' and resid 2433 through 2440 removed outlier: 3.742A pdb=" N GLN C2440 " --> pdb=" O SER C2436 " (cutoff:3.500A) Processing helix chain 'C' and resid 2461 through 2475 removed outlier: 3.999A pdb=" N ALA C2465 " --> pdb=" O PRO C2461 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA C2466 " --> pdb=" O ASP C2462 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C2471 " --> pdb=" O MET C2467 " (cutoff:3.500A) Processing helix chain 'C' and resid 2479 through 2487 removed outlier: 3.929A pdb=" N LEU C2483 " --> pdb=" O VAL C2479 " (cutoff:3.500A) Processing helix chain 'C' and resid 2490 through 2500 removed outlier: 3.566A pdb=" N ALA C2498 " --> pdb=" O ASP C2494 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA C2499 " --> pdb=" O LEU C2495 " (cutoff:3.500A) Processing helix chain 'C' and resid 2511 through 2522 Processing helix chain 'C' and resid 2582 through 2591 removed outlier: 3.959A pdb=" N HIS C2586 " --> pdb=" O SER C2582 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG C2589 " --> pdb=" O GLN C2585 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG C2590 " --> pdb=" O HIS C2586 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU C2591 " --> pdb=" O LEU C2587 " (cutoff:3.500A) Processing helix chain 'C' and resid 2599 through 2614 removed outlier: 3.783A pdb=" N LYS C2603 " --> pdb=" O ASN C2599 " (cutoff:3.500A) Proline residue: C2605 - end of helix removed outlier: 3.783A pdb=" N THR C2610 " --> pdb=" O LEU C2606 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASN C2611 " --> pdb=" O LYS C2607 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N HIS C2612 " --> pdb=" O LEU C2608 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR C2613 " --> pdb=" O LEU C2609 " (cutoff:3.500A) Processing helix chain 'C' and resid 2621 through 2633 Processing helix chain 'C' and resid 2639 through 2650 removed outlier: 4.037A pdb=" N LEU C2643 " --> pdb=" O LEU C2639 " (cutoff:3.500A) Processing helix chain 'C' and resid 2660 through 2675 removed outlier: 3.656A pdb=" N LEU C2665 " --> pdb=" O PHE C2661 " (cutoff:3.500A) Proline residue: C2666 - end of helix removed outlier: 3.903A pdb=" N SER C2669 " --> pdb=" O LEU C2665 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU C2675 " --> pdb=" O VAL C2671 " (cutoff:3.500A) Processing helix chain 'C' and resid 2718 through 2739 Processing helix chain 'C' and resid 2763 through 2785 Proline residue: C2773 - end of helix Processing helix chain 'C' and resid 2816 through 2820 removed outlier: 3.691A pdb=" N GLY C2819 " --> pdb=" O ALA C2816 " (cutoff:3.500A) Processing helix chain 'C' and resid 2833 through 2863 Processing helix chain 'C' and resid 2877 through 2896 removed outlier: 3.935A pdb=" N LYS C2883 " --> pdb=" O LYS C2879 " (cutoff:3.500A) Processing helix chain 'C' and resid 2990 through 3012 removed outlier: 4.295A pdb=" N SER C2996 " --> pdb=" O GLY C2992 " (cutoff:3.500A) Processing helix chain 'C' and resid 3037 through 3050 removed outlier: 3.796A pdb=" N ARG C3042 " --> pdb=" O THR C3038 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS C3046 " --> pdb=" O ARG C3042 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR C3047 " --> pdb=" O THR C3043 " (cutoff:3.500A) Processing helix chain 'C' and resid 3054 through 3063 removed outlier: 3.530A pdb=" N LEU C3060 " --> pdb=" O LEU C3056 " (cutoff:3.500A) Processing helix chain 'C' and resid 3066 through 3083 Processing helix chain 'C' and resid 3090 through 3099 Processing helix chain 'C' and resid 3183 through 3192 Processing helix chain 'C' and resid 3214 through 3225 removed outlier: 4.140A pdb=" N ILE C3218 " --> pdb=" O MET C3214 " (cutoff:3.500A) Processing helix chain 'C' and resid 3238 through 3252 removed outlier: 4.369A pdb=" N TYR C3244 " --> pdb=" O MET C3240 " (cutoff:3.500A) Processing helix chain 'C' and resid 3263 through 3268 removed outlier: 3.700A pdb=" N ALA C3266 " --> pdb=" O CYS C3263 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN C3268 " --> pdb=" O THR C3265 " (cutoff:3.500A) Processing helix chain 'C' and resid 3286 through 3292 Processing helix chain 'C' and resid 3308 through 3324 removed outlier: 4.258A pdb=" N GLN C3312 " --> pdb=" O LYS C3308 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU C3319 " --> pdb=" O LYS C3315 " (cutoff:3.500A) Proline residue: C3320 - end of helix Processing helix chain 'C' and resid 3330 through 3344 Processing helix chain 'C' and resid 3355 through 3374 removed outlier: 4.280A pdb=" N THR C3359 " --> pdb=" O LEU C3355 " (cutoff:3.500A) Proline residue: C3370 - end of helix Processing helix chain 'C' and resid 3405 through 3431 removed outlier: 3.896A pdb=" N VAL C3420 " --> pdb=" O GLN C3416 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN C3421 " --> pdb=" O ASN C3417 " (cutoff:3.500A) Processing helix chain 'C' and resid 3436 through 3473 removed outlier: 4.115A pdb=" N ASP C3456 " --> pdb=" O LYS C3452 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG C3457 " --> pdb=" O ARG C3453 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C3467 " --> pdb=" O SER C3463 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ARG C3471 " --> pdb=" O ALA C3467 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU C3472 " --> pdb=" O ALA C3468 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU C3473 " --> pdb=" O LEU C3469 " (cutoff:3.500A) Processing helix chain 'C' and resid 3473 through 3491 removed outlier: 3.713A pdb=" N LEU C3477 " --> pdb=" O LEU C3473 " (cutoff:3.500A) Proline residue: C3482 - end of helix removed outlier: 3.502A pdb=" N GLN C3485 " --> pdb=" O ALA C3481 " (cutoff:3.500A) Processing helix chain 'C' and resid 3494 through 3508 removed outlier: 4.288A pdb=" N THR C3500 " --> pdb=" O SER C3496 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE C3508 " --> pdb=" O VAL C3504 " (cutoff:3.500A) Processing helix chain 'C' and resid 3513 through 3518 removed outlier: 3.542A pdb=" N LYS C3517 " --> pdb=" O HIS C3513 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU C3518 " --> pdb=" O LEU C3514 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3513 through 3518' Processing helix chain 'C' and resid 3557 through 3566 Processing helix chain 'C' and resid 3615 through 3628 removed outlier: 4.229A pdb=" N SER C3626 " --> pdb=" O GLY C3622 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE C3628 " --> pdb=" O GLU C3624 " (cutoff:3.500A) Processing helix chain 'C' and resid 3628 through 3645 removed outlier: 3.765A pdb=" N HIS C3633 " --> pdb=" O GLU C3629 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR C3634 " --> pdb=" O THR C3630 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE C3635 " --> pdb=" O GLU C3631 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU C3639 " --> pdb=" O PHE C3635 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU C3641 " --> pdb=" O ASP C3637 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP C3642 " --> pdb=" O LYS C3638 " (cutoff:3.500A) Processing helix chain 'C' and resid 3661 through 3676 removed outlier: 3.748A pdb=" N GLN C3665 " --> pdb=" O ASP C3661 " (cutoff:3.500A) Processing helix chain 'C' and resid 3684 through 3698 removed outlier: 3.539A pdb=" N CYS C3698 " --> pdb=" O MET C3694 " (cutoff:3.500A) Processing helix chain 'C' and resid 3715 through 3732 Processing helix chain 'C' and resid 3734 through 3746 Processing helix chain 'C' and resid 3751 through 3766 removed outlier: 3.736A pdb=" N ALA C3756 " --> pdb=" O PRO C3752 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR C3757 " --> pdb=" O MET C3753 " (cutoff:3.500A) Processing helix chain 'C' and resid 3769 through 3784 Processing helix chain 'C' and resid 3786 through 3799 Processing helix chain 'C' and resid 3803 through 3812 removed outlier: 3.566A pdb=" N ARG C3809 " --> pdb=" O ASN C3805 " (cutoff:3.500A) Processing helix chain 'C' and resid 3832 through 3845 Processing helix chain 'C' and resid 3850 through 3857 Processing helix chain 'C' and resid 3868 through 3887 removed outlier: 3.946A pdb=" N SER C3872 " --> pdb=" O ASN C3868 " (cutoff:3.500A) Processing helix chain 'C' and resid 3888 through 3893 removed outlier: 4.038A pdb=" N GLY C3893 " --> pdb=" O TRP C3889 " (cutoff:3.500A) Processing helix chain 'C' and resid 3898 through 3924 removed outlier: 3.537A pdb=" N ARG C3903 " --> pdb=" O GLU C3899 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE C3923 " --> pdb=" O LEU C3919 " (cutoff:3.500A) Processing helix chain 'C' and resid 3927 through 3936 Processing helix chain 'C' and resid 3938 through 3959 removed outlier: 3.783A pdb=" N GLN C3954 " --> pdb=" O PHE C3950 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N MET C3955 " --> pdb=" O ALA C3951 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS C3956 " --> pdb=" O HIS C3952 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN C3959 " --> pdb=" O MET C3955 " (cutoff:3.500A) Processing helix chain 'C' and resid 3964 through 3985 removed outlier: 3.808A pdb=" N LEU C3985 " --> pdb=" O LEU C3981 " (cutoff:3.500A) Processing helix chain 'C' and resid 3992 through 4005 removed outlier: 4.464A pdb=" N GLU C4004 " --> pdb=" O ASP C4000 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER C4005 " --> pdb=" O MET C4001 " (cutoff:3.500A) Processing helix chain 'C' and resid 4005 through 4014 Processing helix chain 'C' and resid 4027 through 4032 removed outlier: 4.361A pdb=" N PHE C4031 " --> pdb=" O SER C4027 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS C4032 " --> pdb=" O SER C4028 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4027 through 4032' Processing helix chain 'C' and resid 4043 through 4051 removed outlier: 3.542A pdb=" N MET C4051 " --> pdb=" O PHE C4047 " (cutoff:3.500A) Processing helix chain 'C' and resid 4062 through 4069 removed outlier: 3.643A pdb=" N LEU C4066 " --> pdb=" O THR C4062 " (cutoff:3.500A) Processing helix chain 'C' and resid 4079 through 4085 removed outlier: 3.696A pdb=" N VAL C4083 " --> pdb=" O TYR C4079 " (cutoff:3.500A) Processing helix chain 'C' and resid 4087 through 4108 removed outlier: 4.339A pdb=" N LYS C4091 " --> pdb=" O HIS C4087 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN C4096 " --> pdb=" O ASP C4092 " (cutoff:3.500A) Processing helix chain 'C' and resid 4111 through 4121 removed outlier: 3.762A pdb=" N GLN C4115 " --> pdb=" O ASP C4111 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR C4116 " --> pdb=" O THR C4112 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE C4117 " --> pdb=" O ARG C4113 " (cutoff:3.500A) Processing helix chain 'C' and resid 4121 through 4129 Processing helix chain 'C' and resid 4152 through 4160 removed outlier: 3.712A pdb=" N GLU C4160 " --> pdb=" O ARG C4156 " (cutoff:3.500A) Processing helix chain 'C' and resid 4161 through 4179 removed outlier: 3.722A pdb=" N ASN C4177 " --> pdb=" O PHE C4173 " (cutoff:3.500A) Processing helix chain 'C' and resid 4182 through 4204 removed outlier: 3.850A pdb=" N GLU C4186 " --> pdb=" O LYS C4182 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN C4204 " --> pdb=" O GLN C4200 " (cutoff:3.500A) Processing helix chain 'C' and resid 4484 through 4496 removed outlier: 3.598A pdb=" N ASN C4496 " --> pdb=" O TYR C4492 " (cutoff:3.500A) Processing helix chain 'C' and resid 4496 through 4515 Processing helix chain 'C' and resid 4516 through 4518 No H-bonds generated for 'chain 'C' and resid 4516 through 4518' Processing helix chain 'C' and resid 4566 through 4593 Processing helix chain 'C' and resid 4593 through 4612 removed outlier: 3.557A pdb=" N VAL C4597 " --> pdb=" O LYS C4593 " (cutoff:3.500A) Processing helix chain 'C' and resid 4624 through 4630 Processing helix chain 'C' and resid 4631 through 4634 Processing helix chain 'C' and resid 4647 through 4661 removed outlier: 4.028A pdb=" N MET C4653 " --> pdb=" O LYS C4649 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP C4654 " --> pdb=" O ARG C4650 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS C4655 " --> pdb=" O LYS C4651 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N GLU C4658 " --> pdb=" O ASP C4654 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N PHE C4659 " --> pdb=" O LYS C4655 " (cutoff:3.500A) Processing helix chain 'C' and resid 4661 through 4670 removed outlier: 3.870A pdb=" N ILE C4665 " --> pdb=" O GLY C4661 " (cutoff:3.500A) Processing helix chain 'C' and resid 4701 through 4715 Processing helix chain 'C' and resid 4715 through 4734 removed outlier: 3.931A pdb=" N HIS C4732 " --> pdb=" O SER C4728 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYR C4733 " --> pdb=" O VAL C4729 " (cutoff:3.500A) Processing helix chain 'C' and resid 4735 through 4743 removed outlier: 3.761A pdb=" N LEU C4743 " --> pdb=" O ALA C4740 " (cutoff:3.500A) Processing helix chain 'C' and resid 4744 through 4749 removed outlier: 3.568A pdb=" N PHE C4749 " --> pdb=" O ILE C4745 " (cutoff:3.500A) Processing helix chain 'C' and resid 4749 through 4762 removed outlier: 3.823A pdb=" N SER C4758 " --> pdb=" O THR C4754 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL C4759 " --> pdb=" O ILE C4755 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASN C4762 " --> pdb=" O SER C4758 " (cutoff:3.500A) Processing helix chain 'C' and resid 4762 through 4787 removed outlier: 3.640A pdb=" N VAL C4767 " --> pdb=" O GLY C4763 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU C4768 " --> pdb=" O LYS C4764 " (cutoff:3.500A) Processing helix chain 'C' and resid 4788 through 4792 Processing helix chain 'C' and resid 4808 through 4818 Processing helix chain 'C' and resid 4825 through 4830 removed outlier: 3.790A pdb=" N ASP C4828 " --> pdb=" O GLY C4825 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE C4830 " --> pdb=" O GLY C4827 " (cutoff:3.500A) Processing helix chain 'C' and resid 4838 through 4853 Processing helix chain 'C' and resid 4855 through 4886 removed outlier: 4.085A pdb=" N ILE C4865 " --> pdb=" O ILE C4861 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE C4866 " --> pdb=" O GLN C4862 " (cutoff:3.500A) Processing helix chain 'C' and resid 4893 through 4898 removed outlier: 3.872A pdb=" N PHE C4897 " --> pdb=" O GLY C4893 " (cutoff:3.500A) Processing helix chain 'C' and resid 4902 through 4910 Processing helix chain 'C' and resid 4913 through 4926 removed outlier: 3.706A pdb=" N LEU C4921 " --> pdb=" O TYR C4917 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET C4922 " --> pdb=" O LEU C4918 " (cutoff:3.500A) Processing helix chain 'C' and resid 4928 through 4932 removed outlier: 3.561A pdb=" N HIS C4932 " --> pdb=" O GLU C4929 " (cutoff:3.500A) Processing helix chain 'C' and resid 4933 through 4946 removed outlier: 3.590A pdb=" N MET C4942 " --> pdb=" O TYR C4938 " (cutoff:3.500A) Processing helix chain 'C' and resid 4956 through 4961 Processing helix chain 'D' and resid 255 through 259 removed outlier: 4.034A pdb=" N THR D 259 " --> pdb=" O GLN D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 438 removed outlier: 4.162A pdb=" N LYS D 438 " --> pdb=" O ASP D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 464 Processing helix chain 'D' and resid 471 through 494 removed outlier: 3.699A pdb=" N MET D 494 " --> pdb=" O GLN D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 506 Processing helix chain 'D' and resid 512 through 518 Processing helix chain 'D' and resid 525 through 543 Processing helix chain 'D' and resid 554 through 563 Processing helix chain 'D' and resid 568 through 582 Processing helix chain 'D' and resid 584 through 588 removed outlier: 3.529A pdb=" N ASN D 587 " --> pdb=" O GLU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 604 Processing helix chain 'D' and resid 609 through 617 removed outlier: 3.917A pdb=" N VAL D 613 " --> pdb=" O LYS D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 636 Processing helix chain 'D' and resid 875 through 877 No H-bonds generated for 'chain 'D' and resid 875 through 877' Processing helix chain 'D' and resid 878 through 901 removed outlier: 3.996A pdb=" N GLY D 901 " --> pdb=" O LYS D 897 " (cutoff:3.500A) Processing helix chain 'D' and resid 909 through 912 Processing helix chain 'D' and resid 925 through 945 Processing helix chain 'D' and resid 965 through 969 removed outlier: 3.672A pdb=" N ASN D 969 " --> pdb=" O LEU D 966 " (cutoff:3.500A) Processing helix chain 'D' and resid 991 through 1015 Processing helix chain 'D' and resid 1043 through 1061 Processing helix chain 'D' and resid 1092 through 1095 Processing helix chain 'D' and resid 1230 through 1235 Processing helix chain 'D' and resid 1633 through 1637 removed outlier: 4.432A pdb=" N ASN D1637 " --> pdb=" O PRO D1634 " (cutoff:3.500A) Processing helix chain 'D' and resid 1648 through 1666 Processing helix chain 'D' and resid 1672 through 1681 removed outlier: 3.554A pdb=" N SER D1679 " --> pdb=" O HIS D1675 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N HIS D1680 " --> pdb=" O ALA D1676 " (cutoff:3.500A) Processing helix chain 'D' and resid 1682 through 1692 Processing helix chain 'D' and resid 1696 through 1712 Processing helix chain 'D' and resid 1713 through 1723 Processing helix chain 'D' and resid 1784 through 1806 removed outlier: 3.653A pdb=" N LEU D1805 " --> pdb=" O LYS D1801 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS D1806 " --> pdb=" O GLU D1802 " (cutoff:3.500A) Processing helix chain 'D' and resid 1814 through 1831 Proline residue: D1821 - end of helix Processing helix chain 'D' and resid 1836 through 1845 removed outlier: 3.629A pdb=" N GLN D1845 " --> pdb=" O LYS D1841 " (cutoff:3.500A) Processing helix chain 'D' and resid 1898 through 1939 removed outlier: 4.304A pdb=" N GLN D1904 " --> pdb=" O PRO D1900 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N MET D1905 " --> pdb=" O VAL D1901 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS D1906 " --> pdb=" O LYS D1902 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU D1907 " --> pdb=" O LEU D1903 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP D1929 " --> pdb=" O VAL D1925 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP D1930 " --> pdb=" O ALA D1926 " (cutoff:3.500A) Processing helix chain 'D' and resid 1952 through 1958 removed outlier: 3.868A pdb=" N LEU D1956 " --> pdb=" O MET D1952 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA D1958 " --> pdb=" O ALA D1954 " (cutoff:3.500A) Processing helix chain 'D' and resid 1999 through 2006 removed outlier: 3.890A pdb=" N MET D2003 " --> pdb=" O HIS D1999 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N CYS D2006 " --> pdb=" O LEU D2002 " (cutoff:3.500A) Processing helix chain 'D' and resid 2010 through 2016 Processing helix chain 'D' and resid 2023 through 2036 removed outlier: 4.524A pdb=" N ARG D2027 " --> pdb=" O THR D2023 " (cutoff:3.500A) Processing helix chain 'D' and resid 2056 through 2072 removed outlier: 3.899A pdb=" N SER D2072 " --> pdb=" O TRP D2068 " (cutoff:3.500A) Processing helix chain 'D' and resid 2076 through 2092 removed outlier: 3.745A pdb=" N VAL D2080 " --> pdb=" O ASP D2076 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN D2090 " --> pdb=" O LEU D2086 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR D2091 " --> pdb=" O LEU D2087 " (cutoff:3.500A) Processing helix chain 'D' and resid 2092 through 2104 Proline residue: D2102 - end of helix Processing helix chain 'D' and resid 2111 through 2127 removed outlier: 4.231A pdb=" N ASN D2117 " --> pdb=" O GLU D2113 " (cutoff:3.500A) Processing helix chain 'D' and resid 2136 through 2150 removed outlier: 4.411A pdb=" N LEU D2140 " --> pdb=" O GLU D2136 " (cutoff:3.500A) Processing helix chain 'D' and resid 2152 through 2157 Processing helix chain 'D' and resid 2158 through 2165 removed outlier: 4.157A pdb=" N ARG D2162 " --> pdb=" O PRO D2158 " (cutoff:3.500A) Processing helix chain 'D' and resid 2165 through 2179 Processing helix chain 'D' and resid 2189 through 2202 removed outlier: 3.998A pdb=" N ALA D2193 " --> pdb=" O PRO D2189 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASN D2194 " --> pdb=" O LYS D2190 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE D2198 " --> pdb=" O ASN D2194 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU D2199 " --> pdb=" O CYS D2195 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS D2200 " --> pdb=" O CYS D2196 " (cutoff:3.500A) Processing helix chain 'D' and resid 2208 through 2215 Processing helix chain 'D' and resid 2216 through 2223 Processing helix chain 'D' and resid 2238 through 2246 removed outlier: 3.817A pdb=" N ALA D2242 " --> pdb=" O PRO D2238 " (cutoff:3.500A) Processing helix chain 'D' and resid 2249 through 2256 removed outlier: 3.551A pdb=" N ALA D2253 " --> pdb=" O ASN D2249 " (cutoff:3.500A) Processing helix chain 'D' and resid 2257 through 2260 removed outlier: 3.565A pdb=" N ASP D2260 " --> pdb=" O ARG D2257 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2257 through 2260' Processing helix chain 'D' and resid 2261 through 2271 removed outlier: 3.809A pdb=" N VAL D2265 " --> pdb=" O LEU D2261 " (cutoff:3.500A) Processing helix chain 'D' and resid 2294 through 2305 removed outlier: 3.686A pdb=" N LEU D2298 " --> pdb=" O GLY D2294 " (cutoff:3.500A) Processing helix chain 'D' and resid 2312 through 2326 removed outlier: 3.768A pdb=" N ALA D2316 " --> pdb=" O VAL D2312 " (cutoff:3.500A) Processing helix chain 'D' and resid 2341 through 2354 removed outlier: 4.649A pdb=" N GLU D2347 " --> pdb=" O LEU D2343 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS D2351 " --> pdb=" O GLU D2347 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE D2352 " --> pdb=" O GLU D2348 " (cutoff:3.500A) Processing helix chain 'D' and resid 2386 through 2402 Processing helix chain 'D' and resid 2415 through 2425 removed outlier: 3.765A pdb=" N ARG D2419 " --> pdb=" O ALA D2415 " (cutoff:3.500A) Processing helix chain 'D' and resid 2430 through 2432 No H-bonds generated for 'chain 'D' and resid 2430 through 2432' Processing helix chain 'D' and resid 2433 through 2440 removed outlier: 3.742A pdb=" N GLN D2440 " --> pdb=" O SER D2436 " (cutoff:3.500A) Processing helix chain 'D' and resid 2461 through 2475 removed outlier: 3.999A pdb=" N ALA D2465 " --> pdb=" O PRO D2461 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA D2466 " --> pdb=" O ASP D2462 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU D2471 " --> pdb=" O MET D2467 " (cutoff:3.500A) Processing helix chain 'D' and resid 2479 through 2487 removed outlier: 3.929A pdb=" N LEU D2483 " --> pdb=" O VAL D2479 " (cutoff:3.500A) Processing helix chain 'D' and resid 2490 through 2500 removed outlier: 3.566A pdb=" N ALA D2498 " --> pdb=" O ASP D2494 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA D2499 " --> pdb=" O LEU D2495 " (cutoff:3.500A) Processing helix chain 'D' and resid 2511 through 2522 Processing helix chain 'D' and resid 2582 through 2591 removed outlier: 3.959A pdb=" N HIS D2586 " --> pdb=" O SER D2582 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG D2589 " --> pdb=" O GLN D2585 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG D2590 " --> pdb=" O HIS D2586 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU D2591 " --> pdb=" O LEU D2587 " (cutoff:3.500A) Processing helix chain 'D' and resid 2599 through 2614 removed outlier: 3.783A pdb=" N LYS D2603 " --> pdb=" O ASN D2599 " (cutoff:3.500A) Proline residue: D2605 - end of helix removed outlier: 3.783A pdb=" N THR D2610 " --> pdb=" O LEU D2606 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASN D2611 " --> pdb=" O LYS D2607 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N HIS D2612 " --> pdb=" O LEU D2608 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR D2613 " --> pdb=" O LEU D2609 " (cutoff:3.500A) Processing helix chain 'D' and resid 2621 through 2633 Processing helix chain 'D' and resid 2639 through 2650 removed outlier: 4.037A pdb=" N LEU D2643 " --> pdb=" O LEU D2639 " (cutoff:3.500A) Processing helix chain 'D' and resid 2660 through 2675 removed outlier: 3.656A pdb=" N LEU D2665 " --> pdb=" O PHE D2661 " (cutoff:3.500A) Proline residue: D2666 - end of helix removed outlier: 3.903A pdb=" N SER D2669 " --> pdb=" O LEU D2665 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU D2675 " --> pdb=" O VAL D2671 " (cutoff:3.500A) Processing helix chain 'D' and resid 2718 through 2739 Processing helix chain 'D' and resid 2763 through 2785 Proline residue: D2773 - end of helix Processing helix chain 'D' and resid 2816 through 2820 removed outlier: 3.691A pdb=" N GLY D2819 " --> pdb=" O ALA D2816 " (cutoff:3.500A) Processing helix chain 'D' and resid 2833 through 2863 Processing helix chain 'D' and resid 2877 through 2896 removed outlier: 3.935A pdb=" N LYS D2883 " --> pdb=" O LYS D2879 " (cutoff:3.500A) Processing helix chain 'D' and resid 2990 through 3012 removed outlier: 4.295A pdb=" N SER D2996 " --> pdb=" O GLY D2992 " (cutoff:3.500A) Processing helix chain 'D' and resid 3037 through 3050 removed outlier: 3.796A pdb=" N ARG D3042 " --> pdb=" O THR D3038 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS D3046 " --> pdb=" O ARG D3042 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR D3047 " --> pdb=" O THR D3043 " (cutoff:3.500A) Processing helix chain 'D' and resid 3054 through 3063 removed outlier: 3.530A pdb=" N LEU D3060 " --> pdb=" O LEU D3056 " (cutoff:3.500A) Processing helix chain 'D' and resid 3066 through 3083 Processing helix chain 'D' and resid 3090 through 3099 Processing helix chain 'D' and resid 3183 through 3192 Processing helix chain 'D' and resid 3214 through 3225 removed outlier: 4.140A pdb=" N ILE D3218 " --> pdb=" O MET D3214 " (cutoff:3.500A) Processing helix chain 'D' and resid 3238 through 3252 removed outlier: 4.369A pdb=" N TYR D3244 " --> pdb=" O MET D3240 " (cutoff:3.500A) Processing helix chain 'D' and resid 3263 through 3268 removed outlier: 3.700A pdb=" N ALA D3266 " --> pdb=" O CYS D3263 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN D3268 " --> pdb=" O THR D3265 " (cutoff:3.500A) Processing helix chain 'D' and resid 3286 through 3292 Processing helix chain 'D' and resid 3308 through 3324 removed outlier: 4.258A pdb=" N GLN D3312 " --> pdb=" O LYS D3308 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D3319 " --> pdb=" O LYS D3315 " (cutoff:3.500A) Proline residue: D3320 - end of helix Processing helix chain 'D' and resid 3330 through 3344 Processing helix chain 'D' and resid 3355 through 3374 removed outlier: 4.280A pdb=" N THR D3359 " --> pdb=" O LEU D3355 " (cutoff:3.500A) Proline residue: D3370 - end of helix Processing helix chain 'D' and resid 3405 through 3431 removed outlier: 3.896A pdb=" N VAL D3420 " --> pdb=" O GLN D3416 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN D3421 " --> pdb=" O ASN D3417 " (cutoff:3.500A) Processing helix chain 'D' and resid 3436 through 3473 removed outlier: 4.115A pdb=" N ASP D3456 " --> pdb=" O LYS D3452 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG D3457 " --> pdb=" O ARG D3453 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA D3467 " --> pdb=" O SER D3463 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ARG D3471 " --> pdb=" O ALA D3467 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU D3472 " --> pdb=" O ALA D3468 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU D3473 " --> pdb=" O LEU D3469 " (cutoff:3.500A) Processing helix chain 'D' and resid 3473 through 3491 removed outlier: 3.713A pdb=" N LEU D3477 " --> pdb=" O LEU D3473 " (cutoff:3.500A) Proline residue: D3482 - end of helix removed outlier: 3.502A pdb=" N GLN D3485 " --> pdb=" O ALA D3481 " (cutoff:3.500A) Processing helix chain 'D' and resid 3494 through 3508 removed outlier: 4.288A pdb=" N THR D3500 " --> pdb=" O SER D3496 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE D3508 " --> pdb=" O VAL D3504 " (cutoff:3.500A) Processing helix chain 'D' and resid 3513 through 3518 removed outlier: 3.542A pdb=" N LYS D3517 " --> pdb=" O HIS D3513 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU D3518 " --> pdb=" O LEU D3514 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3513 through 3518' Processing helix chain 'D' and resid 3557 through 3566 Processing helix chain 'D' and resid 3615 through 3628 removed outlier: 4.229A pdb=" N SER D3626 " --> pdb=" O GLY D3622 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE D3628 " --> pdb=" O GLU D3624 " (cutoff:3.500A) Processing helix chain 'D' and resid 3628 through 3645 removed outlier: 3.765A pdb=" N HIS D3633 " --> pdb=" O GLU D3629 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR D3634 " --> pdb=" O THR D3630 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE D3635 " --> pdb=" O GLU D3631 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU D3639 " --> pdb=" O PHE D3635 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU D3641 " --> pdb=" O ASP D3637 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP D3642 " --> pdb=" O LYS D3638 " (cutoff:3.500A) Processing helix chain 'D' and resid 3661 through 3676 removed outlier: 3.748A pdb=" N GLN D3665 " --> pdb=" O ASP D3661 " (cutoff:3.500A) Processing helix chain 'D' and resid 3684 through 3698 removed outlier: 3.539A pdb=" N CYS D3698 " --> pdb=" O MET D3694 " (cutoff:3.500A) Processing helix chain 'D' and resid 3715 through 3732 Processing helix chain 'D' and resid 3734 through 3746 Processing helix chain 'D' and resid 3751 through 3766 removed outlier: 3.736A pdb=" N ALA D3756 " --> pdb=" O PRO D3752 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR D3757 " --> pdb=" O MET D3753 " (cutoff:3.500A) Processing helix chain 'D' and resid 3769 through 3784 Processing helix chain 'D' and resid 3786 through 3799 Processing helix chain 'D' and resid 3803 through 3812 removed outlier: 3.566A pdb=" N ARG D3809 " --> pdb=" O ASN D3805 " (cutoff:3.500A) Processing helix chain 'D' and resid 3832 through 3845 Processing helix chain 'D' and resid 3850 through 3857 Processing helix chain 'D' and resid 3868 through 3887 removed outlier: 3.946A pdb=" N SER D3872 " --> pdb=" O ASN D3868 " (cutoff:3.500A) Processing helix chain 'D' and resid 3888 through 3893 removed outlier: 4.038A pdb=" N GLY D3893 " --> pdb=" O TRP D3889 " (cutoff:3.500A) Processing helix chain 'D' and resid 3898 through 3924 removed outlier: 3.537A pdb=" N ARG D3903 " --> pdb=" O GLU D3899 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE D3923 " --> pdb=" O LEU D3919 " (cutoff:3.500A) Processing helix chain 'D' and resid 3927 through 3936 Processing helix chain 'D' and resid 3938 through 3959 removed outlier: 3.783A pdb=" N GLN D3954 " --> pdb=" O PHE D3950 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N MET D3955 " --> pdb=" O ALA D3951 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS D3956 " --> pdb=" O HIS D3952 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN D3959 " --> pdb=" O MET D3955 " (cutoff:3.500A) Processing helix chain 'D' and resid 3964 through 3985 removed outlier: 3.808A pdb=" N LEU D3985 " --> pdb=" O LEU D3981 " (cutoff:3.500A) Processing helix chain 'D' and resid 3992 through 4005 removed outlier: 4.464A pdb=" N GLU D4004 " --> pdb=" O ASP D4000 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER D4005 " --> pdb=" O MET D4001 " (cutoff:3.500A) Processing helix chain 'D' and resid 4005 through 4014 Processing helix chain 'D' and resid 4027 through 4032 removed outlier: 4.361A pdb=" N PHE D4031 " --> pdb=" O SER D4027 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS D4032 " --> pdb=" O SER D4028 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4027 through 4032' Processing helix chain 'D' and resid 4043 through 4051 removed outlier: 3.542A pdb=" N MET D4051 " --> pdb=" O PHE D4047 " (cutoff:3.500A) Processing helix chain 'D' and resid 4062 through 4069 removed outlier: 3.643A pdb=" N LEU D4066 " --> pdb=" O THR D4062 " (cutoff:3.500A) Processing helix chain 'D' and resid 4079 through 4085 removed outlier: 3.696A pdb=" N VAL D4083 " --> pdb=" O TYR D4079 " (cutoff:3.500A) Processing helix chain 'D' and resid 4087 through 4108 removed outlier: 4.339A pdb=" N LYS D4091 " --> pdb=" O HIS D4087 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN D4096 " --> pdb=" O ASP D4092 " (cutoff:3.500A) Processing helix chain 'D' and resid 4111 through 4121 removed outlier: 3.762A pdb=" N GLN D4115 " --> pdb=" O ASP D4111 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR D4116 " --> pdb=" O THR D4112 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE D4117 " --> pdb=" O ARG D4113 " (cutoff:3.500A) Processing helix chain 'D' and resid 4121 through 4129 Processing helix chain 'D' and resid 4152 through 4160 removed outlier: 3.712A pdb=" N GLU D4160 " --> pdb=" O ARG D4156 " (cutoff:3.500A) Processing helix chain 'D' and resid 4161 through 4179 removed outlier: 3.722A pdb=" N ASN D4177 " --> pdb=" O PHE D4173 " (cutoff:3.500A) Processing helix chain 'D' and resid 4182 through 4204 removed outlier: 3.850A pdb=" N GLU D4186 " --> pdb=" O LYS D4182 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN D4204 " --> pdb=" O GLN D4200 " (cutoff:3.500A) Processing helix chain 'D' and resid 4484 through 4496 removed outlier: 3.598A pdb=" N ASN D4496 " --> pdb=" O TYR D4492 " (cutoff:3.500A) Processing helix chain 'D' and resid 4496 through 4515 Processing helix chain 'D' and resid 4516 through 4518 No H-bonds generated for 'chain 'D' and resid 4516 through 4518' Processing helix chain 'D' and resid 4566 through 4593 Processing helix chain 'D' and resid 4593 through 4612 removed outlier: 3.557A pdb=" N VAL D4597 " --> pdb=" O LYS D4593 " (cutoff:3.500A) Processing helix chain 'D' and resid 4624 through 4630 Processing helix chain 'D' and resid 4631 through 4634 Processing helix chain 'D' and resid 4647 through 4661 removed outlier: 4.028A pdb=" N MET D4653 " --> pdb=" O LYS D4649 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP D4654 " --> pdb=" O ARG D4650 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS D4655 " --> pdb=" O LYS D4651 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N GLU D4658 " --> pdb=" O ASP D4654 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N PHE D4659 " --> pdb=" O LYS D4655 " (cutoff:3.500A) Processing helix chain 'D' and resid 4661 through 4670 removed outlier: 3.870A pdb=" N ILE D4665 " --> pdb=" O GLY D4661 " (cutoff:3.500A) Processing helix chain 'D' and resid 4701 through 4715 Processing helix chain 'D' and resid 4715 through 4734 removed outlier: 3.931A pdb=" N HIS D4732 " --> pdb=" O SER D4728 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYR D4733 " --> pdb=" O VAL D4729 " (cutoff:3.500A) Processing helix chain 'D' and resid 4735 through 4743 removed outlier: 3.761A pdb=" N LEU D4743 " --> pdb=" O ALA D4740 " (cutoff:3.500A) Processing helix chain 'D' and resid 4744 through 4749 removed outlier: 3.568A pdb=" N PHE D4749 " --> pdb=" O ILE D4745 " (cutoff:3.500A) Processing helix chain 'D' and resid 4749 through 4762 removed outlier: 3.823A pdb=" N SER D4758 " --> pdb=" O THR D4754 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL D4759 " --> pdb=" O ILE D4755 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASN D4762 " --> pdb=" O SER D4758 " (cutoff:3.500A) Processing helix chain 'D' and resid 4762 through 4787 removed outlier: 3.640A pdb=" N VAL D4767 " --> pdb=" O GLY D4763 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU D4768 " --> pdb=" O LYS D4764 " (cutoff:3.500A) Processing helix chain 'D' and resid 4788 through 4792 Processing helix chain 'D' and resid 4808 through 4818 Processing helix chain 'D' and resid 4825 through 4830 removed outlier: 3.790A pdb=" N ASP D4828 " --> pdb=" O GLY D4825 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE D4830 " --> pdb=" O GLY D4827 " (cutoff:3.500A) Processing helix chain 'D' and resid 4838 through 4853 Processing helix chain 'D' and resid 4855 through 4886 removed outlier: 4.085A pdb=" N ILE D4865 " --> pdb=" O ILE D4861 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE D4866 " --> pdb=" O GLN D4862 " (cutoff:3.500A) Processing helix chain 'D' and resid 4893 through 4898 removed outlier: 3.872A pdb=" N PHE D4897 " --> pdb=" O GLY D4893 " (cutoff:3.500A) Processing helix chain 'D' and resid 4902 through 4910 Processing helix chain 'D' and resid 4913 through 4926 removed outlier: 3.706A pdb=" N LEU D4921 " --> pdb=" O TYR D4917 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET D4922 " --> pdb=" O LEU D4918 " (cutoff:3.500A) Processing helix chain 'D' and resid 4928 through 4932 removed outlier: 3.561A pdb=" N HIS D4932 " --> pdb=" O GLU D4929 " (cutoff:3.500A) Processing helix chain 'D' and resid 4933 through 4946 removed outlier: 3.590A pdb=" N MET D4942 " --> pdb=" O TYR D4938 " (cutoff:3.500A) Processing helix chain 'D' and resid 4956 through 4961 Processing helix chain 'E' and resid 56 through 65 removed outlier: 4.286A pdb=" N GLU E 60 " --> pdb=" O ILE E 56 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLN E 65 " --> pdb=" O GLU E 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 65 removed outlier: 4.286A pdb=" N GLU F 60 " --> pdb=" O ILE F 56 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLN F 65 " --> pdb=" O GLU F 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 65 removed outlier: 4.286A pdb=" N GLU G 60 " --> pdb=" O ILE G 56 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLN G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 65 removed outlier: 4.286A pdb=" N GLU H 60 " --> pdb=" O ILE H 56 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLN H 65 " --> pdb=" O GLU H 61 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 51 removed outlier: 5.673A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 10.430A pdb=" N ALA A 39 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 13.536A pdb=" N VAL A 20 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLU A 19 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 162 " --> pdb=" O HIS A 117 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N HIS A 117 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA A 118 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER A 72 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU A 120 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP A 18 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 130 Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 196 removed outlier: 3.504A pdb=" N SER A 195 " --> pdb=" O HIS A 202 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 370 through 371 removed outlier: 3.759A pdb=" N LEU A 403 " --> pdb=" O CYS A 361 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TRP A 275 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 298 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU A 278 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG A 296 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 243 through 246 Processing sheet with id=AA6, first strand: chain 'A' and resid 305 through 309 removed outlier: 4.009A pdb=" N ASN A 313 " --> pdb=" O MET A 309 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 648 through 650 Processing sheet with id=AA8, first strand: chain 'A' and resid 653 through 655 removed outlier: 3.980A pdb=" N SER A 653 " --> pdb=" O PHE A 794 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 794 " --> pdb=" O SER A 653 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 767 through 770 removed outlier: 3.514A pdb=" N SER A 767 " --> pdb=" O CYS A 758 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP A 753 " --> pdb=" O VAL A 679 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 679 " --> pdb=" O ASP A 753 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 755 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR A 675 " --> pdb=" O CYS A 757 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 759 " --> pdb=" O TRP A 673 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TRP A 673 " --> pdb=" O LEU A 759 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 903 through 904 removed outlier: 5.888A pdb=" N GLN A 903 " --> pdb=" O HIS A 915 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 1149 through 1151 removed outlier: 4.096A pdb=" N ALA A1090 " --> pdb=" O PRO A1203 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG A1086 " --> pdb=" O LEU A1207 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE A1087 " --> pdb=" O SER A1252 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1160 through 1161 removed outlier: 3.707A pdb=" N MET A1165 " --> pdb=" O MET A1174 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET A1174 " --> pdb=" O MET A1165 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP A1167 " --> pdb=" O THR A1172 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A1192 " --> pdb=" O MET A1173 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1180 through 1181 removed outlier: 3.531A pdb=" N ASP A1167 " --> pdb=" O THR A1172 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET A1174 " --> pdb=" O MET A1165 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET A1165 " --> pdb=" O MET A1174 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A1104 " --> pdb=" O ASN A1216 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1425 through 1429 removed outlier: 5.782A pdb=" N TYR A1426 " --> pdb=" O VAL A1511 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N VAL A1511 " --> pdb=" O TYR A1426 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR A1520 " --> pdb=" O CYS A1510 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1466 through 1468 Processing sheet with id=AB7, first strand: chain 'A' and resid 1727 through 1728 removed outlier: 4.021A pdb=" N VAL A1728 " --> pdb=" O TYR A2105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 2741 through 2742 removed outlier: 5.748A pdb=" N ILE A2741 " --> pdb=" O GLN A2753 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 2787 through 2790 removed outlier: 3.511A pdb=" N VAL A2901 " --> pdb=" O GLU A2789 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 4132 through 4138 removed outlier: 3.663A pdb=" N PHE A4149 " --> pdb=" O GLY A4133 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 51 removed outlier: 5.673A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 10.430A pdb=" N ALA B 39 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 13.536A pdb=" N VAL B 20 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLU B 19 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 162 " --> pdb=" O HIS B 117 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N HIS B 117 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA B 118 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER B 72 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU B 120 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP B 18 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 129 through 130 Processing sheet with id=AC4, first strand: chain 'B' and resid 191 through 196 removed outlier: 3.504A pdb=" N SER B 195 " --> pdb=" O HIS B 202 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 370 through 371 removed outlier: 3.759A pdb=" N LEU B 403 " --> pdb=" O CYS B 361 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TRP B 275 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG B 298 " --> pdb=" O ARG B 276 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU B 278 " --> pdb=" O ARG B 296 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG B 296 " --> pdb=" O GLU B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 243 through 246 Processing sheet with id=AC7, first strand: chain 'B' and resid 305 through 309 removed outlier: 4.009A pdb=" N ASN B 313 " --> pdb=" O MET B 309 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 648 through 650 Processing sheet with id=AC9, first strand: chain 'B' and resid 653 through 655 removed outlier: 3.980A pdb=" N SER B 653 " --> pdb=" O PHE B 794 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B 794 " --> pdb=" O SER B 653 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 767 through 770 removed outlier: 3.514A pdb=" N SER B 767 " --> pdb=" O CYS B 758 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP B 753 " --> pdb=" O VAL B 679 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 679 " --> pdb=" O ASP B 753 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 755 " --> pdb=" O LEU B 677 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR B 675 " --> pdb=" O CYS B 757 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B 759 " --> pdb=" O TRP B 673 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TRP B 673 " --> pdb=" O LEU B 759 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 903 through 904 removed outlier: 5.888A pdb=" N GLN B 903 " --> pdb=" O HIS B 915 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 1149 through 1151 removed outlier: 4.096A pdb=" N ALA B1090 " --> pdb=" O PRO B1203 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG B1086 " --> pdb=" O LEU B1207 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE B1087 " --> pdb=" O SER B1252 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1160 through 1161 removed outlier: 3.707A pdb=" N MET B1165 " --> pdb=" O MET B1174 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET B1174 " --> pdb=" O MET B1165 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP B1167 " --> pdb=" O THR B1172 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B1192 " --> pdb=" O MET B1173 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1180 through 1181 removed outlier: 3.531A pdb=" N ASP B1167 " --> pdb=" O THR B1172 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET B1174 " --> pdb=" O MET B1165 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET B1165 " --> pdb=" O MET B1174 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B1104 " --> pdb=" O ASN B1216 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1425 through 1429 removed outlier: 5.782A pdb=" N TYR B1426 " --> pdb=" O VAL B1511 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N VAL B1511 " --> pdb=" O TYR B1426 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR B1520 " --> pdb=" O CYS B1510 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1466 through 1468 Processing sheet with id=AD8, first strand: chain 'B' and resid 1727 through 1728 removed outlier: 4.021A pdb=" N VAL B1728 " --> pdb=" O TYR B2105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'B' and resid 2741 through 2742 removed outlier: 5.748A pdb=" N ILE B2741 " --> pdb=" O GLN B2753 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 2787 through 2790 removed outlier: 3.511A pdb=" N VAL B2901 " --> pdb=" O GLU B2789 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 4132 through 4138 removed outlier: 3.663A pdb=" N PHE B4149 " --> pdb=" O GLY B4133 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 47 through 51 removed outlier: 5.673A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 10.430A pdb=" N ALA C 39 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 13.536A pdb=" N VAL C 20 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLU C 19 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE C 162 " --> pdb=" O HIS C 117 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N HIS C 117 " --> pdb=" O ILE C 162 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA C 118 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER C 72 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU C 120 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP C 18 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 129 through 130 Processing sheet with id=AE5, first strand: chain 'C' and resid 191 through 196 removed outlier: 3.504A pdb=" N SER C 195 " --> pdb=" O HIS C 202 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 370 through 371 removed outlier: 3.759A pdb=" N LEU C 403 " --> pdb=" O CYS C 361 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TRP C 275 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG C 298 " --> pdb=" O ARG C 276 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU C 278 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG C 296 " --> pdb=" O GLU C 278 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 243 through 246 Processing sheet with id=AE8, first strand: chain 'C' and resid 305 through 309 removed outlier: 4.009A pdb=" N ASN C 313 " --> pdb=" O MET C 309 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 648 through 650 Processing sheet with id=AF1, first strand: chain 'C' and resid 653 through 655 removed outlier: 3.980A pdb=" N SER C 653 " --> pdb=" O PHE C 794 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE C 794 " --> pdb=" O SER C 653 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 767 through 770 removed outlier: 3.514A pdb=" N SER C 767 " --> pdb=" O CYS C 758 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP C 753 " --> pdb=" O VAL C 679 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C 679 " --> pdb=" O ASP C 753 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE C 755 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR C 675 " --> pdb=" O CYS C 757 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 759 " --> pdb=" O TRP C 673 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TRP C 673 " --> pdb=" O LEU C 759 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 903 through 904 removed outlier: 5.888A pdb=" N GLN C 903 " --> pdb=" O HIS C 915 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'C' and resid 1149 through 1151 removed outlier: 4.096A pdb=" N ALA C1090 " --> pdb=" O PRO C1203 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG C1086 " --> pdb=" O LEU C1207 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE C1087 " --> pdb=" O SER C1252 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1160 through 1161 removed outlier: 3.707A pdb=" N MET C1165 " --> pdb=" O MET C1174 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET C1174 " --> pdb=" O MET C1165 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP C1167 " --> pdb=" O THR C1172 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE C1192 " --> pdb=" O MET C1173 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1180 through 1181 removed outlier: 3.531A pdb=" N ASP C1167 " --> pdb=" O THR C1172 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET C1174 " --> pdb=" O MET C1165 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET C1165 " --> pdb=" O MET C1174 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU C1104 " --> pdb=" O ASN C1216 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1425 through 1429 removed outlier: 5.782A pdb=" N TYR C1426 " --> pdb=" O VAL C1511 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N VAL C1511 " --> pdb=" O TYR C1426 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR C1520 " --> pdb=" O CYS C1510 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1466 through 1468 Processing sheet with id=AF9, first strand: chain 'C' and resid 1727 through 1728 removed outlier: 4.021A pdb=" N VAL C1728 " --> pdb=" O TYR C2105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'C' and resid 2741 through 2742 removed outlier: 5.748A pdb=" N ILE C2741 " --> pdb=" O GLN C2753 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'C' and resid 2787 through 2790 removed outlier: 3.511A pdb=" N VAL C2901 " --> pdb=" O GLU C2789 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 4132 through 4138 removed outlier: 3.663A pdb=" N PHE C4149 " --> pdb=" O GLY C4133 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 47 through 51 removed outlier: 5.673A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 10.430A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 13.536A pdb=" N VAL D 20 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLU D 19 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE D 162 " --> pdb=" O HIS D 117 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N HIS D 117 " --> pdb=" O ILE D 162 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA D 118 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER D 72 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU D 120 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP D 18 " --> pdb=" O LEU D 69 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 129 through 130 Processing sheet with id=AG6, first strand: chain 'D' and resid 191 through 196 removed outlier: 3.504A pdb=" N SER D 195 " --> pdb=" O HIS D 202 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'D' and resid 370 through 371 removed outlier: 3.759A pdb=" N LEU D 403 " --> pdb=" O CYS D 361 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TRP D 275 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG D 298 " --> pdb=" O ARG D 276 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU D 278 " --> pdb=" O ARG D 296 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG D 296 " --> pdb=" O GLU D 278 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'D' and resid 243 through 246 Processing sheet with id=AG9, first strand: chain 'D' and resid 305 through 309 removed outlier: 4.009A pdb=" N ASN D 313 " --> pdb=" O MET D 309 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 648 through 650 Processing sheet with id=AH2, first strand: chain 'D' and resid 653 through 655 removed outlier: 3.980A pdb=" N SER D 653 " --> pdb=" O PHE D 794 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE D 794 " --> pdb=" O SER D 653 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'D' and resid 767 through 770 removed outlier: 3.514A pdb=" N SER D 767 " --> pdb=" O CYS D 758 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP D 753 " --> pdb=" O VAL D 679 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL D 679 " --> pdb=" O ASP D 753 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE D 755 " --> pdb=" O LEU D 677 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR D 675 " --> pdb=" O CYS D 757 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU D 759 " --> pdb=" O TRP D 673 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TRP D 673 " --> pdb=" O LEU D 759 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'D' and resid 903 through 904 removed outlier: 5.888A pdb=" N GLN D 903 " --> pdb=" O HIS D 915 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'D' and resid 1149 through 1151 removed outlier: 4.096A pdb=" N ALA D1090 " --> pdb=" O PRO D1203 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG D1086 " --> pdb=" O LEU D1207 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE D1087 " --> pdb=" O SER D1252 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'D' and resid 1160 through 1161 removed outlier: 3.707A pdb=" N MET D1165 " --> pdb=" O MET D1174 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET D1174 " --> pdb=" O MET D1165 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP D1167 " --> pdb=" O THR D1172 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE D1192 " --> pdb=" O MET D1173 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'D' and resid 1180 through 1181 removed outlier: 3.531A pdb=" N ASP D1167 " --> pdb=" O THR D1172 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET D1174 " --> pdb=" O MET D1165 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET D1165 " --> pdb=" O MET D1174 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU D1104 " --> pdb=" O ASN D1216 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'D' and resid 1425 through 1429 removed outlier: 5.782A pdb=" N TYR D1426 " --> pdb=" O VAL D1511 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N VAL D1511 " --> pdb=" O TYR D1426 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR D1520 " --> pdb=" O CYS D1510 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'D' and resid 1466 through 1468 Processing sheet with id=AI1, first strand: chain 'D' and resid 1727 through 1728 removed outlier: 4.021A pdb=" N VAL D1728 " --> pdb=" O TYR D2105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'D' and resid 2741 through 2742 removed outlier: 5.748A pdb=" N ILE D2741 " --> pdb=" O GLN D2753 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 Processing sheet with id=AI3, first strand: chain 'D' and resid 2787 through 2790 removed outlier: 3.511A pdb=" N VAL D2901 " --> pdb=" O GLU D2789 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'D' and resid 4132 through 4138 removed outlier: 3.663A pdb=" N PHE D4149 " --> pdb=" O GLY D4133 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'E' and resid 3 through 6 removed outlier: 4.132A pdb=" N GLU E 3 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR E 75 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU E 97 " --> pdb=" O CYS E 76 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'E' and resid 3 through 6 removed outlier: 4.132A pdb=" N GLU E 3 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR E 75 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN E 70 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU E 104 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL E 23 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU E 106 " --> pdb=" O THR E 21 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR E 21 " --> pdb=" O LEU E 106 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'F' and resid 3 through 6 removed outlier: 4.132A pdb=" N GLU F 3 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR F 75 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU F 97 " --> pdb=" O CYS F 76 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'F' and resid 3 through 6 removed outlier: 4.132A pdb=" N GLU F 3 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR F 75 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN F 70 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU F 104 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL F 23 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU F 106 " --> pdb=" O THR F 21 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR F 21 " --> pdb=" O LEU F 106 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'G' and resid 3 through 6 removed outlier: 4.132A pdb=" N GLU G 3 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR G 75 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU G 97 " --> pdb=" O CYS G 76 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'G' and resid 3 through 6 removed outlier: 4.132A pdb=" N GLU G 3 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR G 75 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN G 70 " --> pdb=" O LEU G 103 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU G 104 " --> pdb=" O VAL G 23 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL G 23 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU G 106 " --> pdb=" O THR G 21 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR G 21 " --> pdb=" O LEU G 106 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.132A pdb=" N GLU H 3 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR H 75 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU H 97 " --> pdb=" O CYS H 76 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'H' and resid 3 through 6 removed outlier: 4.132A pdb=" N GLU H 3 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR H 75 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN H 70 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU H 104 " --> pdb=" O VAL H 23 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL H 23 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU H 106 " --> pdb=" O THR H 21 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR H 21 " --> pdb=" O LEU H 106 " (cutoff:3.500A) 5584 hydrogen bonds defined for protein. 16236 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: 80.39 Time building geometry restraints manager: 41.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 42652 1.34 - 1.46: 25992 1.46 - 1.58: 62244 1.58 - 1.70: 8 1.70 - 1.82: 1296 Bond restraints: 132192 Sorted by residual: bond pdb=" CB PRO A2189 " pdb=" CG PRO A2189 " ideal model delta sigma weight residual 1.492 1.618 -0.126 5.00e-02 4.00e+02 6.33e+00 bond pdb=" CB PRO B2189 " pdb=" CG PRO B2189 " ideal model delta sigma weight residual 1.492 1.618 -0.126 5.00e-02 4.00e+02 6.33e+00 bond pdb=" CB PRO C2189 " pdb=" CG PRO C2189 " ideal model delta sigma weight residual 1.492 1.618 -0.126 5.00e-02 4.00e+02 6.33e+00 bond pdb=" CB PRO D2189 " pdb=" CG PRO D2189 " ideal model delta sigma weight residual 1.492 1.618 -0.126 5.00e-02 4.00e+02 6.33e+00 bond pdb=" SD MET B2161 " pdb=" CE MET B2161 " ideal model delta sigma weight residual 1.791 1.738 0.053 2.50e-02 1.60e+03 4.43e+00 ... (remaining 132187 not shown) Histogram of bond angle deviations from ideal: 96.01 - 103.64: 1508 103.64 - 111.27: 52312 111.27 - 118.90: 54084 118.90 - 126.53: 69040 126.53 - 134.16: 1956 Bond angle restraints: 178900 Sorted by residual: angle pdb=" CA PRO D2189 " pdb=" N PRO D2189 " pdb=" CD PRO D2189 " ideal model delta sigma weight residual 112.00 103.58 8.42 1.40e+00 5.10e-01 3.62e+01 angle pdb=" CA PRO A2189 " pdb=" N PRO A2189 " pdb=" CD PRO A2189 " ideal model delta sigma weight residual 112.00 103.58 8.42 1.40e+00 5.10e-01 3.62e+01 angle pdb=" CA PRO C2189 " pdb=" N PRO C2189 " pdb=" CD PRO C2189 " ideal model delta sigma weight residual 112.00 103.58 8.42 1.40e+00 5.10e-01 3.62e+01 angle pdb=" CA PRO B2189 " pdb=" N PRO B2189 " pdb=" CD PRO B2189 " ideal model delta sigma weight residual 112.00 103.58 8.42 1.40e+00 5.10e-01 3.62e+01 angle pdb=" C LYS D4021 " pdb=" N LEU D4022 " pdb=" CA LEU D4022 " ideal model delta sigma weight residual 121.54 130.59 -9.05 1.91e+00 2.74e-01 2.24e+01 ... (remaining 178895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 69004 17.91 - 35.82: 7904 35.82 - 53.73: 1860 53.73 - 71.64: 232 71.64 - 89.55: 176 Dihedral angle restraints: 79176 sinusoidal: 30820 harmonic: 48356 Sorted by residual: dihedral pdb=" CA LYS C4023 " pdb=" C LYS C4023 " pdb=" N ASP C4024 " pdb=" CA ASP C4024 " ideal model delta harmonic sigma weight residual 180.00 139.57 40.43 0 5.00e+00 4.00e-02 6.54e+01 dihedral pdb=" CA LYS B4023 " pdb=" C LYS B4023 " pdb=" N ASP B4024 " pdb=" CA ASP B4024 " ideal model delta harmonic sigma weight residual 180.00 139.57 40.43 0 5.00e+00 4.00e-02 6.54e+01 dihedral pdb=" CA LYS D4023 " pdb=" C LYS D4023 " pdb=" N ASP D4024 " pdb=" CA ASP D4024 " ideal model delta harmonic sigma weight residual 180.00 139.57 40.43 0 5.00e+00 4.00e-02 6.54e+01 ... (remaining 79173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 18192 0.072 - 0.145: 1640 0.145 - 0.217: 80 0.217 - 0.290: 8 0.290 - 0.362: 8 Chirality restraints: 19928 Sorted by residual: chirality pdb=" CB VAL C 423 " pdb=" CA VAL C 423 " pdb=" CG1 VAL C 423 " pdb=" CG2 VAL C 423 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CB VAL B 423 " pdb=" CA VAL B 423 " pdb=" CG1 VAL B 423 " pdb=" CG2 VAL B 423 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CB VAL D 423 " pdb=" CA VAL D 423 " pdb=" CG1 VAL D 423 " pdb=" CG2 VAL D 423 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.28e+00 ... (remaining 19925 not shown) Planarity restraints: 23144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B3252 " -0.084 5.00e-02 4.00e+02 1.27e-01 2.59e+01 pdb=" N PRO B3253 " 0.220 5.00e-02 4.00e+02 pdb=" CA PRO B3253 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO B3253 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D3252 " 0.084 5.00e-02 4.00e+02 1.27e-01 2.59e+01 pdb=" N PRO D3253 " -0.220 5.00e-02 4.00e+02 pdb=" CA PRO D3253 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO D3253 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C3252 " -0.084 5.00e-02 4.00e+02 1.27e-01 2.59e+01 pdb=" N PRO C3253 " 0.220 5.00e-02 4.00e+02 pdb=" CA PRO C3253 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO C3253 " -0.067 5.00e-02 4.00e+02 ... (remaining 23141 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 2040 2.67 - 3.23: 123804 3.23 - 3.79: 197144 3.79 - 4.34: 246308 4.34 - 4.90: 405904 Nonbonded interactions: 975200 Sorted by model distance: nonbonded pdb=" O VAL D 418 " pdb=" OG1 THR D 422 " model vdw 2.116 2.440 nonbonded pdb=" O VAL C 418 " pdb=" OG1 THR C 422 " model vdw 2.116 2.440 nonbonded pdb=" O VAL A 418 " pdb=" OG1 THR A 422 " model vdw 2.116 2.440 nonbonded pdb=" O VAL B 418 " pdb=" OG1 THR B 422 " model vdw 2.116 2.440 nonbonded pdb=" OH TYR D4589 " pdb=" OG SER D4717 " model vdw 2.217 2.440 ... (remaining 975195 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 23.990 Check model and map are aligned: 1.400 Set scattering table: 0.920 Process input model: 299.630 Find NCS groups from input model: 6.830 Set up NCS constraints: 0.770 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 340.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6067 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 : 0.003 0.126 132192 Z= 0.195 Angle : 0.721 13.390 178900 Z= 0.368 Chirality : 0.043 0.362 19928 Planarity : 0.005 0.127 23144 Dihedral : 16.282 89.547 47952 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.91 % Favored : 89.92 % Rotamer: Outliers : 0.18 % Allowed : 13.18 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.06), residues: 16464 helix: 0.72 (0.06), residues: 7308 sheet: -0.93 (0.17), residues: 916 loop : -2.82 (0.06), residues: 8240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.001 TRP C1007 HIS 0.012 0.001 HIS D 29 PHE 0.069 0.001 PHE A 685 TYR 0.037 0.001 TYR C 115 ARG 0.012 0.000 ARG D 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 996 residues out of total 14576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 972 time to evaluate : 10.758 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 349 MET cc_start: 0.5697 (mtm) cc_final: 0.5282 (mtt) REVERT: A 1168 MET cc_start: 0.6444 (tpt) cc_final: 0.5668 (tpt) REVERT: A 1173 MET cc_start: 0.3466 (mmp) cc_final: 0.3050 (mmp) REVERT: A 4018 MET cc_start: 0.3389 (mpp) cc_final: 0.3073 (ptp) REVERT: B 1168 MET cc_start: 0.6415 (tpt) cc_final: 0.5573 (tpt) REVERT: B 3977 MET cc_start: 0.8393 (tpp) cc_final: 0.8124 (ttt) REVERT: B 4018 MET cc_start: 0.3268 (mpp) cc_final: 0.2753 (ptp) REVERT: C 1168 MET cc_start: 0.6272 (tpt) cc_final: 0.5281 (tpt) REVERT: C 3977 MET cc_start: 0.8470 (tpp) cc_final: 0.8097 (ttt) REVERT: D 349 MET cc_start: 0.5822 (mtm) cc_final: 0.5383 (mtt) REVERT: D 1168 MET cc_start: 0.6236 (tpt) cc_final: 0.5182 (tpt) REVERT: D 1604 PHE cc_start: 0.5997 (p90) cc_final: 0.5795 (p90) REVERT: E 18 LYS cc_start: 0.8435 (mmmm) cc_final: 0.7691 (mptt) REVERT: H 50 ILE cc_start: 0.8218 (mm) cc_final: 0.7965 (tp) outliers start: 24 outliers final: 12 residues processed: 972 average time/residue: 1.0211 time to fit residues: 1783.4130 Evaluate side-chains 920 residues out of total 14576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 908 time to evaluate : 10.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 1007 TRP Chi-restraints excluded: chain A residue 2265 VAL Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 1007 TRP Chi-restraints excluded: chain B residue 2265 VAL Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 1007 TRP Chi-restraints excluded: chain C residue 2265 VAL Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 1007 TRP Chi-restraints excluded: chain D residue 2265 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1664 random chunks: chunk 1405 optimal weight: 9.9990 chunk 1261 optimal weight: 5.9990 chunk 699 optimal weight: 20.0000 chunk 430 optimal weight: 0.0770 chunk 850 optimal weight: 4.9990 chunk 673 optimal weight: 9.9990 chunk 1304 optimal weight: 50.0000 chunk 504 optimal weight: 5.9990 chunk 793 optimal weight: 0.5980 chunk 970 optimal weight: 9.9990 chunk 1511 optimal weight: 20.0000 overall best weight: 3.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 HIS A 635 ASN ** A 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1436 GLN A1603 GLN ** A1655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2176 ASN ** A2223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3307 ASN ** A3931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3948 HIS ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 HIS B 469 HIS B 635 ASN ** B 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1436 GLN B1603 GLN ** B1655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3307 ASN ** B3931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3948 HIS C 29 HIS ** C 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 HIS C 469 HIS C1436 GLN C1603 GLN ** C1655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3307 ASN ** C3931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3948 HIS D 29 HIS ** D 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 HIS D 469 HIS ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 635 ASN D1436 GLN D1603 GLN ** D1655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3307 ASN ** D3931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3948 HIS E 32 ASN F 32 ASN G 32 ASN H 32 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6274 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 132192 Z= 0.330 Angle : 0.660 12.822 178900 Z= 0.341 Chirality : 0.043 0.217 19928 Planarity : 0.005 0.123 23144 Dihedral : 5.083 43.065 17884 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.23 % Favored : 89.63 % Rotamer: Outliers : 2.00 % Allowed : 14.72 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.06), residues: 16464 helix: 0.82 (0.06), residues: 7340 sheet: -0.92 (0.16), residues: 1032 loop : -2.83 (0.06), residues: 8092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A4644 HIS 0.011 0.001 HIS B 469 PHE 0.038 0.002 PHE A4849 TYR 0.021 0.002 TYR C4724 ARG 0.007 0.001 ARG D 343 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1195 residues out of total 14576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 922 time to evaluate : 10.832 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 495 ILE cc_start: 0.2446 (OUTLIER) cc_final: 0.1535 (tp) REVERT: A 2161 MET cc_start: 0.8281 (mmt) cc_final: 0.7999 (mmt) REVERT: A 3045 MET cc_start: 0.3174 (ppp) cc_final: 0.1553 (tmm) REVERT: A 3322 MET cc_start: 0.2975 (mmt) cc_final: 0.2766 (mmt) REVERT: A 4500 MET cc_start: 0.8423 (ptp) cc_final: 0.8095 (ptp) REVERT: B 495 ILE cc_start: 0.2339 (OUTLIER) cc_final: 0.1461 (tp) REVERT: B 1168 MET cc_start: 0.6627 (tpt) cc_final: 0.5573 (tpt) REVERT: B 3045 MET cc_start: 0.3093 (ppp) cc_final: 0.1540 (tmm) REVERT: B 3322 MET cc_start: 0.2881 (mmt) cc_final: 0.2647 (mmt) REVERT: B 3977 MET cc_start: 0.8695 (tpp) cc_final: 0.8220 (ttp) REVERT: B 4500 MET cc_start: 0.8435 (ptp) cc_final: 0.8091 (ptp) REVERT: B 4808 MET cc_start: 0.8906 (tpt) cc_final: 0.8700 (tpt) REVERT: C 495 ILE cc_start: 0.2137 (OUTLIER) cc_final: 0.1238 (tp) REVERT: C 1168 MET cc_start: 0.6603 (tpt) cc_final: 0.5326 (tpt) REVERT: C 3045 MET cc_start: 0.2997 (ppp) cc_final: 0.1355 (tmm) REVERT: C 3322 MET cc_start: 0.2908 (mmt) cc_final: 0.2514 (mmt) REVERT: C 3977 MET cc_start: 0.8720 (tpp) cc_final: 0.8221 (ttp) REVERT: C 4500 MET cc_start: 0.8445 (ptp) cc_final: 0.8101 (ptp) REVERT: D 495 ILE cc_start: 0.2240 (OUTLIER) cc_final: 0.1310 (tp) REVERT: D 1168 MET cc_start: 0.6601 (tpt) cc_final: 0.5324 (tpt) REVERT: D 3045 MET cc_start: 0.3094 (ppp) cc_final: 0.1412 (tmm) REVERT: D 3322 MET cc_start: 0.3131 (mmt) cc_final: 0.2772 (mmt) REVERT: D 4500 MET cc_start: 0.8429 (ptp) cc_final: 0.8103 (ptp) REVERT: E 18 LYS cc_start: 0.8511 (mmmm) cc_final: 0.7744 (mptt) REVERT: F 18 LYS cc_start: 0.8467 (mmmm) cc_final: 0.7665 (mptt) REVERT: G 18 LYS cc_start: 0.8430 (mmmm) cc_final: 0.7649 (mptt) REVERT: H 18 LYS cc_start: 0.8470 (mmmm) cc_final: 0.7673 (mptt) outliers start: 273 outliers final: 127 residues processed: 1148 average time/residue: 0.9797 time to fit residues: 2033.7162 Evaluate side-chains 993 residues out of total 14576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 862 time to evaluate : 10.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1530 THR Chi-restraints excluded: chain A residue 1609 VAL Chi-restraints excluded: chain A residue 1631 LEU Chi-restraints excluded: chain A residue 1941 PHE Chi-restraints excluded: chain A residue 1944 ASN Chi-restraints excluded: chain A residue 2060 LEU Chi-restraints excluded: chain A residue 2192 VAL Chi-restraints excluded: chain A residue 2199 LEU Chi-restraints excluded: chain A residue 2217 LEU Chi-restraints excluded: chain A residue 2265 VAL Chi-restraints excluded: chain A residue 2286 ASP Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain A residue 4026 THR Chi-restraints excluded: chain A residue 4502 MET Chi-restraints excluded: chain A residue 4696 VAL Chi-restraints excluded: chain A residue 4735 ASN Chi-restraints excluded: chain A residue 4757 SER Chi-restraints excluded: chain A residue 4922 MET Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 964 MET Chi-restraints excluded: chain B residue 1430 VAL Chi-restraints excluded: chain B residue 1443 VAL Chi-restraints excluded: chain B residue 1530 THR Chi-restraints excluded: chain B residue 1609 VAL Chi-restraints excluded: chain B residue 1631 LEU Chi-restraints excluded: chain B residue 1728 VAL Chi-restraints excluded: chain B residue 1941 PHE Chi-restraints excluded: chain B residue 1944 ASN Chi-restraints excluded: chain B residue 2060 LEU Chi-restraints excluded: chain B residue 2192 VAL Chi-restraints excluded: chain B residue 2199 LEU Chi-restraints excluded: chain B residue 2217 LEU Chi-restraints excluded: chain B residue 2265 VAL Chi-restraints excluded: chain B residue 2286 ASP Chi-restraints excluded: chain B residue 2519 LEU Chi-restraints excluded: chain B residue 3730 LEU Chi-restraints excluded: chain B residue 4026 THR Chi-restraints excluded: chain B residue 4502 MET Chi-restraints excluded: chain B residue 4696 VAL Chi-restraints excluded: chain B residue 4735 ASN Chi-restraints excluded: chain B residue 4757 SER Chi-restraints excluded: chain B residue 4922 MET Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 800 VAL Chi-restraints excluded: chain C residue 964 MET Chi-restraints excluded: chain C residue 1430 VAL Chi-restraints excluded: chain C residue 1443 VAL Chi-restraints excluded: chain C residue 1530 THR Chi-restraints excluded: chain C residue 1609 VAL Chi-restraints excluded: chain C residue 1631 LEU Chi-restraints excluded: chain C residue 1728 VAL Chi-restraints excluded: chain C residue 1941 PHE Chi-restraints excluded: chain C residue 1944 ASN Chi-restraints excluded: chain C residue 2060 LEU Chi-restraints excluded: chain C residue 2192 VAL Chi-restraints excluded: chain C residue 2199 LEU Chi-restraints excluded: chain C residue 2217 LEU Chi-restraints excluded: chain C residue 2265 VAL Chi-restraints excluded: chain C residue 2286 ASP Chi-restraints excluded: chain C residue 2519 LEU Chi-restraints excluded: chain C residue 3730 LEU Chi-restraints excluded: chain C residue 4026 THR Chi-restraints excluded: chain C residue 4502 MET Chi-restraints excluded: chain C residue 4696 VAL Chi-restraints excluded: chain C residue 4735 ASN Chi-restraints excluded: chain C residue 4757 SER Chi-restraints excluded: chain C residue 4922 MET Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 495 ILE Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 615 CYS Chi-restraints excluded: chain D residue 800 VAL Chi-restraints excluded: chain D residue 964 MET Chi-restraints excluded: chain D residue 1430 VAL Chi-restraints excluded: chain D residue 1443 VAL Chi-restraints excluded: chain D residue 1530 THR Chi-restraints excluded: chain D residue 1609 VAL Chi-restraints excluded: chain D residue 1631 LEU Chi-restraints excluded: chain D residue 1728 VAL Chi-restraints excluded: chain D residue 1941 PHE Chi-restraints excluded: chain D residue 1944 ASN Chi-restraints excluded: chain D residue 2060 LEU Chi-restraints excluded: chain D residue 2192 VAL Chi-restraints excluded: chain D residue 2265 VAL Chi-restraints excluded: chain D residue 2286 ASP Chi-restraints excluded: chain D residue 2519 LEU Chi-restraints excluded: chain D residue 3730 LEU Chi-restraints excluded: chain D residue 4026 THR Chi-restraints excluded: chain D residue 4502 MET Chi-restraints excluded: chain D residue 4696 VAL Chi-restraints excluded: chain D residue 4735 ASN Chi-restraints excluded: chain D residue 4757 SER Chi-restraints excluded: chain D residue 4922 MET Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 32 ASN Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 90 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1664 random chunks: chunk 839 optimal weight: 10.0000 chunk 468 optimal weight: 5.9990 chunk 1257 optimal weight: 6.9990 chunk 1028 optimal weight: 20.0000 chunk 416 optimal weight: 10.0000 chunk 1513 optimal weight: 30.0000 chunk 1635 optimal weight: 20.0000 chunk 1348 optimal weight: 4.9990 chunk 1501 optimal weight: 30.0000 chunk 516 optimal weight: 20.0000 chunk 1214 optimal weight: 4.9990 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1123 GLN ** A1655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1845 GLN A2088 HIS ** A2157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2889 GLN ** A3914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3924 GLN A3991 ASN A4499 ASN B 29 HIS ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1123 GLN ** B1655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1845 GLN B2088 HIS ** B2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2889 GLN ** B3731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3924 GLN B3991 ASN B4499 ASN B4786 ASN B4932 HIS ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 635 ASN C1123 GLN ** C1655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1845 GLN C2088 HIS ** C2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2889 GLN C3924 GLN C3991 ASN C4499 ASN C4932 HIS ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1123 GLN ** D1655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1711 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1845 GLN D2088 HIS ** D2157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2889 GLN D3924 GLN D3991 ASN D4499 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.114 132192 Z= 0.555 Angle : 0.813 18.629 178900 Z= 0.419 Chirality : 0.048 0.282 19928 Planarity : 0.006 0.119 23144 Dihedral : 5.599 46.721 17864 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.60 % Favored : 88.25 % Rotamer: Outliers : 3.62 % Allowed : 16.58 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.06), residues: 16464 helix: 0.27 (0.06), residues: 7336 sheet: -1.32 (0.16), residues: 1020 loop : -2.99 (0.06), residues: 8108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D1007 HIS 0.012 0.002 HIS C1680 PHE 0.078 0.003 PHE D4849 TYR 0.035 0.002 TYR A4724 ARG 0.010 0.001 ARG A 626 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1406 residues out of total 14576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 494 poor density : 912 time to evaluate : 11.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 393 MET cc_start: 0.3368 (mmp) cc_final: 0.3112 (mmp) REVERT: A 558 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8071 (mm) REVERT: A 617 LEU cc_start: 0.8858 (mt) cc_final: 0.8635 (mt) REVERT: A 1927 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.7187 (t80) REVERT: A 2199 LEU cc_start: 0.5558 (OUTLIER) cc_final: 0.5293 (mp) REVERT: A 3045 MET cc_start: 0.3516 (ppp) cc_final: 0.2059 (tmm) REVERT: A 3866 THR cc_start: 0.8310 (OUTLIER) cc_final: 0.8107 (p) REVERT: A 4490 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7302 (mp) REVERT: A 4909 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8600 (mt) REVERT: B 393 MET cc_start: 0.3278 (mmp) cc_final: 0.3029 (mmp) REVERT: B 617 LEU cc_start: 0.8898 (mt) cc_final: 0.8656 (mt) REVERT: B 630 HIS cc_start: 0.7795 (OUTLIER) cc_final: 0.6857 (t70) REVERT: B 1927 PHE cc_start: 0.7595 (OUTLIER) cc_final: 0.7105 (t80) REVERT: B 2324 ILE cc_start: 0.7455 (mm) cc_final: 0.7047 (mm) REVERT: B 3045 MET cc_start: 0.3395 (ppp) cc_final: 0.1975 (tmm) REVERT: B 3866 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.8100 (p) REVERT: B 3977 MET cc_start: 0.8762 (tpp) cc_final: 0.8343 (ttp) REVERT: B 4017 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7590 (p0) REVERT: B 4490 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7284 (mp) REVERT: B 4909 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8557 (mt) REVERT: C 393 MET cc_start: 0.3357 (mmp) cc_final: 0.3098 (mmp) REVERT: C 617 LEU cc_start: 0.8951 (mt) cc_final: 0.8683 (mt) REVERT: C 630 HIS cc_start: 0.7813 (OUTLIER) cc_final: 0.6902 (t70) REVERT: C 1168 MET cc_start: 0.6757 (tpt) cc_final: 0.5690 (tpt) REVERT: C 1604 PHE cc_start: 0.6321 (p90) cc_final: 0.5989 (p90) REVERT: C 1927 PHE cc_start: 0.7637 (OUTLIER) cc_final: 0.7192 (t80) REVERT: C 2324 ILE cc_start: 0.7327 (mm) cc_final: 0.6921 (mm) REVERT: C 3045 MET cc_start: 0.3486 (ppp) cc_final: 0.2102 (tmm) REVERT: C 3866 THR cc_start: 0.8323 (OUTLIER) cc_final: 0.8093 (p) REVERT: C 3977 MET cc_start: 0.8773 (tpp) cc_final: 0.8330 (ttp) REVERT: C 4017 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7715 (p0) REVERT: C 4490 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7279 (mp) REVERT: C 4909 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8590 (mt) REVERT: D 393 MET cc_start: 0.3380 (mmp) cc_final: 0.3125 (mmp) REVERT: D 504 ARG cc_start: 0.6559 (tpt170) cc_final: 0.6089 (tmt-80) REVERT: D 558 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8064 (mm) REVERT: D 617 LEU cc_start: 0.8915 (mt) cc_final: 0.8673 (mt) REVERT: D 630 HIS cc_start: 0.7849 (OUTLIER) cc_final: 0.6860 (t70) REVERT: D 1113 MET cc_start: 0.6910 (mtp) cc_final: 0.6639 (mtm) REVERT: D 1168 MET cc_start: 0.6762 (tpt) cc_final: 0.5695 (tpt) REVERT: D 1927 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.7253 (t80) REVERT: D 2324 ILE cc_start: 0.7303 (mm) cc_final: 0.6908 (mm) REVERT: D 3045 MET cc_start: 0.3465 (ppp) cc_final: 0.2135 (tmm) REVERT: D 3866 THR cc_start: 0.8320 (OUTLIER) cc_final: 0.8096 (p) REVERT: D 4490 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7294 (mp) REVERT: D 4909 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8615 (mt) REVERT: E 18 LYS cc_start: 0.8551 (mmmm) cc_final: 0.7878 (mptt) REVERT: F 18 LYS cc_start: 0.8553 (mmmm) cc_final: 0.7810 (mptt) REVERT: G 18 LYS cc_start: 0.8491 (mmmm) cc_final: 0.7799 (mptt) REVERT: G 73 LYS cc_start: 0.8341 (tttm) cc_final: 0.8014 (ttmm) REVERT: H 23 VAL cc_start: 0.7492 (OUTLIER) cc_final: 0.7108 (m) REVERT: H 73 LYS cc_start: 0.8338 (tttm) cc_final: 0.8013 (ttmm) outliers start: 494 outliers final: 213 residues processed: 1331 average time/residue: 1.0953 time to fit residues: 2663.6160 Evaluate side-chains 1115 residues out of total 14576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 877 time to evaluate : 10.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 608 HIS Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1443 VAL Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain A residue 1530 THR Chi-restraints excluded: chain A residue 1609 VAL Chi-restraints excluded: chain A residue 1629 MET Chi-restraints excluded: chain A residue 1631 LEU Chi-restraints excluded: chain A residue 1728 VAL Chi-restraints excluded: chain A residue 1796 LEU Chi-restraints excluded: chain A residue 1917 VAL Chi-restraints excluded: chain A residue 1927 PHE Chi-restraints excluded: chain A residue 1932 VAL Chi-restraints excluded: chain A residue 1941 PHE Chi-restraints excluded: chain A residue 1944 ASN Chi-restraints excluded: chain A residue 2032 VAL Chi-restraints excluded: chain A residue 2060 LEU Chi-restraints excluded: chain A residue 2086 LEU Chi-restraints excluded: chain A residue 2131 VAL Chi-restraints excluded: chain A residue 2192 VAL Chi-restraints excluded: chain A residue 2199 LEU Chi-restraints excluded: chain A residue 2265 VAL Chi-restraints excluded: chain A residue 2286 ASP Chi-restraints excluded: chain A residue 2290 ASN Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain A residue 2781 MET Chi-restraints excluded: chain A residue 3237 VAL Chi-restraints excluded: chain A residue 3643 LEU Chi-restraints excluded: chain A residue 3730 LEU Chi-restraints excluded: chain A residue 3762 ILE Chi-restraints excluded: chain A residue 3829 LEU Chi-restraints excluded: chain A residue 3866 THR Chi-restraints excluded: chain A residue 4011 MET Chi-restraints excluded: chain A residue 4195 THR Chi-restraints excluded: chain A residue 4490 LEU Chi-restraints excluded: chain A residue 4502 MET Chi-restraints excluded: chain A residue 4521 SER Chi-restraints excluded: chain A residue 4696 VAL Chi-restraints excluded: chain A residue 4712 VAL Chi-restraints excluded: chain A residue 4735 ASN Chi-restraints excluded: chain A residue 4809 LEU Chi-restraints excluded: chain A residue 4830 ILE Chi-restraints excluded: chain A residue 4909 LEU Chi-restraints excluded: chain A residue 4922 MET Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 608 HIS Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 630 HIS Chi-restraints excluded: chain B residue 641 ASP Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 964 MET Chi-restraints excluded: chain B residue 1430 VAL Chi-restraints excluded: chain B residue 1443 VAL Chi-restraints excluded: chain B residue 1519 LEU Chi-restraints excluded: chain B residue 1528 LEU Chi-restraints excluded: chain B residue 1530 THR Chi-restraints excluded: chain B residue 1609 VAL Chi-restraints excluded: chain B residue 1629 MET Chi-restraints excluded: chain B residue 1631 LEU Chi-restraints excluded: chain B residue 1728 VAL Chi-restraints excluded: chain B residue 1796 LEU Chi-restraints excluded: chain B residue 1917 VAL Chi-restraints excluded: chain B residue 1927 PHE Chi-restraints excluded: chain B residue 1932 VAL Chi-restraints excluded: chain B residue 1941 PHE Chi-restraints excluded: chain B residue 1944 ASN Chi-restraints excluded: chain B residue 2032 VAL Chi-restraints excluded: chain B residue 2060 LEU Chi-restraints excluded: chain B residue 2086 LEU Chi-restraints excluded: chain B residue 2192 VAL Chi-restraints excluded: chain B residue 2199 LEU Chi-restraints excluded: chain B residue 2265 VAL Chi-restraints excluded: chain B residue 2286 ASP Chi-restraints excluded: chain B residue 2290 ASN Chi-restraints excluded: chain B residue 2425 LEU Chi-restraints excluded: chain B residue 2519 LEU Chi-restraints excluded: chain B residue 3237 VAL Chi-restraints excluded: chain B residue 3643 LEU Chi-restraints excluded: chain B residue 3730 LEU Chi-restraints excluded: chain B residue 3762 ILE Chi-restraints excluded: chain B residue 3829 LEU Chi-restraints excluded: chain B residue 3866 THR Chi-restraints excluded: chain B residue 4011 MET Chi-restraints excluded: chain B residue 4017 ASP Chi-restraints excluded: chain B residue 4195 THR Chi-restraints excluded: chain B residue 4490 LEU Chi-restraints excluded: chain B residue 4502 MET Chi-restraints excluded: chain B residue 4521 SER Chi-restraints excluded: chain B residue 4696 VAL Chi-restraints excluded: chain B residue 4712 VAL Chi-restraints excluded: chain B residue 4735 ASN Chi-restraints excluded: chain B residue 4809 LEU Chi-restraints excluded: chain B residue 4830 ILE Chi-restraints excluded: chain B residue 4909 LEU Chi-restraints excluded: chain B residue 4922 MET Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 608 HIS Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 630 HIS Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 964 MET Chi-restraints excluded: chain C residue 1430 VAL Chi-restraints excluded: chain C residue 1443 VAL Chi-restraints excluded: chain C residue 1519 LEU Chi-restraints excluded: chain C residue 1528 LEU Chi-restraints excluded: chain C residue 1530 THR Chi-restraints excluded: chain C residue 1609 VAL Chi-restraints excluded: chain C residue 1629 MET Chi-restraints excluded: chain C residue 1631 LEU Chi-restraints excluded: chain C residue 1728 VAL Chi-restraints excluded: chain C residue 1917 VAL Chi-restraints excluded: chain C residue 1927 PHE Chi-restraints excluded: chain C residue 1932 VAL Chi-restraints excluded: chain C residue 1941 PHE Chi-restraints excluded: chain C residue 1944 ASN Chi-restraints excluded: chain C residue 2032 VAL Chi-restraints excluded: chain C residue 2060 LEU Chi-restraints excluded: chain C residue 2086 LEU Chi-restraints excluded: chain C residue 2192 VAL Chi-restraints excluded: chain C residue 2199 LEU Chi-restraints excluded: chain C residue 2265 VAL Chi-restraints excluded: chain C residue 2286 ASP Chi-restraints excluded: chain C residue 2290 ASN Chi-restraints excluded: chain C residue 2519 LEU Chi-restraints excluded: chain C residue 3237 VAL Chi-restraints excluded: chain C residue 3643 LEU Chi-restraints excluded: chain C residue 3730 LEU Chi-restraints excluded: chain C residue 3762 ILE Chi-restraints excluded: chain C residue 3829 LEU Chi-restraints excluded: chain C residue 3866 THR Chi-restraints excluded: chain C residue 4011 MET Chi-restraints excluded: chain C residue 4017 ASP Chi-restraints excluded: chain C residue 4195 THR Chi-restraints excluded: chain C residue 4490 LEU Chi-restraints excluded: chain C residue 4502 MET Chi-restraints excluded: chain C residue 4521 SER Chi-restraints excluded: chain C residue 4696 VAL Chi-restraints excluded: chain C residue 4712 VAL Chi-restraints excluded: chain C residue 4735 ASN Chi-restraints excluded: chain C residue 4809 LEU Chi-restraints excluded: chain C residue 4830 ILE Chi-restraints excluded: chain C residue 4909 LEU Chi-restraints excluded: chain C residue 4922 MET Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 608 HIS Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 615 CYS Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 630 HIS Chi-restraints excluded: chain D residue 964 MET Chi-restraints excluded: chain D residue 1430 VAL Chi-restraints excluded: chain D residue 1443 VAL Chi-restraints excluded: chain D residue 1519 LEU Chi-restraints excluded: chain D residue 1530 THR Chi-restraints excluded: chain D residue 1604 PHE Chi-restraints excluded: chain D residue 1609 VAL Chi-restraints excluded: chain D residue 1629 MET Chi-restraints excluded: chain D residue 1631 LEU Chi-restraints excluded: chain D residue 1728 VAL Chi-restraints excluded: chain D residue 1796 LEU Chi-restraints excluded: chain D residue 1917 VAL Chi-restraints excluded: chain D residue 1927 PHE Chi-restraints excluded: chain D residue 1941 PHE Chi-restraints excluded: chain D residue 1944 ASN Chi-restraints excluded: chain D residue 2032 VAL Chi-restraints excluded: chain D residue 2060 LEU Chi-restraints excluded: chain D residue 2086 LEU Chi-restraints excluded: chain D residue 2131 VAL Chi-restraints excluded: chain D residue 2192 VAL Chi-restraints excluded: chain D residue 2199 LEU Chi-restraints excluded: chain D residue 2265 VAL Chi-restraints excluded: chain D residue 2286 ASP Chi-restraints excluded: chain D residue 2290 ASN Chi-restraints excluded: chain D residue 2387 ILE Chi-restraints excluded: chain D residue 2519 LEU Chi-restraints excluded: chain D residue 3237 VAL Chi-restraints excluded: chain D residue 3643 LEU Chi-restraints excluded: chain D residue 3730 LEU Chi-restraints excluded: chain D residue 3762 ILE Chi-restraints excluded: chain D residue 3829 LEU Chi-restraints excluded: chain D residue 3866 THR Chi-restraints excluded: chain D residue 4011 MET Chi-restraints excluded: chain D residue 4132 LEU Chi-restraints excluded: chain D residue 4195 THR Chi-restraints excluded: chain D residue 4490 LEU Chi-restraints excluded: chain D residue 4502 MET Chi-restraints excluded: chain D residue 4521 SER Chi-restraints excluded: chain D residue 4566 TYR Chi-restraints excluded: chain D residue 4696 VAL Chi-restraints excluded: chain D residue 4712 VAL Chi-restraints excluded: chain D residue 4735 ASN Chi-restraints excluded: chain D residue 4809 LEU Chi-restraints excluded: chain D residue 4830 ILE Chi-restraints excluded: chain D residue 4909 LEU Chi-restraints excluded: chain D residue 4922 MET Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 77 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1664 random chunks: chunk 1495 optimal weight: 40.0000 chunk 1138 optimal weight: 0.8980 chunk 785 optimal weight: 4.9990 chunk 167 optimal weight: 0.9990 chunk 722 optimal weight: 0.7980 chunk 1016 optimal weight: 0.9990 chunk 1519 optimal weight: 9.9990 chunk 1608 optimal weight: 0.9990 chunk 793 optimal weight: 0.8980 chunk 1439 optimal weight: 0.7980 chunk 433 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 HIS ** A1655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1711 HIS ** A2223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3952 HIS ** A4735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 HIS ** B1655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1711 HIS ** B2223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3952 HIS ** B4735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 651 HIS ** C1655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1711 HIS ** C2223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3952 HIS C3954 GLN ** C4735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN ** D 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 HIS ** D1655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1711 HIS ** D2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3952 HIS ** D4735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 132192 Z= 0.165 Angle : 0.588 14.236 178900 Z= 0.302 Chirality : 0.040 0.283 19928 Planarity : 0.004 0.117 23144 Dihedral : 5.067 42.159 17864 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.89 % Favored : 89.98 % Rotamer: Outliers : 2.37 % Allowed : 18.57 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.46 (0.06), residues: 16464 helix: 0.88 (0.06), residues: 7304 sheet: -1.19 (0.16), residues: 1096 loop : -2.86 (0.06), residues: 8064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP D1007 HIS 0.008 0.001 HIS D 29 PHE 0.025 0.001 PHE D2202 TYR 0.021 0.001 TYR B3623 ARG 0.005 0.000 ARG D 343 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1264 residues out of total 14576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 323 poor density : 941 time to evaluate : 11.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1113 MET cc_start: 0.6784 (mtp) cc_final: 0.6535 (mtm) REVERT: A 1168 MET cc_start: 0.6745 (tpt) cc_final: 0.5871 (tpt) REVERT: A 1927 PHE cc_start: 0.7521 (OUTLIER) cc_final: 0.7146 (t80) REVERT: A 3020 LEU cc_start: 0.0705 (OUTLIER) cc_final: 0.0237 (mp) REVERT: A 3045 MET cc_start: 0.3524 (ppp) cc_final: 0.3105 (ppp) REVERT: A 3322 MET cc_start: 0.3028 (mmt) cc_final: 0.2775 (mmt) REVERT: A 3796 MET cc_start: 0.8008 (mtp) cc_final: 0.7772 (mtp) REVERT: B 1113 MET cc_start: 0.6744 (mtp) cc_final: 0.6500 (mtm) REVERT: B 1927 PHE cc_start: 0.7468 (OUTLIER) cc_final: 0.7017 (t80) REVERT: B 3020 LEU cc_start: 0.0828 (OUTLIER) cc_final: 0.0430 (mp) REVERT: B 3045 MET cc_start: 0.3507 (ppp) cc_final: 0.2365 (tmm) REVERT: B 3314 LEU cc_start: 0.1564 (OUTLIER) cc_final: 0.0426 (mt) REVERT: B 3718 MET cc_start: 0.7496 (tpt) cc_final: 0.7240 (tpp) REVERT: B 3796 MET cc_start: 0.8003 (mtp) cc_final: 0.7743 (mtp) REVERT: B 3977 MET cc_start: 0.8694 (tpp) cc_final: 0.8437 (ttp) REVERT: C 1113 MET cc_start: 0.6719 (mtp) cc_final: 0.6508 (mtm) REVERT: C 1604 PHE cc_start: 0.6209 (p90) cc_final: 0.5962 (p90) REVERT: C 1927 PHE cc_start: 0.7553 (OUTLIER) cc_final: 0.7159 (t80) REVERT: C 2397 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6886 (tp) REVERT: C 3020 LEU cc_start: 0.0831 (OUTLIER) cc_final: 0.0418 (mp) REVERT: C 3045 MET cc_start: 0.3391 (ppp) cc_final: 0.2311 (tmm) REVERT: C 3796 MET cc_start: 0.8003 (mtp) cc_final: 0.7759 (mtp) REVERT: C 3977 MET cc_start: 0.8691 (tpp) cc_final: 0.8390 (ttp) REVERT: D 1113 MET cc_start: 0.6834 (mtp) cc_final: 0.6573 (mtm) REVERT: D 1927 PHE cc_start: 0.7407 (OUTLIER) cc_final: 0.7068 (t80) REVERT: D 3020 LEU cc_start: 0.0917 (OUTLIER) cc_final: 0.0450 (mp) REVERT: D 3045 MET cc_start: 0.3514 (ppp) cc_final: 0.3121 (ppp) REVERT: E 18 LYS cc_start: 0.8524 (mmmm) cc_final: 0.7866 (mptt) REVERT: F 18 LYS cc_start: 0.8470 (mmmm) cc_final: 0.7811 (mptt) REVERT: F 48 PHE cc_start: 0.7830 (p90) cc_final: 0.7588 (p90) REVERT: G 18 LYS cc_start: 0.8408 (mmmm) cc_final: 0.7788 (mptt) REVERT: G 73 LYS cc_start: 0.8330 (tttm) cc_final: 0.7990 (ttmm) REVERT: H 18 LYS cc_start: 0.8456 (mmmm) cc_final: 0.7798 (mptt) REVERT: H 73 LYS cc_start: 0.8350 (tttm) cc_final: 0.8021 (ttmm) outliers start: 323 outliers final: 199 residues processed: 1193 average time/residue: 1.0067 time to fit residues: 2174.3892 Evaluate side-chains 1130 residues out of total 14576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 921 time to evaluate : 10.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 398 HIS Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1608 ASP Chi-restraints excluded: chain A residue 1631 LEU Chi-restraints excluded: chain A residue 1665 VAL Chi-restraints excluded: chain A residue 1927 PHE Chi-restraints excluded: chain A residue 1941 PHE Chi-restraints excluded: chain A residue 1944 ASN Chi-restraints excluded: chain A residue 1957 THR Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2032 VAL Chi-restraints excluded: chain A residue 2060 LEU Chi-restraints excluded: chain A residue 2086 LEU Chi-restraints excluded: chain A residue 2129 LEU Chi-restraints excluded: chain A residue 2171 MET Chi-restraints excluded: chain A residue 2192 VAL Chi-restraints excluded: chain A residue 2199 LEU Chi-restraints excluded: chain A residue 2265 VAL Chi-restraints excluded: chain A residue 2286 ASP Chi-restraints excluded: chain A residue 2388 MET Chi-restraints excluded: chain A residue 2781 MET Chi-restraints excluded: chain A residue 3020 LEU Chi-restraints excluded: chain A residue 3713 PHE Chi-restraints excluded: chain A residue 3730 LEU Chi-restraints excluded: chain A residue 3954 GLN Chi-restraints excluded: chain A residue 4011 MET Chi-restraints excluded: chain A residue 4026 THR Chi-restraints excluded: chain A residue 4594 VAL Chi-restraints excluded: chain A residue 4696 VAL Chi-restraints excluded: chain A residue 4735 ASN Chi-restraints excluded: chain A residue 4813 MET Chi-restraints excluded: chain A residue 4830 ILE Chi-restraints excluded: chain A residue 4922 MET Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 398 HIS Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 630 HIS Chi-restraints excluded: chain B residue 964 MET Chi-restraints excluded: chain B residue 1430 VAL Chi-restraints excluded: chain B residue 1608 ASP Chi-restraints excluded: chain B residue 1631 LEU Chi-restraints excluded: chain B residue 1665 VAL Chi-restraints excluded: chain B residue 1927 PHE Chi-restraints excluded: chain B residue 1941 PHE Chi-restraints excluded: chain B residue 1944 ASN Chi-restraints excluded: chain B residue 1957 THR Chi-restraints excluded: chain B residue 1991 ILE Chi-restraints excluded: chain B residue 2032 VAL Chi-restraints excluded: chain B residue 2060 LEU Chi-restraints excluded: chain B residue 2086 LEU Chi-restraints excluded: chain B residue 2129 LEU Chi-restraints excluded: chain B residue 2192 VAL Chi-restraints excluded: chain B residue 2199 LEU Chi-restraints excluded: chain B residue 2217 LEU Chi-restraints excluded: chain B residue 2265 VAL Chi-restraints excluded: chain B residue 2388 MET Chi-restraints excluded: chain B residue 2425 LEU Chi-restraints excluded: chain B residue 2781 MET Chi-restraints excluded: chain B residue 3020 LEU Chi-restraints excluded: chain B residue 3314 LEU Chi-restraints excluded: chain B residue 3713 PHE Chi-restraints excluded: chain B residue 3730 LEU Chi-restraints excluded: chain B residue 3954 GLN Chi-restraints excluded: chain B residue 4011 MET Chi-restraints excluded: chain B residue 4026 THR Chi-restraints excluded: chain B residue 4594 VAL Chi-restraints excluded: chain B residue 4696 VAL Chi-restraints excluded: chain B residue 4735 ASN Chi-restraints excluded: chain B residue 4809 LEU Chi-restraints excluded: chain B residue 4830 ILE Chi-restraints excluded: chain B residue 4922 MET Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 398 HIS Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 630 HIS Chi-restraints excluded: chain C residue 964 MET Chi-restraints excluded: chain C residue 1430 VAL Chi-restraints excluded: chain C residue 1631 LEU Chi-restraints excluded: chain C residue 1665 VAL Chi-restraints excluded: chain C residue 1927 PHE Chi-restraints excluded: chain C residue 1941 PHE Chi-restraints excluded: chain C residue 1944 ASN Chi-restraints excluded: chain C residue 1957 THR Chi-restraints excluded: chain C residue 1991 ILE Chi-restraints excluded: chain C residue 2032 VAL Chi-restraints excluded: chain C residue 2060 LEU Chi-restraints excluded: chain C residue 2086 LEU Chi-restraints excluded: chain C residue 2129 LEU Chi-restraints excluded: chain C residue 2171 MET Chi-restraints excluded: chain C residue 2192 VAL Chi-restraints excluded: chain C residue 2199 LEU Chi-restraints excluded: chain C residue 2217 LEU Chi-restraints excluded: chain C residue 2265 VAL Chi-restraints excluded: chain C residue 2387 ILE Chi-restraints excluded: chain C residue 2388 MET Chi-restraints excluded: chain C residue 2397 LEU Chi-restraints excluded: chain C residue 2781 MET Chi-restraints excluded: chain C residue 3020 LEU Chi-restraints excluded: chain C residue 3713 PHE Chi-restraints excluded: chain C residue 3730 LEU Chi-restraints excluded: chain C residue 4011 MET Chi-restraints excluded: chain C residue 4026 THR Chi-restraints excluded: chain C residue 4594 VAL Chi-restraints excluded: chain C residue 4696 VAL Chi-restraints excluded: chain C residue 4735 ASN Chi-restraints excluded: chain C residue 4813 MET Chi-restraints excluded: chain C residue 4830 ILE Chi-restraints excluded: chain C residue 4922 MET Chi-restraints excluded: chain D residue 132 CYS Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 398 HIS Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 630 HIS Chi-restraints excluded: chain D residue 964 MET Chi-restraints excluded: chain D residue 1430 VAL Chi-restraints excluded: chain D residue 1631 LEU Chi-restraints excluded: chain D residue 1665 VAL Chi-restraints excluded: chain D residue 1927 PHE Chi-restraints excluded: chain D residue 1941 PHE Chi-restraints excluded: chain D residue 1944 ASN Chi-restraints excluded: chain D residue 1957 THR Chi-restraints excluded: chain D residue 1991 ILE Chi-restraints excluded: chain D residue 2032 VAL Chi-restraints excluded: chain D residue 2060 LEU Chi-restraints excluded: chain D residue 2086 LEU Chi-restraints excluded: chain D residue 2129 LEU Chi-restraints excluded: chain D residue 2171 MET Chi-restraints excluded: chain D residue 2192 VAL Chi-restraints excluded: chain D residue 2199 LEU Chi-restraints excluded: chain D residue 2265 VAL Chi-restraints excluded: chain D residue 2286 ASP Chi-restraints excluded: chain D residue 2387 ILE Chi-restraints excluded: chain D residue 2388 MET Chi-restraints excluded: chain D residue 2781 MET Chi-restraints excluded: chain D residue 3020 LEU Chi-restraints excluded: chain D residue 3713 PHE Chi-restraints excluded: chain D residue 3730 LEU Chi-restraints excluded: chain D residue 3954 GLN Chi-restraints excluded: chain D residue 4011 MET Chi-restraints excluded: chain D residue 4026 THR Chi-restraints excluded: chain D residue 4142 LYS Chi-restraints excluded: chain D residue 4594 VAL Chi-restraints excluded: chain D residue 4696 VAL Chi-restraints excluded: chain D residue 4735 ASN Chi-restraints excluded: chain D residue 4813 MET Chi-restraints excluded: chain D residue 4830 ILE Chi-restraints excluded: chain D residue 4922 MET Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 32 ASN Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 90 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1664 random chunks: chunk 1339 optimal weight: 9.9990 chunk 913 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 chunk 1197 optimal weight: 1.9990 chunk 663 optimal weight: 30.0000 chunk 1372 optimal weight: 0.9980 chunk 1111 optimal weight: 30.0000 chunk 1 optimal weight: 6.9990 chunk 821 optimal weight: 9.9990 chunk 1443 optimal weight: 6.9990 chunk 405 optimal weight: 1.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1603 GLN A1655 HIS ** A2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4786 ASN B 29 HIS ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1603 GLN B1655 HIS ** B2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1603 GLN C1655 HIS ** C2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4786 ASN D 29 HIS D 150 GLN ** D 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1655 HIS ** D2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4786 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6380 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 132192 Z= 0.333 Angle : 0.659 15.614 178900 Z= 0.337 Chirality : 0.043 0.263 19928 Planarity : 0.004 0.115 23144 Dihedral : 5.148 46.330 17864 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.05 % Favored : 88.82 % Rotamer: Outliers : 3.35 % Allowed : 19.02 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.06), residues: 16464 helix: 0.79 (0.06), residues: 7272 sheet: -1.23 (0.16), residues: 1056 loop : -2.87 (0.06), residues: 8136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP C1007 HIS 0.016 0.001 HIS D1711 PHE 0.033 0.002 PHE B4849 TYR 0.023 0.002 TYR D3690 ARG 0.008 0.000 ARG C 626 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1376 residues out of total 14576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 456 poor density : 920 time to evaluate : 10.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.3836 (ttp) cc_final: 0.3630 (ttp) REVERT: A 393 MET cc_start: 0.3375 (mmp) cc_final: 0.3094 (mmp) REVERT: A 535 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.5918 (tt0) REVERT: A 558 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8226 (mm) REVERT: A 617 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8693 (mp) REVERT: A 868 ASP cc_start: 0.3997 (OUTLIER) cc_final: 0.2674 (t0) REVERT: A 874 LEU cc_start: 0.0150 (OUTLIER) cc_final: -0.0468 (tt) REVERT: A 1168 MET cc_start: 0.6947 (tpt) cc_final: 0.5930 (tpt) REVERT: A 1596 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7652 (tt) REVERT: A 1927 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.7051 (t80) REVERT: A 2397 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6993 (tp) REVERT: A 3020 LEU cc_start: 0.1097 (OUTLIER) cc_final: 0.0617 (mp) REVERT: A 3045 MET cc_start: 0.3600 (ppp) cc_final: 0.3331 (ppp) REVERT: A 3866 THR cc_start: 0.8198 (OUTLIER) cc_final: 0.7969 (p) REVERT: B 393 MET cc_start: 0.3384 (mmp) cc_final: 0.3095 (mmp) REVERT: B 535 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.5877 (tt0) REVERT: B 617 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8605 (mp) REVERT: B 874 LEU cc_start: 0.0222 (OUTLIER) cc_final: -0.0389 (tt) REVERT: B 1596 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7592 (tt) REVERT: B 1604 PHE cc_start: 0.6464 (p90) cc_final: 0.6129 (p90) REVERT: B 1927 PHE cc_start: 0.7454 (OUTLIER) cc_final: 0.6958 (t80) REVERT: B 1947 MET cc_start: -0.0791 (mmt) cc_final: -0.3470 (ptt) REVERT: B 2324 ILE cc_start: 0.7657 (mm) cc_final: 0.7325 (mm) REVERT: B 3020 LEU cc_start: 0.0735 (OUTLIER) cc_final: 0.0286 (mp) REVERT: B 3045 MET cc_start: 0.3495 (ppp) cc_final: 0.3220 (ppp) REVERT: B 3866 THR cc_start: 0.8194 (OUTLIER) cc_final: 0.7964 (p) REVERT: B 3977 MET cc_start: 0.8715 (tpp) cc_final: 0.8393 (ttp) REVERT: C 393 MET cc_start: 0.3446 (mmp) cc_final: 0.3158 (mmp) REVERT: C 535 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.5778 (tt0) REVERT: C 617 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8617 (mp) REVERT: C 874 LEU cc_start: 0.0330 (OUTLIER) cc_final: -0.0225 (tt) REVERT: C 1596 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7581 (tt) REVERT: C 1604 PHE cc_start: 0.6308 (p90) cc_final: 0.6045 (p90) REVERT: C 1927 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.7009 (t80) REVERT: C 2397 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.6969 (tp) REVERT: C 3020 LEU cc_start: 0.0648 (OUTLIER) cc_final: 0.0179 (mp) REVERT: C 3045 MET cc_start: 0.3494 (ppp) cc_final: 0.3246 (ppp) REVERT: C 3853 PHE cc_start: 0.8948 (OUTLIER) cc_final: 0.8744 (t80) REVERT: C 3977 MET cc_start: 0.8711 (tpp) cc_final: 0.8389 (ttp) REVERT: C 4566 TYR cc_start: 0.5392 (OUTLIER) cc_final: 0.4850 (t80) REVERT: D 309 MET cc_start: 0.3865 (ttp) cc_final: 0.3656 (ttp) REVERT: D 535 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.5798 (tt0) REVERT: D 558 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8207 (mm) REVERT: D 630 HIS cc_start: 0.7634 (OUTLIER) cc_final: 0.6673 (t70) REVERT: D 868 ASP cc_start: 0.3985 (OUTLIER) cc_final: 0.2746 (t0) REVERT: D 874 LEU cc_start: 0.0482 (OUTLIER) cc_final: 0.0276 (tt) REVERT: D 1596 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7654 (tt) REVERT: D 1604 PHE cc_start: 0.6435 (p90) cc_final: 0.6130 (p90) REVERT: D 1927 PHE cc_start: 0.7491 (OUTLIER) cc_final: 0.7119 (t80) REVERT: D 2397 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6963 (tp) REVERT: D 3020 LEU cc_start: 0.1051 (OUTLIER) cc_final: 0.0572 (mp) REVERT: D 3045 MET cc_start: 0.3572 (ppp) cc_final: 0.3352 (ppp) REVERT: D 3322 MET cc_start: 0.2799 (mmt) cc_final: 0.2313 (mmt) REVERT: D 3853 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8715 (t80) REVERT: D 3977 MET cc_start: 0.8725 (tpp) cc_final: 0.8313 (ttp) REVERT: D 4566 TYR cc_start: 0.5344 (OUTLIER) cc_final: 0.4812 (t80) REVERT: E 18 LYS cc_start: 0.8584 (mmmm) cc_final: 0.7872 (mptt) REVERT: F 18 LYS cc_start: 0.8482 (mmmm) cc_final: 0.7797 (mptt) REVERT: G 18 LYS cc_start: 0.8453 (mmmm) cc_final: 0.7799 (mptt) REVERT: G 73 LYS cc_start: 0.8350 (tttm) cc_final: 0.8010 (ttmm) REVERT: H 18 LYS cc_start: 0.8487 (mmmm) cc_final: 0.7810 (mptt) REVERT: H 23 VAL cc_start: 0.7640 (OUTLIER) cc_final: 0.7271 (m) REVERT: H 73 LYS cc_start: 0.8347 (tttm) cc_final: 0.8008 (ttmm) outliers start: 456 outliers final: 308 residues processed: 1285 average time/residue: 1.0511 time to fit residues: 2453.4438 Evaluate side-chains 1245 residues out of total 14576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 346 poor density : 899 time to evaluate : 10.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 608 HIS Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 1007 TRP Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1300 MET Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1510 CYS Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain A residue 1530 THR Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1609 VAL Chi-restraints excluded: chain A residue 1629 MET Chi-restraints excluded: chain A residue 1631 LEU Chi-restraints excluded: chain A residue 1665 VAL Chi-restraints excluded: chain A residue 1814 THR Chi-restraints excluded: chain A residue 1927 PHE Chi-restraints excluded: chain A residue 1928 SER Chi-restraints excluded: chain A residue 1941 PHE Chi-restraints excluded: chain A residue 1944 ASN Chi-restraints excluded: chain A residue 1957 THR Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2032 VAL Chi-restraints excluded: chain A residue 2060 LEU Chi-restraints excluded: chain A residue 2086 LEU Chi-restraints excluded: chain A residue 2116 ILE Chi-restraints excluded: chain A residue 2129 LEU Chi-restraints excluded: chain A residue 2171 MET Chi-restraints excluded: chain A residue 2192 VAL Chi-restraints excluded: chain A residue 2199 LEU Chi-restraints excluded: chain A residue 2265 VAL Chi-restraints excluded: chain A residue 2282 LYS Chi-restraints excluded: chain A residue 2286 ASP Chi-restraints excluded: chain A residue 2290 ASN Chi-restraints excluded: chain A residue 2397 LEU Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain A residue 2781 MET Chi-restraints excluded: chain A residue 3020 LEU Chi-restraints excluded: chain A residue 3237 VAL Chi-restraints excluded: chain A residue 3636 GLU Chi-restraints excluded: chain A residue 3730 LEU Chi-restraints excluded: chain A residue 3786 VAL Chi-restraints excluded: chain A residue 3829 LEU Chi-restraints excluded: chain A residue 3866 THR Chi-restraints excluded: chain A residue 3954 GLN Chi-restraints excluded: chain A residue 4011 MET Chi-restraints excluded: chain A residue 4026 THR Chi-restraints excluded: chain A residue 4502 MET Chi-restraints excluded: chain A residue 4521 SER Chi-restraints excluded: chain A residue 4594 VAL Chi-restraints excluded: chain A residue 4735 ASN Chi-restraints excluded: chain A residue 4755 ILE Chi-restraints excluded: chain A residue 4809 LEU Chi-restraints excluded: chain A residue 4813 MET Chi-restraints excluded: chain A residue 4830 ILE Chi-restraints excluded: chain A residue 4922 MET Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 201 TRP Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 608 HIS Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 630 HIS Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 964 MET Chi-restraints excluded: chain B residue 1007 TRP Chi-restraints excluded: chain B residue 1166 VAL Chi-restraints excluded: chain B residue 1430 VAL Chi-restraints excluded: chain B residue 1510 CYS Chi-restraints excluded: chain B residue 1519 LEU Chi-restraints excluded: chain B residue 1530 THR Chi-restraints excluded: chain B residue 1596 LEU Chi-restraints excluded: chain B residue 1609 VAL Chi-restraints excluded: chain B residue 1631 LEU Chi-restraints excluded: chain B residue 1665 VAL Chi-restraints excluded: chain B residue 1814 THR Chi-restraints excluded: chain B residue 1927 PHE Chi-restraints excluded: chain B residue 1941 PHE Chi-restraints excluded: chain B residue 1944 ASN Chi-restraints excluded: chain B residue 1957 THR Chi-restraints excluded: chain B residue 1991 ILE Chi-restraints excluded: chain B residue 2032 VAL Chi-restraints excluded: chain B residue 2060 LEU Chi-restraints excluded: chain B residue 2086 LEU Chi-restraints excluded: chain B residue 2116 ILE Chi-restraints excluded: chain B residue 2129 LEU Chi-restraints excluded: chain B residue 2192 VAL Chi-restraints excluded: chain B residue 2199 LEU Chi-restraints excluded: chain B residue 2217 LEU Chi-restraints excluded: chain B residue 2265 VAL Chi-restraints excluded: chain B residue 2282 LYS Chi-restraints excluded: chain B residue 2286 ASP Chi-restraints excluded: chain B residue 2290 ASN Chi-restraints excluded: chain B residue 2328 GLU Chi-restraints excluded: chain B residue 2425 LEU Chi-restraints excluded: chain B residue 2519 LEU Chi-restraints excluded: chain B residue 2781 MET Chi-restraints excluded: chain B residue 3020 LEU Chi-restraints excluded: chain B residue 3237 VAL Chi-restraints excluded: chain B residue 3636 GLU Chi-restraints excluded: chain B residue 3730 LEU Chi-restraints excluded: chain B residue 3786 VAL Chi-restraints excluded: chain B residue 3829 LEU Chi-restraints excluded: chain B residue 3866 THR Chi-restraints excluded: chain B residue 3954 GLN Chi-restraints excluded: chain B residue 4011 MET Chi-restraints excluded: chain B residue 4026 THR Chi-restraints excluded: chain B residue 4502 MET Chi-restraints excluded: chain B residue 4521 SER Chi-restraints excluded: chain B residue 4594 VAL Chi-restraints excluded: chain B residue 4696 VAL Chi-restraints excluded: chain B residue 4735 ASN Chi-restraints excluded: chain B residue 4755 ILE Chi-restraints excluded: chain B residue 4809 LEU Chi-restraints excluded: chain B residue 4830 ILE Chi-restraints excluded: chain B residue 4922 MET Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 201 TRP Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 398 HIS Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 608 HIS Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 617 LEU Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 630 HIS Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 964 MET Chi-restraints excluded: chain C residue 1007 TRP Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1300 MET Chi-restraints excluded: chain C residue 1430 VAL Chi-restraints excluded: chain C residue 1510 CYS Chi-restraints excluded: chain C residue 1519 LEU Chi-restraints excluded: chain C residue 1530 THR Chi-restraints excluded: chain C residue 1596 LEU Chi-restraints excluded: chain C residue 1608 ASP Chi-restraints excluded: chain C residue 1609 VAL Chi-restraints excluded: chain C residue 1631 LEU Chi-restraints excluded: chain C residue 1633 ILE Chi-restraints excluded: chain C residue 1665 VAL Chi-restraints excluded: chain C residue 1796 LEU Chi-restraints excluded: chain C residue 1814 THR Chi-restraints excluded: chain C residue 1917 VAL Chi-restraints excluded: chain C residue 1927 PHE Chi-restraints excluded: chain C residue 1928 SER Chi-restraints excluded: chain C residue 1941 PHE Chi-restraints excluded: chain C residue 1944 ASN Chi-restraints excluded: chain C residue 1957 THR Chi-restraints excluded: chain C residue 1991 ILE Chi-restraints excluded: chain C residue 2032 VAL Chi-restraints excluded: chain C residue 2060 LEU Chi-restraints excluded: chain C residue 2086 LEU Chi-restraints excluded: chain C residue 2116 ILE Chi-restraints excluded: chain C residue 2129 LEU Chi-restraints excluded: chain C residue 2171 MET Chi-restraints excluded: chain C residue 2192 VAL Chi-restraints excluded: chain C residue 2199 LEU Chi-restraints excluded: chain C residue 2217 LEU Chi-restraints excluded: chain C residue 2265 VAL Chi-restraints excluded: chain C residue 2282 LYS Chi-restraints excluded: chain C residue 2286 ASP Chi-restraints excluded: chain C residue 2290 ASN Chi-restraints excluded: chain C residue 2387 ILE Chi-restraints excluded: chain C residue 2397 LEU Chi-restraints excluded: chain C residue 2519 LEU Chi-restraints excluded: chain C residue 2781 MET Chi-restraints excluded: chain C residue 3020 LEU Chi-restraints excluded: chain C residue 3237 VAL Chi-restraints excluded: chain C residue 3730 LEU Chi-restraints excluded: chain C residue 3786 VAL Chi-restraints excluded: chain C residue 3795 LEU Chi-restraints excluded: chain C residue 3829 LEU Chi-restraints excluded: chain C residue 3853 PHE Chi-restraints excluded: chain C residue 3954 GLN Chi-restraints excluded: chain C residue 4011 MET Chi-restraints excluded: chain C residue 4026 THR Chi-restraints excluded: chain C residue 4502 MET Chi-restraints excluded: chain C residue 4521 SER Chi-restraints excluded: chain C residue 4566 TYR Chi-restraints excluded: chain C residue 4594 VAL Chi-restraints excluded: chain C residue 4696 VAL Chi-restraints excluded: chain C residue 4735 ASN Chi-restraints excluded: chain C residue 4755 ILE Chi-restraints excluded: chain C residue 4757 SER Chi-restraints excluded: chain C residue 4809 LEU Chi-restraints excluded: chain C residue 4813 MET Chi-restraints excluded: chain C residue 4830 ILE Chi-restraints excluded: chain C residue 4922 MET Chi-restraints excluded: chain D residue 132 CYS Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 201 TRP Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 398 HIS Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 608 HIS Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 615 CYS Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 630 HIS Chi-restraints excluded: chain D residue 868 ASP Chi-restraints excluded: chain D residue 874 LEU Chi-restraints excluded: chain D residue 964 MET Chi-restraints excluded: chain D residue 1007 TRP Chi-restraints excluded: chain D residue 1166 VAL Chi-restraints excluded: chain D residue 1300 MET Chi-restraints excluded: chain D residue 1430 VAL Chi-restraints excluded: chain D residue 1510 CYS Chi-restraints excluded: chain D residue 1519 LEU Chi-restraints excluded: chain D residue 1530 THR Chi-restraints excluded: chain D residue 1596 LEU Chi-restraints excluded: chain D residue 1608 ASP Chi-restraints excluded: chain D residue 1629 MET Chi-restraints excluded: chain D residue 1631 LEU Chi-restraints excluded: chain D residue 1665 VAL Chi-restraints excluded: chain D residue 1814 THR Chi-restraints excluded: chain D residue 1917 VAL Chi-restraints excluded: chain D residue 1927 PHE Chi-restraints excluded: chain D residue 1928 SER Chi-restraints excluded: chain D residue 1932 VAL Chi-restraints excluded: chain D residue 1941 PHE Chi-restraints excluded: chain D residue 1944 ASN Chi-restraints excluded: chain D residue 1957 THR Chi-restraints excluded: chain D residue 1991 ILE Chi-restraints excluded: chain D residue 2032 VAL Chi-restraints excluded: chain D residue 2060 LEU Chi-restraints excluded: chain D residue 2086 LEU Chi-restraints excluded: chain D residue 2116 ILE Chi-restraints excluded: chain D residue 2129 LEU Chi-restraints excluded: chain D residue 2171 MET Chi-restraints excluded: chain D residue 2192 VAL Chi-restraints excluded: chain D residue 2199 LEU Chi-restraints excluded: chain D residue 2265 VAL Chi-restraints excluded: chain D residue 2282 LYS Chi-restraints excluded: chain D residue 2286 ASP Chi-restraints excluded: chain D residue 2290 ASN Chi-restraints excluded: chain D residue 2387 ILE Chi-restraints excluded: chain D residue 2397 LEU Chi-restraints excluded: chain D residue 2519 LEU Chi-restraints excluded: chain D residue 2781 MET Chi-restraints excluded: chain D residue 3020 LEU Chi-restraints excluded: chain D residue 3237 VAL Chi-restraints excluded: chain D residue 3636 GLU Chi-restraints excluded: chain D residue 3730 LEU Chi-restraints excluded: chain D residue 3786 VAL Chi-restraints excluded: chain D residue 3795 LEU Chi-restraints excluded: chain D residue 3829 LEU Chi-restraints excluded: chain D residue 3853 PHE Chi-restraints excluded: chain D residue 3954 GLN Chi-restraints excluded: chain D residue 4011 MET Chi-restraints excluded: chain D residue 4026 THR Chi-restraints excluded: chain D residue 4142 LYS Chi-restraints excluded: chain D residue 4502 MET Chi-restraints excluded: chain D residue 4521 SER Chi-restraints excluded: chain D residue 4566 TYR Chi-restraints excluded: chain D residue 4594 VAL Chi-restraints excluded: chain D residue 4696 VAL Chi-restraints excluded: chain D residue 4735 ASN Chi-restraints excluded: chain D residue 4755 ILE Chi-restraints excluded: chain D residue 4757 SER Chi-restraints excluded: chain D residue 4809 LEU Chi-restraints excluded: chain D residue 4813 MET Chi-restraints excluded: chain D residue 4830 ILE Chi-restraints excluded: chain D residue 4922 MET Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 25 HIS Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 25 HIS Chi-restraints excluded: chain G residue 32 ASN Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 25 HIS Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 90 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1664 random chunks: chunk 541 optimal weight: 20.0000 chunk 1448 optimal weight: 40.0000 chunk 317 optimal weight: 0.8980 chunk 944 optimal weight: 9.9990 chunk 397 optimal weight: 2.9990 chunk 1609 optimal weight: 0.6980 chunk 1336 optimal weight: 9.9990 chunk 745 optimal weight: 0.9980 chunk 133 optimal weight: 40.0000 chunk 532 optimal weight: 20.0000 chunk 845 optimal weight: 20.0000 overall best weight: 3.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 HIS A1169 ASN A1603 GLN ** A2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2249 ASN A2340 ASN ** A4735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1169 ASN B1603 GLN ** B2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2249 ASN ** B4735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 ASN C1169 ASN C1603 GLN ** C2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2249 ASN ** C4735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1169 ASN ** D2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2249 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 132192 Z= 0.288 Angle : 0.628 15.394 178900 Z= 0.322 Chirality : 0.042 0.267 19928 Planarity : 0.004 0.113 23144 Dihedral : 5.112 45.193 17864 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.88 % Favored : 89.00 % Rotamer: Outliers : 3.46 % Allowed : 19.50 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.50 (0.06), residues: 16464 helix: 0.86 (0.06), residues: 7268 sheet: -1.27 (0.16), residues: 1060 loop : -2.86 (0.06), residues: 8136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP D1007 HIS 0.011 0.001 HIS A1711 PHE 0.031 0.002 PHE D2202 TYR 0.022 0.001 TYR C3690 ARG 0.013 0.000 ARG A 626 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1383 residues out of total 14576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 471 poor density : 912 time to evaluate : 10.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 ASP cc_start: 0.6960 (OUTLIER) cc_final: 0.6712 (p0) REVERT: A 535 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.5887 (tt0) REVERT: A 868 ASP cc_start: 0.3960 (OUTLIER) cc_final: 0.2687 (t0) REVERT: A 874 LEU cc_start: 0.0182 (OUTLIER) cc_final: -0.0037 (tt) REVERT: A 1168 MET cc_start: 0.6988 (tpt) cc_final: 0.6006 (tpt) REVERT: A 1173 MET cc_start: 0.3891 (mmp) cc_final: 0.3136 (mmp) REVERT: A 1927 PHE cc_start: 0.7449 (OUTLIER) cc_final: 0.7038 (t80) REVERT: A 2213 MET cc_start: 0.7170 (mpp) cc_final: 0.6940 (mpp) REVERT: A 2397 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6953 (tp) REVERT: A 2467 MET cc_start: 0.6688 (mmp) cc_final: 0.6467 (mmp) REVERT: A 3020 LEU cc_start: 0.0783 (OUTLIER) cc_final: 0.0314 (mp) REVERT: A 3469 LEU cc_start: 0.1071 (OUTLIER) cc_final: 0.0677 (pp) REVERT: A 3866 THR cc_start: 0.8164 (OUTLIER) cc_final: 0.7935 (p) REVERT: B 535 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.5860 (tt0) REVERT: B 630 HIS cc_start: 0.7604 (OUTLIER) cc_final: 0.6667 (t70) REVERT: B 868 ASP cc_start: 0.4002 (OUTLIER) cc_final: 0.2705 (t0) REVERT: B 874 LEU cc_start: 0.0235 (OUTLIER) cc_final: -0.0339 (tt) REVERT: B 1604 PHE cc_start: 0.6323 (p90) cc_final: 0.6002 (p90) REVERT: B 1927 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.6914 (t80) REVERT: B 1947 MET cc_start: -0.0831 (mmt) cc_final: -0.3360 (ptt) REVERT: B 2191 MET cc_start: 0.7214 (pmm) cc_final: 0.6925 (pmm) REVERT: B 2467 MET cc_start: 0.6686 (mmp) cc_final: 0.6475 (mmp) REVERT: B 3020 LEU cc_start: 0.0833 (OUTLIER) cc_final: 0.0400 (mp) REVERT: B 3233 MET cc_start: 0.4182 (ptt) cc_final: 0.3904 (ptt) REVERT: B 3469 LEU cc_start: 0.1110 (OUTLIER) cc_final: 0.0720 (pp) REVERT: B 3977 MET cc_start: 0.8708 (tpp) cc_final: 0.8447 (ttp) REVERT: C 535 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.5791 (tt0) REVERT: C 628 ASN cc_start: 0.3444 (OUTLIER) cc_final: 0.3213 (m110) REVERT: C 630 HIS cc_start: 0.7572 (OUTLIER) cc_final: 0.6746 (t70) REVERT: C 868 ASP cc_start: 0.3815 (OUTLIER) cc_final: 0.2526 (t0) REVERT: C 874 LEU cc_start: 0.0560 (OUTLIER) cc_final: 0.0353 (tt) REVERT: C 1604 PHE cc_start: 0.6223 (p90) cc_final: 0.5992 (p90) REVERT: C 1927 PHE cc_start: 0.7405 (OUTLIER) cc_final: 0.6924 (t80) REVERT: C 2213 MET cc_start: 0.7257 (tpp) cc_final: 0.6928 (mpp) REVERT: C 2397 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.7011 (tp) REVERT: C 3020 LEU cc_start: 0.0948 (OUTLIER) cc_final: 0.0474 (mp) REVERT: C 3469 LEU cc_start: 0.1230 (OUTLIER) cc_final: 0.0789 (pp) REVERT: C 3853 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8644 (t80) REVERT: C 3977 MET cc_start: 0.8708 (tpp) cc_final: 0.8377 (ttp) REVERT: D 311 ASP cc_start: 0.6929 (OUTLIER) cc_final: 0.6710 (p0) REVERT: D 535 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.5796 (tt0) REVERT: D 630 HIS cc_start: 0.7574 (OUTLIER) cc_final: 0.6703 (t70) REVERT: D 868 ASP cc_start: 0.3945 (OUTLIER) cc_final: 0.2719 (t0) REVERT: D 1604 PHE cc_start: 0.6193 (p90) cc_final: 0.5990 (p90) REVERT: D 1927 PHE cc_start: 0.7393 (OUTLIER) cc_final: 0.6995 (t80) REVERT: D 2213 MET cc_start: 0.7274 (tpp) cc_final: 0.6910 (mpp) REVERT: D 2397 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.7044 (tp) REVERT: D 3020 LEU cc_start: 0.0804 (OUTLIER) cc_final: 0.0312 (mp) REVERT: D 3469 LEU cc_start: 0.1230 (OUTLIER) cc_final: 0.0767 (pp) REVERT: D 3853 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.8575 (t80) REVERT: D 3977 MET cc_start: 0.8690 (tpp) cc_final: 0.8352 (ttp) REVERT: D 4018 MET cc_start: 0.4732 (OUTLIER) cc_final: 0.4500 (mtp) REVERT: E 18 LYS cc_start: 0.8589 (mmmm) cc_final: 0.7890 (mptt) REVERT: E 48 PHE cc_start: 0.8021 (p90) cc_final: 0.7703 (p90) REVERT: F 18 LYS cc_start: 0.8493 (mmmm) cc_final: 0.7821 (mptt) REVERT: F 23 VAL cc_start: 0.7812 (OUTLIER) cc_final: 0.7602 (m) REVERT: G 18 LYS cc_start: 0.8461 (mmmm) cc_final: 0.7829 (mptt) REVERT: G 23 VAL cc_start: 0.7752 (OUTLIER) cc_final: 0.7474 (m) REVERT: G 73 LYS cc_start: 0.8357 (tttm) cc_final: 0.8015 (ttmm) REVERT: H 18 LYS cc_start: 0.8532 (mmmm) cc_final: 0.7935 (mptt) REVERT: H 23 VAL cc_start: 0.7812 (OUTLIER) cc_final: 0.7584 (m) REVERT: H 73 LYS cc_start: 0.8356 (tttm) cc_final: 0.8022 (ttmm) outliers start: 471 outliers final: 317 residues processed: 1291 average time/residue: 0.9782 time to fit residues: 2295.1268 Evaluate side-chains 1250 residues out of total 14576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 356 poor density : 894 time to evaluate : 10.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 398 HIS Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 608 HIS Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain A residue 781 ASN Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 1007 TRP Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1300 MET Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1510 CYS Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain A residue 1530 THR Chi-restraints excluded: chain A residue 1608 ASP Chi-restraints excluded: chain A residue 1629 MET Chi-restraints excluded: chain A residue 1631 LEU Chi-restraints excluded: chain A residue 1633 ILE Chi-restraints excluded: chain A residue 1814 THR Chi-restraints excluded: chain A residue 1917 VAL Chi-restraints excluded: chain A residue 1927 PHE Chi-restraints excluded: chain A residue 1928 SER Chi-restraints excluded: chain A residue 1941 PHE Chi-restraints excluded: chain A residue 1944 ASN Chi-restraints excluded: chain A residue 1957 THR Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2032 VAL Chi-restraints excluded: chain A residue 2060 LEU Chi-restraints excluded: chain A residue 2086 LEU Chi-restraints excluded: chain A residue 2116 ILE Chi-restraints excluded: chain A residue 2129 LEU Chi-restraints excluded: chain A residue 2171 MET Chi-restraints excluded: chain A residue 2199 LEU Chi-restraints excluded: chain A residue 2265 VAL Chi-restraints excluded: chain A residue 2282 LYS Chi-restraints excluded: chain A residue 2286 ASP Chi-restraints excluded: chain A residue 2387 ILE Chi-restraints excluded: chain A residue 2397 LEU Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain A residue 2781 MET Chi-restraints excluded: chain A residue 2902 VAL Chi-restraints excluded: chain A residue 3020 LEU Chi-restraints excluded: chain A residue 3228 THR Chi-restraints excluded: chain A residue 3469 LEU Chi-restraints excluded: chain A residue 3636 GLU Chi-restraints excluded: chain A residue 3643 LEU Chi-restraints excluded: chain A residue 3697 SER Chi-restraints excluded: chain A residue 3730 LEU Chi-restraints excluded: chain A residue 3750 THR Chi-restraints excluded: chain A residue 3786 VAL Chi-restraints excluded: chain A residue 3866 THR Chi-restraints excluded: chain A residue 3954 GLN Chi-restraints excluded: chain A residue 4011 MET Chi-restraints excluded: chain A residue 4026 THR Chi-restraints excluded: chain A residue 4195 THR Chi-restraints excluded: chain A residue 4521 SER Chi-restraints excluded: chain A residue 4594 VAL Chi-restraints excluded: chain A residue 4696 VAL Chi-restraints excluded: chain A residue 4735 ASN Chi-restraints excluded: chain A residue 4809 LEU Chi-restraints excluded: chain A residue 4813 MET Chi-restraints excluded: chain A residue 4830 ILE Chi-restraints excluded: chain A residue 4922 MET Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 201 TRP Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 398 HIS Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 608 HIS Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 630 HIS Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 868 ASP Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 964 MET Chi-restraints excluded: chain B residue 1007 TRP Chi-restraints excluded: chain B residue 1166 VAL Chi-restraints excluded: chain B residue 1430 VAL Chi-restraints excluded: chain B residue 1510 CYS Chi-restraints excluded: chain B residue 1530 THR Chi-restraints excluded: chain B residue 1608 ASP Chi-restraints excluded: chain B residue 1629 MET Chi-restraints excluded: chain B residue 1631 LEU Chi-restraints excluded: chain B residue 1633 ILE Chi-restraints excluded: chain B residue 1665 VAL Chi-restraints excluded: chain B residue 1814 THR Chi-restraints excluded: chain B residue 1917 VAL Chi-restraints excluded: chain B residue 1927 PHE Chi-restraints excluded: chain B residue 1928 SER Chi-restraints excluded: chain B residue 1941 PHE Chi-restraints excluded: chain B residue 1944 ASN Chi-restraints excluded: chain B residue 1957 THR Chi-restraints excluded: chain B residue 1991 ILE Chi-restraints excluded: chain B residue 2032 VAL Chi-restraints excluded: chain B residue 2060 LEU Chi-restraints excluded: chain B residue 2086 LEU Chi-restraints excluded: chain B residue 2116 ILE Chi-restraints excluded: chain B residue 2129 LEU Chi-restraints excluded: chain B residue 2199 LEU Chi-restraints excluded: chain B residue 2217 LEU Chi-restraints excluded: chain B residue 2265 VAL Chi-restraints excluded: chain B residue 2282 LYS Chi-restraints excluded: chain B residue 2286 ASP Chi-restraints excluded: chain B residue 2328 GLU Chi-restraints excluded: chain B residue 2425 LEU Chi-restraints excluded: chain B residue 2503 THR Chi-restraints excluded: chain B residue 2519 LEU Chi-restraints excluded: chain B residue 2781 MET Chi-restraints excluded: chain B residue 2902 VAL Chi-restraints excluded: chain B residue 3020 LEU Chi-restraints excluded: chain B residue 3228 THR Chi-restraints excluded: chain B residue 3469 LEU Chi-restraints excluded: chain B residue 3636 GLU Chi-restraints excluded: chain B residue 3643 LEU Chi-restraints excluded: chain B residue 3697 SER Chi-restraints excluded: chain B residue 3730 LEU Chi-restraints excluded: chain B residue 3750 THR Chi-restraints excluded: chain B residue 3786 VAL Chi-restraints excluded: chain B residue 3954 GLN Chi-restraints excluded: chain B residue 4011 MET Chi-restraints excluded: chain B residue 4026 THR Chi-restraints excluded: chain B residue 4521 SER Chi-restraints excluded: chain B residue 4594 VAL Chi-restraints excluded: chain B residue 4696 VAL Chi-restraints excluded: chain B residue 4735 ASN Chi-restraints excluded: chain B residue 4809 LEU Chi-restraints excluded: chain B residue 4830 ILE Chi-restraints excluded: chain B residue 4922 MET Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 201 TRP Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 398 HIS Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 529 ILE Chi-restraints excluded: chain C residue 534 TYR Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 608 HIS Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 625 VAL Chi-restraints excluded: chain C residue 628 ASN Chi-restraints excluded: chain C residue 630 HIS Chi-restraints excluded: chain C residue 781 ASN Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 868 ASP Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 964 MET Chi-restraints excluded: chain C residue 1007 TRP Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1430 VAL Chi-restraints excluded: chain C residue 1510 CYS Chi-restraints excluded: chain C residue 1530 THR Chi-restraints excluded: chain C residue 1608 ASP Chi-restraints excluded: chain C residue 1629 MET Chi-restraints excluded: chain C residue 1631 LEU Chi-restraints excluded: chain C residue 1633 ILE Chi-restraints excluded: chain C residue 1665 VAL Chi-restraints excluded: chain C residue 1783 PHE Chi-restraints excluded: chain C residue 1796 LEU Chi-restraints excluded: chain C residue 1814 THR Chi-restraints excluded: chain C residue 1927 PHE Chi-restraints excluded: chain C residue 1928 SER Chi-restraints excluded: chain C residue 1941 PHE Chi-restraints excluded: chain C residue 1944 ASN Chi-restraints excluded: chain C residue 1957 THR Chi-restraints excluded: chain C residue 1991 ILE Chi-restraints excluded: chain C residue 2032 VAL Chi-restraints excluded: chain C residue 2060 LEU Chi-restraints excluded: chain C residue 2086 LEU Chi-restraints excluded: chain C residue 2116 ILE Chi-restraints excluded: chain C residue 2129 LEU Chi-restraints excluded: chain C residue 2171 MET Chi-restraints excluded: chain C residue 2199 LEU Chi-restraints excluded: chain C residue 2217 LEU Chi-restraints excluded: chain C residue 2265 VAL Chi-restraints excluded: chain C residue 2282 LYS Chi-restraints excluded: chain C residue 2286 ASP Chi-restraints excluded: chain C residue 2387 ILE Chi-restraints excluded: chain C residue 2397 LEU Chi-restraints excluded: chain C residue 2519 LEU Chi-restraints excluded: chain C residue 2667 CYS Chi-restraints excluded: chain C residue 2781 MET Chi-restraints excluded: chain C residue 2902 VAL Chi-restraints excluded: chain C residue 3020 LEU Chi-restraints excluded: chain C residue 3228 THR Chi-restraints excluded: chain C residue 3237 VAL Chi-restraints excluded: chain C residue 3469 LEU Chi-restraints excluded: chain C residue 3636 GLU Chi-restraints excluded: chain C residue 3643 LEU Chi-restraints excluded: chain C residue 3697 SER Chi-restraints excluded: chain C residue 3730 LEU Chi-restraints excluded: chain C residue 3786 VAL Chi-restraints excluded: chain C residue 3795 LEU Chi-restraints excluded: chain C residue 3853 PHE Chi-restraints excluded: chain C residue 3954 GLN Chi-restraints excluded: chain C residue 4011 MET Chi-restraints excluded: chain C residue 4026 THR Chi-restraints excluded: chain C residue 4521 SER Chi-restraints excluded: chain C residue 4594 VAL Chi-restraints excluded: chain C residue 4696 VAL Chi-restraints excluded: chain C residue 4735 ASN Chi-restraints excluded: chain C residue 4809 LEU Chi-restraints excluded: chain C residue 4813 MET Chi-restraints excluded: chain C residue 4830 ILE Chi-restraints excluded: chain C residue 4922 MET Chi-restraints excluded: chain D residue 132 CYS Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 201 TRP Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 534 TYR Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 608 HIS Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 615 CYS Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 630 HIS Chi-restraints excluded: chain D residue 781 ASN Chi-restraints excluded: chain D residue 868 ASP Chi-restraints excluded: chain D residue 964 MET Chi-restraints excluded: chain D residue 1007 TRP Chi-restraints excluded: chain D residue 1166 VAL Chi-restraints excluded: chain D residue 1300 MET Chi-restraints excluded: chain D residue 1430 VAL Chi-restraints excluded: chain D residue 1510 CYS Chi-restraints excluded: chain D residue 1530 THR Chi-restraints excluded: chain D residue 1608 ASP Chi-restraints excluded: chain D residue 1629 MET Chi-restraints excluded: chain D residue 1631 LEU Chi-restraints excluded: chain D residue 1633 ILE Chi-restraints excluded: chain D residue 1665 VAL Chi-restraints excluded: chain D residue 1783 PHE Chi-restraints excluded: chain D residue 1814 THR Chi-restraints excluded: chain D residue 1927 PHE Chi-restraints excluded: chain D residue 1928 SER Chi-restraints excluded: chain D residue 1941 PHE Chi-restraints excluded: chain D residue 1944 ASN Chi-restraints excluded: chain D residue 1957 THR Chi-restraints excluded: chain D residue 1991 ILE Chi-restraints excluded: chain D residue 2032 VAL Chi-restraints excluded: chain D residue 2060 LEU Chi-restraints excluded: chain D residue 2086 LEU Chi-restraints excluded: chain D residue 2116 ILE Chi-restraints excluded: chain D residue 2129 LEU Chi-restraints excluded: chain D residue 2199 LEU Chi-restraints excluded: chain D residue 2265 VAL Chi-restraints excluded: chain D residue 2282 LYS Chi-restraints excluded: chain D residue 2286 ASP Chi-restraints excluded: chain D residue 2387 ILE Chi-restraints excluded: chain D residue 2397 LEU Chi-restraints excluded: chain D residue 2519 LEU Chi-restraints excluded: chain D residue 2781 MET Chi-restraints excluded: chain D residue 2902 VAL Chi-restraints excluded: chain D residue 3020 LEU Chi-restraints excluded: chain D residue 3228 THR Chi-restraints excluded: chain D residue 3237 VAL Chi-restraints excluded: chain D residue 3469 LEU Chi-restraints excluded: chain D residue 3636 GLU Chi-restraints excluded: chain D residue 3643 LEU Chi-restraints excluded: chain D residue 3697 SER Chi-restraints excluded: chain D residue 3730 LEU Chi-restraints excluded: chain D residue 3786 VAL Chi-restraints excluded: chain D residue 3795 LEU Chi-restraints excluded: chain D residue 3853 PHE Chi-restraints excluded: chain D residue 3954 GLN Chi-restraints excluded: chain D residue 4011 MET Chi-restraints excluded: chain D residue 4018 MET Chi-restraints excluded: chain D residue 4026 THR Chi-restraints excluded: chain D residue 4142 LYS Chi-restraints excluded: chain D residue 4195 THR Chi-restraints excluded: chain D residue 4521 SER Chi-restraints excluded: chain D residue 4522 THR Chi-restraints excluded: chain D residue 4566 TYR Chi-restraints excluded: chain D residue 4594 VAL Chi-restraints excluded: chain D residue 4696 VAL Chi-restraints excluded: chain D residue 4735 ASN Chi-restraints excluded: chain D residue 4809 LEU Chi-restraints excluded: chain D residue 4813 MET Chi-restraints excluded: chain D residue 4830 ILE Chi-restraints excluded: chain D residue 4922 MET Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 25 HIS Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain G residue 25 HIS Chi-restraints excluded: chain G residue 32 ASN Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 25 HIS Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 90 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1664 random chunks: chunk 1552 optimal weight: 3.9990 chunk 181 optimal weight: 8.9990 chunk 917 optimal weight: 5.9990 chunk 1175 optimal weight: 0.9990 chunk 910 optimal weight: 7.9990 chunk 1355 optimal weight: 20.0000 chunk 899 optimal weight: 8.9990 chunk 1603 optimal weight: 0.8980 chunk 1003 optimal weight: 7.9990 chunk 977 optimal weight: 0.0370 chunk 740 optimal weight: 4.9990 overall best weight: 2.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 ASN ** A 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 HIS ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 ASN ** B 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1603 GLN ** B2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2721 ASN C 29 HIS ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 630 HIS C1603 GLN ** C2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2176 ASN C2340 ASN D 29 HIS D 150 GLN ** D2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 132192 Z= 0.232 Angle : 0.610 14.512 178900 Z= 0.311 Chirality : 0.041 0.255 19928 Planarity : 0.004 0.112 23144 Dihedral : 5.018 45.419 17864 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.81 % Favored : 89.10 % Rotamer: Outliers : 3.30 % Allowed : 20.19 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.39 (0.06), residues: 16464 helix: 0.97 (0.06), residues: 7300 sheet: -1.28 (0.16), residues: 1068 loop : -2.84 (0.06), residues: 8096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP D1007 HIS 0.021 0.001 HIS A 270 PHE 0.029 0.001 PHE D2202 TYR 0.019 0.001 TYR A3623 ARG 0.012 0.000 ARG C 626 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1379 residues out of total 14576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 450 poor density : 929 time to evaluate : 11.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 311 ASP cc_start: 0.7028 (OUTLIER) cc_final: 0.6822 (p0) REVERT: A 535 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.5836 (tt0) REVERT: A 628 ASN cc_start: 0.3508 (OUTLIER) cc_final: 0.3223 (m110) REVERT: A 1168 MET cc_start: 0.7038 (tpt) cc_final: 0.6057 (tpt) REVERT: A 1604 PHE cc_start: 0.6265 (p90) cc_final: 0.6022 (p90) REVERT: A 1927 PHE cc_start: 0.7374 (OUTLIER) cc_final: 0.6983 (t80) REVERT: A 2397 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.7013 (tp) REVERT: A 2716 LEU cc_start: 0.0456 (OUTLIER) cc_final: -0.0547 (mm) REVERT: A 3020 LEU cc_start: 0.0783 (OUTLIER) cc_final: 0.0315 (mp) REVERT: A 3045 MET cc_start: 0.3841 (ppp) cc_final: 0.2595 (tmm) REVERT: A 4821 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.6174 (mtp180) REVERT: B 535 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.5832 (tt0) REVERT: B 628 ASN cc_start: 0.3556 (OUTLIER) cc_final: 0.3302 (m110) REVERT: B 868 ASP cc_start: 0.4013 (OUTLIER) cc_final: 0.2746 (t0) REVERT: B 874 LEU cc_start: 0.0323 (OUTLIER) cc_final: 0.0092 (tt) REVERT: B 1927 PHE cc_start: 0.7346 (OUTLIER) cc_final: 0.6896 (t80) REVERT: B 1947 MET cc_start: -0.0946 (mmt) cc_final: -0.3358 (ptt) REVERT: B 2716 LEU cc_start: 0.0239 (OUTLIER) cc_final: -0.0787 (mm) REVERT: B 3020 LEU cc_start: 0.0826 (OUTLIER) cc_final: 0.0402 (mp) REVERT: B 3045 MET cc_start: 0.3185 (ppp) cc_final: 0.1916 (tmm) REVERT: B 3233 MET cc_start: 0.4175 (ptt) cc_final: 0.3884 (ptt) REVERT: B 3977 MET cc_start: 0.8683 (tpp) cc_final: 0.8451 (ttp) REVERT: B 4821 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.6490 (mtp180) REVERT: C 535 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.5723 (tt0) REVERT: C 868 ASP cc_start: 0.3994 (OUTLIER) cc_final: 0.2779 (t0) REVERT: C 874 LEU cc_start: 0.0569 (OUTLIER) cc_final: 0.0352 (tt) REVERT: C 1927 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6911 (t80) REVERT: C 2213 MET cc_start: 0.7221 (tpp) cc_final: 0.6908 (mpp) REVERT: C 2397 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6979 (tp) REVERT: C 2716 LEU cc_start: 0.0350 (OUTLIER) cc_final: -0.0783 (mm) REVERT: C 3020 LEU cc_start: 0.1017 (OUTLIER) cc_final: 0.0565 (mp) REVERT: C 3045 MET cc_start: 0.3168 (ppp) cc_final: 0.1899 (tmm) REVERT: C 3977 MET cc_start: 0.8701 (tpp) cc_final: 0.8456 (ttp) REVERT: C 4018 MET cc_start: 0.4622 (OUTLIER) cc_final: 0.4386 (mtp) REVERT: C 4821 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.6647 (ptt-90) REVERT: D 535 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.5771 (tt0) REVERT: D 868 ASP cc_start: 0.3941 (OUTLIER) cc_final: 0.2742 (t0) REVERT: D 1927 PHE cc_start: 0.7386 (OUTLIER) cc_final: 0.7011 (t80) REVERT: D 2397 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.7039 (tp) REVERT: D 2716 LEU cc_start: 0.0373 (OUTLIER) cc_final: -0.0686 (mm) REVERT: D 3020 LEU cc_start: 0.0813 (OUTLIER) cc_final: 0.0322 (mp) REVERT: D 3045 MET cc_start: 0.4009 (ppp) cc_final: 0.2675 (tmm) REVERT: D 3322 MET cc_start: 0.2690 (mmt) cc_final: 0.1996 (mmt) REVERT: D 3977 MET cc_start: 0.8680 (tpp) cc_final: 0.8421 (ttp) REVERT: D 4018 MET cc_start: 0.4646 (OUTLIER) cc_final: 0.4433 (mtp) REVERT: D 4821 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.6197 (mtp180) REVERT: E 18 LYS cc_start: 0.8584 (mmmm) cc_final: 0.7905 (mptt) REVERT: E 48 PHE cc_start: 0.8000 (p90) cc_final: 0.7657 (p90) REVERT: F 18 LYS cc_start: 0.8479 (mmmm) cc_final: 0.7813 (mptt) REVERT: F 23 VAL cc_start: 0.7866 (OUTLIER) cc_final: 0.7661 (m) REVERT: G 18 LYS cc_start: 0.8459 (mmmm) cc_final: 0.7805 (mptt) REVERT: G 73 LYS cc_start: 0.8352 (tttm) cc_final: 0.8014 (ttmm) REVERT: H 18 LYS cc_start: 0.8523 (mmmm) cc_final: 0.7936 (mptt) REVERT: H 73 LYS cc_start: 0.8357 (tttm) cc_final: 0.8013 (ttmm) outliers start: 450 outliers final: 322 residues processed: 1285 average time/residue: 0.9962 time to fit residues: 2323.5250 Evaluate side-chains 1260 residues out of total 14576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 356 poor density : 904 time to evaluate : 10.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 398 HIS Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 608 HIS Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 1007 TRP Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1300 MET Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1510 CYS Chi-restraints excluded: chain A residue 1530 THR Chi-restraints excluded: chain A residue 1608 ASP Chi-restraints excluded: chain A residue 1631 LEU Chi-restraints excluded: chain A residue 1633 ILE Chi-restraints excluded: chain A residue 1665 VAL Chi-restraints excluded: chain A residue 1673 VAL Chi-restraints excluded: chain A residue 1796 LEU Chi-restraints excluded: chain A residue 1814 THR Chi-restraints excluded: chain A residue 1917 VAL Chi-restraints excluded: chain A residue 1927 PHE Chi-restraints excluded: chain A residue 1928 SER Chi-restraints excluded: chain A residue 1941 PHE Chi-restraints excluded: chain A residue 1944 ASN Chi-restraints excluded: chain A residue 1957 THR Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2032 VAL Chi-restraints excluded: chain A residue 2060 LEU Chi-restraints excluded: chain A residue 2086 LEU Chi-restraints excluded: chain A residue 2129 LEU Chi-restraints excluded: chain A residue 2171 MET Chi-restraints excluded: chain A residue 2199 LEU Chi-restraints excluded: chain A residue 2264 VAL Chi-restraints excluded: chain A residue 2265 VAL Chi-restraints excluded: chain A residue 2282 LYS Chi-restraints excluded: chain A residue 2286 ASP Chi-restraints excluded: chain A residue 2397 LEU Chi-restraints excluded: chain A residue 2425 LEU Chi-restraints excluded: chain A residue 2503 THR Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain A residue 2667 CYS Chi-restraints excluded: chain A residue 2716 LEU Chi-restraints excluded: chain A residue 2781 MET Chi-restraints excluded: chain A residue 3020 LEU Chi-restraints excluded: chain A residue 3228 THR Chi-restraints excluded: chain A residue 3636 GLU Chi-restraints excluded: chain A residue 3697 SER Chi-restraints excluded: chain A residue 3730 LEU Chi-restraints excluded: chain A residue 3786 VAL Chi-restraints excluded: chain A residue 3829 LEU Chi-restraints excluded: chain A residue 3954 GLN Chi-restraints excluded: chain A residue 4011 MET Chi-restraints excluded: chain A residue 4017 ASP Chi-restraints excluded: chain A residue 4026 THR Chi-restraints excluded: chain A residue 4502 MET Chi-restraints excluded: chain A residue 4521 SER Chi-restraints excluded: chain A residue 4594 VAL Chi-restraints excluded: chain A residue 4696 VAL Chi-restraints excluded: chain A residue 4735 ASN Chi-restraints excluded: chain A residue 4813 MET Chi-restraints excluded: chain A residue 4821 ARG Chi-restraints excluded: chain A residue 4830 ILE Chi-restraints excluded: chain A residue 4922 MET Chi-restraints excluded: chain B residue 47 CYS Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 201 TRP Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 398 HIS Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 608 HIS Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 630 HIS Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 868 ASP Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 964 MET Chi-restraints excluded: chain B residue 1007 TRP Chi-restraints excluded: chain B residue 1166 VAL Chi-restraints excluded: chain B residue 1304 LEU Chi-restraints excluded: chain B residue 1430 VAL Chi-restraints excluded: chain B residue 1510 CYS Chi-restraints excluded: chain B residue 1519 LEU Chi-restraints excluded: chain B residue 1530 THR Chi-restraints excluded: chain B residue 1608 ASP Chi-restraints excluded: chain B residue 1629 MET Chi-restraints excluded: chain B residue 1631 LEU Chi-restraints excluded: chain B residue 1633 ILE Chi-restraints excluded: chain B residue 1665 VAL Chi-restraints excluded: chain B residue 1814 THR Chi-restraints excluded: chain B residue 1917 VAL Chi-restraints excluded: chain B residue 1927 PHE Chi-restraints excluded: chain B residue 1928 SER Chi-restraints excluded: chain B residue 1941 PHE Chi-restraints excluded: chain B residue 1944 ASN Chi-restraints excluded: chain B residue 1957 THR Chi-restraints excluded: chain B residue 1991 ILE Chi-restraints excluded: chain B residue 2032 VAL Chi-restraints excluded: chain B residue 2060 LEU Chi-restraints excluded: chain B residue 2086 LEU Chi-restraints excluded: chain B residue 2129 LEU Chi-restraints excluded: chain B residue 2199 LEU Chi-restraints excluded: chain B residue 2217 LEU Chi-restraints excluded: chain B residue 2264 VAL Chi-restraints excluded: chain B residue 2265 VAL Chi-restraints excluded: chain B residue 2282 LYS Chi-restraints excluded: chain B residue 2286 ASP Chi-restraints excluded: chain B residue 2290 ASN Chi-restraints excluded: chain B residue 2328 GLU Chi-restraints excluded: chain B residue 2519 LEU Chi-restraints excluded: chain B residue 2667 CYS Chi-restraints excluded: chain B residue 2716 LEU Chi-restraints excluded: chain B residue 2781 MET Chi-restraints excluded: chain B residue 3020 LEU Chi-restraints excluded: chain B residue 3228 THR Chi-restraints excluded: chain B residue 3636 GLU Chi-restraints excluded: chain B residue 3697 SER Chi-restraints excluded: chain B residue 3713 PHE Chi-restraints excluded: chain B residue 3730 LEU Chi-restraints excluded: chain B residue 3786 VAL Chi-restraints excluded: chain B residue 3829 LEU Chi-restraints excluded: chain B residue 3954 GLN Chi-restraints excluded: chain B residue 4011 MET Chi-restraints excluded: chain B residue 4026 THR Chi-restraints excluded: chain B residue 4195 THR Chi-restraints excluded: chain B residue 4502 MET Chi-restraints excluded: chain B residue 4521 SER Chi-restraints excluded: chain B residue 4594 VAL Chi-restraints excluded: chain B residue 4696 VAL Chi-restraints excluded: chain B residue 4735 ASN Chi-restraints excluded: chain B residue 4821 ARG Chi-restraints excluded: chain B residue 4830 ILE Chi-restraints excluded: chain B residue 4922 MET Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 201 TRP Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 398 HIS Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 608 HIS Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 630 HIS Chi-restraints excluded: chain C residue 781 ASN Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 868 ASP Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 964 MET Chi-restraints excluded: chain C residue 1007 TRP Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1304 LEU Chi-restraints excluded: chain C residue 1430 VAL Chi-restraints excluded: chain C residue 1510 CYS Chi-restraints excluded: chain C residue 1519 LEU Chi-restraints excluded: chain C residue 1530 THR Chi-restraints excluded: chain C residue 1608 ASP Chi-restraints excluded: chain C residue 1629 MET Chi-restraints excluded: chain C residue 1631 LEU Chi-restraints excluded: chain C residue 1633 ILE Chi-restraints excluded: chain C residue 1665 VAL Chi-restraints excluded: chain C residue 1728 VAL Chi-restraints excluded: chain C residue 1796 LEU Chi-restraints excluded: chain C residue 1814 THR Chi-restraints excluded: chain C residue 1927 PHE Chi-restraints excluded: chain C residue 1928 SER Chi-restraints excluded: chain C residue 1941 PHE Chi-restraints excluded: chain C residue 1944 ASN Chi-restraints excluded: chain C residue 1957 THR Chi-restraints excluded: chain C residue 1991 ILE Chi-restraints excluded: chain C residue 2032 VAL Chi-restraints excluded: chain C residue 2060 LEU Chi-restraints excluded: chain C residue 2086 LEU Chi-restraints excluded: chain C residue 2129 LEU Chi-restraints excluded: chain C residue 2199 LEU Chi-restraints excluded: chain C residue 2217 LEU Chi-restraints excluded: chain C residue 2264 VAL Chi-restraints excluded: chain C residue 2265 VAL Chi-restraints excluded: chain C residue 2282 LYS Chi-restraints excluded: chain C residue 2286 ASP Chi-restraints excluded: chain C residue 2387 ILE Chi-restraints excluded: chain C residue 2397 LEU Chi-restraints excluded: chain C residue 2503 THR Chi-restraints excluded: chain C residue 2519 LEU Chi-restraints excluded: chain C residue 2716 LEU Chi-restraints excluded: chain C residue 2781 MET Chi-restraints excluded: chain C residue 3020 LEU Chi-restraints excluded: chain C residue 3228 THR Chi-restraints excluded: chain C residue 3636 GLU Chi-restraints excluded: chain C residue 3697 SER Chi-restraints excluded: chain C residue 3730 LEU Chi-restraints excluded: chain C residue 3786 VAL Chi-restraints excluded: chain C residue 3829 LEU Chi-restraints excluded: chain C residue 3954 GLN Chi-restraints excluded: chain C residue 4011 MET Chi-restraints excluded: chain C residue 4018 MET Chi-restraints excluded: chain C residue 4026 THR Chi-restraints excluded: chain C residue 4195 THR Chi-restraints excluded: chain C residue 4502 MET Chi-restraints excluded: chain C residue 4521 SER Chi-restraints excluded: chain C residue 4566 TYR Chi-restraints excluded: chain C residue 4594 VAL Chi-restraints excluded: chain C residue 4696 VAL Chi-restraints excluded: chain C residue 4735 ASN Chi-restraints excluded: chain C residue 4813 MET Chi-restraints excluded: chain C residue 4821 ARG Chi-restraints excluded: chain C residue 4830 ILE Chi-restraints excluded: chain C residue 4922 MET Chi-restraints excluded: chain D residue 132 CYS Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 201 TRP Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 398 HIS Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 608 HIS Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 615 CYS Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 630 HIS Chi-restraints excluded: chain D residue 781 ASN Chi-restraints excluded: chain D residue 868 ASP Chi-restraints excluded: chain D residue 964 MET Chi-restraints excluded: chain D residue 1007 TRP Chi-restraints excluded: chain D residue 1166 VAL Chi-restraints excluded: chain D residue 1300 MET Chi-restraints excluded: chain D residue 1304 LEU Chi-restraints excluded: chain D residue 1430 VAL Chi-restraints excluded: chain D residue 1510 CYS Chi-restraints excluded: chain D residue 1519 LEU Chi-restraints excluded: chain D residue 1530 THR Chi-restraints excluded: chain D residue 1608 ASP Chi-restraints excluded: chain D residue 1629 MET Chi-restraints excluded: chain D residue 1631 LEU Chi-restraints excluded: chain D residue 1633 ILE Chi-restraints excluded: chain D residue 1665 VAL Chi-restraints excluded: chain D residue 1673 VAL Chi-restraints excluded: chain D residue 1814 THR Chi-restraints excluded: chain D residue 1927 PHE Chi-restraints excluded: chain D residue 1928 SER Chi-restraints excluded: chain D residue 1941 PHE Chi-restraints excluded: chain D residue 1944 ASN Chi-restraints excluded: chain D residue 1957 THR Chi-restraints excluded: chain D residue 1991 ILE Chi-restraints excluded: chain D residue 2032 VAL Chi-restraints excluded: chain D residue 2060 LEU Chi-restraints excluded: chain D residue 2086 LEU Chi-restraints excluded: chain D residue 2129 LEU Chi-restraints excluded: chain D residue 2192 VAL Chi-restraints excluded: chain D residue 2199 LEU Chi-restraints excluded: chain D residue 2265 VAL Chi-restraints excluded: chain D residue 2282 LYS Chi-restraints excluded: chain D residue 2286 ASP Chi-restraints excluded: chain D residue 2290 ASN Chi-restraints excluded: chain D residue 2387 ILE Chi-restraints excluded: chain D residue 2397 LEU Chi-restraints excluded: chain D residue 2503 THR Chi-restraints excluded: chain D residue 2519 LEU Chi-restraints excluded: chain D residue 2667 CYS Chi-restraints excluded: chain D residue 2716 LEU Chi-restraints excluded: chain D residue 2781 MET Chi-restraints excluded: chain D residue 3020 LEU Chi-restraints excluded: chain D residue 3228 THR Chi-restraints excluded: chain D residue 3636 GLU Chi-restraints excluded: chain D residue 3697 SER Chi-restraints excluded: chain D residue 3730 LEU Chi-restraints excluded: chain D residue 3786 VAL Chi-restraints excluded: chain D residue 3795 LEU Chi-restraints excluded: chain D residue 3829 LEU Chi-restraints excluded: chain D residue 3954 GLN Chi-restraints excluded: chain D residue 4011 MET Chi-restraints excluded: chain D residue 4017 ASP Chi-restraints excluded: chain D residue 4018 MET Chi-restraints excluded: chain D residue 4026 THR Chi-restraints excluded: chain D residue 4142 LYS Chi-restraints excluded: chain D residue 4502 MET Chi-restraints excluded: chain D residue 4521 SER Chi-restraints excluded: chain D residue 4566 TYR Chi-restraints excluded: chain D residue 4594 VAL Chi-restraints excluded: chain D residue 4609 LEU Chi-restraints excluded: chain D residue 4696 VAL Chi-restraints excluded: chain D residue 4735 ASN Chi-restraints excluded: chain D residue 4813 MET Chi-restraints excluded: chain D residue 4821 ARG Chi-restraints excluded: chain D residue 4830 ILE Chi-restraints excluded: chain D residue 4922 MET Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 25 HIS Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 32 ASN Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 90 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1664 random chunks: chunk 992 optimal weight: 1.9990 chunk 640 optimal weight: 50.0000 chunk 957 optimal weight: 0.0470 chunk 483 optimal weight: 30.0000 chunk 315 optimal weight: 3.9990 chunk 310 optimal weight: 0.0980 chunk 1019 optimal weight: 20.0000 chunk 1092 optimal weight: 30.0000 chunk 792 optimal weight: 0.5980 chunk 149 optimal weight: 5.9990 chunk 1260 optimal weight: 0.8980 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 ASN A2151 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 HIS ** B 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2176 ASN B2340 ASN B2721 ASN ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1603 GLN ** C2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN D 628 ASN D 630 HIS ** D2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.083 132192 Z= 0.160 Angle : 0.580 12.315 178900 Z= 0.294 Chirality : 0.040 0.259 19928 Planarity : 0.004 0.110 23144 Dihedral : 4.839 42.687 17864 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.82 % Favored : 90.11 % Rotamer: Outliers : 2.49 % Allowed : 21.25 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.07), residues: 16464 helix: 1.17 (0.06), residues: 7332 sheet: -1.31 (0.16), residues: 1108 loop : -2.82 (0.06), residues: 8024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP D1007 HIS 0.020 0.001 HIS A 270 PHE 0.026 0.001 PHE A 685 TYR 0.018 0.001 TYR A3623 ARG 0.015 0.000 ARG B 626 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1281 residues out of total 14576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 339 poor density : 942 time to evaluate : 10.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.5733 (tt0) REVERT: A 628 ASN cc_start: 0.3920 (OUTLIER) cc_final: 0.3662 (m110) REVERT: A 1113 MET cc_start: 0.6683 (mtp) cc_final: 0.6481 (mtm) REVERT: A 1487 MET cc_start: 0.3040 (ptt) cc_final: 0.2601 (ttp) REVERT: A 1927 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.7090 (t80) REVERT: A 2282 LYS cc_start: 0.6601 (OUTLIER) cc_final: 0.4842 (mtmm) REVERT: A 2397 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6980 (tp) REVERT: A 2467 MET cc_start: 0.6503 (mmp) cc_final: 0.6249 (mmp) REVERT: A 2716 LEU cc_start: 0.0445 (OUTLIER) cc_final: -0.0539 (mm) REVERT: A 3020 LEU cc_start: 0.0687 (OUTLIER) cc_final: 0.0248 (mp) REVERT: A 3045 MET cc_start: 0.3826 (ppp) cc_final: 0.2701 (tmm) REVERT: A 3469 LEU cc_start: 0.1094 (OUTLIER) cc_final: 0.0683 (pp) REVERT: A 3796 MET cc_start: 0.8016 (mtp) cc_final: 0.7780 (mtp) REVERT: A 4821 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.6523 (ptt-90) REVERT: B 535 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.5739 (tt0) REVERT: B 868 ASP cc_start: 0.4105 (OUTLIER) cc_final: 0.2878 (t0) REVERT: B 1927 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6952 (t80) REVERT: B 1947 MET cc_start: -0.1313 (mmt) cc_final: -0.3542 (ptt) REVERT: B 2191 MET cc_start: 0.7373 (pmm) cc_final: 0.7037 (pmm) REVERT: B 2716 LEU cc_start: 0.0362 (OUTLIER) cc_final: -0.0689 (mm) REVERT: B 3020 LEU cc_start: 0.0486 (OUTLIER) cc_final: 0.0077 (mp) REVERT: B 3045 MET cc_start: 0.3263 (ppp) cc_final: 0.1995 (tmm) REVERT: B 3233 MET cc_start: 0.4076 (ptt) cc_final: 0.3801 (ptt) REVERT: B 3796 MET cc_start: 0.8017 (mtp) cc_final: 0.7780 (mtp) REVERT: B 4821 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.6290 (mtp180) REVERT: C 535 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.5630 (tt0) REVERT: C 868 ASP cc_start: 0.3940 (OUTLIER) cc_final: 0.2820 (t0) REVERT: C 1730 MET cc_start: 0.6394 (mmm) cc_final: 0.6038 (mmm) REVERT: C 1927 PHE cc_start: 0.7393 (OUTLIER) cc_final: 0.6973 (t80) REVERT: C 2397 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6973 (tp) REVERT: C 2716 LEU cc_start: 0.0471 (OUTLIER) cc_final: -0.0697 (mm) REVERT: C 3020 LEU cc_start: 0.0984 (OUTLIER) cc_final: 0.0582 (mp) REVERT: C 3045 MET cc_start: 0.3159 (ppp) cc_final: 0.1885 (tmm) REVERT: C 3469 LEU cc_start: 0.1247 (OUTLIER) cc_final: 0.0786 (pp) REVERT: C 3796 MET cc_start: 0.8040 (mtp) cc_final: 0.7807 (mtp) REVERT: C 4018 MET cc_start: 0.4729 (OUTLIER) cc_final: 0.4422 (mtp) REVERT: C 4821 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.6302 (mtp180) REVERT: D 535 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.5707 (tt0) REVERT: D 1487 MET cc_start: 0.3036 (ptt) cc_final: 0.2612 (ttp) REVERT: D 1730 MET cc_start: 0.6458 (mmm) cc_final: 0.6109 (mmm) REVERT: D 1927 PHE cc_start: 0.7286 (OUTLIER) cc_final: 0.6932 (t80) REVERT: D 2397 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6967 (tp) REVERT: D 2716 LEU cc_start: 0.0492 (OUTLIER) cc_final: -0.0608 (mm) REVERT: D 3020 LEU cc_start: 0.0728 (OUTLIER) cc_final: 0.0266 (mp) REVERT: D 3045 MET cc_start: 0.3894 (ppp) cc_final: 0.2702 (tmm) REVERT: D 3322 MET cc_start: 0.2684 (mmt) cc_final: 0.2147 (mmt) REVERT: D 3469 LEU cc_start: 0.1413 (OUTLIER) cc_final: 0.0938 (pp) REVERT: D 3796 MET cc_start: 0.8061 (mtp) cc_final: 0.7812 (mtp) REVERT: D 4821 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.6339 (mtp180) REVERT: E 18 LYS cc_start: 0.8565 (mmmm) cc_final: 0.7903 (mptt) REVERT: F 18 LYS cc_start: 0.8534 (mmmm) cc_final: 0.7825 (mptt) REVERT: G 18 LYS cc_start: 0.8506 (mmmm) cc_final: 0.7809 (mptt) REVERT: G 73 LYS cc_start: 0.8340 (tttm) cc_final: 0.8000 (ttmm) REVERT: H 18 LYS cc_start: 0.8479 (mmmm) cc_final: 0.7934 (mptt) REVERT: H 73 LYS cc_start: 0.8350 (tttm) cc_final: 0.8023 (ttmm) outliers start: 339 outliers final: 238 residues processed: 1216 average time/residue: 0.9956 time to fit residues: 2197.1432 Evaluate side-chains 1183 residues out of total 14576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 914 time to evaluate : 10.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 398 HIS Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain A residue 781 ASN Chi-restraints excluded: chain A residue 791 VAL Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1510 CYS Chi-restraints excluded: chain A residue 1530 THR Chi-restraints excluded: chain A residue 1608 ASP Chi-restraints excluded: chain A residue 1626 LEU Chi-restraints excluded: chain A residue 1631 LEU Chi-restraints excluded: chain A residue 1796 LEU Chi-restraints excluded: chain A residue 1927 PHE Chi-restraints excluded: chain A residue 1928 SER Chi-restraints excluded: chain A residue 1941 PHE Chi-restraints excluded: chain A residue 1944 ASN Chi-restraints excluded: chain A residue 1957 THR Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2060 LEU Chi-restraints excluded: chain A residue 2086 LEU Chi-restraints excluded: chain A residue 2129 LEU Chi-restraints excluded: chain A residue 2171 MET Chi-restraints excluded: chain A residue 2199 LEU Chi-restraints excluded: chain A residue 2282 LYS Chi-restraints excluded: chain A residue 2290 ASN Chi-restraints excluded: chain A residue 2397 LEU Chi-restraints excluded: chain A residue 2503 THR Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain A residue 2667 CYS Chi-restraints excluded: chain A residue 2716 LEU Chi-restraints excluded: chain A residue 2781 MET Chi-restraints excluded: chain A residue 3020 LEU Chi-restraints excluded: chain A residue 3469 LEU Chi-restraints excluded: chain A residue 3636 GLU Chi-restraints excluded: chain A residue 3730 LEU Chi-restraints excluded: chain A residue 3829 LEU Chi-restraints excluded: chain A residue 3954 GLN Chi-restraints excluded: chain A residue 4011 MET Chi-restraints excluded: chain A residue 4026 THR Chi-restraints excluded: chain A residue 4696 VAL Chi-restraints excluded: chain A residue 4735 ASN Chi-restraints excluded: chain A residue 4813 MET Chi-restraints excluded: chain A residue 4821 ARG Chi-restraints excluded: chain A residue 4830 ILE Chi-restraints excluded: chain B residue 47 CYS Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 201 TRP Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 398 HIS Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 630 HIS Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 868 ASP Chi-restraints excluded: chain B residue 964 MET Chi-restraints excluded: chain B residue 1007 TRP Chi-restraints excluded: chain B residue 1166 VAL Chi-restraints excluded: chain B residue 1304 LEU Chi-restraints excluded: chain B residue 1430 VAL Chi-restraints excluded: chain B residue 1510 CYS Chi-restraints excluded: chain B residue 1608 ASP Chi-restraints excluded: chain B residue 1631 LEU Chi-restraints excluded: chain B residue 1665 VAL Chi-restraints excluded: chain B residue 1796 LEU Chi-restraints excluded: chain B residue 1917 VAL Chi-restraints excluded: chain B residue 1927 PHE Chi-restraints excluded: chain B residue 1928 SER Chi-restraints excluded: chain B residue 1941 PHE Chi-restraints excluded: chain B residue 1944 ASN Chi-restraints excluded: chain B residue 1957 THR Chi-restraints excluded: chain B residue 1991 ILE Chi-restraints excluded: chain B residue 2060 LEU Chi-restraints excluded: chain B residue 2086 LEU Chi-restraints excluded: chain B residue 2129 LEU Chi-restraints excluded: chain B residue 2192 VAL Chi-restraints excluded: chain B residue 2199 LEU Chi-restraints excluded: chain B residue 2264 VAL Chi-restraints excluded: chain B residue 2282 LYS Chi-restraints excluded: chain B residue 2286 ASP Chi-restraints excluded: chain B residue 2290 ASN Chi-restraints excluded: chain B residue 2425 LEU Chi-restraints excluded: chain B residue 2503 THR Chi-restraints excluded: chain B residue 2519 LEU Chi-restraints excluded: chain B residue 2667 CYS Chi-restraints excluded: chain B residue 2716 LEU Chi-restraints excluded: chain B residue 2781 MET Chi-restraints excluded: chain B residue 3020 LEU Chi-restraints excluded: chain B residue 3636 GLU Chi-restraints excluded: chain B residue 3713 PHE Chi-restraints excluded: chain B residue 3730 LEU Chi-restraints excluded: chain B residue 3954 GLN Chi-restraints excluded: chain B residue 4026 THR Chi-restraints excluded: chain B residue 4521 SER Chi-restraints excluded: chain B residue 4696 VAL Chi-restraints excluded: chain B residue 4735 ASN Chi-restraints excluded: chain B residue 4821 ARG Chi-restraints excluded: chain B residue 4830 ILE Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 201 TRP Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 398 HIS Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 868 ASP Chi-restraints excluded: chain C residue 964 MET Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1304 LEU Chi-restraints excluded: chain C residue 1430 VAL Chi-restraints excluded: chain C residue 1510 CYS Chi-restraints excluded: chain C residue 1530 THR Chi-restraints excluded: chain C residue 1608 ASP Chi-restraints excluded: chain C residue 1631 LEU Chi-restraints excluded: chain C residue 1665 VAL Chi-restraints excluded: chain C residue 1728 VAL Chi-restraints excluded: chain C residue 1927 PHE Chi-restraints excluded: chain C residue 1928 SER Chi-restraints excluded: chain C residue 1941 PHE Chi-restraints excluded: chain C residue 1944 ASN Chi-restraints excluded: chain C residue 1957 THR Chi-restraints excluded: chain C residue 1991 ILE Chi-restraints excluded: chain C residue 2060 LEU Chi-restraints excluded: chain C residue 2086 LEU Chi-restraints excluded: chain C residue 2129 LEU Chi-restraints excluded: chain C residue 2192 VAL Chi-restraints excluded: chain C residue 2199 LEU Chi-restraints excluded: chain C residue 2282 LYS Chi-restraints excluded: chain C residue 2286 ASP Chi-restraints excluded: chain C residue 2290 ASN Chi-restraints excluded: chain C residue 2397 LEU Chi-restraints excluded: chain C residue 2503 THR Chi-restraints excluded: chain C residue 2519 LEU Chi-restraints excluded: chain C residue 2667 CYS Chi-restraints excluded: chain C residue 2716 LEU Chi-restraints excluded: chain C residue 2781 MET Chi-restraints excluded: chain C residue 3020 LEU Chi-restraints excluded: chain C residue 3469 LEU Chi-restraints excluded: chain C residue 3636 GLU Chi-restraints excluded: chain C residue 3713 PHE Chi-restraints excluded: chain C residue 3730 LEU Chi-restraints excluded: chain C residue 3954 GLN Chi-restraints excluded: chain C residue 4011 MET Chi-restraints excluded: chain C residue 4018 MET Chi-restraints excluded: chain C residue 4026 THR Chi-restraints excluded: chain C residue 4502 MET Chi-restraints excluded: chain C residue 4521 SER Chi-restraints excluded: chain C residue 4696 VAL Chi-restraints excluded: chain C residue 4735 ASN Chi-restraints excluded: chain C residue 4813 MET Chi-restraints excluded: chain C residue 4821 ARG Chi-restraints excluded: chain C residue 4830 ILE Chi-restraints excluded: chain D residue 47 CYS Chi-restraints excluded: chain D residue 132 CYS Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 201 TRP Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 615 CYS Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 630 HIS Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain D residue 964 MET Chi-restraints excluded: chain D residue 1166 VAL Chi-restraints excluded: chain D residue 1304 LEU Chi-restraints excluded: chain D residue 1430 VAL Chi-restraints excluded: chain D residue 1510 CYS Chi-restraints excluded: chain D residue 1530 THR Chi-restraints excluded: chain D residue 1608 ASP Chi-restraints excluded: chain D residue 1631 LEU Chi-restraints excluded: chain D residue 1665 VAL Chi-restraints excluded: chain D residue 1796 LEU Chi-restraints excluded: chain D residue 1927 PHE Chi-restraints excluded: chain D residue 1941 PHE Chi-restraints excluded: chain D residue 1944 ASN Chi-restraints excluded: chain D residue 1957 THR Chi-restraints excluded: chain D residue 2060 LEU Chi-restraints excluded: chain D residue 2086 LEU Chi-restraints excluded: chain D residue 2129 LEU Chi-restraints excluded: chain D residue 2192 VAL Chi-restraints excluded: chain D residue 2199 LEU Chi-restraints excluded: chain D residue 2217 LEU Chi-restraints excluded: chain D residue 2282 LYS Chi-restraints excluded: chain D residue 2397 LEU Chi-restraints excluded: chain D residue 2503 THR Chi-restraints excluded: chain D residue 2519 LEU Chi-restraints excluded: chain D residue 2667 CYS Chi-restraints excluded: chain D residue 2716 LEU Chi-restraints excluded: chain D residue 2781 MET Chi-restraints excluded: chain D residue 3020 LEU Chi-restraints excluded: chain D residue 3469 LEU Chi-restraints excluded: chain D residue 3636 GLU Chi-restraints excluded: chain D residue 3730 LEU Chi-restraints excluded: chain D residue 3954 GLN Chi-restraints excluded: chain D residue 4011 MET Chi-restraints excluded: chain D residue 4026 THR Chi-restraints excluded: chain D residue 4502 MET Chi-restraints excluded: chain D residue 4609 LEU Chi-restraints excluded: chain D residue 4696 VAL Chi-restraints excluded: chain D residue 4735 ASN Chi-restraints excluded: chain D residue 4813 MET Chi-restraints excluded: chain D residue 4821 ARG Chi-restraints excluded: chain D residue 4830 ILE Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 25 HIS Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 32 ASN Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 90 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1664 random chunks: chunk 1458 optimal weight: 40.0000 chunk 1536 optimal weight: 2.9990 chunk 1401 optimal weight: 3.9990 chunk 1494 optimal weight: 9.9990 chunk 899 optimal weight: 9.9990 chunk 651 optimal weight: 0.0270 chunk 1173 optimal weight: 3.9990 chunk 458 optimal weight: 10.0000 chunk 1350 optimal weight: 8.9990 chunk 1413 optimal weight: 4.9990 chunk 1489 optimal weight: 50.0000 overall best weight: 3.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 628 ASN ** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1603 GLN B 29 HIS ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 ASN B1603 GLN B2090 GLN ** B2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1603 GLN ** C2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 HIS D 150 GLN ** D2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6372 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 : 0.005 0.081 132192 Z= 0.298 Angle : 0.644 14.299 178900 Z= 0.326 Chirality : 0.042 0.237 19928 Planarity : 0.004 0.109 23144 Dihedral : 4.960 46.701 17860 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.95 % Favored : 88.98 % Rotamer: Outliers : 2.88 % Allowed : 21.07 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.34 (0.07), residues: 16464 helix: 1.04 (0.06), residues: 7304 sheet: -1.33 (0.16), residues: 1116 loop : -2.84 (0.06), residues: 8044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP D1007 HIS 0.015 0.001 HIS A 270 PHE 0.028 0.002 PHE D2202 TYR 0.018 0.002 TYR B3623 ARG 0.011 0.000 ARG B 626 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1316 residues out of total 14576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 393 poor density : 923 time to evaluate : 10.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 535 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.5899 (tt0) REVERT: A 628 ASN cc_start: 0.3698 (OUTLIER) cc_final: 0.3257 (m110) REVERT: A 868 ASP cc_start: 0.3778 (OUTLIER) cc_final: 0.2493 (t0) REVERT: A 1174 MET cc_start: 0.6357 (ppp) cc_final: 0.5925 (ppp) REVERT: A 1927 PHE cc_start: 0.7390 (OUTLIER) cc_final: 0.7006 (t80) REVERT: A 2213 MET cc_start: 0.7310 (mpp) cc_final: 0.7035 (mpp) REVERT: A 2397 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6991 (tp) REVERT: A 2467 MET cc_start: 0.6520 (mmp) cc_final: 0.6266 (mmp) REVERT: A 2716 LEU cc_start: 0.0542 (OUTLIER) cc_final: -0.0549 (mm) REVERT: A 3020 LEU cc_start: 0.0715 (OUTLIER) cc_final: 0.0250 (mp) REVERT: A 3045 MET cc_start: 0.3921 (ppp) cc_final: 0.2724 (tmm) REVERT: A 3469 LEU cc_start: 0.1110 (OUTLIER) cc_final: 0.0709 (pp) REVERT: A 4821 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.6411 (mtp180) REVERT: B 29 HIS cc_start: 0.6058 (OUTLIER) cc_final: 0.5775 (m-70) REVERT: B 535 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.5912 (tt0) REVERT: B 628 ASN cc_start: 0.3562 (OUTLIER) cc_final: 0.3149 (m110) REVERT: B 868 ASP cc_start: 0.3991 (OUTLIER) cc_final: 0.2740 (t0) REVERT: B 1927 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.6920 (t80) REVERT: B 1947 MET cc_start: -0.1125 (mmt) cc_final: -0.3389 (ptt) REVERT: B 2191 MET cc_start: 0.7467 (pmm) cc_final: 0.7148 (pmm) REVERT: B 2213 MET cc_start: 0.7291 (mpp) cc_final: 0.7042 (mpp) REVERT: B 2716 LEU cc_start: 0.0441 (OUTLIER) cc_final: -0.0668 (mm) REVERT: B 3020 LEU cc_start: 0.0582 (OUTLIER) cc_final: 0.0138 (mp) REVERT: B 3045 MET cc_start: 0.3377 (ppp) cc_final: 0.2040 (tmm) REVERT: B 3233 MET cc_start: 0.4109 (ptt) cc_final: 0.3837 (ptt) REVERT: B 3469 LEU cc_start: 0.1119 (OUTLIER) cc_final: 0.0738 (pp) REVERT: B 4821 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.6307 (mtp180) REVERT: C 29 HIS cc_start: 0.6051 (OUTLIER) cc_final: 0.5814 (m90) REVERT: C 81 MET cc_start: 0.4619 (mmm) cc_final: 0.4256 (mmm) REVERT: C 535 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.5842 (tt0) REVERT: C 868 ASP cc_start: 0.3839 (OUTLIER) cc_final: 0.2607 (t0) REVERT: C 1927 PHE cc_start: 0.7390 (OUTLIER) cc_final: 0.6937 (t80) REVERT: C 2397 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.7036 (tp) REVERT: C 2467 MET cc_start: 0.6498 (mmp) cc_final: 0.6246 (mmp) REVERT: C 3020 LEU cc_start: 0.0788 (OUTLIER) cc_final: 0.0319 (mp) REVERT: C 3045 MET cc_start: 0.3359 (ppp) cc_final: 0.2015 (tmm) REVERT: C 3469 LEU cc_start: 0.1258 (OUTLIER) cc_final: 0.0795 (pp) REVERT: C 4018 MET cc_start: 0.4772 (OUTLIER) cc_final: 0.4546 (mtp) REVERT: C 4821 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.6398 (mtp180) REVERT: D 29 HIS cc_start: 0.6081 (OUTLIER) cc_final: 0.5783 (m-70) REVERT: D 535 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.5872 (tt0) REVERT: D 868 ASP cc_start: 0.3916 (OUTLIER) cc_final: 0.2705 (t0) REVERT: D 1927 PHE cc_start: 0.7399 (OUTLIER) cc_final: 0.7021 (t80) REVERT: D 2397 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7112 (tp) REVERT: D 2716 LEU cc_start: 0.0468 (OUTLIER) cc_final: -0.0699 (mm) REVERT: D 3020 LEU cc_start: 0.0839 (OUTLIER) cc_final: 0.0340 (mp) REVERT: D 3045 MET cc_start: 0.3973 (ppp) cc_final: 0.2777 (tmm) REVERT: D 3322 MET cc_start: 0.2892 (mmt) cc_final: 0.2450 (mmt) REVERT: D 3469 LEU cc_start: 0.1430 (OUTLIER) cc_final: 0.0950 (pp) REVERT: D 4018 MET cc_start: 0.4796 (OUTLIER) cc_final: 0.4542 (mtp) REVERT: D 4821 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.6364 (mtp180) REVERT: E 18 LYS cc_start: 0.8584 (mmmm) cc_final: 0.7943 (mptt) REVERT: E 48 PHE cc_start: 0.7995 (p90) cc_final: 0.7733 (p90) REVERT: F 5 GLU cc_start: 0.8191 (mp0) cc_final: 0.7938 (mp0) REVERT: F 18 LYS cc_start: 0.8499 (mmmm) cc_final: 0.7825 (mptt) REVERT: F 48 PHE cc_start: 0.7997 (p90) cc_final: 0.7629 (p90) REVERT: G 18 LYS cc_start: 0.8455 (mmmm) cc_final: 0.7796 (mptt) REVERT: G 73 LYS cc_start: 0.8340 (tttm) cc_final: 0.8014 (ttmm) REVERT: H 18 LYS cc_start: 0.8513 (mmmm) cc_final: 0.7962 (mptt) REVERT: H 73 LYS cc_start: 0.8317 (tttm) cc_final: 0.8000 (ttmm) outliers start: 393 outliers final: 300 residues processed: 1239 average time/residue: 0.9989 time to fit residues: 2247.5351 Evaluate side-chains 1238 residues out of total 14576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 337 poor density : 901 time to evaluate : 10.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 CYS Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 398 HIS Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 608 HIS Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 628 ASN Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain A residue 781 ASN Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 868 ASP Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 1007 TRP Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1510 CYS Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain A residue 1530 THR Chi-restraints excluded: chain A residue 1608 ASP Chi-restraints excluded: chain A residue 1626 LEU Chi-restraints excluded: chain A residue 1631 LEU Chi-restraints excluded: chain A residue 1633 ILE Chi-restraints excluded: chain A residue 1665 VAL Chi-restraints excluded: chain A residue 1796 LEU Chi-restraints excluded: chain A residue 1917 VAL Chi-restraints excluded: chain A residue 1927 PHE Chi-restraints excluded: chain A residue 1928 SER Chi-restraints excluded: chain A residue 1941 PHE Chi-restraints excluded: chain A residue 1944 ASN Chi-restraints excluded: chain A residue 1957 THR Chi-restraints excluded: chain A residue 2032 VAL Chi-restraints excluded: chain A residue 2060 LEU Chi-restraints excluded: chain A residue 2086 LEU Chi-restraints excluded: chain A residue 2116 ILE Chi-restraints excluded: chain A residue 2129 LEU Chi-restraints excluded: chain A residue 2171 MET Chi-restraints excluded: chain A residue 2192 VAL Chi-restraints excluded: chain A residue 2199 LEU Chi-restraints excluded: chain A residue 2264 VAL Chi-restraints excluded: chain A residue 2282 LYS Chi-restraints excluded: chain A residue 2290 ASN Chi-restraints excluded: chain A residue 2397 LEU Chi-restraints excluded: chain A residue 2425 LEU Chi-restraints excluded: chain A residue 2503 THR Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain A residue 2667 CYS Chi-restraints excluded: chain A residue 2716 LEU Chi-restraints excluded: chain A residue 2781 MET Chi-restraints excluded: chain A residue 3020 LEU Chi-restraints excluded: chain A residue 3228 THR Chi-restraints excluded: chain A residue 3469 LEU Chi-restraints excluded: chain A residue 3636 GLU Chi-restraints excluded: chain A residue 3697 SER Chi-restraints excluded: chain A residue 3730 LEU Chi-restraints excluded: chain A residue 3786 VAL Chi-restraints excluded: chain A residue 3829 LEU Chi-restraints excluded: chain A residue 3954 GLN Chi-restraints excluded: chain A residue 4011 MET Chi-restraints excluded: chain A residue 4026 THR Chi-restraints excluded: chain A residue 4521 SER Chi-restraints excluded: chain A residue 4566 TYR Chi-restraints excluded: chain A residue 4696 VAL Chi-restraints excluded: chain A residue 4735 ASN Chi-restraints excluded: chain A residue 4813 MET Chi-restraints excluded: chain A residue 4821 ARG Chi-restraints excluded: chain A residue 4830 ILE Chi-restraints excluded: chain B residue 29 HIS Chi-restraints excluded: chain B residue 47 CYS Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 201 TRP Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 398 HIS Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 534 TYR Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 608 HIS Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 628 ASN Chi-restraints excluded: chain B residue 630 HIS Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 868 ASP Chi-restraints excluded: chain B residue 964 MET Chi-restraints excluded: chain B residue 1007 TRP Chi-restraints excluded: chain B residue 1166 VAL Chi-restraints excluded: chain B residue 1304 LEU Chi-restraints excluded: chain B residue 1430 VAL Chi-restraints excluded: chain B residue 1510 CYS Chi-restraints excluded: chain B residue 1519 LEU Chi-restraints excluded: chain B residue 1530 THR Chi-restraints excluded: chain B residue 1608 ASP Chi-restraints excluded: chain B residue 1626 LEU Chi-restraints excluded: chain B residue 1631 LEU Chi-restraints excluded: chain B residue 1633 ILE Chi-restraints excluded: chain B residue 1665 VAL Chi-restraints excluded: chain B residue 1796 LEU Chi-restraints excluded: chain B residue 1814 THR Chi-restraints excluded: chain B residue 1917 VAL Chi-restraints excluded: chain B residue 1927 PHE Chi-restraints excluded: chain B residue 1928 SER Chi-restraints excluded: chain B residue 1941 PHE Chi-restraints excluded: chain B residue 1944 ASN Chi-restraints excluded: chain B residue 1957 THR Chi-restraints excluded: chain B residue 1991 ILE Chi-restraints excluded: chain B residue 2032 VAL Chi-restraints excluded: chain B residue 2060 LEU Chi-restraints excluded: chain B residue 2086 LEU Chi-restraints excluded: chain B residue 2116 ILE Chi-restraints excluded: chain B residue 2129 LEU Chi-restraints excluded: chain B residue 2192 VAL Chi-restraints excluded: chain B residue 2199 LEU Chi-restraints excluded: chain B residue 2264 VAL Chi-restraints excluded: chain B residue 2265 VAL Chi-restraints excluded: chain B residue 2282 LYS Chi-restraints excluded: chain B residue 2286 ASP Chi-restraints excluded: chain B residue 2290 ASN Chi-restraints excluded: chain B residue 2425 LEU Chi-restraints excluded: chain B residue 2503 THR Chi-restraints excluded: chain B residue 2519 LEU Chi-restraints excluded: chain B residue 2667 CYS Chi-restraints excluded: chain B residue 2716 LEU Chi-restraints excluded: chain B residue 2781 MET Chi-restraints excluded: chain B residue 3020 LEU Chi-restraints excluded: chain B residue 3469 LEU Chi-restraints excluded: chain B residue 3636 GLU Chi-restraints excluded: chain B residue 3697 SER Chi-restraints excluded: chain B residue 3730 LEU Chi-restraints excluded: chain B residue 3786 VAL Chi-restraints excluded: chain B residue 3829 LEU Chi-restraints excluded: chain B residue 3954 GLN Chi-restraints excluded: chain B residue 4026 THR Chi-restraints excluded: chain B residue 4195 THR Chi-restraints excluded: chain B residue 4521 SER Chi-restraints excluded: chain B residue 4696 VAL Chi-restraints excluded: chain B residue 4735 ASN Chi-restraints excluded: chain B residue 4821 ARG Chi-restraints excluded: chain B residue 4830 ILE Chi-restraints excluded: chain B residue 4922 MET Chi-restraints excluded: chain C residue 29 HIS Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 201 TRP Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 398 HIS Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 630 HIS Chi-restraints excluded: chain C residue 781 ASN Chi-restraints excluded: chain C residue 868 ASP Chi-restraints excluded: chain C residue 964 MET Chi-restraints excluded: chain C residue 1007 TRP Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1430 VAL Chi-restraints excluded: chain C residue 1510 CYS Chi-restraints excluded: chain C residue 1530 THR Chi-restraints excluded: chain C residue 1608 ASP Chi-restraints excluded: chain C residue 1631 LEU Chi-restraints excluded: chain C residue 1665 VAL Chi-restraints excluded: chain C residue 1728 VAL Chi-restraints excluded: chain C residue 1783 PHE Chi-restraints excluded: chain C residue 1814 THR Chi-restraints excluded: chain C residue 1917 VAL Chi-restraints excluded: chain C residue 1927 PHE Chi-restraints excluded: chain C residue 1928 SER Chi-restraints excluded: chain C residue 1941 PHE Chi-restraints excluded: chain C residue 1944 ASN Chi-restraints excluded: chain C residue 1957 THR Chi-restraints excluded: chain C residue 2032 VAL Chi-restraints excluded: chain C residue 2060 LEU Chi-restraints excluded: chain C residue 2086 LEU Chi-restraints excluded: chain C residue 2129 LEU Chi-restraints excluded: chain C residue 2192 VAL Chi-restraints excluded: chain C residue 2199 LEU Chi-restraints excluded: chain C residue 2264 VAL Chi-restraints excluded: chain C residue 2282 LYS Chi-restraints excluded: chain C residue 2286 ASP Chi-restraints excluded: chain C residue 2290 ASN Chi-restraints excluded: chain C residue 2397 LEU Chi-restraints excluded: chain C residue 2503 THR Chi-restraints excluded: chain C residue 2519 LEU Chi-restraints excluded: chain C residue 2667 CYS Chi-restraints excluded: chain C residue 2716 LEU Chi-restraints excluded: chain C residue 2781 MET Chi-restraints excluded: chain C residue 3020 LEU Chi-restraints excluded: chain C residue 3469 LEU Chi-restraints excluded: chain C residue 3636 GLU Chi-restraints excluded: chain C residue 3697 SER Chi-restraints excluded: chain C residue 3730 LEU Chi-restraints excluded: chain C residue 3786 VAL Chi-restraints excluded: chain C residue 3954 GLN Chi-restraints excluded: chain C residue 4011 MET Chi-restraints excluded: chain C residue 4018 MET Chi-restraints excluded: chain C residue 4026 THR Chi-restraints excluded: chain C residue 4195 THR Chi-restraints excluded: chain C residue 4502 MET Chi-restraints excluded: chain C residue 4521 SER Chi-restraints excluded: chain C residue 4566 TYR Chi-restraints excluded: chain C residue 4696 VAL Chi-restraints excluded: chain C residue 4735 ASN Chi-restraints excluded: chain C residue 4813 MET Chi-restraints excluded: chain C residue 4821 ARG Chi-restraints excluded: chain C residue 4830 ILE Chi-restraints excluded: chain C residue 4922 MET Chi-restraints excluded: chain D residue 29 HIS Chi-restraints excluded: chain D residue 47 CYS Chi-restraints excluded: chain D residue 132 CYS Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 201 TRP Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 362 TYR Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 534 TYR Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 615 CYS Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 625 VAL Chi-restraints excluded: chain D residue 630 HIS Chi-restraints excluded: chain D residue 781 ASN Chi-restraints excluded: chain D residue 868 ASP Chi-restraints excluded: chain D residue 964 MET Chi-restraints excluded: chain D residue 1007 TRP Chi-restraints excluded: chain D residue 1166 VAL Chi-restraints excluded: chain D residue 1304 LEU Chi-restraints excluded: chain D residue 1430 VAL Chi-restraints excluded: chain D residue 1510 CYS Chi-restraints excluded: chain D residue 1519 LEU Chi-restraints excluded: chain D residue 1530 THR Chi-restraints excluded: chain D residue 1608 ASP Chi-restraints excluded: chain D residue 1631 LEU Chi-restraints excluded: chain D residue 1665 VAL Chi-restraints excluded: chain D residue 1796 LEU Chi-restraints excluded: chain D residue 1917 VAL Chi-restraints excluded: chain D residue 1927 PHE Chi-restraints excluded: chain D residue 1928 SER Chi-restraints excluded: chain D residue 1941 PHE Chi-restraints excluded: chain D residue 1944 ASN Chi-restraints excluded: chain D residue 1957 THR Chi-restraints excluded: chain D residue 2032 VAL Chi-restraints excluded: chain D residue 2060 LEU Chi-restraints excluded: chain D residue 2086 LEU Chi-restraints excluded: chain D residue 2116 ILE Chi-restraints excluded: chain D residue 2129 LEU Chi-restraints excluded: chain D residue 2192 VAL Chi-restraints excluded: chain D residue 2199 LEU Chi-restraints excluded: chain D residue 2264 VAL Chi-restraints excluded: chain D residue 2282 LYS Chi-restraints excluded: chain D residue 2290 ASN Chi-restraints excluded: chain D residue 2397 LEU Chi-restraints excluded: chain D residue 2503 THR Chi-restraints excluded: chain D residue 2519 LEU Chi-restraints excluded: chain D residue 2667 CYS Chi-restraints excluded: chain D residue 2716 LEU Chi-restraints excluded: chain D residue 2781 MET Chi-restraints excluded: chain D residue 3020 LEU Chi-restraints excluded: chain D residue 3228 THR Chi-restraints excluded: chain D residue 3469 LEU Chi-restraints excluded: chain D residue 3636 GLU Chi-restraints excluded: chain D residue 3697 SER Chi-restraints excluded: chain D residue 3730 LEU Chi-restraints excluded: chain D residue 3829 LEU Chi-restraints excluded: chain D residue 3954 GLN Chi-restraints excluded: chain D residue 4011 MET Chi-restraints excluded: chain D residue 4018 MET Chi-restraints excluded: chain D residue 4026 THR Chi-restraints excluded: chain D residue 4195 THR Chi-restraints excluded: chain D residue 4502 MET Chi-restraints excluded: chain D residue 4521 SER Chi-restraints excluded: chain D residue 4609 LEU Chi-restraints excluded: chain D residue 4696 VAL Chi-restraints excluded: chain D residue 4735 ASN Chi-restraints excluded: chain D residue 4813 MET Chi-restraints excluded: chain D residue 4821 ARG Chi-restraints excluded: chain D residue 4830 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 25 HIS Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 32 ASN Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 90 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1664 random chunks: chunk 981 optimal weight: 0.9980 chunk 1580 optimal weight: 0.5980 chunk 964 optimal weight: 2.9990 chunk 749 optimal weight: 5.9990 chunk 1098 optimal weight: 30.0000 chunk 1657 optimal weight: 10.0000 chunk 1525 optimal weight: 0.9990 chunk 1320 optimal weight: 0.0010 chunk 137 optimal weight: 20.0000 chunk 1019 optimal weight: 1.9990 chunk 809 optimal weight: 0.9980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1603 GLN ** A2176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 HIS ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2090 GLN ** B2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 HIS ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1603 GLN ** C2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 HIS D 150 GLN ** D2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.082 132192 Z= 0.159 Angle : 0.595 12.358 178900 Z= 0.300 Chirality : 0.040 0.252 19928 Planarity : 0.004 0.108 23144 Dihedral : 4.801 42.435 17860 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.44 % Favored : 90.48 % Rotamer: Outliers : 2.22 % Allowed : 21.81 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.16 (0.07), residues: 16464 helix: 1.23 (0.06), residues: 7344 sheet: -1.26 (0.16), residues: 1112 loop : -2.79 (0.06), residues: 8008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP B1007 HIS 0.017 0.001 HIS A 270 PHE 0.024 0.001 PHE D2202 TYR 0.018 0.001 TYR A3623 ARG 0.015 0.000 ARG B 626 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32928 Ramachandran restraints generated. 16464 Oldfield, 0 Emsley, 16464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1231 residues out of total 14576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 929 time to evaluate : 11.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 MET cc_start: 0.4786 (OUTLIER) cc_final: 0.4560 (ttm) REVERT: A 535 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.5751 (tt0) REVERT: A 1113 MET cc_start: 0.6704 (mtp) cc_final: 0.6452 (mtm) REVERT: A 1174 MET cc_start: 0.6398 (ppp) cc_final: 0.5885 (ppp) REVERT: A 1927 PHE cc_start: 0.7456 (OUTLIER) cc_final: 0.7127 (t80) REVERT: A 1952 MET cc_start: 0.2362 (tpt) cc_final: 0.1881 (tpt) REVERT: A 2397 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6938 (tp) REVERT: A 2467 MET cc_start: 0.6648 (mmp) cc_final: 0.6432 (mmp) REVERT: A 2716 LEU cc_start: 0.0511 (OUTLIER) cc_final: -0.0549 (mm) REVERT: A 3020 LEU cc_start: 0.0636 (OUTLIER) cc_final: 0.0201 (mp) REVERT: A 3045 MET cc_start: 0.3799 (ppp) cc_final: 0.2717 (tmm) REVERT: A 3469 LEU cc_start: 0.1132 (OUTLIER) cc_final: 0.0693 (pp) REVERT: A 3796 MET cc_start: 0.7999 (mtp) cc_final: 0.7732 (mtp) REVERT: A 3984 MET cc_start: 0.8612 (mmm) cc_final: 0.8399 (tpp) REVERT: A 4108 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7558 (mmm) REVERT: A 4500 MET cc_start: 0.7955 (ptp) cc_final: 0.7755 (mpp) REVERT: A 4821 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.6358 (mtp180) REVERT: B 317 MET cc_start: 0.4622 (OUTLIER) cc_final: 0.4414 (ttm) REVERT: B 535 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.5752 (tt0) REVERT: B 1113 MET cc_start: 0.6156 (OUTLIER) cc_final: 0.5924 (mtm) REVERT: B 1927 PHE cc_start: 0.7372 (OUTLIER) cc_final: 0.6991 (t80) REVERT: B 1947 MET cc_start: -0.1224 (mmt) cc_final: -0.3361 (ptt) REVERT: B 1952 MET cc_start: 0.2036 (tpt) cc_final: 0.1574 (tpt) REVERT: B 2191 MET cc_start: 0.7405 (pmm) cc_final: 0.7125 (pmm) REVERT: B 2716 LEU cc_start: 0.0405 (OUTLIER) cc_final: -0.0668 (mm) REVERT: B 3020 LEU cc_start: 0.0525 (OUTLIER) cc_final: 0.0107 (mp) REVERT: B 3045 MET cc_start: 0.3555 (ppp) cc_final: 0.2227 (tmm) REVERT: B 3233 MET cc_start: 0.4247 (ptt) cc_final: 0.3976 (ptt) REVERT: B 3469 LEU cc_start: 0.1141 (OUTLIER) cc_final: 0.0728 (pp) REVERT: B 3796 MET cc_start: 0.7980 (mtp) cc_final: 0.7714 (mtp) REVERT: B 3984 MET cc_start: 0.8592 (mmm) cc_final: 0.8361 (tpp) REVERT: B 4108 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7563 (mmm) REVERT: B 4821 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.6261 (mtp180) REVERT: C 317 MET cc_start: 0.4759 (OUTLIER) cc_final: 0.4551 (ttm) REVERT: C 535 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.5680 (tt0) REVERT: C 868 ASP cc_start: 0.3503 (OUTLIER) cc_final: 0.2813 (t0) REVERT: C 935 MET cc_start: 0.4038 (ppp) cc_final: 0.3555 (pmm) REVERT: C 1927 PHE cc_start: 0.7396 (OUTLIER) cc_final: 0.7004 (t80) REVERT: C 1952 MET cc_start: 0.1874 (tpt) cc_final: 0.1470 (tpt) REVERT: C 2397 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6948 (tp) REVERT: C 3020 LEU cc_start: 0.0834 (OUTLIER) cc_final: 0.0409 (mp) REVERT: C 3045 MET cc_start: 0.3580 (ppp) cc_final: 0.2258 (tmm) REVERT: C 3469 LEU cc_start: 0.1286 (OUTLIER) cc_final: 0.0823 (pp) REVERT: C 3796 MET cc_start: 0.8004 (mtp) cc_final: 0.7732 (mtp) REVERT: C 3984 MET cc_start: 0.8598 (mmm) cc_final: 0.8371 (tpp) REVERT: C 4018 MET cc_start: 0.4552 (OUTLIER) cc_final: 0.4214 (mtp) REVERT: C 4108 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7558 (mmm) REVERT: C 4821 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.6286 (mtp180) REVERT: D 535 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.5748 (tt0) REVERT: D 868 ASP cc_start: 0.4039 (OUTLIER) cc_final: 0.2979 (t0) REVERT: D 1927 PHE cc_start: 0.7317 (OUTLIER) cc_final: 0.6978 (t80) REVERT: D 1952 MET cc_start: 0.2142 (tpt) cc_final: 0.1702 (tpt) REVERT: D 2397 LEU cc_start: 0.7225 (OUTLIER) cc_final: 0.6987 (tp) REVERT: D 2716 LEU cc_start: 0.0791 (OUTLIER) cc_final: -0.0477 (mm) REVERT: D 3020 LEU cc_start: 0.0763 (OUTLIER) cc_final: 0.0292 (mp) REVERT: D 3045 MET cc_start: 0.3865 (ppp) cc_final: 0.2720 (tmm) REVERT: D 3322 MET cc_start: 0.2771 (mmt) cc_final: 0.2493 (mmt) REVERT: D 3469 LEU cc_start: 0.1284 (OUTLIER) cc_final: 0.0797 (pp) REVERT: D 3796 MET cc_start: 0.8051 (mtp) cc_final: 0.7796 (mtp) REVERT: D 4018 MET cc_start: 0.4489 (OUTLIER) cc_final: 0.4182 (mtp) REVERT: D 4108 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7530 (mmm) REVERT: D 4821 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.6302 (mtp180) REVERT: E 18 LYS cc_start: 0.8585 (mmmm) cc_final: 0.7962 (mptt) REVERT: E 48 PHE cc_start: 0.7898 (p90) cc_final: 0.7613 (p90) REVERT: F 5 GLU cc_start: 0.8157 (mp0) cc_final: 0.7932 (mp0) REVERT: F 18 LYS cc_start: 0.8496 (mmmm) cc_final: 0.7820 (mptt) REVERT: F 48 PHE cc_start: 0.7903 (p90) cc_final: 0.7516 (p90) REVERT: G 18 LYS cc_start: 0.8509 (mmmm) cc_final: 0.7826 (mptt) REVERT: G 73 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7998 (ttmm) REVERT: H 18 LYS cc_start: 0.8475 (mmmm) cc_final: 0.7955 (mptt) REVERT: H 73 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8017 (ttmm) outliers start: 302 outliers final: 227 residues processed: 1165 average time/residue: 1.0171 time to fit residues: 2154.2169 Evaluate side-chains 1180 residues out of total 14576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 913 time to evaluate : 10.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 398 HIS Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 535 GLU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 615 CYS Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 781 ASN Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 964 MET Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1510 CYS Chi-restraints excluded: chain A residue 1530 THR Chi-restraints excluded: chain A residue 1608 ASP Chi-restraints excluded: chain A residue 1631 LEU Chi-restraints excluded: chain A residue 1665 VAL Chi-restraints excluded: chain A residue 1796 LEU Chi-restraints excluded: chain A residue 1917 VAL Chi-restraints excluded: chain A residue 1927 PHE Chi-restraints excluded: chain A residue 1928 SER Chi-restraints excluded: chain A residue 1941 PHE Chi-restraints excluded: chain A residue 1944 ASN Chi-restraints excluded: chain A residue 1957 THR Chi-restraints excluded: chain A residue 2060 LEU Chi-restraints excluded: chain A residue 2086 LEU Chi-restraints excluded: chain A residue 2129 LEU Chi-restraints excluded: chain A residue 2192 VAL Chi-restraints excluded: chain A residue 2199 LEU Chi-restraints excluded: chain A residue 2264 VAL Chi-restraints excluded: chain A residue 2397 LEU Chi-restraints excluded: chain A residue 2503 THR Chi-restraints excluded: chain A residue 2519 LEU Chi-restraints excluded: chain A residue 2667 CYS Chi-restraints excluded: chain A residue 2716 LEU Chi-restraints excluded: chain A residue 2781 MET Chi-restraints excluded: chain A residue 3020 LEU Chi-restraints excluded: chain A residue 3469 LEU Chi-restraints excluded: chain A residue 3636 GLU Chi-restraints excluded: chain A residue 3730 LEU Chi-restraints excluded: chain A residue 3954 GLN Chi-restraints excluded: chain A residue 4011 MET Chi-restraints excluded: chain A residue 4026 THR Chi-restraints excluded: chain A residue 4108 MET Chi-restraints excluded: chain A residue 4521 SER Chi-restraints excluded: chain A residue 4696 VAL Chi-restraints excluded: chain A residue 4735 ASN Chi-restraints excluded: chain A residue 4813 MET Chi-restraints excluded: chain A residue 4821 ARG Chi-restraints excluded: chain A residue 4830 ILE Chi-restraints excluded: chain B residue 47 CYS Chi-restraints excluded: chain B residue 132 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 201 TRP Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 398 HIS Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 535 GLU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain B residue 964 MET Chi-restraints excluded: chain B residue 1113 MET Chi-restraints excluded: chain B residue 1304 LEU Chi-restraints excluded: chain B residue 1430 VAL Chi-restraints excluded: chain B residue 1510 CYS Chi-restraints excluded: chain B residue 1530 THR Chi-restraints excluded: chain B residue 1608 ASP Chi-restraints excluded: chain B residue 1631 LEU Chi-restraints excluded: chain B residue 1665 VAL Chi-restraints excluded: chain B residue 1796 LEU Chi-restraints excluded: chain B residue 1927 PHE Chi-restraints excluded: chain B residue 1928 SER Chi-restraints excluded: chain B residue 1941 PHE Chi-restraints excluded: chain B residue 1944 ASN Chi-restraints excluded: chain B residue 1957 THR Chi-restraints excluded: chain B residue 1991 ILE Chi-restraints excluded: chain B residue 2060 LEU Chi-restraints excluded: chain B residue 2086 LEU Chi-restraints excluded: chain B residue 2129 LEU Chi-restraints excluded: chain B residue 2192 VAL Chi-restraints excluded: chain B residue 2199 LEU Chi-restraints excluded: chain B residue 2264 VAL Chi-restraints excluded: chain B residue 2265 VAL Chi-restraints excluded: chain B residue 2286 ASP Chi-restraints excluded: chain B residue 2425 LEU Chi-restraints excluded: chain B residue 2503 THR Chi-restraints excluded: chain B residue 2519 LEU Chi-restraints excluded: chain B residue 2667 CYS Chi-restraints excluded: chain B residue 2716 LEU Chi-restraints excluded: chain B residue 2781 MET Chi-restraints excluded: chain B residue 3020 LEU Chi-restraints excluded: chain B residue 3469 LEU Chi-restraints excluded: chain B residue 3636 GLU Chi-restraints excluded: chain B residue 3730 LEU Chi-restraints excluded: chain B residue 4026 THR Chi-restraints excluded: chain B residue 4108 MET Chi-restraints excluded: chain B residue 4502 MET Chi-restraints excluded: chain B residue 4521 SER Chi-restraints excluded: chain B residue 4696 VAL Chi-restraints excluded: chain B residue 4735 ASN Chi-restraints excluded: chain B residue 4821 ARG Chi-restraints excluded: chain B residue 4830 ILE Chi-restraints excluded: chain C residue 47 CYS Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 201 TRP Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 398 HIS Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 535 GLU Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 608 HIS Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 781 ASN Chi-restraints excluded: chain C residue 791 VAL Chi-restraints excluded: chain C residue 868 ASP Chi-restraints excluded: chain C residue 964 MET Chi-restraints excluded: chain C residue 1304 LEU Chi-restraints excluded: chain C residue 1430 VAL Chi-restraints excluded: chain C residue 1510 CYS Chi-restraints excluded: chain C residue 1608 ASP Chi-restraints excluded: chain C residue 1631 LEU Chi-restraints excluded: chain C residue 1665 VAL Chi-restraints excluded: chain C residue 1728 VAL Chi-restraints excluded: chain C residue 1927 PHE Chi-restraints excluded: chain C residue 1928 SER Chi-restraints excluded: chain C residue 1941 PHE Chi-restraints excluded: chain C residue 1944 ASN Chi-restraints excluded: chain C residue 1957 THR Chi-restraints excluded: chain C residue 2060 LEU Chi-restraints excluded: chain C residue 2086 LEU Chi-restraints excluded: chain C residue 2129 LEU Chi-restraints excluded: chain C residue 2192 VAL Chi-restraints excluded: chain C residue 2199 LEU Chi-restraints excluded: chain C residue 2264 VAL Chi-restraints excluded: chain C residue 2286 ASP Chi-restraints excluded: chain C residue 2397 LEU Chi-restraints excluded: chain C residue 2503 THR Chi-restraints excluded: chain C residue 2519 LEU Chi-restraints excluded: chain C residue 2667 CYS Chi-restraints excluded: chain C residue 2716 LEU Chi-restraints excluded: chain C residue 2781 MET Chi-restraints excluded: chain C residue 3020 LEU Chi-restraints excluded: chain C residue 3228 THR Chi-restraints excluded: chain C residue 3469 LEU Chi-restraints excluded: chain C residue 3636 GLU Chi-restraints excluded: chain C residue 3713 PHE Chi-restraints excluded: chain C residue 3730 LEU Chi-restraints excluded: chain C residue 4011 MET Chi-restraints excluded: chain C residue 4018 MET Chi-restraints excluded: chain C residue 4026 THR Chi-restraints excluded: chain C residue 4108 MET Chi-restraints excluded: chain C residue 4502 MET Chi-restraints excluded: chain C residue 4521 SER Chi-restraints excluded: chain C residue 4696 VAL Chi-restraints excluded: chain C residue 4735 ASN Chi-restraints excluded: chain C residue 4813 MET Chi-restraints excluded: chain C residue 4821 ARG Chi-restraints excluded: chain C residue 4830 ILE Chi-restraints excluded: chain C residue 4922 MET Chi-restraints excluded: chain D residue 47 CYS Chi-restraints excluded: chain D residue 132 CYS Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 201 TRP Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 362 TYR Chi-restraints excluded: chain D residue 474 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 615 CYS Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 781 ASN Chi-restraints excluded: chain D residue 868 ASP Chi-restraints excluded: chain D residue 964 MET Chi-restraints excluded: chain D residue 1166 VAL Chi-restraints excluded: chain D residue 1304 LEU Chi-restraints excluded: chain D residue 1430 VAL Chi-restraints excluded: chain D residue 1510 CYS Chi-restraints excluded: chain D residue 1530 THR Chi-restraints excluded: chain D residue 1608 ASP Chi-restraints excluded: chain D residue 1631 LEU Chi-restraints excluded: chain D residue 1665 VAL Chi-restraints excluded: chain D residue 1796 LEU Chi-restraints excluded: chain D residue 1927 PHE Chi-restraints excluded: chain D residue 1928 SER Chi-restraints excluded: chain D residue 1941 PHE Chi-restraints excluded: chain D residue 1944 ASN Chi-restraints excluded: chain D residue 1957 THR Chi-restraints excluded: chain D residue 2060 LEU Chi-restraints excluded: chain D residue 2086 LEU Chi-restraints excluded: chain D residue 2129 LEU Chi-restraints excluded: chain D residue 2192 VAL Chi-restraints excluded: chain D residue 2199 LEU Chi-restraints excluded: chain D residue 2264 VAL Chi-restraints excluded: chain D residue 2282 LYS Chi-restraints excluded: chain D residue 2397 LEU Chi-restraints excluded: chain D residue 2503 THR Chi-restraints excluded: chain D residue 2519 LEU Chi-restraints excluded: chain D residue 2667 CYS Chi-restraints excluded: chain D residue 2716 LEU Chi-restraints excluded: chain D residue 2781 MET Chi-restraints excluded: chain D residue 3020 LEU Chi-restraints excluded: chain D residue 3228 THR Chi-restraints excluded: chain D residue 3469 LEU Chi-restraints excluded: chain D residue 3636 GLU Chi-restraints excluded: chain D residue 3730 LEU Chi-restraints excluded: chain D residue 4011 MET Chi-restraints excluded: chain D residue 4018 MET Chi-restraints excluded: chain D residue 4026 THR Chi-restraints excluded: chain D residue 4108 MET Chi-restraints excluded: chain D residue 4502 MET Chi-restraints excluded: chain D residue 4521 SER Chi-restraints excluded: chain D residue 4609 LEU Chi-restraints excluded: chain D residue 4696 VAL Chi-restraints excluded: chain D residue 4735 ASN Chi-restraints excluded: chain D residue 4813 MET Chi-restraints excluded: chain D residue 4821 ARG Chi-restraints excluded: chain D residue 4830 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 32 ASN Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain F residue 25 HIS Chi-restraints excluded: chain F residue 32 ASN Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain G residue 32 ASN Chi-restraints excluded: chain G residue 73 LYS Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 90 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1664 random chunks: chunk 1048 optimal weight: 0.9980 chunk 1406 optimal weight: 9.9990 chunk 404 optimal weight: 3.9990 chunk 1217 optimal weight: 3.9990 chunk 194 optimal weight: 2.9990 chunk 366 optimal weight: 2.9990 chunk 1322 optimal weight: 9.9990 chunk 553 optimal weight: 5.9990 chunk 1357 optimal weight: 4.9990 chunk 167 optimal weight: 8.9990 chunk 243 optimal weight: 50.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 GLN A 630 HIS A1603 GLN A2090 GLN A2340 ASN A2721 ASN ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 ASN B1603 GLN ** B2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 GLN ** C 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1603 GLN ** C2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2721 ASN ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN D 209 GLN D2090 GLN ** D2151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.170778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.148319 restraints weight = 303610.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.147275 restraints weight = 631201.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.145217 restraints weight = 418299.267| |-----------------------------------------------------------------------------| r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4168 r_free = 0.4168 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4168 r_free = 0.4168 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.4168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 132192 Z= 0.279 Angle : 0.638 13.865 178900 Z= 0.322 Chirality : 0.042 0.229 19928 Planarity : 0.004 0.114 23144 Dihedral : 4.906 46.254 17860 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.87 % Favored : 89.06 % Rotamer: Outliers : 2.67 % Allowed : 21.43 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.28 (0.07), residues: 16464 helix: 1.09 (0.06), residues: 7328 sheet: -1.27 (0.16), residues: 1112 loop : -2.81 (0.06), residues: 8024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP B1007 HIS 0.013 0.001 HIS A 270 PHE 0.027 0.001 PHE D2202 TYR 0.017 0.001 TYR B3623 ARG 0.009 0.000 ARG A 626 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33869.05 seconds wall clock time: 591 minutes 17.08 seconds (35477.08 seconds total)