Starting phenix.real_space_refine on Fri Mar 15 21:13:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dty_27711/03_2024/8dty_27711.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dty_27711/03_2024/8dty_27711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dty_27711/03_2024/8dty_27711.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dty_27711/03_2024/8dty_27711.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dty_27711/03_2024/8dty_27711.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dty_27711/03_2024/8dty_27711.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.065 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 808 5.16 5 C 81800 2.51 5 N 21996 2.21 5 O 24164 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 31": "OE1" <-> "OE2" Residue "A PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 61": "OD1" <-> "OD2" Residue "A TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 320": "OE1" <-> "OE2" Residue "A ASP 458": "OD1" <-> "OD2" Residue "A GLU 492": "OE1" <-> "OE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 680": "OD1" <-> "OD2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1819": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2037": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2114": "OD1" <-> "OD2" Residue "A GLU 2182": "OE1" <-> "OE2" Residue "A PHE 2198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2215": "OD1" <-> "OD2" Residue "A GLU 2222": "OE1" <-> "OE2" Residue "A GLU 2258": "OE1" <-> "OE2" Residue "A GLU 2681": "OE1" <-> "OE2" Residue "A GLU 3636": "OE1" <-> "OE2" Residue "A ASP 3642": "OD1" <-> "OD2" Residue "A ASP 3832": "OD1" <-> "OD2" Residue "A TYR 3891": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3941": "OD1" <-> "OD2" Residue "A PHE 4117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4119": "OE1" <-> "OE2" Residue "A TYR 4558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4604": "OE1" <-> "OE2" Residue "A PHE 4659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4881": "OE1" <-> "OE2" Residue "B GLU 31": "OE1" <-> "OE2" Residue "B PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 61": "OD1" <-> "OD2" Residue "B TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 320": "OE1" <-> "OE2" Residue "B ASP 458": "OD1" <-> "OD2" Residue "B GLU 492": "OE1" <-> "OE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 680": "OD1" <-> "OD2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1819": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2037": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2114": "OD1" <-> "OD2" Residue "B GLU 2182": "OE1" <-> "OE2" Residue "B PHE 2198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2215": "OD1" <-> "OD2" Residue "B GLU 2222": "OE1" <-> "OE2" Residue "B GLU 2258": "OE1" <-> "OE2" Residue "B GLU 2681": "OE1" <-> "OE2" Residue "B GLU 3636": "OE1" <-> "OE2" Residue "B ASP 3642": "OD1" <-> "OD2" Residue "B ASP 3832": "OD1" <-> "OD2" Residue "B TYR 3891": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 3941": "OD1" <-> "OD2" Residue "B PHE 4117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4119": "OE1" <-> "OE2" Residue "B TYR 4558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4604": "OE1" <-> "OE2" Residue "B PHE 4659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4881": "OE1" <-> "OE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 61": "OD1" <-> "OD2" Residue "C TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 320": "OE1" <-> "OE2" Residue "C ASP 458": "OD1" <-> "OD2" Residue "C GLU 492": "OE1" <-> "OE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 680": "OD1" <-> "OD2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1819": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2037": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 2114": "OD1" <-> "OD2" Residue "C GLU 2182": "OE1" <-> "OE2" Residue "C PHE 2198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 2215": "OD1" <-> "OD2" Residue "C GLU 2222": "OE1" <-> "OE2" Residue "C GLU 2258": "OE1" <-> "OE2" Residue "C GLU 2681": "OE1" <-> "OE2" Residue "C GLU 3636": "OE1" <-> "OE2" Residue "C ASP 3642": "OD1" <-> "OD2" Residue "C ASP 3832": "OD1" <-> "OD2" Residue "C TYR 3891": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 3905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 3941": "OD1" <-> "OD2" Residue "C PHE 4117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4119": "OE1" <-> "OE2" Residue "C TYR 4558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4604": "OE1" <-> "OE2" Residue "C PHE 4659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4881": "OE1" <-> "OE2" Residue "D GLU 31": "OE1" <-> "OE2" Residue "D PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 61": "OD1" <-> "OD2" Residue "D TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 320": "OE1" <-> "OE2" Residue "D ASP 458": "OD1" <-> "OD2" Residue "D GLU 492": "OE1" <-> "OE2" Residue "D TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 680": "OD1" <-> "OD2" Residue "D PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1819": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2037": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 2114": "OD1" <-> "OD2" Residue "D GLU 2182": "OE1" <-> "OE2" Residue "D PHE 2198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 2215": "OD1" <-> "OD2" Residue "D GLU 2222": "OE1" <-> "OE2" Residue "D GLU 2258": "OE1" <-> "OE2" Residue "D GLU 2681": "OE1" <-> "OE2" Residue "D GLU 3636": "OE1" <-> "OE2" Residue "D ASP 3642": "OD1" <-> "OD2" Residue "D ASP 3832": "OD1" <-> "OD2" Residue "D TYR 3891": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 3905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 3941": "OD1" <-> "OD2" Residue "D PHE 4117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4119": "OE1" <-> "OE2" Residue "D TYR 4558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4604": "OE1" <-> "OE2" Residue "D PHE 4659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4881": "OE1" <-> "OE2" Time to flip residues: 0.38s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 128772 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 31374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4004, 31374 Classifications: {'peptide': 4004} Incomplete info: {'truncation_to_alanine': 177} Link IDs: {'PTRANS': 143, 'TRANS': 3860} Chain breaks: 25 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 678 Unresolved non-hydrogen angles: 830 Unresolved non-hydrogen dihedrals: 569 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 2, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 21, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 358 Chain: "B" Number of atoms: 31374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4004, 31374 Classifications: {'peptide': 4004} Incomplete info: {'truncation_to_alanine': 177} Link IDs: {'PTRANS': 143, 'TRANS': 3860} Chain breaks: 25 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 678 Unresolved non-hydrogen angles: 830 Unresolved non-hydrogen dihedrals: 569 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 2, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 21, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 358 Chain: "C" Number of atoms: 31374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4004, 31374 Classifications: {'peptide': 4004} Incomplete info: {'truncation_to_alanine': 177} Link IDs: {'PTRANS': 143, 'TRANS': 3860} Chain breaks: 25 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 678 Unresolved non-hydrogen angles: 830 Unresolved non-hydrogen dihedrals: 569 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 2, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 21, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 358 Chain: "D" Number of atoms: 31374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4004, 31374 Classifications: {'peptide': 4004} Incomplete info: {'truncation_to_alanine': 177} Link IDs: {'PTRANS': 143, 'TRANS': 3860} Chain breaks: 25 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 678 Unresolved non-hydrogen angles: 830 Unresolved non-hydrogen dihedrals: 569 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 2, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 21, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 358 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 30695 SG CYS A4887 203.703 193.256 125.437 1.00 34.84 S ATOM 30720 SG CYS A4890 203.691 195.557 122.597 1.00 29.46 S ATOM 62069 SG CYS B4887 182.604 203.688 125.426 1.00 34.84 S ATOM 62094 SG CYS B4890 180.302 203.677 122.587 1.00 29.46 S ATOM 93443 SG CYS C4887 193.259 172.132 125.431 1.00 34.84 S ATOM 93468 SG CYS C4890 195.560 172.144 122.591 1.00 29.46 S ATOM A0J5D SG CYS D4887 172.128 182.579 125.426 1.00 34.84 S ATOM A0J62 SG CYS D4890 172.140 180.278 122.586 1.00 29.46 S Residues with excluded nonbonded symmetry interactions: 28 residue: pdb=" N VAL A 663 " occ=0.82 ... (5 atoms not shown) pdb=" CG2 VAL A 663 " occ=0.82 residue: pdb=" N GLN A 669 " occ=0.96 ... (7 atoms not shown) pdb=" NE2 GLN A 669 " occ=0.96 residue: pdb=" N CYS A 736 " occ=0.13 ... (4 atoms not shown) pdb=" SG CYS A 736 " occ=0.13 residue: pdb=" N ARG A 739 " occ=0.94 ... (9 atoms not shown) pdb=" NH2 ARG A 739 " occ=0.94 residue: pdb=" N SER A 742 " occ=0.75 ... (4 atoms not shown) pdb=" OG SER A 742 " occ=0.75 residue: pdb=" N ASP A 752 " occ=0.56 ... (6 atoms not shown) pdb=" OD2 ASP A 752 " occ=0.56 residue: pdb=" N HIS A 808 " occ=0.97 ... (8 atoms not shown) pdb=" NE2 HIS A 808 " occ=0.97 residue: pdb=" N VAL B 663 " occ=0.82 ... (5 atoms not shown) pdb=" CG2 VAL B 663 " occ=0.82 residue: pdb=" N GLN B 669 " occ=0.96 ... (7 atoms not shown) pdb=" NE2 GLN B 669 " occ=0.96 residue: pdb=" N CYS B 736 " occ=0.13 ... (4 atoms not shown) pdb=" SG CYS B 736 " occ=0.13 residue: pdb=" N ARG B 739 " occ=0.94 ... (9 atoms not shown) pdb=" NH2 ARG B 739 " occ=0.94 residue: pdb=" N SER B 742 " occ=0.75 ... (4 atoms not shown) pdb=" OG SER B 742 " occ=0.75 ... (remaining 16 not shown) Time building chain proxies: 48.16, per 1000 atoms: 0.37 Number of scatterers: 128772 At special positions: 0 Unit cell: (376.92, 376.92, 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 808 16.00 O 24164 8.00 N 21996 7.00 C 81800 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: 36.36 Conformation dependent library (CDL) restraints added in 16.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A6000 " pdb="ZN ZN A6000 " - pdb=" ND1 HIS A4912 " pdb="ZN ZN A6000 " - pdb=" NE2 HIS A4907 " pdb="ZN ZN A6000 " - pdb=" SG CYS A4887 " pdb="ZN ZN A6000 " - pdb=" SG CYS A4890 " pdb=" ZN B6000 " pdb="ZN ZN B6000 " - pdb=" ND1 HIS B4912 " pdb="ZN ZN B6000 " - pdb=" NE2 HIS B4907 " pdb="ZN ZN B6000 " - pdb=" SG CYS B4887 " pdb="ZN ZN B6000 " - pdb=" SG CYS B4890 " pdb=" ZN C6000 " pdb="ZN ZN C6000 " - pdb=" ND1 HIS C4912 " pdb="ZN ZN C6000 " - pdb=" NE2 HIS C4907 " pdb="ZN ZN C6000 " - pdb=" SG CYS C4887 " pdb="ZN ZN C6000 " - pdb=" SG CYS C4890 " pdb=" ZN D6000 " pdb="ZN ZN D6000 " - pdb=" ND1 HIS D4912 " pdb="ZN ZN D6000 " - pdb=" NE2 HIS D4907 " pdb="ZN ZN D6000 " - pdb=" SG CYS D4887 " pdb="ZN ZN D6000 " - pdb=" SG CYS D4890 " Number of angles added : 8 32456 Ramachandran restraints generated. 16228 Oldfield, 0 Emsley, 16228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 30768 Finding SS restraints... Secondary structure from input PDB file: 587 helices and 104 sheets defined 49.0% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 16.03 Creating SS restraints... Processing helix chain 'A' and resid 249 through 253 removed outlier: 4.338A pdb=" N HIS A 252 " --> pdb=" O SER A 249 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY A 253 " --> pdb=" O GLY A 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 249 through 253' Processing helix chain 'A' and resid 265 through 270 removed outlier: 3.535A pdb=" N VAL A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 435 removed outlier: 4.089A pdb=" N ARG A 414 " --> pdb=" O HIS A 410 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N THR A 415 " --> pdb=" O GLU A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 463 Processing helix chain 'A' and resid 471 through 494 Processing helix chain 'A' and resid 498 through 506 Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 525 through 543 removed outlier: 3.529A pdb=" N GLY A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 563 Processing helix chain 'A' and resid 568 through 582 Processing helix chain 'A' and resid 590 through 604 removed outlier: 3.935A pdb=" N LEU A 601 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP A 602 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 615 removed outlier: 3.692A pdb=" N ASP A 612 " --> pdb=" O HIS A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 628 through 636 Processing helix chain 'A' and resid 878 through 901 removed outlier: 4.201A pdb=" N GLY A 901 " --> pdb=" O LYS A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 946 Processing helix chain 'A' and resid 965 through 969 removed outlier: 4.038A pdb=" N ASN A 969 " --> pdb=" O LEU A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1015 removed outlier: 3.854A pdb=" N GLU A 993 " --> pdb=" O THR A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1060 Processing helix chain 'A' and resid 1092 through 1095 removed outlier: 3.774A pdb=" N ALA A1095 " --> pdb=" O LYS A1092 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1092 through 1095' Processing helix chain 'A' and resid 1230 through 1235 removed outlier: 3.714A pdb=" N GLU A1234 " --> pdb=" O CYS A1230 " (cutoff:3.500A) Processing helix chain 'A' and resid 1643 through 1647 Processing helix chain 'A' and resid 1648 through 1666 removed outlier: 3.588A pdb=" N CYS A1666 " --> pdb=" O TYR A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1672 through 1681 removed outlier: 3.521A 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 1711 Processing helix chain 'A' and resid 1713 through 1723 Processing helix chain 'A' and resid 1784 through 1806 removed outlier: 3.859A pdb=" N ALA A1790 " --> pdb=" O ASP A1786 " (cutoff:3.500A) Processing helix chain 'A' and resid 1819 through 1831 Processing helix chain 'A' and resid 1836 through 1848 Processing helix chain 'A' and resid 1898 through 1942 removed outlier: 3.803A pdb=" N ASP A1930 " --> pdb=" O ALA A1926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1952 through 1956 Processing helix chain 'A' and resid 1999 through 2006 removed outlier: 4.049A pdb=" N MET A2003 " --> pdb=" O HIS A1999 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS A2006 " --> pdb=" O LEU A2002 " (cutoff:3.500A) Processing helix chain 'A' and resid 2010 through 2015 Processing helix chain 'A' and resid 2024 through 2036 removed outlier: 3.528A pdb=" N THR A2036 " --> pdb=" O VAL A2032 " (cutoff:3.500A) Processing helix chain 'A' and resid 2056 through 2072 removed outlier: 4.623A pdb=" N SER A2072 " --> pdb=" O TRP A2068 " (cutoff:3.500A) Processing helix chain 'A' and resid 2076 through 2092 removed outlier: 3.630A pdb=" N VAL A2080 " --> pdb=" O ASP A2076 " (cutoff:3.500A) Processing helix chain 'A' and resid 2092 through 2101 Processing helix chain 'A' and resid 2102 through 2104 No H-bonds generated for 'chain 'A' and resid 2102 through 2104' Processing helix chain 'A' and resid 2108 through 2110 No H-bonds generated for 'chain 'A' and resid 2108 through 2110' Processing helix chain 'A' and resid 2111 through 2131 removed outlier: 3.573A pdb=" N LEU A2118 " --> pdb=" O ASP A2114 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER A2130 " --> pdb=" O ARG A2126 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL A2131 " --> pdb=" O SER A2127 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2150 removed outlier: 3.722A pdb=" N LYS A2139 " --> pdb=" O LYS A2135 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN A2150 " --> pdb=" O GLY A2146 " (cutoff:3.500A) Processing helix chain 'A' and resid 2157 through 2164 Processing helix chain 'A' and resid 2165 through 2179 removed outlier: 3.691A pdb=" N THR A2169 " --> pdb=" O GLY A2165 " (cutoff:3.500A) Processing helix chain 'A' and resid 2190 through 2201 Processing helix chain 'A' and resid 2207 through 2223 removed outlier: 3.652A pdb=" N ASP A2215 " --> pdb=" O LYS A2211 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS A2216 " --> pdb=" O ALA A2212 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER A2218 " --> pdb=" O PHE A2214 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N TYR A2219 " --> pdb=" O ASP A2215 " (cutoff:3.500A) Processing helix chain 'A' and resid 2238 through 2246 removed outlier: 3.707A pdb=" N ALA A2242 " --> pdb=" O PRO A2238 " (cutoff:3.500A) Processing helix chain 'A' and resid 2249 through 2255 Processing helix chain 'A' and resid 2257 through 2270 removed outlier: 4.096A pdb=" N LEU A2261 " --> pdb=" O ARG A2257 " (cutoff:3.500A) Processing helix chain 'A' and resid 2295 through 2306 Processing helix chain 'A' and resid 2312 through 2326 removed outlier: 3.722A pdb=" N VAL A2318 " --> pdb=" O GLU A2314 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG A2326 " --> pdb=" O LEU A2322 " (cutoff:3.500A) Processing helix chain 'A' and resid 2341 through 2354 removed outlier: 4.816A pdb=" N GLU A2347 " --> pdb=" O LEU A2343 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A2354 " --> pdb=" O ILE A2350 " (cutoff:3.500A) Processing helix chain 'A' and resid 2384 through 2402 removed outlier: 4.460A pdb=" N MET A2388 " --> pdb=" O GLY A2384 " (cutoff:3.500A) Processing helix chain 'A' and resid 2414 through 2425 removed outlier: 4.120A pdb=" N ILE A2418 " --> pdb=" O GLU A2414 " (cutoff:3.500A) Processing helix chain 'A' and resid 2434 through 2440 removed outlier: 3.524A pdb=" N GLN A2440 " --> pdb=" O SER A2436 " (cutoff:3.500A) Processing helix chain 'A' and resid 2460 through 2475 removed outlier: 4.063A pdb=" N LYS A2464 " --> pdb=" O CYS A2460 " (cutoff:3.500A) Processing helix chain 'A' and resid 2479 through 2487 removed outlier: 4.000A pdb=" N LEU A2483 " --> pdb=" O VAL A2479 " (cutoff:3.500A) Processing helix chain 'A' and resid 2490 through 2500 removed outlier: 3.638A pdb=" N ASP A2494 " --> pdb=" O GLY A2490 " (cutoff:3.500A) Processing helix chain 'A' and resid 2511 through 2521 Processing helix chain 'A' and resid 2582 through 2592 removed outlier: 4.002A pdb=" N HIS A2586 " --> pdb=" O SER A2582 " (cutoff:3.500A) Processing helix chain 'A' and resid 2599 through 2602 Processing helix chain 'A' and resid 2603 through 2614 removed outlier: 4.120A pdb=" N HIS A2612 " --> pdb=" O LEU A2608 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR A2613 " --> pdb=" O LEU A2609 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU A2614 " --> pdb=" O THR A2610 " (cutoff:3.500A) Processing helix chain 'A' and resid 2615 through 2619 removed outlier: 3.709A pdb=" N TYR A2619 " --> pdb=" O CYS A2616 " (cutoff:3.500A) Processing helix chain 'A' and resid 2621 through 2633 Processing helix chain 'A' and resid 2639 through 2652 removed outlier: 4.035A pdb=" N LEU A2643 " --> pdb=" O LEU A2639 " (cutoff:3.500A) Processing helix chain 'A' and resid 2663 through 2674 removed outlier: 3.525A pdb=" N CYS A2667 " --> pdb=" O LEU A2663 " (cutoff:3.500A) Processing helix chain 'A' and resid 2686 through 2694 removed outlier: 4.293A pdb=" N GLU A2689 " --> pdb=" O SER A2686 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLN A2691 " --> pdb=" O MET A2688 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER A2692 " --> pdb=" O GLU A2689 " (cutoff:3.500A) Processing helix chain 'A' and resid 2718 through 2739 Processing helix chain 'A' and resid 2758 through 2762 Processing helix chain 'A' and resid 2763 through 2785 Proline residue: A2773 - end of helix removed outlier: 3.658A pdb=" N TRP A2784 " --> pdb=" O THR A2780 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY A2785 " --> pdb=" O MET A2781 " (cutoff:3.500A) Processing helix chain 'A' and resid 2791 through 2795 removed outlier: 3.507A pdb=" N GLY A2794 " --> pdb=" O THR A2791 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP A2795 " --> pdb=" O ARG A2792 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2791 through 2795' Processing helix chain 'A' and resid 2833 through 2863 Processing helix chain 'A' and resid 2872 through 2876 Processing helix chain 'A' and resid 2877 through 2897 removed outlier: 3.958A pdb=" N LYS A2883 " --> pdb=" O LYS A2879 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE A2897 " --> pdb=" O LYS A2893 " (cutoff:3.500A) Processing helix chain 'A' and resid 2898 through 2900 No H-bonds generated for 'chain 'A' and resid 2898 through 2900' Processing helix chain 'A' and resid 2990 through 3014 Processing helix chain 'A' and resid 3036 through 3050 removed outlier: 3.974A pdb=" N ASP A3050 " --> pdb=" O LYS A3046 " (cutoff:3.500A) Processing helix chain 'A' and resid 3054 through 3063 removed outlier: 3.503A pdb=" N ALA A3063 " --> pdb=" O PHE A3059 " (cutoff:3.500A) Processing helix chain 'A' and resid 3065 through 3084 removed outlier: 4.404A pdb=" N LYS A3069 " --> pdb=" O GLU A3065 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER A3084 " --> pdb=" O THR A3080 " (cutoff:3.500A) Processing helix chain 'A' and resid 3090 through 3099 Processing helix chain 'A' and resid 3183 through 3193 Processing helix chain 'A' and resid 3214 through 3225 removed outlier: 4.229A pdb=" N ILE A3218 " --> pdb=" O MET A3214 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A3222 " --> pdb=" O ILE A3218 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER A3223 " --> pdb=" O GLU A3219 " (cutoff:3.500A) Processing helix chain 'A' and resid 3237 through 3252 Processing helix chain 'A' and resid 3283 through 3292 Processing helix chain 'A' and resid 3308 through 3324 Proline residue: A3320 - end of helix Processing helix chain 'A' and resid 3331 through 3344 Processing helix chain 'A' and resid 3355 through 3375 Proline residue: A3370 - end of helix Processing helix chain 'A' and resid 3405 through 3431 removed outlier: 4.251A pdb=" N ILE A3431 " --> pdb=" O MET A3427 " (cutoff:3.500A) Processing helix chain 'A' and resid 3436 through 3472 removed outlier: 3.776A pdb=" N LYS A3440 " --> pdb=" O SER A3436 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG A3457 " --> pdb=" O ARG A3453 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER A3463 " --> pdb=" O SER A3459 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LEU A3464 " --> pdb=" O MET A3460 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ARG A3471 " --> pdb=" O ALA A3467 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU A3472 " --> pdb=" O ALA A3468 " (cutoff:3.500A) Processing helix chain 'A' and resid 3474 through 3493 Proline residue: A3482 - end of helix removed outlier: 4.330A pdb=" N ASN A3493 " --> pdb=" O ALA A3489 " (cutoff:3.500A) Processing helix chain 'A' and resid 3495 through 3508 removed outlier: 4.129A pdb=" N GLU A3502 " --> pdb=" O LYS A3498 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU A3503 " --> pdb=" O ASP A3499 " (cutoff:3.500A) Processing helix chain 'A' and resid 3557 through 3566 removed outlier: 3.759A pdb=" N TYR A3566 " --> pdb=" O GLN A3562 " (cutoff:3.500A) Processing helix chain 'A' and resid 3614 through 3643 removed outlier: 3.553A pdb=" N LEU A3618 " --> pdb=" O ARG A3614 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE A3628 " --> pdb=" O GLU A3624 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLU A3629 " --> pdb=" O LYS A3625 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THR A3630 " --> pdb=" O SER A3626 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLU A3631 " --> pdb=" O TRP A3627 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP A3637 " --> pdb=" O HIS A3633 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LYS A3638 " --> pdb=" O TYR A3634 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU A3639 " --> pdb=" O PHE A3635 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE A3640 " --> pdb=" O GLU A3636 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU A3641 " --> pdb=" O ASP A3637 " (cutoff:3.500A) Processing helix chain 'A' and resid 3661 through 3676 removed outlier: 3.913A pdb=" N GLN A3665 " --> pdb=" O ASP A3661 " (cutoff:3.500A) Processing helix chain 'A' and resid 3684 through 3699 Processing helix chain 'A' and resid 3715 through 3732 Processing helix chain 'A' and resid 3734 through 3746 removed outlier: 3.790A pdb=" N SER A3746 " --> pdb=" O THR A3742 " (cutoff:3.500A) Processing helix chain 'A' and resid 3751 through 3765 Processing helix chain 'A' and resid 3770 through 3784 Processing helix chain 'A' and resid 3786 through 3798 removed outlier: 3.653A pdb=" N GLN A3790 " --> pdb=" O VAL A3786 " (cutoff:3.500A) Processing helix chain 'A' and resid 3803 through 3812 removed outlier: 3.655A pdb=" N LYS A3812 " --> pdb=" O GLU A3808 " (cutoff:3.500A) Processing helix chain 'A' and resid 3832 through 3847 Processing helix chain 'A' and resid 3850 through 3857 removed outlier: 3.525A pdb=" N LEU A3857 " --> pdb=" O PHE A3853 " (cutoff:3.500A) Processing helix chain 'A' and resid 3868 through 3892 removed outlier: 3.621A pdb=" N SER A3872 " --> pdb=" O ASN A3868 " (cutoff:3.500A) Processing helix chain 'A' and resid 3898 through 3923 removed outlier: 3.512A 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 3960 removed outlier: 3.694A pdb=" N ALA A3942 " --> pdb=" O ARG A3938 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N HIS A3952 " --> pdb=" O HIS A3948 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N MET A3955 " --> pdb=" O ALA A3951 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN A3959 " --> pdb=" O MET A3955 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP A3960 " --> pdb=" O LYS A3956 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3985 removed outlier: 4.075A pdb=" N LEU A3985 " --> pdb=" O LEU A3981 " (cutoff:3.500A) Processing helix chain 'A' and resid 3992 through 4005 Processing helix chain 'A' and resid 4005 through 4014 Processing helix chain 'A' and resid 4026 through 4030 removed outlier: 3.557A pdb=" N ASP A4029 " --> pdb=" O THR A4026 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N THR A4030 " --> pdb=" O SER A4027 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4026 through 4030' Processing helix chain 'A' and resid 4044 through 4051 removed outlier: 3.904A pdb=" N MET A4051 " --> pdb=" O PHE A4047 " (cutoff:3.500A) Processing helix chain 'A' and resid 4061 through 4069 removed outlier: 3.661A pdb=" N LEU A4065 " --> pdb=" O GLU A4061 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU A4066 " --> pdb=" O THR A4062 " (cutoff:3.500A) Processing helix chain 'A' and resid 4080 through 4085 removed outlier: 3.590A pdb=" N ARG A4085 " --> pdb=" O GLU A4081 " (cutoff:3.500A) Processing helix chain 'A' and resid 4092 through 4108 Processing helix chain 'A' and resid 4111 through 4121 removed outlier: 3.898A pdb=" N THR A4116 " --> pdb=" O THR A4112 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A4117 " --> pdb=" O ARG A4113 " (cutoff:3.500A) Processing helix chain 'A' and resid 4121 through 4128 removed outlier: 3.510A pdb=" N LEU A4125 " --> pdb=" O ALA A4121 " (cutoff:3.500A) Processing helix chain 'A' and resid 4152 through 4159 Processing helix chain 'A' and resid 4161 through 4179 Processing helix chain 'A' and resid 4181 through 4204 removed outlier: 3.795A pdb=" N MET A4185 " --> pdb=" O GLU A4181 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU A4186 " --> pdb=" O LYS A4182 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN A4204 " --> pdb=" O GLN A4200 " (cutoff:3.500A) Processing helix chain 'A' and resid 4484 through 4496 removed outlier: 3.549A pdb=" N ASN A4496 " --> pdb=" O TYR A4492 " (cutoff:3.500A) Processing helix chain 'A' and resid 4496 through 4516 Processing helix chain 'A' and resid 4569 through 4593 Processing helix chain 'A' and resid 4593 through 4612 removed outlier: 3.743A pdb=" N VAL A4597 " --> pdb=" O LYS A4593 " (cutoff:3.500A) Processing helix chain 'A' and resid 4624 through 4631 Processing helix chain 'A' and resid 4647 through 4661 removed outlier: 5.655A pdb=" N GLU A4658 " --> pdb=" O ASP A4654 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N PHE A4659 " --> pdb=" O LYS A4655 " (cutoff:3.500A) Processing helix chain 'A' and resid 4662 through 4670 Processing helix chain 'A' and resid 4701 through 4714 removed outlier: 3.716A pdb=" N THR A4714 " --> pdb=" O GLY A4710 " (cutoff:3.500A) Processing helix chain 'A' and resid 4715 through 4734 removed outlier: 4.006A pdb=" N HIS A4732 " --> pdb=" O SER A4728 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR A4733 " --> pdb=" O VAL A4729 " (cutoff:3.500A) Processing helix chain 'A' and resid 4735 through 4743 removed outlier: 3.642A pdb=" N PHE A4738 " --> pdb=" O ASN A4735 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A4740 " --> pdb=" O PHE A4737 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A4743 " --> pdb=" O ALA A4740 " (cutoff:3.500A) Processing helix chain 'A' and resid 4744 through 4749 removed outlier: 3.779A pdb=" N PHE A4749 " --> pdb=" O ILE A4745 " (cutoff:3.500A) Processing helix chain 'A' and resid 4749 through 4762 removed outlier: 3.896A pdb=" N ILE A4755 " --> pdb=" O THR A4751 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER A4758 " --> pdb=" O THR A4754 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL A4759 " --> pdb=" O ILE A4755 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN A4762 " --> pdb=" O SER A4758 " (cutoff:3.500A) Processing helix chain 'A' and resid 4762 through 4788 removed outlier: 3.842A pdb=" N VAL A4767 " --> pdb=" O GLY A4763 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A4768 " --> pdb=" O LYS A4764 " (cutoff:3.500A) Processing helix chain 'A' and resid 4789 through 4791 No H-bonds generated for 'chain 'A' and resid 4789 through 4791' Processing helix chain 'A' and resid 4807 through 4818 Processing helix chain 'A' and resid 4824 through 4829 removed outlier: 4.279A pdb=" N GLY A4827 " --> pdb=" O GLY A4824 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP A4828 " --> pdb=" O GLY A4825 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU A4829 " --> pdb=" O ILE A4826 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4824 through 4829' Processing helix chain 'A' and resid 4838 through 4854 Processing helix chain 'A' and resid 4855 through 4886 removed outlier: 3.672A pdb=" N ILE A4865 " --> pdb=" O ILE A4861 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A4886 " --> pdb=" O ASP A4882 " (cutoff:3.500A) Processing helix chain 'A' and resid 4893 through 4898 removed outlier: 3.970A pdb=" N PHE A4897 " --> pdb=" O GLY A4893 " (cutoff:3.500A) Processing helix chain 'A' and resid 4902 through 4911 Processing helix chain 'A' and resid 4913 through 4926 Processing helix chain 'A' and resid 4928 through 4932 Processing helix chain 'A' and resid 4933 through 4946 Processing helix chain 'A' and resid 4956 through 4961 Processing helix chain 'B' and resid 249 through 253 removed outlier: 4.338A pdb=" N HIS B 252 " --> pdb=" O SER B 249 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY B 253 " --> pdb=" O GLY B 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 249 through 253' Processing helix chain 'B' and resid 265 through 270 removed outlier: 3.534A pdb=" N VAL B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 435 removed outlier: 4.089A pdb=" N ARG B 414 " --> pdb=" O HIS B 410 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N THR B 415 " --> pdb=" O GLU B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 463 Processing helix chain 'B' and resid 471 through 494 Processing helix chain 'B' and resid 498 through 506 Processing helix chain 'B' and resid 512 through 518 Processing helix chain 'B' and resid 525 through 543 removed outlier: 3.529A pdb=" N GLY B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 563 Processing helix chain 'B' and resid 568 through 582 Processing helix chain 'B' and resid 590 through 604 removed outlier: 3.936A pdb=" N LEU B 601 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP B 602 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 615 removed outlier: 3.692A pdb=" N ASP B 612 " --> pdb=" O HIS B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 628 through 636 Processing helix chain 'B' and resid 878 through 901 removed outlier: 4.201A pdb=" N GLY B 901 " --> pdb=" O LYS B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 946 Processing helix chain 'B' and resid 965 through 969 removed outlier: 4.038A pdb=" N ASN B 969 " --> pdb=" O LEU B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1015 removed outlier: 3.854A pdb=" N GLU B 993 " --> pdb=" O THR B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 1043 through 1060 Processing helix chain 'B' and resid 1092 through 1095 removed outlier: 3.774A pdb=" N ALA B1095 " --> pdb=" O LYS B1092 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1092 through 1095' Processing helix chain 'B' and resid 1230 through 1235 removed outlier: 3.713A pdb=" N GLU B1234 " --> pdb=" O CYS B1230 " (cutoff:3.500A) Processing helix chain 'B' and resid 1643 through 1647 Processing helix chain 'B' and resid 1648 through 1666 removed outlier: 3.588A pdb=" N CYS B1666 " --> pdb=" O TYR B1662 " (cutoff:3.500A) Processing helix chain 'B' and resid 1672 through 1681 removed outlier: 3.522A 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 1711 Processing helix chain 'B' and resid 1713 through 1723 Processing helix chain 'B' and resid 1784 through 1806 removed outlier: 3.860A pdb=" N ALA B1790 " --> pdb=" O ASP B1786 " (cutoff:3.500A) Processing helix chain 'B' and resid 1819 through 1831 Processing helix chain 'B' and resid 1836 through 1848 Processing helix chain 'B' and resid 1898 through 1942 removed outlier: 3.803A pdb=" N ASP B1930 " --> pdb=" O ALA B1926 " (cutoff:3.500A) Processing helix chain 'B' and resid 1952 through 1956 Processing helix chain 'B' and resid 1999 through 2006 removed outlier: 4.050A pdb=" N MET B2003 " --> pdb=" O HIS B1999 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS B2006 " --> pdb=" O LEU B2002 " (cutoff:3.500A) Processing helix chain 'B' and resid 2010 through 2015 Processing helix chain 'B' and resid 2024 through 2036 removed outlier: 3.528A pdb=" N THR B2036 " --> pdb=" O VAL B2032 " (cutoff:3.500A) Processing helix chain 'B' and resid 2056 through 2072 removed outlier: 4.623A pdb=" N SER B2072 " --> pdb=" O TRP B2068 " (cutoff:3.500A) Processing helix chain 'B' and resid 2076 through 2092 removed outlier: 3.630A pdb=" N VAL B2080 " --> pdb=" O ASP B2076 " (cutoff:3.500A) Processing helix chain 'B' and resid 2092 through 2101 Processing helix chain 'B' and resid 2102 through 2104 No H-bonds generated for 'chain 'B' and resid 2102 through 2104' Processing helix chain 'B' and resid 2108 through 2110 No H-bonds generated for 'chain 'B' and resid 2108 through 2110' Processing helix chain 'B' and resid 2111 through 2131 removed outlier: 3.574A pdb=" N LEU B2118 " --> pdb=" O ASP B2114 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER B2130 " --> pdb=" O ARG B2126 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL B2131 " --> pdb=" O SER B2127 " (cutoff:3.500A) Processing helix chain 'B' and resid 2135 through 2150 removed outlier: 3.721A pdb=" N LYS B2139 " --> pdb=" O LYS B2135 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN B2150 " --> pdb=" O GLY B2146 " (cutoff:3.500A) Processing helix chain 'B' and resid 2157 through 2164 Processing helix chain 'B' and resid 2165 through 2179 removed outlier: 3.690A pdb=" N THR B2169 " --> pdb=" O GLY B2165 " (cutoff:3.500A) Processing helix chain 'B' and resid 2190 through 2201 Processing helix chain 'B' and resid 2207 through 2223 removed outlier: 3.652A pdb=" N ASP B2215 " --> pdb=" O LYS B2211 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS B2216 " --> pdb=" O ALA B2212 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER B2218 " --> pdb=" O PHE B2214 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N TYR B2219 " --> pdb=" O ASP B2215 " (cutoff:3.500A) Processing helix chain 'B' and resid 2238 through 2246 removed outlier: 3.706A pdb=" N ALA B2242 " --> pdb=" O PRO B2238 " (cutoff:3.500A) Processing helix chain 'B' and resid 2249 through 2255 Processing helix chain 'B' and resid 2257 through 2270 removed outlier: 4.095A pdb=" N LEU B2261 " --> pdb=" O ARG B2257 " (cutoff:3.500A) Processing helix chain 'B' and resid 2295 through 2306 Processing helix chain 'B' and resid 2312 through 2326 removed outlier: 3.722A pdb=" N VAL B2318 " --> pdb=" O GLU B2314 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG B2326 " --> pdb=" O LEU B2322 " (cutoff:3.500A) Processing helix chain 'B' and resid 2341 through 2354 removed outlier: 4.816A pdb=" N GLU B2347 " --> pdb=" O LEU B2343 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU B2354 " --> pdb=" O ILE B2350 " (cutoff:3.500A) Processing helix chain 'B' and resid 2384 through 2402 removed outlier: 4.460A pdb=" N MET B2388 " --> pdb=" O GLY B2384 " (cutoff:3.500A) Processing helix chain 'B' and resid 2414 through 2425 removed outlier: 4.119A pdb=" N ILE B2418 " --> pdb=" O GLU B2414 " (cutoff:3.500A) Processing helix chain 'B' and resid 2434 through 2440 removed outlier: 3.525A pdb=" N GLN B2440 " --> pdb=" O SER B2436 " (cutoff:3.500A) Processing helix chain 'B' and resid 2460 through 2475 removed outlier: 4.064A pdb=" N LYS B2464 " --> pdb=" O CYS B2460 " (cutoff:3.500A) Processing helix chain 'B' and resid 2479 through 2487 removed outlier: 4.001A pdb=" N LEU B2483 " --> pdb=" O VAL B2479 " (cutoff:3.500A) Processing helix chain 'B' and resid 2490 through 2500 removed outlier: 3.640A pdb=" N ASP B2494 " --> pdb=" O GLY B2490 " (cutoff:3.500A) Processing helix chain 'B' and resid 2511 through 2521 Processing helix chain 'B' and resid 2582 through 2592 removed outlier: 4.001A pdb=" N HIS B2586 " --> pdb=" O SER B2582 " (cutoff:3.500A) Processing helix chain 'B' and resid 2599 through 2602 Processing helix chain 'B' and resid 2603 through 2614 removed outlier: 4.118A pdb=" N HIS B2612 " --> pdb=" O LEU B2608 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR B2613 " --> pdb=" O LEU B2609 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU B2614 " --> pdb=" O THR B2610 " (cutoff:3.500A) Processing helix chain 'B' and resid 2615 through 2619 removed outlier: 3.708A pdb=" N TYR B2619 " --> pdb=" O CYS B2616 " (cutoff:3.500A) Processing helix chain 'B' and resid 2621 through 2633 Processing helix chain 'B' and resid 2639 through 2652 removed outlier: 4.035A pdb=" N LEU B2643 " --> pdb=" O LEU B2639 " (cutoff:3.500A) Processing helix chain 'B' and resid 2663 through 2674 removed outlier: 3.524A pdb=" N CYS B2667 " --> pdb=" O LEU B2663 " (cutoff:3.500A) Processing helix chain 'B' and resid 2686 through 2694 removed outlier: 4.293A pdb=" N GLU B2689 " --> pdb=" O SER B2686 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLN B2691 " --> pdb=" O MET B2688 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B2692 " --> pdb=" O GLU B2689 " (cutoff:3.500A) Processing helix chain 'B' and resid 2718 through 2739 Processing helix chain 'B' and resid 2758 through 2762 Processing helix chain 'B' and resid 2763 through 2785 Proline residue: B2773 - end of helix removed outlier: 3.659A pdb=" N TRP B2784 " --> pdb=" O THR B2780 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY B2785 " --> pdb=" O MET B2781 " (cutoff:3.500A) Processing helix chain 'B' and resid 2791 through 2795 removed outlier: 3.507A pdb=" N GLY B2794 " --> pdb=" O THR B2791 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP B2795 " --> pdb=" O ARG B2792 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2791 through 2795' Processing helix chain 'B' and resid 2833 through 2863 Processing helix chain 'B' and resid 2872 through 2876 Processing helix chain 'B' and resid 2877 through 2897 removed outlier: 3.958A pdb=" N LYS B2883 " --> pdb=" O LYS B2879 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE B2897 " --> pdb=" O LYS B2893 " (cutoff:3.500A) Processing helix chain 'B' and resid 2898 through 2900 No H-bonds generated for 'chain 'B' and resid 2898 through 2900' Processing helix chain 'B' and resid 2990 through 3014 Processing helix chain 'B' and resid 3036 through 3050 removed outlier: 3.974A pdb=" N ASP B3050 " --> pdb=" O LYS B3046 " (cutoff:3.500A) Processing helix chain 'B' and resid 3054 through 3063 removed outlier: 3.504A pdb=" N ALA B3063 " --> pdb=" O PHE B3059 " (cutoff:3.500A) Processing helix chain 'B' and resid 3065 through 3084 removed outlier: 4.404A pdb=" N LYS B3069 " --> pdb=" O GLU B3065 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER B3084 " --> pdb=" O THR B3080 " (cutoff:3.500A) Processing helix chain 'B' and resid 3090 through 3099 Processing helix chain 'B' and resid 3183 through 3193 Processing helix chain 'B' and resid 3214 through 3225 removed outlier: 4.229A pdb=" N ILE B3218 " --> pdb=" O MET B3214 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU B3222 " --> pdb=" O ILE B3218 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER B3223 " --> pdb=" O GLU B3219 " (cutoff:3.500A) Processing helix chain 'B' and resid 3237 through 3252 Processing helix chain 'B' and resid 3283 through 3292 Processing helix chain 'B' and resid 3308 through 3324 Proline residue: B3320 - end of helix Processing helix chain 'B' and resid 3331 through 3344 Processing helix chain 'B' and resid 3355 through 3375 Proline residue: B3370 - end of helix Processing helix chain 'B' and resid 3405 through 3431 removed outlier: 4.251A pdb=" N ILE B3431 " --> pdb=" O MET B3427 " (cutoff:3.500A) Processing helix chain 'B' and resid 3436 through 3472 removed outlier: 3.778A pdb=" N LYS B3440 " --> pdb=" O SER B3436 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG B3457 " --> pdb=" O ARG B3453 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER B3463 " --> pdb=" O SER B3459 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LEU B3464 " --> pdb=" O MET B3460 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG B3471 " --> pdb=" O ALA B3467 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU B3472 " --> pdb=" O ALA B3468 " (cutoff:3.500A) Processing helix chain 'B' and resid 3474 through 3493 Proline residue: B3482 - end of helix removed outlier: 4.331A pdb=" N ASN B3493 " --> pdb=" O ALA B3489 " (cutoff:3.500A) Processing helix chain 'B' and resid 3495 through 3508 removed outlier: 4.130A pdb=" N GLU B3502 " --> pdb=" O LYS B3498 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU B3503 " --> pdb=" O ASP B3499 " (cutoff:3.500A) Processing helix chain 'B' and resid 3557 through 3566 removed outlier: 3.759A pdb=" N TYR B3566 " --> pdb=" O GLN B3562 " (cutoff:3.500A) Processing helix chain 'B' and resid 3614 through 3643 removed outlier: 3.553A pdb=" N LEU B3618 " --> pdb=" O ARG B3614 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE B3628 " --> pdb=" O GLU B3624 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLU B3629 " --> pdb=" O LYS B3625 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THR B3630 " --> pdb=" O SER B3626 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU B3631 " --> pdb=" O TRP B3627 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP B3637 " --> pdb=" O HIS B3633 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LYS B3638 " --> pdb=" O TYR B3634 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU B3639 " --> pdb=" O PHE B3635 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE B3640 " --> pdb=" O GLU B3636 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU B3641 " --> pdb=" O ASP B3637 " (cutoff:3.500A) Processing helix chain 'B' and resid 3661 through 3676 removed outlier: 3.913A pdb=" N GLN B3665 " --> pdb=" O ASP B3661 " (cutoff:3.500A) Processing helix chain 'B' and resid 3684 through 3699 Processing helix chain 'B' and resid 3715 through 3732 Processing helix chain 'B' and resid 3734 through 3746 removed outlier: 3.790A pdb=" N SER B3746 " --> pdb=" O THR B3742 " (cutoff:3.500A) Processing helix chain 'B' and resid 3751 through 3765 Processing helix chain 'B' and resid 3770 through 3784 Processing helix chain 'B' and resid 3786 through 3798 removed outlier: 3.655A pdb=" N GLN B3790 " --> pdb=" O VAL B3786 " (cutoff:3.500A) Processing helix chain 'B' and resid 3803 through 3812 removed outlier: 3.655A pdb=" N LYS B3812 " --> pdb=" O GLU B3808 " (cutoff:3.500A) Processing helix chain 'B' and resid 3832 through 3847 Processing helix chain 'B' and resid 3850 through 3857 removed outlier: 3.525A pdb=" N LEU B3857 " --> pdb=" O PHE B3853 " (cutoff:3.500A) Processing helix chain 'B' and resid 3868 through 3892 removed outlier: 3.620A pdb=" N SER B3872 " --> pdb=" O ASN B3868 " (cutoff:3.500A) Processing helix chain 'B' and resid 3898 through 3923 removed outlier: 3.511A 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 3960 removed outlier: 3.694A pdb=" N ALA B3942 " --> pdb=" O ARG B3938 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N HIS B3952 " --> pdb=" O HIS B3948 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N MET B3955 " --> pdb=" O ALA B3951 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN B3959 " --> pdb=" O MET B3955 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP B3960 " --> pdb=" O LYS B3956 " (cutoff:3.500A) Processing helix chain 'B' and resid 3964 through 3985 removed outlier: 4.075A pdb=" N LEU B3985 " --> pdb=" O LEU B3981 " (cutoff:3.500A) Processing helix chain 'B' and resid 3992 through 4005 Processing helix chain 'B' and resid 4005 through 4014 Processing helix chain 'B' and resid 4026 through 4030 removed outlier: 3.558A pdb=" N ASP B4029 " --> pdb=" O THR B4026 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N THR B4030 " --> pdb=" O SER B4027 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4026 through 4030' Processing helix chain 'B' and resid 4044 through 4051 removed outlier: 3.903A pdb=" N MET B4051 " --> pdb=" O PHE B4047 " (cutoff:3.500A) Processing helix chain 'B' and resid 4061 through 4069 removed outlier: 3.662A pdb=" N LEU B4065 " --> pdb=" O GLU B4061 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU B4066 " --> pdb=" O THR B4062 " (cutoff:3.500A) Processing helix chain 'B' and resid 4080 through 4085 removed outlier: 3.590A pdb=" N ARG B4085 " --> pdb=" O GLU B4081 " (cutoff:3.500A) Processing helix chain 'B' and resid 4092 through 4108 Processing helix chain 'B' and resid 4111 through 4121 removed outlier: 3.897A pdb=" N THR B4116 " --> pdb=" O THR B4112 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B4117 " --> pdb=" O ARG B4113 " (cutoff:3.500A) Processing helix chain 'B' and resid 4121 through 4128 removed outlier: 3.509A pdb=" N LEU B4125 " --> pdb=" O ALA B4121 " (cutoff:3.500A) Processing helix chain 'B' and resid 4152 through 4159 Processing helix chain 'B' and resid 4161 through 4179 Processing helix chain 'B' and resid 4181 through 4204 removed outlier: 3.795A pdb=" N MET B4185 " --> pdb=" O GLU B4181 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU B4186 " --> pdb=" O LYS B4182 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN B4204 " --> pdb=" O GLN B4200 " (cutoff:3.500A) Processing helix chain 'B' and resid 4484 through 4496 removed outlier: 3.549A pdb=" N ASN B4496 " --> pdb=" O TYR B4492 " (cutoff:3.500A) Processing helix chain 'B' and resid 4496 through 4516 Processing helix chain 'B' and resid 4569 through 4593 Processing helix chain 'B' and resid 4593 through 4612 removed outlier: 3.742A pdb=" N VAL B4597 " --> pdb=" O LYS B4593 " (cutoff:3.500A) Processing helix chain 'B' and resid 4624 through 4631 Processing helix chain 'B' and resid 4647 through 4661 removed outlier: 5.655A pdb=" N GLU B4658 " --> pdb=" O ASP B4654 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N PHE B4659 " --> pdb=" O LYS B4655 " (cutoff:3.500A) Processing helix chain 'B' and resid 4662 through 4670 Processing helix chain 'B' and resid 4701 through 4714 removed outlier: 3.716A pdb=" N THR B4714 " --> pdb=" O GLY B4710 " (cutoff:3.500A) Processing helix chain 'B' and resid 4715 through 4734 removed outlier: 4.005A pdb=" N HIS B4732 " --> pdb=" O SER B4728 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TYR B4733 " --> pdb=" O VAL B4729 " (cutoff:3.500A) Processing helix chain 'B' and resid 4735 through 4743 removed outlier: 3.642A pdb=" N PHE B4738 " --> pdb=" O ASN B4735 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA B4740 " --> pdb=" O PHE B4737 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B4743 " --> pdb=" O ALA B4740 " (cutoff:3.500A) Processing helix chain 'B' and resid 4744 through 4749 removed outlier: 3.779A pdb=" N PHE B4749 " --> pdb=" O ILE B4745 " (cutoff:3.500A) Processing helix chain 'B' and resid 4749 through 4762 removed outlier: 3.896A pdb=" N ILE B4755 " --> pdb=" O THR B4751 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER B4758 " --> pdb=" O THR B4754 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL B4759 " --> pdb=" O ILE B4755 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN B4762 " --> pdb=" O SER B4758 " (cutoff:3.500A) Processing helix chain 'B' and resid 4762 through 4788 removed outlier: 3.842A pdb=" N VAL B4767 " --> pdb=" O GLY B4763 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU B4768 " --> pdb=" O LYS B4764 " (cutoff:3.500A) Processing helix chain 'B' and resid 4789 through 4791 No H-bonds generated for 'chain 'B' and resid 4789 through 4791' Processing helix chain 'B' and resid 4807 through 4818 Processing helix chain 'B' and resid 4824 through 4829 removed outlier: 4.279A pdb=" N GLY B4827 " --> pdb=" O GLY B4824 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP B4828 " --> pdb=" O GLY B4825 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B4829 " --> pdb=" O ILE B4826 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4824 through 4829' Processing helix chain 'B' and resid 4838 through 4854 Processing helix chain 'B' and resid 4855 through 4886 removed outlier: 3.672A pdb=" N ILE B4865 " --> pdb=" O ILE B4861 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS B4886 " --> pdb=" O ASP B4882 " (cutoff:3.500A) Processing helix chain 'B' and resid 4893 through 4898 removed outlier: 3.970A pdb=" N PHE B4897 " --> pdb=" O GLY B4893 " (cutoff:3.500A) Processing helix chain 'B' and resid 4902 through 4911 Processing helix chain 'B' and resid 4913 through 4926 Processing helix chain 'B' and resid 4928 through 4932 Processing helix chain 'B' and resid 4933 through 4946 Processing helix chain 'B' and resid 4956 through 4961 Processing helix chain 'C' and resid 249 through 253 removed outlier: 4.338A pdb=" N HIS C 252 " --> pdb=" O SER C 249 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY C 253 " --> pdb=" O GLY C 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 249 through 253' Processing helix chain 'C' and resid 265 through 270 removed outlier: 3.535A pdb=" N VAL C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 435 removed outlier: 4.089A pdb=" N ARG C 414 " --> pdb=" O HIS C 410 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N THR C 415 " --> pdb=" O GLU C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 463 Processing helix chain 'C' and resid 471 through 494 Processing helix chain 'C' and resid 498 through 506 Processing helix chain 'C' and resid 512 through 518 Processing helix chain 'C' and resid 525 through 543 removed outlier: 3.529A pdb=" N GLY C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 563 Processing helix chain 'C' and resid 568 through 582 Processing helix chain 'C' and resid 590 through 604 removed outlier: 3.935A pdb=" N LEU C 601 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP C 602 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 615 removed outlier: 3.692A pdb=" N ASP C 612 " --> pdb=" O HIS C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 618 No H-bonds generated for 'chain 'C' and resid 616 through 618' Processing helix chain 'C' and resid 628 through 636 Processing helix chain 'C' and resid 878 through 901 removed outlier: 4.202A pdb=" N GLY C 901 " --> pdb=" O LYS C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 946 Processing helix chain 'C' and resid 965 through 969 removed outlier: 4.039A pdb=" N ASN C 969 " --> pdb=" O LEU C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1015 removed outlier: 3.854A pdb=" N GLU C 993 " --> pdb=" O THR C 989 " (cutoff:3.500A) Processing helix chain 'C' and resid 1043 through 1060 Processing helix chain 'C' and resid 1092 through 1095 removed outlier: 3.774A pdb=" N ALA C1095 " --> pdb=" O LYS C1092 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1092 through 1095' Processing helix chain 'C' and resid 1230 through 1235 removed outlier: 3.714A pdb=" N GLU C1234 " --> pdb=" O CYS C1230 " (cutoff:3.500A) Processing helix chain 'C' and resid 1643 through 1647 Processing helix chain 'C' and resid 1648 through 1666 removed outlier: 3.588A pdb=" N CYS C1666 " --> pdb=" O TYR C1662 " (cutoff:3.500A) Processing helix chain 'C' and resid 1672 through 1681 removed outlier: 3.522A 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 1711 Processing helix chain 'C' and resid 1713 through 1723 Processing helix chain 'C' and resid 1784 through 1806 removed outlier: 3.859A pdb=" N ALA C1790 " --> pdb=" O ASP C1786 " (cutoff:3.500A) Processing helix chain 'C' and resid 1819 through 1831 Processing helix chain 'C' and resid 1836 through 1848 Processing helix chain 'C' and resid 1898 through 1942 removed outlier: 3.803A pdb=" N ASP C1930 " --> pdb=" O ALA C1926 " (cutoff:3.500A) Processing helix chain 'C' and resid 1952 through 1956 Processing helix chain 'C' and resid 1999 through 2006 removed outlier: 4.049A pdb=" N MET C2003 " --> pdb=" O HIS C1999 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS C2006 " --> pdb=" O LEU C2002 " (cutoff:3.500A) Processing helix chain 'C' and resid 2010 through 2015 Processing helix chain 'C' and resid 2024 through 2036 removed outlier: 3.529A pdb=" N THR C2036 " --> pdb=" O VAL C2032 " (cutoff:3.500A) Processing helix chain 'C' and resid 2056 through 2072 removed outlier: 4.623A pdb=" N SER C2072 " --> pdb=" O TRP C2068 " (cutoff:3.500A) Processing helix chain 'C' and resid 2076 through 2092 removed outlier: 3.630A pdb=" N VAL C2080 " --> pdb=" O ASP C2076 " (cutoff:3.500A) Processing helix chain 'C' and resid 2092 through 2101 Processing helix chain 'C' and resid 2102 through 2104 No H-bonds generated for 'chain 'C' and resid 2102 through 2104' Processing helix chain 'C' and resid 2108 through 2110 No H-bonds generated for 'chain 'C' and resid 2108 through 2110' Processing helix chain 'C' and resid 2111 through 2131 removed outlier: 3.572A pdb=" N LEU C2118 " --> pdb=" O ASP C2114 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER C2130 " --> pdb=" O ARG C2126 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL C2131 " --> pdb=" O SER C2127 " (cutoff:3.500A) Processing helix chain 'C' and resid 2135 through 2150 removed outlier: 3.722A pdb=" N LYS C2139 " --> pdb=" O LYS C2135 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN C2150 " --> pdb=" O GLY C2146 " (cutoff:3.500A) Processing helix chain 'C' and resid 2157 through 2164 Processing helix chain 'C' and resid 2165 through 2179 removed outlier: 3.690A pdb=" N THR C2169 " --> pdb=" O GLY C2165 " (cutoff:3.500A) Processing helix chain 'C' and resid 2190 through 2201 Processing helix chain 'C' and resid 2207 through 2223 removed outlier: 3.652A pdb=" N ASP C2215 " --> pdb=" O LYS C2211 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS C2216 " --> pdb=" O ALA C2212 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER C2218 " --> pdb=" O PHE C2214 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N TYR C2219 " --> pdb=" O ASP C2215 " (cutoff:3.500A) Processing helix chain 'C' and resid 2238 through 2246 removed outlier: 3.706A pdb=" N ALA C2242 " --> pdb=" O PRO C2238 " (cutoff:3.500A) Processing helix chain 'C' and resid 2249 through 2255 Processing helix chain 'C' and resid 2257 through 2270 removed outlier: 4.095A pdb=" N LEU C2261 " --> pdb=" O ARG C2257 " (cutoff:3.500A) Processing helix chain 'C' and resid 2295 through 2306 Processing helix chain 'C' and resid 2312 through 2326 removed outlier: 3.723A pdb=" N VAL C2318 " --> pdb=" O GLU C2314 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG C2326 " --> pdb=" O LEU C2322 " (cutoff:3.500A) Processing helix chain 'C' and resid 2341 through 2354 removed outlier: 4.817A pdb=" N GLU C2347 " --> pdb=" O LEU C2343 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C2354 " --> pdb=" O ILE C2350 " (cutoff:3.500A) Processing helix chain 'C' and resid 2384 through 2402 removed outlier: 4.459A pdb=" N MET C2388 " --> pdb=" O GLY C2384 " (cutoff:3.500A) Processing helix chain 'C' and resid 2414 through 2425 removed outlier: 4.120A pdb=" N ILE C2418 " --> pdb=" O GLU C2414 " (cutoff:3.500A) Processing helix chain 'C' and resid 2434 through 2440 removed outlier: 3.524A pdb=" N GLN C2440 " --> pdb=" O SER C2436 " (cutoff:3.500A) Processing helix chain 'C' and resid 2460 through 2475 removed outlier: 4.063A pdb=" N LYS C2464 " --> pdb=" O CYS C2460 " (cutoff:3.500A) Processing helix chain 'C' and resid 2479 through 2487 removed outlier: 4.000A pdb=" N LEU C2483 " --> pdb=" O VAL C2479 " (cutoff:3.500A) Processing helix chain 'C' and resid 2490 through 2500 removed outlier: 3.639A pdb=" N ASP C2494 " --> pdb=" O GLY C2490 " (cutoff:3.500A) Processing helix chain 'C' and resid 2511 through 2521 Processing helix chain 'C' and resid 2582 through 2592 removed outlier: 4.003A pdb=" N HIS C2586 " --> pdb=" O SER C2582 " (cutoff:3.500A) Processing helix chain 'C' and resid 2599 through 2602 Processing helix chain 'C' and resid 2603 through 2614 removed outlier: 4.119A pdb=" N HIS C2612 " --> pdb=" O LEU C2608 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR C2613 " --> pdb=" O LEU C2609 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU C2614 " --> pdb=" O THR C2610 " (cutoff:3.500A) Processing helix chain 'C' and resid 2615 through 2619 removed outlier: 3.709A pdb=" N TYR C2619 " --> pdb=" O CYS C2616 " (cutoff:3.500A) Processing helix chain 'C' and resid 2621 through 2633 Processing helix chain 'C' and resid 2639 through 2652 removed outlier: 4.035A pdb=" N LEU C2643 " --> pdb=" O LEU C2639 " (cutoff:3.500A) Processing helix chain 'C' and resid 2663 through 2674 removed outlier: 3.524A pdb=" N CYS C2667 " --> pdb=" O LEU C2663 " (cutoff:3.500A) Processing helix chain 'C' and resid 2681 through 2685 removed outlier: 4.274A pdb=" N TYR C2684 " --> pdb=" O GLU C2681 " (cutoff:3.500A) Processing helix chain 'C' and resid 2686 through 2694 removed outlier: 4.293A pdb=" N GLU C2689 " --> pdb=" O SER C2686 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLN C2691 " --> pdb=" O MET C2688 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER C2692 " --> pdb=" O GLU C2689 " (cutoff:3.500A) Processing helix chain 'C' and resid 2718 through 2739 Processing helix chain 'C' and resid 2758 through 2762 Processing helix chain 'C' and resid 2763 through 2785 Proline residue: C2773 - end of helix removed outlier: 3.657A pdb=" N TRP C2784 " --> pdb=" O THR C2780 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY C2785 " --> pdb=" O MET C2781 " (cutoff:3.500A) Processing helix chain 'C' and resid 2791 through 2795 removed outlier: 3.506A pdb=" N GLY C2794 " --> pdb=" O THR C2791 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP C2795 " --> pdb=" O ARG C2792 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2791 through 2795' Processing helix chain 'C' and resid 2833 through 2863 Processing helix chain 'C' and resid 2872 through 2876 Processing helix chain 'C' and resid 2877 through 2897 removed outlier: 3.958A pdb=" N LYS C2883 " --> pdb=" O LYS C2879 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE C2897 " --> pdb=" O LYS C2893 " (cutoff:3.500A) Processing helix chain 'C' and resid 2898 through 2900 No H-bonds generated for 'chain 'C' and resid 2898 through 2900' Processing helix chain 'C' and resid 2990 through 3014 Processing helix chain 'C' and resid 3036 through 3050 removed outlier: 3.974A pdb=" N ASP C3050 " --> pdb=" O LYS C3046 " (cutoff:3.500A) Processing helix chain 'C' and resid 3054 through 3063 removed outlier: 3.503A pdb=" N ALA C3063 " --> pdb=" O PHE C3059 " (cutoff:3.500A) Processing helix chain 'C' and resid 3065 through 3084 removed outlier: 4.404A pdb=" N LYS C3069 " --> pdb=" O GLU C3065 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER C3084 " --> pdb=" O THR C3080 " (cutoff:3.500A) Processing helix chain 'C' and resid 3090 through 3099 Processing helix chain 'C' and resid 3183 through 3193 Processing helix chain 'C' and resid 3214 through 3225 removed outlier: 4.229A pdb=" N ILE C3218 " --> pdb=" O MET C3214 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU C3222 " --> pdb=" O ILE C3218 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER C3223 " --> pdb=" O GLU C3219 " (cutoff:3.500A) Processing helix chain 'C' and resid 3237 through 3252 Processing helix chain 'C' and resid 3283 through 3292 Processing helix chain 'C' and resid 3308 through 3324 Proline residue: C3320 - end of helix Processing helix chain 'C' and resid 3331 through 3344 Processing helix chain 'C' and resid 3355 through 3375 Proline residue: C3370 - end of helix Processing helix chain 'C' and resid 3405 through 3431 removed outlier: 4.251A pdb=" N ILE C3431 " --> pdb=" O MET C3427 " (cutoff:3.500A) Processing helix chain 'C' and resid 3436 through 3472 removed outlier: 3.777A pdb=" N LYS C3440 " --> pdb=" O SER C3436 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG C3457 " --> pdb=" O ARG C3453 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER C3463 " --> pdb=" O SER C3459 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LEU C3464 " --> pdb=" O MET C3460 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ARG C3471 " --> pdb=" O ALA C3467 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU C3472 " --> pdb=" O ALA C3468 " (cutoff:3.500A) Processing helix chain 'C' and resid 3474 through 3493 Proline residue: C3482 - end of helix removed outlier: 4.329A pdb=" N ASN C3493 " --> pdb=" O ALA C3489 " (cutoff:3.500A) Processing helix chain 'C' and resid 3495 through 3508 removed outlier: 4.130A pdb=" N GLU C3502 " --> pdb=" O LYS C3498 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU C3503 " --> pdb=" O ASP C3499 " (cutoff:3.500A) Processing helix chain 'C' and resid 3557 through 3566 removed outlier: 3.759A pdb=" N TYR C3566 " --> pdb=" O GLN C3562 " (cutoff:3.500A) Processing helix chain 'C' and resid 3614 through 3643 removed outlier: 3.553A pdb=" N LEU C3618 " --> pdb=" O ARG C3614 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE C3628 " --> pdb=" O GLU C3624 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLU C3629 " --> pdb=" O LYS C3625 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THR C3630 " --> pdb=" O SER C3626 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU C3631 " --> pdb=" O TRP C3627 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP C3637 " --> pdb=" O HIS C3633 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LYS C3638 " --> pdb=" O TYR C3634 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU C3639 " --> pdb=" O PHE C3635 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE C3640 " --> pdb=" O GLU C3636 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU C3641 " --> pdb=" O ASP C3637 " (cutoff:3.500A) Processing helix chain 'C' and resid 3661 through 3676 removed outlier: 3.914A pdb=" N GLN C3665 " --> pdb=" O ASP C3661 " (cutoff:3.500A) Processing helix chain 'C' and resid 3684 through 3699 Processing helix chain 'C' and resid 3715 through 3732 Processing helix chain 'C' and resid 3734 through 3746 removed outlier: 3.789A pdb=" N SER C3746 " --> pdb=" O THR C3742 " (cutoff:3.500A) Processing helix chain 'C' and resid 3751 through 3765 Processing helix chain 'C' and resid 3770 through 3784 Processing helix chain 'C' and resid 3786 through 3798 removed outlier: 3.653A pdb=" N GLN C3790 " --> pdb=" O VAL C3786 " (cutoff:3.500A) Processing helix chain 'C' and resid 3803 through 3812 removed outlier: 3.655A pdb=" N LYS C3812 " --> pdb=" O GLU C3808 " (cutoff:3.500A) Processing helix chain 'C' and resid 3832 through 3847 Processing helix chain 'C' and resid 3850 through 3857 removed outlier: 3.525A pdb=" N LEU C3857 " --> pdb=" O PHE C3853 " (cutoff:3.500A) Processing helix chain 'C' and resid 3868 through 3892 removed outlier: 3.620A pdb=" N SER C3872 " --> pdb=" O ASN C3868 " (cutoff:3.500A) Processing helix chain 'C' and resid 3898 through 3923 removed outlier: 3.512A 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 3960 removed outlier: 3.694A pdb=" N ALA C3942 " --> pdb=" O ARG C3938 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N HIS C3952 " --> pdb=" O HIS C3948 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N MET C3955 " --> pdb=" O ALA C3951 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN C3959 " --> pdb=" O MET C3955 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP C3960 " --> pdb=" O LYS C3956 " (cutoff:3.500A) Processing helix chain 'C' and resid 3964 through 3985 removed outlier: 4.074A pdb=" N LEU C3985 " --> pdb=" O LEU C3981 " (cutoff:3.500A) Processing helix chain 'C' and resid 3992 through 4005 Processing helix chain 'C' and resid 4005 through 4014 Processing helix chain 'C' and resid 4026 through 4030 removed outlier: 3.557A pdb=" N ASP C4029 " --> pdb=" O THR C4026 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N THR C4030 " --> pdb=" O SER C4027 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4026 through 4030' Processing helix chain 'C' and resid 4044 through 4051 removed outlier: 3.903A pdb=" N MET C4051 " --> pdb=" O PHE C4047 " (cutoff:3.500A) Processing helix chain 'C' and resid 4061 through 4069 removed outlier: 3.662A pdb=" N LEU C4065 " --> pdb=" O GLU C4061 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU C4066 " --> pdb=" O THR C4062 " (cutoff:3.500A) Processing helix chain 'C' and resid 4080 through 4085 removed outlier: 3.591A pdb=" N ARG C4085 " --> pdb=" O GLU C4081 " (cutoff:3.500A) Processing helix chain 'C' and resid 4092 through 4108 Processing helix chain 'C' and resid 4111 through 4121 removed outlier: 3.897A pdb=" N THR C4116 " --> pdb=" O THR C4112 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE C4117 " --> pdb=" O ARG C4113 " (cutoff:3.500A) Processing helix chain 'C' and resid 4121 through 4128 removed outlier: 3.508A pdb=" N LEU C4125 " --> pdb=" O ALA C4121 " (cutoff:3.500A) Processing helix chain 'C' and resid 4152 through 4159 Processing helix chain 'C' and resid 4161 through 4179 Processing helix chain 'C' and resid 4181 through 4204 removed outlier: 3.794A pdb=" N MET C4185 " --> pdb=" O GLU C4181 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU C4186 " --> pdb=" O LYS C4182 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLN C4204 " --> pdb=" O GLN C4200 " (cutoff:3.500A) Processing helix chain 'C' and resid 4484 through 4496 removed outlier: 3.549A pdb=" N ASN C4496 " --> pdb=" O TYR C4492 " (cutoff:3.500A) Processing helix chain 'C' and resid 4496 through 4516 Processing helix chain 'C' and resid 4569 through 4593 Processing helix chain 'C' and resid 4593 through 4612 removed outlier: 3.743A pdb=" N VAL C4597 " --> pdb=" O LYS C4593 " (cutoff:3.500A) Processing helix chain 'C' and resid 4624 through 4631 Processing helix chain 'C' and resid 4647 through 4661 removed outlier: 5.655A pdb=" N GLU C4658 " --> pdb=" O ASP C4654 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N PHE C4659 " --> pdb=" O LYS C4655 " (cutoff:3.500A) Processing helix chain 'C' and resid 4662 through 4670 Processing helix chain 'C' and resid 4701 through 4714 removed outlier: 3.717A pdb=" N THR C4714 " --> pdb=" O GLY C4710 " (cutoff:3.500A) Processing helix chain 'C' and resid 4715 through 4734 removed outlier: 4.005A pdb=" N HIS C4732 " --> pdb=" O SER C4728 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR C4733 " --> pdb=" O VAL C4729 " (cutoff:3.500A) Processing helix chain 'C' and resid 4735 through 4743 removed outlier: 3.642A pdb=" N PHE C4738 " --> pdb=" O ASN C4735 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA C4740 " --> pdb=" O PHE C4737 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU C4743 " --> pdb=" O ALA C4740 " (cutoff:3.500A) Processing helix chain 'C' and resid 4744 through 4749 removed outlier: 3.779A pdb=" N PHE C4749 " --> pdb=" O ILE C4745 " (cutoff:3.500A) Processing helix chain 'C' and resid 4749 through 4762 removed outlier: 3.895A pdb=" N ILE C4755 " --> pdb=" O THR C4751 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER C4758 " --> pdb=" O THR C4754 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL C4759 " --> pdb=" O ILE C4755 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN C4762 " --> pdb=" O SER C4758 " (cutoff:3.500A) Processing helix chain 'C' and resid 4762 through 4788 removed outlier: 3.843A pdb=" N VAL C4767 " --> pdb=" O GLY C4763 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU C4768 " --> pdb=" O LYS C4764 " (cutoff:3.500A) Processing helix chain 'C' and resid 4789 through 4791 No H-bonds generated for 'chain 'C' and resid 4789 through 4791' Processing helix chain 'C' and resid 4807 through 4818 Processing helix chain 'C' and resid 4824 through 4829 removed outlier: 4.279A pdb=" N GLY C4827 " --> pdb=" O GLY C4824 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP C4828 " --> pdb=" O GLY C4825 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU C4829 " --> pdb=" O ILE C4826 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4824 through 4829' Processing helix chain 'C' and resid 4838 through 4854 Processing helix chain 'C' and resid 4855 through 4886 removed outlier: 3.672A pdb=" N ILE C4865 " --> pdb=" O ILE C4861 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS C4886 " --> pdb=" O ASP C4882 " (cutoff:3.500A) Processing helix chain 'C' and resid 4893 through 4898 removed outlier: 3.970A pdb=" N PHE C4897 " --> pdb=" O GLY C4893 " (cutoff:3.500A) Processing helix chain 'C' and resid 4902 through 4911 Processing helix chain 'C' and resid 4913 through 4926 Processing helix chain 'C' and resid 4928 through 4932 Processing helix chain 'C' and resid 4933 through 4946 Processing helix chain 'C' and resid 4956 through 4961 Processing helix chain 'D' and resid 249 through 253 removed outlier: 4.338A pdb=" N HIS D 252 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLY D 253 " --> pdb=" O GLY D 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 249 through 253' Processing helix chain 'D' and resid 265 through 270 removed outlier: 3.535A pdb=" N VAL D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 435 removed outlier: 4.088A pdb=" N ARG D 414 " --> pdb=" O HIS D 410 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N THR D 415 " --> pdb=" O GLU D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 463 Processing helix chain 'D' and resid 471 through 494 Processing helix chain 'D' and resid 498 through 506 Processing helix chain 'D' and resid 512 through 518 Processing helix chain 'D' and resid 525 through 543 removed outlier: 3.528A pdb=" N GLY D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 563 Processing helix chain 'D' and resid 568 through 582 Processing helix chain 'D' and resid 590 through 604 removed outlier: 3.935A pdb=" N LEU D 601 " --> pdb=" O ILE D 597 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP D 602 " --> pdb=" O ILE D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 615 removed outlier: 3.692A pdb=" N ASP D 612 " --> pdb=" O HIS D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 618 No H-bonds generated for 'chain 'D' and resid 616 through 618' Processing helix chain 'D' and resid 628 through 636 Processing helix chain 'D' and resid 878 through 901 removed outlier: 4.201A pdb=" N GLY D 901 " --> pdb=" O LYS D 897 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 946 Processing helix chain 'D' and resid 965 through 969 removed outlier: 4.037A pdb=" N ASN D 969 " --> pdb=" O LEU D 966 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 1015 removed outlier: 3.854A pdb=" N GLU D 993 " --> pdb=" O THR D 989 " (cutoff:3.500A) Processing helix chain 'D' and resid 1043 through 1060 Processing helix chain 'D' and resid 1092 through 1095 removed outlier: 3.773A pdb=" N ALA D1095 " --> pdb=" O LYS D1092 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1092 through 1095' Processing helix chain 'D' and resid 1230 through 1235 removed outlier: 3.713A pdb=" N GLU D1234 " --> pdb=" O CYS D1230 " (cutoff:3.500A) Processing helix chain 'D' and resid 1643 through 1647 Processing helix chain 'D' and resid 1648 through 1666 removed outlier: 3.588A pdb=" N CYS D1666 " --> pdb=" O TYR D1662 " (cutoff:3.500A) Processing helix chain 'D' and resid 1672 through 1681 removed outlier: 3.522A 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 1711 Processing helix chain 'D' and resid 1713 through 1723 Processing helix chain 'D' and resid 1784 through 1806 removed outlier: 3.860A pdb=" N ALA D1790 " --> pdb=" O ASP D1786 " (cutoff:3.500A) Processing helix chain 'D' and resid 1819 through 1831 Processing helix chain 'D' and resid 1836 through 1848 Processing helix chain 'D' and resid 1898 through 1942 removed outlier: 3.803A pdb=" N ASP D1930 " --> pdb=" O ALA D1926 " (cutoff:3.500A) Processing helix chain 'D' and resid 1952 through 1956 Processing helix chain 'D' and resid 1999 through 2006 removed outlier: 4.050A pdb=" N MET D2003 " --> pdb=" O HIS D1999 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS D2006 " --> pdb=" O LEU D2002 " (cutoff:3.500A) Processing helix chain 'D' and resid 2010 through 2015 Processing helix chain 'D' and resid 2024 through 2036 removed outlier: 3.529A pdb=" N THR D2036 " --> pdb=" O VAL D2032 " (cutoff:3.500A) Processing helix chain 'D' and resid 2056 through 2072 removed outlier: 4.624A pdb=" N SER D2072 " --> pdb=" O TRP D2068 " (cutoff:3.500A) Processing helix chain 'D' and resid 2076 through 2092 removed outlier: 3.630A pdb=" N VAL D2080 " --> pdb=" O ASP D2076 " (cutoff:3.500A) Processing helix chain 'D' and resid 2092 through 2101 Processing helix chain 'D' and resid 2102 through 2104 No H-bonds generated for 'chain 'D' and resid 2102 through 2104' Processing helix chain 'D' and resid 2108 through 2110 No H-bonds generated for 'chain 'D' and resid 2108 through 2110' Processing helix chain 'D' and resid 2111 through 2131 removed outlier: 3.574A pdb=" N LEU D2118 " --> pdb=" O ASP D2114 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER D2130 " --> pdb=" O ARG D2126 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL D2131 " --> pdb=" O SER D2127 " (cutoff:3.500A) Processing helix chain 'D' and resid 2135 through 2150 removed outlier: 3.722A pdb=" N LYS D2139 " --> pdb=" O LYS D2135 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN D2150 " --> pdb=" O GLY D2146 " (cutoff:3.500A) Processing helix chain 'D' and resid 2157 through 2164 Processing helix chain 'D' and resid 2165 through 2179 removed outlier: 3.691A pdb=" N THR D2169 " --> pdb=" O GLY D2165 " (cutoff:3.500A) Processing helix chain 'D' and resid 2190 through 2201 Processing helix chain 'D' and resid 2207 through 2223 removed outlier: 3.652A pdb=" N ASP D2215 " --> pdb=" O LYS D2211 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS D2216 " --> pdb=" O ALA D2212 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER D2218 " --> pdb=" O PHE D2214 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N TYR D2219 " --> pdb=" O ASP D2215 " (cutoff:3.500A) Processing helix chain 'D' and resid 2238 through 2246 removed outlier: 3.707A pdb=" N ALA D2242 " --> pdb=" O PRO D2238 " (cutoff:3.500A) Processing helix chain 'D' and resid 2249 through 2255 Processing helix chain 'D' and resid 2257 through 2270 removed outlier: 4.095A pdb=" N LEU D2261 " --> pdb=" O ARG D2257 " (cutoff:3.500A) Processing helix chain 'D' and resid 2295 through 2306 Processing helix chain 'D' and resid 2312 through 2326 removed outlier: 3.721A pdb=" N VAL D2318 " --> pdb=" O GLU D2314 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG D2326 " --> pdb=" O LEU D2322 " (cutoff:3.500A) Processing helix chain 'D' and resid 2341 through 2354 removed outlier: 4.817A pdb=" N GLU D2347 " --> pdb=" O LEU D2343 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU D2354 " --> pdb=" O ILE D2350 " (cutoff:3.500A) Processing helix chain 'D' and resid 2384 through 2402 removed outlier: 4.460A pdb=" N MET D2388 " --> pdb=" O GLY D2384 " (cutoff:3.500A) Processing helix chain 'D' and resid 2414 through 2425 removed outlier: 4.120A pdb=" N ILE D2418 " --> pdb=" O GLU D2414 " (cutoff:3.500A) Processing helix chain 'D' and resid 2434 through 2440 removed outlier: 3.524A pdb=" N GLN D2440 " --> pdb=" O SER D2436 " (cutoff:3.500A) Processing helix chain 'D' and resid 2460 through 2475 removed outlier: 4.063A pdb=" N LYS D2464 " --> pdb=" O CYS D2460 " (cutoff:3.500A) Processing helix chain 'D' and resid 2479 through 2487 removed outlier: 4.000A pdb=" N LEU D2483 " --> pdb=" O VAL D2479 " (cutoff:3.500A) Processing helix chain 'D' and resid 2490 through 2500 removed outlier: 3.639A pdb=" N ASP D2494 " --> pdb=" O GLY D2490 " (cutoff:3.500A) Processing helix chain 'D' and resid 2511 through 2521 Processing helix chain 'D' and resid 2582 through 2592 removed outlier: 4.001A pdb=" N HIS D2586 " --> pdb=" O SER D2582 " (cutoff:3.500A) Processing helix chain 'D' and resid 2599 through 2602 Processing helix chain 'D' and resid 2603 through 2614 removed outlier: 4.119A pdb=" N HIS D2612 " --> pdb=" O LEU D2608 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR D2613 " --> pdb=" O LEU D2609 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU D2614 " --> pdb=" O THR D2610 " (cutoff:3.500A) Processing helix chain 'D' and resid 2615 through 2619 removed outlier: 3.709A pdb=" N TYR D2619 " --> pdb=" O CYS D2616 " (cutoff:3.500A) Processing helix chain 'D' and resid 2621 through 2633 Processing helix chain 'D' and resid 2639 through 2652 removed outlier: 4.035A pdb=" N LEU D2643 " --> pdb=" O LEU D2639 " (cutoff:3.500A) Processing helix chain 'D' and resid 2663 through 2674 removed outlier: 3.524A pdb=" N CYS D2667 " --> pdb=" O LEU D2663 " (cutoff:3.500A) Processing helix chain 'D' and resid 2681 through 2685 removed outlier: 4.274A pdb=" N TYR D2684 " --> pdb=" O GLU D2681 " (cutoff:3.500A) Processing helix chain 'D' and resid 2686 through 2694 removed outlier: 4.294A pdb=" N GLU D2689 " --> pdb=" O SER D2686 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLN D2691 " --> pdb=" O MET D2688 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER D2692 " --> pdb=" O GLU D2689 " (cutoff:3.500A) Processing helix chain 'D' and resid 2718 through 2739 Processing helix chain 'D' and resid 2758 through 2762 Processing helix chain 'D' and resid 2763 through 2785 Proline residue: D2773 - end of helix removed outlier: 3.658A pdb=" N TRP D2784 " --> pdb=" O THR D2780 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY D2785 " --> pdb=" O MET D2781 " (cutoff:3.500A) Processing helix chain 'D' and resid 2791 through 2795 removed outlier: 3.506A pdb=" N GLY D2794 " --> pdb=" O THR D2791 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP D2795 " --> pdb=" O ARG D2792 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2791 through 2795' Processing helix chain 'D' and resid 2833 through 2863 Processing helix chain 'D' and resid 2872 through 2876 Processing helix chain 'D' and resid 2877 through 2897 removed outlier: 3.959A pdb=" N LYS D2883 " --> pdb=" O LYS D2879 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE D2897 " --> pdb=" O LYS D2893 " (cutoff:3.500A) Processing helix chain 'D' and resid 2898 through 2900 No H-bonds generated for 'chain 'D' and resid 2898 through 2900' Processing helix chain 'D' and resid 2990 through 3014 Processing helix chain 'D' and resid 3036 through 3050 removed outlier: 3.973A pdb=" N ASP D3050 " --> pdb=" O LYS D3046 " (cutoff:3.500A) Processing helix chain 'D' and resid 3054 through 3063 removed outlier: 3.504A pdb=" N ALA D3063 " --> pdb=" O PHE D3059 " (cutoff:3.500A) Processing helix chain 'D' and resid 3065 through 3084 removed outlier: 4.404A pdb=" N LYS D3069 " --> pdb=" O GLU D3065 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER D3084 " --> pdb=" O THR D3080 " (cutoff:3.500A) Processing helix chain 'D' and resid 3090 through 3099 Processing helix chain 'D' and resid 3183 through 3193 Processing helix chain 'D' and resid 3214 through 3225 removed outlier: 4.229A pdb=" N ILE D3218 " --> pdb=" O MET D3214 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU D3222 " --> pdb=" O ILE D3218 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER D3223 " --> pdb=" O GLU D3219 " (cutoff:3.500A) Processing helix chain 'D' and resid 3237 through 3252 Processing helix chain 'D' and resid 3283 through 3292 Processing helix chain 'D' and resid 3303 through 3307 removed outlier: 3.593A pdb=" N ASN D3307 " --> pdb=" O PRO D3304 " (cutoff:3.500A) Processing helix chain 'D' and resid 3308 through 3324 Proline residue: D3320 - end of helix Processing helix chain 'D' and resid 3331 through 3344 Processing helix chain 'D' and resid 3355 through 3375 Proline residue: D3370 - end of helix Processing helix chain 'D' and resid 3405 through 3431 removed outlier: 4.251A pdb=" N ILE D3431 " --> pdb=" O MET D3427 " (cutoff:3.500A) Processing helix chain 'D' and resid 3436 through 3472 removed outlier: 3.777A pdb=" N LYS D3440 " --> pdb=" O SER D3436 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG D3457 " --> pdb=" O ARG D3453 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER D3463 " --> pdb=" O SER D3459 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LEU D3464 " --> pdb=" O MET D3460 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ARG D3471 " --> pdb=" O ALA D3467 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU D3472 " --> pdb=" O ALA D3468 " (cutoff:3.500A) Processing helix chain 'D' and resid 3474 through 3493 Proline residue: D3482 - end of helix removed outlier: 4.329A pdb=" N ASN D3493 " --> pdb=" O ALA D3489 " (cutoff:3.500A) Processing helix chain 'D' and resid 3495 through 3508 removed outlier: 4.129A pdb=" N GLU D3502 " --> pdb=" O LYS D3498 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU D3503 " --> pdb=" O ASP D3499 " (cutoff:3.500A) Processing helix chain 'D' and resid 3557 through 3566 removed outlier: 3.760A pdb=" N TYR D3566 " --> pdb=" O GLN D3562 " (cutoff:3.500A) Processing helix chain 'D' and resid 3614 through 3643 removed outlier: 3.553A pdb=" N LEU D3618 " --> pdb=" O ARG D3614 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE D3628 " --> pdb=" O GLU D3624 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLU D3629 " --> pdb=" O LYS D3625 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N THR D3630 " --> pdb=" O SER D3626 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU D3631 " --> pdb=" O TRP D3627 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP D3637 " --> pdb=" O HIS D3633 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LYS D3638 " --> pdb=" O TYR D3634 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU D3639 " --> pdb=" O PHE D3635 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE D3640 " --> pdb=" O GLU D3636 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU D3641 " --> pdb=" O ASP D3637 " (cutoff:3.500A) Processing helix chain 'D' and resid 3661 through 3676 removed outlier: 3.913A pdb=" N GLN D3665 " --> pdb=" O ASP D3661 " (cutoff:3.500A) Processing helix chain 'D' and resid 3684 through 3699 Processing helix chain 'D' and resid 3715 through 3732 Processing helix chain 'D' and resid 3734 through 3746 removed outlier: 3.789A pdb=" N SER D3746 " --> pdb=" O THR D3742 " (cutoff:3.500A) Processing helix chain 'D' and resid 3751 through 3765 Processing helix chain 'D' and resid 3770 through 3784 Processing helix chain 'D' and resid 3786 through 3798 removed outlier: 3.653A pdb=" N GLN D3790 " --> pdb=" O VAL D3786 " (cutoff:3.500A) Processing helix chain 'D' and resid 3803 through 3812 removed outlier: 3.655A pdb=" N LYS D3812 " --> pdb=" O GLU D3808 " (cutoff:3.500A) Processing helix chain 'D' and resid 3832 through 3847 Processing helix chain 'D' and resid 3850 through 3857 removed outlier: 3.525A pdb=" N LEU D3857 " --> pdb=" O PHE D3853 " (cutoff:3.500A) Processing helix chain 'D' and resid 3868 through 3892 removed outlier: 3.622A pdb=" N SER D3872 " --> pdb=" O ASN D3868 " (cutoff:3.500A) Processing helix chain 'D' and resid 3898 through 3923 removed outlier: 3.512A 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 3960 removed outlier: 3.694A pdb=" N ALA D3942 " --> pdb=" O ARG D3938 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N HIS D3952 " --> pdb=" O HIS D3948 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N MET D3955 " --> pdb=" O ALA D3951 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN D3959 " --> pdb=" O MET D3955 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP D3960 " --> pdb=" O LYS D3956 " (cutoff:3.500A) Processing helix chain 'D' and resid 3964 through 3985 removed outlier: 4.075A pdb=" N LEU D3985 " --> pdb=" O LEU D3981 " (cutoff:3.500A) Processing helix chain 'D' and resid 3992 through 4005 Processing helix chain 'D' and resid 4005 through 4014 Processing helix chain 'D' and resid 4026 through 4030 removed outlier: 3.557A pdb=" N ASP D4029 " --> pdb=" O THR D4026 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N THR D4030 " --> pdb=" O SER D4027 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4026 through 4030' Processing helix chain 'D' and resid 4044 through 4051 removed outlier: 3.904A pdb=" N MET D4051 " --> pdb=" O PHE D4047 " (cutoff:3.500A) Processing helix chain 'D' and resid 4061 through 4069 removed outlier: 3.661A pdb=" N LEU D4065 " --> pdb=" O GLU D4061 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU D4066 " --> pdb=" O THR D4062 " (cutoff:3.500A) Processing helix chain 'D' and resid 4080 through 4085 removed outlier: 3.590A pdb=" N ARG D4085 " --> pdb=" O GLU D4081 " (cutoff:3.500A) Processing helix chain 'D' and resid 4092 through 4108 Processing helix chain 'D' and resid 4111 through 4121 removed outlier: 3.897A pdb=" N THR D4116 " --> pdb=" O THR D4112 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE D4117 " --> pdb=" O ARG D4113 " (cutoff:3.500A) Processing helix chain 'D' and resid 4121 through 4128 removed outlier: 3.508A pdb=" N LEU D4125 " --> pdb=" O ALA D4121 " (cutoff:3.500A) Processing helix chain 'D' and resid 4152 through 4159 Processing helix chain 'D' and resid 4161 through 4179 Processing helix chain 'D' and resid 4181 through 4204 removed outlier: 3.795A pdb=" N MET D4185 " --> pdb=" O GLU D4181 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU D4186 " --> pdb=" O LYS D4182 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN D4204 " --> pdb=" O GLN D4200 " (cutoff:3.500A) Processing helix chain 'D' and resid 4484 through 4496 removed outlier: 3.547A pdb=" N ASN D4496 " --> pdb=" O TYR D4492 " (cutoff:3.500A) Processing helix chain 'D' and resid 4496 through 4516 Processing helix chain 'D' and resid 4569 through 4593 Processing helix chain 'D' and resid 4593 through 4612 removed outlier: 3.743A pdb=" N VAL D4597 " --> pdb=" O LYS D4593 " (cutoff:3.500A) Processing helix chain 'D' and resid 4624 through 4631 Processing helix chain 'D' and resid 4647 through 4661 removed outlier: 5.655A pdb=" N GLU D4658 " --> pdb=" O ASP D4654 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N PHE D4659 " --> pdb=" O LYS D4655 " (cutoff:3.500A) Processing helix chain 'D' and resid 4662 through 4670 Processing helix chain 'D' and resid 4701 through 4714 removed outlier: 3.716A pdb=" N THR D4714 " --> pdb=" O GLY D4710 " (cutoff:3.500A) Processing helix chain 'D' and resid 4715 through 4734 removed outlier: 4.006A pdb=" N HIS D4732 " --> pdb=" O SER D4728 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR D4733 " --> pdb=" O VAL D4729 " (cutoff:3.500A) Processing helix chain 'D' and resid 4735 through 4743 removed outlier: 3.642A pdb=" N PHE D4738 " --> pdb=" O ASN D4735 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA D4740 " --> pdb=" O PHE D4737 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU D4743 " --> pdb=" O ALA D4740 " (cutoff:3.500A) Processing helix chain 'D' and resid 4744 through 4749 removed outlier: 3.779A pdb=" N PHE D4749 " --> pdb=" O ILE D4745 " (cutoff:3.500A) Processing helix chain 'D' and resid 4749 through 4762 removed outlier: 3.895A pdb=" N ILE D4755 " --> pdb=" O THR D4751 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER D4758 " --> pdb=" O THR D4754 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL D4759 " --> pdb=" O ILE D4755 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN D4762 " --> pdb=" O SER D4758 " (cutoff:3.500A) Processing helix chain 'D' and resid 4762 through 4788 removed outlier: 3.842A pdb=" N VAL D4767 " --> pdb=" O GLY D4763 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU D4768 " --> pdb=" O LYS D4764 " (cutoff:3.500A) Processing helix chain 'D' and resid 4789 through 4791 No H-bonds generated for 'chain 'D' and resid 4789 through 4791' Processing helix chain 'D' and resid 4807 through 4818 Processing helix chain 'D' and resid 4824 through 4829 removed outlier: 4.279A pdb=" N GLY D4827 " --> pdb=" O GLY D4824 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP D4828 " --> pdb=" O GLY D4825 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU D4829 " --> pdb=" O ILE D4826 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4824 through 4829' Processing helix chain 'D' and resid 4838 through 4854 Processing helix chain 'D' and resid 4855 through 4886 removed outlier: 3.672A pdb=" N ILE D4865 " --> pdb=" O ILE D4861 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS D4886 " --> pdb=" O ASP D4882 " (cutoff:3.500A) Processing helix chain 'D' and resid 4893 through 4898 removed outlier: 3.969A pdb=" N PHE D4897 " --> pdb=" O GLY D4893 " (cutoff:3.500A) Processing helix chain 'D' and resid 4902 through 4911 Processing helix chain 'D' and resid 4913 through 4926 Processing helix chain 'D' and resid 4928 through 4932 Processing helix chain 'D' and resid 4933 through 4946 Processing helix chain 'D' and resid 4956 through 4961 Processing helix chain 'E' and resid 31 through 35 removed outlier: 4.140A pdb=" N GLY E 34 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 64 removed outlier: 3.990A pdb=" N GLU E 61 " --> pdb=" O ILE E 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 35 removed outlier: 4.140A pdb=" N GLY F 34 " --> pdb=" O LEU F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 64 removed outlier: 3.989A pdb=" N GLU F 61 " --> pdb=" O ILE F 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 35 removed outlier: 4.140A pdb=" N GLY G 34 " --> pdb=" O LEU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 64 removed outlier: 3.989A pdb=" N GLU G 61 " --> pdb=" O ILE G 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 35 removed outlier: 4.141A pdb=" N GLY H 34 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 64 removed outlier: 3.989A pdb=" N GLU H 61 " --> pdb=" O ILE H 57 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 removed outlier: 5.573A pdb=" N LEU A 69 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ARG A 122 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLN A 71 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 38 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 131 removed outlier: 3.571A pdb=" N GLN A 150 " --> pdb=" O TYR A 129 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N CYS A 131 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY A 148 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 193 Processing sheet with id=AA4, first strand: chain 'A' and resid 233 through 237 removed outlier: 3.695A 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 removed outlier: 3.811A pdb=" N CYS A 244 " --> pdb=" O GLU A 263 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 263 " --> pdb=" O CYS A 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 371 through 374 removed outlier: 3.515A pdb=" N ILE A 392 " --> pdb=" O THR A 373 " (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 Processing sheet with id=AA9, first strand: chain 'A' and resid 755 through 756 removed outlier: 3.711A pdb=" N ILE A 755 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 677 " --> pdb=" O ILE A 755 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL A 800 " --> pdb=" O VAL A1620 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL A1620 " --> pdb=" O VAL A 800 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A1621 " --> pdb=" O ILE A1612 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE A1612 " --> pdb=" O GLN A1621 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 769 through 770 Processing sheet with id=AB2, first strand: chain 'A' and resid 778 through 780 removed outlier: 4.334A pdb=" N MET A 778 " --> pdb=" O THR A1468 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A1468 " --> pdb=" O MET A 778 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU A 780 " --> pdb=" O THR A1466 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 849 through 851 Processing sheet with id=AB4, first strand: chain 'A' and resid 903 through 904 removed outlier: 6.419A pdb=" N GLN A 903 " --> pdb=" O HIS A 915 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1116 through 1118 removed outlier: 3.700A pdb=" N ALA A1090 " --> pdb=" O PRO A1203 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG A1086 " --> pdb=" O LEU A1207 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ILE A1087 " --> pdb=" O SER A1252 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1101 through 1102 Processing sheet with id=AB7, first strand: chain 'A' and resid 1136 through 1138 removed outlier: 3.753A pdb=" N ALA A1136 " --> pdb=" O TRP A1145 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A1138 " --> pdb=" O GLN A1143 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU A1150 " --> pdb=" O ARG A1144 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1172 through 1173 removed outlier: 3.808A pdb=" N PHE A1192 " --> pdb=" O MET A1173 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1176 through 1177 Processing sheet with id=AC1, first strand: chain 'A' and resid 1301 through 1303 Processing sheet with id=AC2, first strand: chain 'A' and resid 1443 through 1445 removed outlier: 3.690A pdb=" N VAL A1443 " --> pdb=" O CYS A1489 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N MET A1487 " --> pdb=" O TRP A1445 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 2787 through 2788 removed outlier: 3.659A pdb=" N SER A2903 " --> pdb=" O ARG A2787 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 4132 through 4138 removed outlier: 3.760A pdb=" N PHE A4149 " --> pdb=" O GLY A4133 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 4518 through 4519 Processing sheet with id=AC6, first strand: chain 'A' and resid 4793 through 4794 removed outlier: 4.176A pdb=" N MET A4803 " --> pdb=" O LYS A4794 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 19 through 20 removed outlier: 5.573A pdb=" N LEU B 69 " --> pdb=" O ARG B 122 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ARG B 122 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLN B 71 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 38 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 129 through 131 removed outlier: 3.570A pdb=" N GLN B 150 " --> pdb=" O TYR B 129 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N CYS B 131 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY B 148 " --> pdb=" O CYS B 131 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 191 through 193 Processing sheet with id=AD1, first strand: chain 'B' and resid 233 through 237 removed outlier: 3.695A pdb=" N ARG B 296 " --> pdb=" O GLU B 278 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 243 through 246 removed outlier: 3.812A pdb=" N CYS B 244 " --> pdb=" O GLU B 263 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU B 263 " --> pdb=" O CYS B 244 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 371 through 374 removed outlier: 3.514A pdb=" N ILE B 392 " --> pdb=" O THR B 373 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 648 through 650 Processing sheet with id=AD5, first strand: chain 'B' and resid 653 through 655 Processing sheet with id=AD6, first strand: chain 'B' and resid 755 through 756 removed outlier: 3.711A pdb=" N ILE B 755 " --> pdb=" O LEU B 677 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 677 " --> pdb=" O ILE B 755 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL B 800 " --> pdb=" O VAL B1620 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL B1620 " --> pdb=" O VAL B 800 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN B1621 " --> pdb=" O ILE B1612 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE B1612 " --> pdb=" O GLN B1621 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 769 through 770 Processing sheet with id=AD8, first strand: chain 'B' and resid 778 through 780 removed outlier: 4.333A pdb=" N MET B 778 " --> pdb=" O THR B1468 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR B1468 " --> pdb=" O MET B 778 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU B 780 " --> pdb=" O THR B1466 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 849 through 851 Processing sheet with id=AE1, first strand: chain 'B' and resid 903 through 904 removed outlier: 6.419A pdb=" N GLN B 903 " --> pdb=" O HIS B 915 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'B' and resid 1116 through 1118 removed outlier: 3.699A pdb=" N ALA B1090 " --> pdb=" O PRO B1203 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG B1086 " --> pdb=" O LEU B1207 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ILE B1087 " --> pdb=" O SER B1252 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1101 through 1102 Processing sheet with id=AE4, first strand: chain 'B' and resid 1136 through 1138 removed outlier: 3.753A pdb=" N ALA B1136 " --> pdb=" O TRP B1145 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP B1138 " --> pdb=" O GLN B1143 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU B1150 " --> pdb=" O ARG B1144 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 1172 through 1173 removed outlier: 3.809A pdb=" N PHE B1192 " --> pdb=" O MET B1173 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 1176 through 1177 Processing sheet with id=AE7, first strand: chain 'B' and resid 1301 through 1303 Processing sheet with id=AE8, first strand: chain 'B' and resid 1443 through 1445 removed outlier: 3.690A pdb=" N VAL B1443 " --> pdb=" O CYS B1489 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N MET B1487 " --> pdb=" O TRP B1445 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 2787 through 2788 removed outlier: 3.658A pdb=" N SER B2903 " --> pdb=" O ARG B2787 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 4132 through 4138 removed outlier: 3.759A pdb=" N PHE B4149 " --> pdb=" O GLY B4133 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 4518 through 4519 Processing sheet with id=AF3, first strand: chain 'B' and resid 4793 through 4794 removed outlier: 4.175A pdb=" N MET B4803 " --> pdb=" O LYS B4794 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 19 through 20 removed outlier: 5.574A pdb=" N LEU C 69 " --> pdb=" O ARG C 122 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ARG C 122 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLN C 71 " --> pdb=" O LEU C 120 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA C 38 " --> pdb=" O PHE C 48 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 129 through 131 removed outlier: 3.570A pdb=" N GLN C 150 " --> pdb=" O TYR C 129 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N CYS C 131 " --> pdb=" O GLY C 148 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY C 148 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 191 through 193 Processing sheet with id=AF7, first strand: chain 'C' and resid 233 through 237 removed outlier: 3.694A pdb=" N ARG C 296 " --> pdb=" O GLU C 278 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 243 through 246 removed outlier: 3.811A pdb=" N CYS C 244 " --> pdb=" O GLU C 263 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU C 263 " --> pdb=" O CYS C 244 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 371 through 374 removed outlier: 3.515A pdb=" N ILE C 392 " --> pdb=" O THR C 373 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 648 through 650 Processing sheet with id=AG2, first strand: chain 'C' and resid 653 through 655 Processing sheet with id=AG3, first strand: chain 'C' and resid 755 through 756 removed outlier: 3.711A pdb=" N ILE C 755 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 677 " --> pdb=" O ILE C 755 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL C 800 " --> pdb=" O VAL C1620 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL C1620 " --> pdb=" O VAL C 800 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN C1621 " --> pdb=" O ILE C1612 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE C1612 " --> pdb=" O GLN C1621 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 769 through 770 Processing sheet with id=AG5, first strand: chain 'C' and resid 778 through 780 removed outlier: 4.334A pdb=" N MET C 778 " --> pdb=" O THR C1468 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR C1468 " --> pdb=" O MET C 778 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU C 780 " --> pdb=" O THR C1466 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 849 through 851 Processing sheet with id=AG7, first strand: chain 'C' and resid 903 through 904 removed outlier: 6.420A pdb=" N GLN C 903 " --> pdb=" O HIS C 915 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'C' and resid 1116 through 1118 removed outlier: 3.699A pdb=" N ALA C1090 " --> pdb=" O PRO C1203 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG C1086 " --> pdb=" O LEU C1207 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ILE C1087 " --> pdb=" O SER C1252 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 1101 through 1102 Processing sheet with id=AH1, first strand: chain 'C' and resid 1136 through 1138 removed outlier: 3.752A pdb=" N ALA C1136 " --> pdb=" O TRP C1145 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP C1138 " --> pdb=" O GLN C1143 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU C1150 " --> pdb=" O ARG C1144 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 1172 through 1173 removed outlier: 3.809A pdb=" N PHE C1192 " --> pdb=" O MET C1173 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 1176 through 1177 Processing sheet with id=AH4, first strand: chain 'C' and resid 1301 through 1303 Processing sheet with id=AH5, first strand: chain 'C' and resid 1443 through 1445 removed outlier: 3.689A pdb=" N VAL C1443 " --> pdb=" O CYS C1489 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N MET C1487 " --> pdb=" O TRP C1445 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 2787 through 2788 removed outlier: 3.658A pdb=" N SER C2903 " --> pdb=" O ARG C2787 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'C' and resid 4132 through 4138 removed outlier: 3.760A pdb=" N PHE C4149 " --> pdb=" O GLY C4133 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'C' and resid 4518 through 4519 Processing sheet with id=AH9, first strand: chain 'C' and resid 4793 through 4794 removed outlier: 4.175A pdb=" N MET C4803 " --> pdb=" O LYS C4794 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'D' and resid 19 through 20 removed outlier: 5.573A pdb=" N LEU D 69 " --> pdb=" O ARG D 122 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ARG D 122 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLN D 71 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA D 38 " --> pdb=" O PHE D 48 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'D' and resid 129 through 131 removed outlier: 3.570A pdb=" N GLN D 150 " --> pdb=" O TYR D 129 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N CYS D 131 " --> pdb=" O GLY D 148 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY D 148 " --> pdb=" O CYS D 131 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'D' and resid 191 through 193 Processing sheet with id=AI4, first strand: chain 'D' and resid 233 through 237 removed outlier: 3.695A pdb=" N ARG D 296 " --> pdb=" O GLU D 278 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'D' and resid 243 through 246 removed outlier: 3.812A pdb=" N CYS D 244 " --> pdb=" O GLU D 263 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU D 263 " --> pdb=" O CYS D 244 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'D' and resid 371 through 374 removed outlier: 3.514A pdb=" N ILE D 392 " --> pdb=" O THR D 373 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'D' and resid 648 through 650 Processing sheet with id=AI8, first strand: chain 'D' and resid 653 through 655 Processing sheet with id=AI9, first strand: chain 'D' and resid 755 through 756 removed outlier: 3.711A pdb=" N ILE D 755 " --> pdb=" O LEU D 677 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D 677 " --> pdb=" O ILE D 755 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL D 800 " --> pdb=" O VAL D1620 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL D1620 " --> pdb=" O VAL D 800 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN D1621 " --> pdb=" O ILE D1612 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE D1612 " --> pdb=" O GLN D1621 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'D' and resid 769 through 770 Processing sheet with id=AJ2, first strand: chain 'D' and resid 778 through 780 removed outlier: 4.333A pdb=" N MET D 778 " --> pdb=" O THR D1468 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR D1468 " --> pdb=" O MET D 778 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU D 780 " --> pdb=" O THR D1466 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'D' and resid 849 through 851 Processing sheet with id=AJ4, first strand: chain 'D' and resid 903 through 904 removed outlier: 6.420A pdb=" N GLN D 903 " --> pdb=" O HIS D 915 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ4 Processing sheet with id=AJ5, first strand: chain 'D' and resid 1116 through 1118 removed outlier: 3.699A pdb=" N ALA D1090 " --> pdb=" O PRO D1203 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG D1086 " --> pdb=" O LEU D1207 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ILE D1087 " --> pdb=" O SER D1252 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'D' and resid 1101 through 1102 Processing sheet with id=AJ7, first strand: chain 'D' and resid 1136 through 1138 removed outlier: 3.752A pdb=" N ALA D1136 " --> pdb=" O TRP D1145 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP D1138 " --> pdb=" O GLN D1143 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU D1150 " --> pdb=" O ARG D1144 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'D' and resid 1172 through 1173 removed outlier: 3.809A pdb=" N PHE D1192 " --> pdb=" O MET D1173 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'D' and resid 1176 through 1177 Processing sheet with id=AK1, first strand: chain 'D' and resid 1301 through 1303 Processing sheet with id=AK2, first strand: chain 'D' and resid 1443 through 1445 removed outlier: 3.691A pdb=" N VAL D1443 " --> pdb=" O CYS D1489 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N MET D1487 " --> pdb=" O TRP D1445 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'D' and resid 2787 through 2788 removed outlier: 3.658A pdb=" N SER D2903 " --> pdb=" O ARG D2787 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'D' and resid 4132 through 4138 removed outlier: 3.760A pdb=" N PHE D4149 " --> pdb=" O GLY D4133 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'D' and resid 4518 through 4519 Processing sheet with id=AK6, first strand: chain 'D' and resid 4793 through 4794 removed outlier: 4.175A pdb=" N MET D4803 " --> pdb=" O LYS D4794 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.896A pdb=" N GLU E 4 " --> pdb=" O THR E 76 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR E 76 " --> pdb=" O GLU E 4 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU E 98 " --> pdb=" O CYS E 77 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'E' and resid 47 through 50 removed outlier: 3.625A pdb=" N PHE E 47 " --> pdb=" O VAL E 25 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE E 49 " --> pdb=" O CYS E 23 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR E 22 " --> pdb=" O GLU E 108 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASN E 106 " --> pdb=" O VAL E 24 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.895A pdb=" N GLU F 4 " --> pdb=" O THR F 76 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR F 76 " --> pdb=" O GLU F 4 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU F 98 " --> pdb=" O CYS F 77 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'F' and resid 47 through 50 removed outlier: 3.625A pdb=" N PHE F 47 " --> pdb=" O VAL F 25 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE F 49 " --> pdb=" O CYS F 23 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR F 22 " --> pdb=" O GLU F 108 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASN F 106 " --> pdb=" O VAL F 24 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.896A pdb=" N GLU G 4 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR G 76 " --> pdb=" O GLU G 4 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU G 98 " --> pdb=" O CYS G 77 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'G' and resid 47 through 50 removed outlier: 3.625A pdb=" N PHE G 47 " --> pdb=" O VAL G 25 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE G 49 " --> pdb=" O CYS G 23 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR G 22 " --> pdb=" O GLU G 108 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASN G 106 " --> pdb=" O VAL G 24 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.895A pdb=" N GLU H 4 " --> pdb=" O THR H 76 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR H 76 " --> pdb=" O GLU H 4 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU H 98 " --> pdb=" O CYS H 77 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'H' and resid 47 through 50 removed outlier: 3.626A pdb=" N PHE H 47 " --> pdb=" O VAL H 25 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE H 49 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR H 22 " --> pdb=" O GLU H 108 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASN H 106 " --> pdb=" O VAL H 24 " (cutoff:3.500A) 5623 hydrogen bonds defined for protein. 16320 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: 81.34 Time building geometry restraints manager: 40.32 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: 42533 1.34 - 1.47: 30198 1.47 - 1.59: 57401 1.59 - 1.71: 0 1.71 - 1.83: 1308 Bond restraints: 131440 Sorted by residual: bond pdb=" CB ARG C 414 " pdb=" CG ARG C 414 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.29e+00 bond pdb=" CA LYS H 36 " pdb=" CB LYS H 36 " ideal model delta sigma weight residual 1.535 1.509 0.026 1.71e-02 3.42e+03 2.28e+00 bond pdb=" CB ARG D 414 " pdb=" CG ARG D 414 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.27e+00 bond pdb=" CB ARG A 414 " pdb=" CG ARG A 414 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.27e+00 bond pdb=" CB ARG B 414 " pdb=" CG ARG B 414 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.22e+00 ... (remaining 131435 not shown) Histogram of bond angle deviations from ideal: 98.69 - 105.78: 2397 105.78 - 112.86: 69823 112.86 - 119.94: 44849 119.94 - 127.02: 59219 127.02 - 134.10: 1464 Bond angle restraints: 177752 Sorted by residual: angle pdb=" CB MET B 964 " pdb=" CG MET B 964 " pdb=" SD MET B 964 " ideal model delta sigma weight residual 112.70 127.48 -14.78 3.00e+00 1.11e-01 2.43e+01 angle pdb=" CB MET A 964 " pdb=" CG MET A 964 " pdb=" SD MET A 964 " ideal model delta sigma weight residual 112.70 127.47 -14.77 3.00e+00 1.11e-01 2.42e+01 angle pdb=" CB MET C 964 " pdb=" CG MET C 964 " pdb=" SD MET C 964 " ideal model delta sigma weight residual 112.70 127.45 -14.75 3.00e+00 1.11e-01 2.42e+01 angle pdb=" CB MET D 964 " pdb=" CG MET D 964 " pdb=" SD MET D 964 " ideal model delta sigma weight residual 112.70 127.45 -14.75 3.00e+00 1.11e-01 2.42e+01 angle pdb=" CA ARG A 414 " pdb=" CB ARG A 414 " pdb=" CG ARG A 414 " ideal model delta sigma weight residual 114.10 123.13 -9.03 2.00e+00 2.50e-01 2.04e+01 ... (remaining 177747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 68350 17.56 - 35.12: 8175 35.12 - 52.68: 1827 52.68 - 70.24: 292 70.24 - 87.80: 140 Dihedral angle restraints: 78784 sinusoidal: 31108 harmonic: 47676 Sorted by residual: dihedral pdb=" CA MET C 494 " pdb=" C MET C 494 " pdb=" N ILE C 495 " pdb=" CA ILE C 495 " ideal model delta harmonic sigma weight residual 180.00 152.62 27.38 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA MET D 494 " pdb=" C MET D 494 " pdb=" N ILE D 495 " pdb=" CA ILE D 495 " ideal model delta harmonic sigma weight residual 180.00 152.64 27.36 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA MET B 494 " pdb=" C MET B 494 " pdb=" N ILE B 495 " pdb=" CA ILE B 495 " ideal model delta harmonic sigma weight residual 180.00 152.66 27.34 0 5.00e+00 4.00e-02 2.99e+01 ... (remaining 78781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 15300 0.045 - 0.089: 3513 0.089 - 0.134: 836 0.134 - 0.179: 27 0.179 - 0.224: 12 Chirality restraints: 19688 Sorted by residual: chirality pdb=" CA MET A 494 " pdb=" N MET A 494 " pdb=" C MET A 494 " pdb=" CB MET A 494 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA MET D 494 " pdb=" N MET D 494 " pdb=" C MET D 494 " pdb=" CB MET D 494 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA MET B 494 " pdb=" N MET B 494 " pdb=" C MET B 494 " pdb=" CB MET B 494 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 19685 not shown) Planarity restraints: 22980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 464 " -0.043 5.00e-02 4.00e+02 6.59e-02 6.96e+00 pdb=" N PRO C 465 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 465 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 465 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 464 " 0.043 5.00e-02 4.00e+02 6.57e-02 6.90e+00 pdb=" N PRO B 465 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 465 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 465 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 464 " -0.043 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO A 465 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 465 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 465 " -0.036 5.00e-02 4.00e+02 ... (remaining 22977 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 5950 2.73 - 3.27: 125922 3.27 - 3.82: 208181 3.82 - 4.36: 220818 4.36 - 4.90: 394424 Nonbonded interactions: 955295 Sorted by model distance: nonbonded pdb=" O ASN B1670 " pdb=" OH TYR B1777 " model vdw 2.188 2.440 nonbonded pdb=" O ASN A1670 " pdb=" OH TYR A1777 " model vdw 2.188 2.440 nonbonded pdb=" O ASN C1670 " pdb=" OH TYR C1777 " model vdw 2.188 2.440 nonbonded pdb=" O ASN D1670 " pdb=" OH TYR D1777 " model vdw 2.188 2.440 nonbonded pdb=" OG SER A 166 " pdb=" OE1 GLN A 168 " model vdw 2.193 2.440 ... (remaining 955290 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: 4.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.130 Extract box with map and model: 23.610 Check model and map are aligned: 1.600 Set scattering table: 0.860 Process input model: 300.730 Find NCS groups from input model: 6.710 Set up NCS constraints: 0.820 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: 0.030 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 341.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 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 0.048 131440 Z= 0.180 Angle : 0.613 14.780 177752 Z= 0.305 Chirality : 0.039 0.224 19688 Planarity : 0.004 0.078 22980 Dihedral : 15.938 87.805 48016 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.66 % Favored : 94.19 % Rotamer: Outliers : 0.23 % Allowed : 10.96 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.07), residues: 16228 helix: 1.56 (0.06), residues: 7396 sheet: -0.40 (0.17), residues: 976 loop : -2.26 (0.06), residues: 7856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP D 893 HIS 0.006 0.001 HIS D 469 PHE 0.016 0.001 PHE B4845 TYR 0.024 0.001 TYR C4938 ARG 0.014 0.000 ARG B 647 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32456 Ramachandran restraints generated. 16228 Oldfield, 0 Emsley, 16228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32456 Ramachandran restraints generated. 16228 Oldfield, 0 Emsley, 16228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1094 residues out of total 14384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1063 time to evaluate : 10.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.4879 (mmp) cc_final: 0.4632 (mmt) REVERT: A 895 MET cc_start: 0.4703 (mmp) cc_final: 0.3840 (mtp) REVERT: A 3245 MET cc_start: -0.1947 (mpp) cc_final: -0.2214 (mpp) REVERT: A 3331 MET cc_start: 0.6185 (ppp) cc_final: 0.5155 (tpp) REVERT: A 4881 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7422 (tm-30) REVERT: A 4898 ASP cc_start: 0.6608 (m-30) cc_final: 0.6332 (m-30) REVERT: B 309 MET cc_start: 0.4774 (mmp) cc_final: 0.4510 (mmt) REVERT: B 895 MET cc_start: 0.4395 (mmp) cc_final: 0.3511 (mtp) REVERT: B 3245 MET cc_start: -0.1838 (mpp) cc_final: -0.2125 (mpp) REVERT: B 3331 MET cc_start: 0.6223 (ppp) cc_final: 0.5227 (tpp) REVERT: C 309 MET cc_start: 0.4882 (mmp) cc_final: 0.4636 (mmt) REVERT: C 895 MET cc_start: 0.4744 (mmp) cc_final: 0.3866 (mtp) REVERT: C 1629 MET cc_start: 0.5813 (pmm) cc_final: 0.4699 (ptp) REVERT: C 3245 MET cc_start: -0.1915 (mpp) cc_final: -0.2174 (mpp) REVERT: C 3331 MET cc_start: 0.6228 (ppp) cc_final: 0.5210 (tpp) REVERT: C 4881 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7428 (tm-30) REVERT: C 4898 ASP cc_start: 0.6638 (m-30) cc_final: 0.6355 (m-30) REVERT: D 895 MET cc_start: 0.4714 (mmp) cc_final: 0.3854 (mtp) REVERT: D 1629 MET cc_start: 0.5779 (pmm) cc_final: 0.4656 (ptp) REVERT: D 3245 MET cc_start: -0.1917 (mpp) cc_final: -0.2180 (mpp) REVERT: D 3331 MET cc_start: 0.6090 (ppp) cc_final: 0.5110 (tpp) REVERT: D 4846 ASP cc_start: 0.7380 (m-30) cc_final: 0.7176 (m-30) REVERT: D 4898 ASP cc_start: 0.6633 (m-30) cc_final: 0.6347 (m-30) outliers start: 31 outliers final: 15 residues processed: 1071 average time/residue: 1.0292 time to fit residues: 1987.5769 Evaluate side-chains 1042 residues out of total 14384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1027 time to evaluate : 10.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1722 MET Chi-restraints excluded: chain A residue 1818 LEU Chi-restraints excluded: chain A residue 2091 TYR Chi-restraints excluded: chain A residue 4747 MET Chi-restraints excluded: chain B residue 1722 MET Chi-restraints excluded: chain B residue 1818 LEU Chi-restraints excluded: chain B residue 2405 MET Chi-restraints excluded: chain B residue 4747 MET Chi-restraints excluded: chain C residue 1722 MET Chi-restraints excluded: chain C residue 1818 LEU Chi-restraints excluded: chain C residue 2091 TYR Chi-restraints excluded: chain D residue 1722 MET Chi-restraints excluded: chain D residue 1818 LEU Chi-restraints excluded: chain D residue 2091 TYR Chi-restraints excluded: chain D residue 2405 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1640 random chunks: chunk 1384 optimal weight: 7.9990 chunk 1243 optimal weight: 6.9990 chunk 689 optimal weight: 30.0000 chunk 424 optimal weight: 10.0000 chunk 838 optimal weight: 3.9990 chunk 664 optimal weight: 50.0000 chunk 1285 optimal weight: 0.3980 chunk 497 optimal weight: 50.0000 chunk 781 optimal weight: 1.9990 chunk 956 optimal weight: 4.9990 chunk 1489 optimal weight: 30.0000 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 496 ASN A 692 HIS A1244 ASN ** A1484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2223 ASN A2340 ASN A2516 ASN A2599 ASN A3617 ASN A3665 GLN A3849 HIS B 23 GLN ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 HIS B1244 ASN B1440 ASN ** B1484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2223 ASN B2340 ASN B2516 ASN B2599 ASN B3617 ASN B3849 HIS C 23 GLN ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 HIS C1244 ASN ** C1484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2223 ASN C2340 ASN C2516 ASN C2599 ASN C3617 ASN C3665 GLN C3849 HIS D 23 GLN ** D 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 692 HIS D1244 ASN D1440 ASN ** D1484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2223 ASN D2340 ASN D2516 ASN D2599 ASN D3617 ASN D3849 HIS E 32 GLN F 32 GLN G 32 GLN H 32 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 131440 Z= 0.406 Angle : 0.667 9.562 177752 Z= 0.342 Chirality : 0.043 0.168 19688 Planarity : 0.005 0.066 22980 Dihedral : 4.083 50.254 17698 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.37 % Favored : 93.48 % Rotamer: Outliers : 2.36 % Allowed : 12.78 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.07), residues: 16228 helix: 1.51 (0.06), residues: 7476 sheet: -0.83 (0.16), residues: 1044 loop : -2.30 (0.06), residues: 7708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C4644 HIS 0.016 0.001 HIS A 630 PHE 0.034 0.002 PHE B4845 TYR 0.033 0.002 TYR B4792 ARG 0.008 0.001 ARG A3614 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32456 Ramachandran restraints generated. 16228 Oldfield, 0 Emsley, 16228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32456 Ramachandran restraints generated. 16228 Oldfield, 0 Emsley, 16228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1423 residues out of total 14384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 323 poor density : 1100 time to evaluate : 10.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8049 (mp10) REVERT: A 393 MET cc_start: 0.3494 (mmm) cc_final: 0.3192 (mmm) REVERT: A 494 MET cc_start: 0.1469 (pmm) cc_final: 0.1109 (pmm) REVERT: A 935 MET cc_start: 0.5922 (tmm) cc_final: 0.5042 (ptt) REVERT: A 981 MET cc_start: 0.1227 (ppp) cc_final: 0.0145 (ptp) REVERT: A 1131 ASP cc_start: 0.7829 (p0) cc_final: 0.7582 (p0) REVERT: A 1199 ASP cc_start: 0.8477 (p0) cc_final: 0.8050 (p0) REVERT: A 1641 ASP cc_start: 0.6818 (m-30) cc_final: 0.6407 (m-30) REVERT: A 1764 PHE cc_start: 0.5729 (p90) cc_final: 0.5479 (p90) REVERT: A 1768 SER cc_start: 0.5572 (m) cc_final: 0.5302 (p) REVERT: A 1897 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8397 (mt) REVERT: A 2781 MET cc_start: 0.0050 (ptp) cc_final: -0.0993 (mmp) REVERT: A 3245 MET cc_start: -0.1711 (mpp) cc_final: -0.2096 (mpp) REVERT: A 3331 MET cc_start: 0.6177 (ppp) cc_final: 0.5259 (tpp) REVERT: A 3998 MET cc_start: 0.8654 (tpp) cc_final: 0.8223 (ttt) REVERT: A 4153 GLU cc_start: 0.7981 (tp30) cc_final: 0.7741 (tp30) REVERT: A 4862 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7578 (mp10) REVERT: A 4881 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7449 (tm-30) REVERT: B 23 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8041 (mp10) REVERT: B 494 MET cc_start: 0.1468 (pmm) cc_final: 0.1112 (pmm) REVERT: B 935 MET cc_start: 0.5810 (tmm) cc_final: 0.5008 (ptt) REVERT: B 981 MET cc_start: 0.1395 (ppp) cc_final: 0.0331 (ptp) REVERT: B 1131 ASP cc_start: 0.7812 (p0) cc_final: 0.7572 (p0) REVERT: B 1199 ASP cc_start: 0.8488 (p0) cc_final: 0.8133 (p0) REVERT: B 1605 LEU cc_start: 0.6459 (mt) cc_final: 0.6258 (mt) REVERT: B 1641 ASP cc_start: 0.6861 (m-30) cc_final: 0.6434 (m-30) REVERT: B 1764 PHE cc_start: 0.5690 (p90) cc_final: 0.5481 (p90) REVERT: B 1768 SER cc_start: 0.5546 (m) cc_final: 0.5278 (p) REVERT: B 1897 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8432 (mt) REVERT: B 2694 MET cc_start: -0.0434 (tpt) cc_final: -0.0746 (tpp) REVERT: B 2781 MET cc_start: -0.0020 (ptp) cc_final: -0.1122 (mmp) REVERT: B 3245 MET cc_start: -0.1713 (mpp) cc_final: -0.2127 (mpp) REVERT: B 3331 MET cc_start: 0.6189 (ppp) cc_final: 0.5291 (tpp) REVERT: B 3718 MET cc_start: 0.7314 (tpp) cc_final: 0.6987 (tpp) REVERT: B 3998 MET cc_start: 0.8649 (tpp) cc_final: 0.8233 (ttt) REVERT: B 4153 GLU cc_start: 0.7973 (tp30) cc_final: 0.7687 (tp30) REVERT: B 4862 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7565 (mp10) REVERT: C 23 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8053 (mp10) REVERT: C 393 MET cc_start: 0.3362 (mmm) cc_final: 0.3110 (mmm) REVERT: C 494 MET cc_start: 0.1471 (pmm) cc_final: 0.1111 (pmm) REVERT: C 935 MET cc_start: 0.5881 (tmm) cc_final: 0.4980 (ptt) REVERT: C 1131 ASP cc_start: 0.7831 (p0) cc_final: 0.7584 (p0) REVERT: C 1199 ASP cc_start: 0.8474 (p0) cc_final: 0.8052 (p0) REVERT: C 1641 ASP cc_start: 0.6835 (m-30) cc_final: 0.6421 (m-30) REVERT: C 1764 PHE cc_start: 0.5720 (p90) cc_final: 0.5471 (p90) REVERT: C 1768 SER cc_start: 0.5586 (m) cc_final: 0.5314 (p) REVERT: C 1897 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8403 (mt) REVERT: C 2781 MET cc_start: -0.0124 (ptp) cc_final: -0.1214 (mmp) REVERT: C 3245 MET cc_start: -0.1885 (mpp) cc_final: -0.2227 (mpp) REVERT: C 3331 MET cc_start: 0.6214 (ppp) cc_final: 0.5274 (tpp) REVERT: C 3998 MET cc_start: 0.8654 (tpp) cc_final: 0.8219 (ttt) REVERT: C 4153 GLU cc_start: 0.7978 (tp30) cc_final: 0.7733 (tp30) REVERT: C 4862 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7582 (mp10) REVERT: C 4881 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7448 (tm-30) REVERT: D 23 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8056 (mp10) REVERT: D 393 MET cc_start: 0.3363 (mmm) cc_final: 0.3107 (mmm) REVERT: D 494 MET cc_start: 0.1466 (pmm) cc_final: 0.1109 (pmm) REVERT: D 935 MET cc_start: 0.5909 (tmm) cc_final: 0.5040 (ptt) REVERT: D 1131 ASP cc_start: 0.7964 (p0) cc_final: 0.7700 (p0) REVERT: D 1199 ASP cc_start: 0.8468 (p0) cc_final: 0.8046 (p0) REVERT: D 1641 ASP cc_start: 0.6825 (m-30) cc_final: 0.6422 (m-30) REVERT: D 1764 PHE cc_start: 0.5704 (p90) cc_final: 0.5456 (p90) REVERT: D 1768 SER cc_start: 0.5551 (m) cc_final: 0.5283 (p) REVERT: D 1832 MET cc_start: 0.9026 (mtp) cc_final: 0.8803 (mtp) REVERT: D 1897 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8408 (mt) REVERT: D 2781 MET cc_start: 0.0005 (ptp) cc_final: -0.1122 (mmp) REVERT: D 3245 MET cc_start: -0.1696 (mpp) cc_final: -0.2086 (mpp) REVERT: D 3331 MET cc_start: 0.6218 (ppp) cc_final: 0.5276 (tpp) REVERT: D 3998 MET cc_start: 0.8652 (tpp) cc_final: 0.8219 (ttt) REVERT: D 4153 GLU cc_start: 0.7986 (tp30) cc_final: 0.7736 (tp30) REVERT: D 4862 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7583 (mp10) REVERT: E 26 HIS cc_start: 0.7737 (OUTLIER) cc_final: 0.7361 (t-90) REVERT: E 46 PRO cc_start: 0.8262 (Cg_exo) cc_final: 0.7921 (Cg_endo) REVERT: F 26 HIS cc_start: 0.7450 (OUTLIER) cc_final: 0.7122 (t-90) REVERT: F 46 PRO cc_start: 0.8142 (Cg_exo) cc_final: 0.7832 (Cg_endo) REVERT: G 6 GLU cc_start: 0.7680 (mp0) cc_final: 0.7478 (mp0) REVERT: G 26 HIS cc_start: 0.7763 (OUTLIER) cc_final: 0.7369 (t-90) REVERT: G 46 PRO cc_start: 0.8265 (Cg_exo) cc_final: 0.7922 (Cg_endo) REVERT: H 26 HIS cc_start: 0.7727 (OUTLIER) cc_final: 0.7340 (t-90) REVERT: H 46 PRO cc_start: 0.8269 (Cg_exo) cc_final: 0.7918 (Cg_endo) outliers start: 323 outliers final: 172 residues processed: 1341 average time/residue: 0.9706 time to fit residues: 2352.7796 Evaluate side-chains 1167 residues out of total 14384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 979 time to evaluate : 10.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 608 HIS Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 1202 ILE Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1607 VAL Chi-restraints excluded: chain A residue 1783 PHE Chi-restraints excluded: chain A residue 1818 LEU Chi-restraints excluded: chain A residue 1819 PHE Chi-restraints excluded: chain A residue 1897 LEU Chi-restraints excluded: chain A residue 2060 LEU Chi-restraints excluded: chain A residue 2150 ASN Chi-restraints excluded: chain A residue 2195 CYS Chi-restraints excluded: chain A residue 2196 CYS Chi-restraints excluded: chain A residue 2305 VAL Chi-restraints excluded: chain A residue 2342 LEU Chi-restraints excluded: chain A residue 2383 MET Chi-restraints excluded: chain A residue 2405 MET Chi-restraints excluded: chain A residue 2425 LEU Chi-restraints excluded: chain A residue 2598 LEU Chi-restraints excluded: chain A residue 2675 LEU Chi-restraints excluded: chain A residue 3262 MET Chi-restraints excluded: chain A residue 3616 VAL Chi-restraints excluded: chain A residue 3786 VAL Chi-restraints excluded: chain A residue 3934 LEU Chi-restraints excluded: chain A residue 3970 LEU Chi-restraints excluded: chain A residue 3989 VAL Chi-restraints excluded: chain A residue 4016 PHE Chi-restraints excluded: chain A residue 4515 LEU Chi-restraints excluded: chain A residue 4807 ASP Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4862 GLN Chi-restraints excluded: chain B residue 23 GLN Chi-restraints excluded: chain B residue 42 PHE Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 608 HIS Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 1166 VAL Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1251 LEU Chi-restraints excluded: chain B residue 1297 THR Chi-restraints excluded: chain B residue 1511 VAL Chi-restraints excluded: chain B residue 1607 VAL Chi-restraints excluded: chain B residue 1658 THR Chi-restraints excluded: chain B residue 1721 MET Chi-restraints excluded: chain B residue 1783 PHE Chi-restraints excluded: chain B residue 1818 LEU Chi-restraints excluded: chain B residue 1819 PHE Chi-restraints excluded: chain B residue 1897 LEU Chi-restraints excluded: chain B residue 2060 LEU Chi-restraints excluded: chain B residue 2150 ASN Chi-restraints excluded: chain B residue 2195 CYS Chi-restraints excluded: chain B residue 2196 CYS Chi-restraints excluded: chain B residue 2305 VAL Chi-restraints excluded: chain B residue 2342 LEU Chi-restraints excluded: chain B residue 2383 MET Chi-restraints excluded: chain B residue 2598 LEU Chi-restraints excluded: chain B residue 2675 LEU Chi-restraints excluded: chain B residue 3262 MET Chi-restraints excluded: chain B residue 3616 VAL Chi-restraints excluded: chain B residue 3786 VAL Chi-restraints excluded: chain B residue 3934 LEU Chi-restraints excluded: chain B residue 3970 LEU Chi-restraints excluded: chain B residue 3989 VAL Chi-restraints excluded: chain B residue 4016 PHE Chi-restraints excluded: chain B residue 4515 LEU Chi-restraints excluded: chain B residue 4807 ASP Chi-restraints excluded: chain B residue 4862 GLN Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 42 PHE Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 608 HIS Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1202 ILE Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1297 THR Chi-restraints excluded: chain C residue 1511 VAL Chi-restraints excluded: chain C residue 1607 VAL Chi-restraints excluded: chain C residue 1783 PHE Chi-restraints excluded: chain C residue 1818 LEU Chi-restraints excluded: chain C residue 1819 PHE Chi-restraints excluded: chain C residue 1897 LEU Chi-restraints excluded: chain C residue 2060 LEU Chi-restraints excluded: chain C residue 2150 ASN Chi-restraints excluded: chain C residue 2195 CYS Chi-restraints excluded: chain C residue 2196 CYS Chi-restraints excluded: chain C residue 2305 VAL Chi-restraints excluded: chain C residue 2342 LEU Chi-restraints excluded: chain C residue 2383 MET Chi-restraints excluded: chain C residue 2405 MET Chi-restraints excluded: chain C residue 2526 LEU Chi-restraints excluded: chain C residue 2598 LEU Chi-restraints excluded: chain C residue 2675 LEU Chi-restraints excluded: chain C residue 2682 SER Chi-restraints excluded: chain C residue 3262 MET Chi-restraints excluded: chain C residue 3616 VAL Chi-restraints excluded: chain C residue 3786 VAL Chi-restraints excluded: chain C residue 3934 LEU Chi-restraints excluded: chain C residue 3970 LEU Chi-restraints excluded: chain C residue 3989 VAL Chi-restraints excluded: chain C residue 4016 PHE Chi-restraints excluded: chain C residue 4515 LEU Chi-restraints excluded: chain C residue 4747 MET Chi-restraints excluded: chain C residue 4807 ASP Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4862 GLN Chi-restraints excluded: chain D residue 23 GLN Chi-restraints excluded: chain D residue 42 PHE Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 492 GLU Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 608 HIS Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 798 ILE Chi-restraints excluded: chain D residue 1166 VAL Chi-restraints excluded: chain D residue 1202 ILE Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1297 THR Chi-restraints excluded: chain D residue 1511 VAL Chi-restraints excluded: chain D residue 1607 VAL Chi-restraints excluded: chain D residue 1783 PHE Chi-restraints excluded: chain D residue 1818 LEU Chi-restraints excluded: chain D residue 1819 PHE Chi-restraints excluded: chain D residue 1897 LEU Chi-restraints excluded: chain D residue 2060 LEU Chi-restraints excluded: chain D residue 2150 ASN Chi-restraints excluded: chain D residue 2195 CYS Chi-restraints excluded: chain D residue 2196 CYS Chi-restraints excluded: chain D residue 2305 VAL Chi-restraints excluded: chain D residue 2342 LEU Chi-restraints excluded: chain D residue 2383 MET Chi-restraints excluded: chain D residue 2526 LEU Chi-restraints excluded: chain D residue 2598 LEU Chi-restraints excluded: chain D residue 2675 LEU Chi-restraints excluded: chain D residue 3262 MET Chi-restraints excluded: chain D residue 3616 VAL Chi-restraints excluded: chain D residue 3786 VAL Chi-restraints excluded: chain D residue 3934 LEU Chi-restraints excluded: chain D residue 3970 LEU Chi-restraints excluded: chain D residue 3989 VAL Chi-restraints excluded: chain D residue 4016 PHE Chi-restraints excluded: chain D residue 4515 LEU Chi-restraints excluded: chain D residue 4747 MET Chi-restraints excluded: chain D residue 4807 ASP Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4862 GLN Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain H residue 102 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1640 random chunks: chunk 827 optimal weight: 20.0000 chunk 462 optimal weight: 20.0000 chunk 1239 optimal weight: 7.9990 chunk 1014 optimal weight: 8.9990 chunk 410 optimal weight: 6.9990 chunk 1491 optimal weight: 9.9990 chunk 1611 optimal weight: 20.0000 chunk 1328 optimal weight: 8.9990 chunk 1479 optimal weight: 50.0000 chunk 508 optimal weight: 9.9990 chunk 1196 optimal weight: 0.8980 overall best weight: 6.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 HIS A 487 ASN ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 ASN ** A 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 859 GLN A 915 HIS A1014 GLN A1146 HIS ** A1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1440 ASN ** A1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1675 HIS A1680 HIS A1774 ASN ** A2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2409 HIS ** A2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3073 ASN A3633 HIS ** A3773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3959 GLN ** A4628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A4637 GLN A4793 ASN A4902 HIS B 410 HIS B 487 ASN ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 ASN B 531 ASN ** B 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 859 GLN B 915 HIS B1014 GLN B1146 HIS ** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1484 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1675 HIS B1680 HIS B1774 ASN ** B2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2409 HIS ** B2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3073 ASN B3633 HIS ** B3773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B4637 GLN B4793 ASN B4902 HIS C 410 HIS C 487 ASN ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 ASN ** C 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 859 GLN C 915 HIS C1014 GLN C1146 HIS ** C1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1440 ASN ** C1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1675 HIS C1680 HIS C1774 ASN ** C2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2409 HIS ** C2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3073 ASN C3633 HIS ** C3902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C4637 GLN C4793 ASN C4902 HIS D 410 HIS D 487 ASN ** D 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 496 ASN ** D 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 859 GLN D 915 HIS D1014 GLN D1146 HIS ** D1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1675 HIS D1680 HIS D1774 ASN ** D2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2409 HIS ** D2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3073 ASN D3633 HIS D3665 GLN ** D3902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D4637 GLN D4793 ASN D4902 HIS E 32 GLN F 32 GLN G 32 GLN H 32 GLN Total number of N/Q/H flips: 73 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.158 131440 Z= 0.671 Angle : 0.882 16.182 177752 Z= 0.456 Chirality : 0.050 0.324 19688 Planarity : 0.006 0.117 22980 Dihedral : 5.199 53.016 17668 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.67 % Favored : 91.13 % Rotamer: Outliers : 4.96 % Allowed : 15.43 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.06), residues: 16228 helix: 0.81 (0.06), residues: 7468 sheet: -1.18 (0.16), residues: 1124 loop : -2.64 (0.06), residues: 7636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 893 HIS 0.016 0.002 HIS B1711 PHE 0.037 0.003 PHE C4845 TYR 0.040 0.003 TYR B2679 ARG 0.025 0.001 ARG B2641 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32456 Ramachandran restraints generated. 16228 Oldfield, 0 Emsley, 16228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32456 Ramachandran restraints generated. 16228 Oldfield, 0 Emsley, 16228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1742 residues out of total 14384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 679 poor density : 1063 time to evaluate : 10.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 HIS cc_start: 0.8416 (OUTLIER) cc_final: 0.7305 (m90) REVERT: A 152 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8065 (p0) REVERT: A 245 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6819 (mm) REVERT: A 362 TYR cc_start: 0.7516 (m-80) cc_final: 0.7095 (m-80) REVERT: A 484 ASN cc_start: 0.9124 (OUTLIER) cc_final: 0.8799 (t0) REVERT: A 584 GLU cc_start: 0.7348 (pp20) cc_final: 0.6717 (pp20) REVERT: A 981 MET cc_start: 0.0944 (ppp) cc_final: -0.0108 (ptp) REVERT: A 1199 ASP cc_start: 0.8850 (p0) cc_final: 0.8532 (p0) REVERT: A 1641 ASP cc_start: 0.6301 (m-30) cc_final: 0.6077 (m-30) REVERT: A 1897 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8543 (mt) REVERT: A 2174 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7743 (mtp) REVERT: A 2178 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7524 (mm) REVERT: A 2190 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7287 (ptmm) REVERT: A 2198 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.8164 (t80) REVERT: A 2408 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8125 (tt) REVERT: A 2689 GLU cc_start: 0.7536 (mp0) cc_final: 0.7221 (mt-10) REVERT: A 2781 MET cc_start: -0.0610 (ptp) cc_final: -0.1487 (mmp) REVERT: A 3245 MET cc_start: -0.1516 (mpp) cc_final: -0.1875 (mpp) REVERT: A 3331 MET cc_start: 0.6368 (ppp) cc_final: 0.5470 (tpp) REVERT: A 3672 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7902 (ptp-170) REVERT: A 3998 MET cc_start: 0.8720 (tpp) cc_final: 0.8263 (ttt) REVERT: A 4117 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.8167 (t80) REVERT: A 4921 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8393 (tp) REVERT: B 117 HIS cc_start: 0.8460 (OUTLIER) cc_final: 0.7331 (m90) REVERT: B 152 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.8067 (p0) REVERT: B 245 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6849 (mm) REVERT: B 362 TYR cc_start: 0.7526 (m-80) cc_final: 0.7044 (m-80) REVERT: B 484 ASN cc_start: 0.9125 (OUTLIER) cc_final: 0.8799 (t0) REVERT: B 584 GLU cc_start: 0.7403 (pp20) cc_final: 0.6769 (pp20) REVERT: B 981 MET cc_start: 0.1076 (ppp) cc_final: 0.0046 (ptp) REVERT: B 1199 ASP cc_start: 0.8742 (p0) cc_final: 0.8477 (p0) REVERT: B 1641 ASP cc_start: 0.6417 (m-30) cc_final: 0.6185 (m-30) REVERT: B 1722 MET cc_start: 0.6799 (ptt) cc_final: 0.6495 (tmm) REVERT: B 1897 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8549 (mt) REVERT: B 2174 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7743 (mtp) REVERT: B 2178 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7507 (mm) REVERT: B 2190 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7297 (ptmm) REVERT: B 2198 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.8162 (t80) REVERT: B 2689 GLU cc_start: 0.7525 (mp0) cc_final: 0.7215 (mt-10) REVERT: B 2781 MET cc_start: -0.0546 (ptp) cc_final: -0.1428 (mmp) REVERT: B 3245 MET cc_start: -0.1610 (mpp) cc_final: -0.1973 (mpp) REVERT: B 3331 MET cc_start: 0.6375 (ppp) cc_final: 0.5500 (tpp) REVERT: B 3672 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7893 (ptp-170) REVERT: B 3718 MET cc_start: 0.7498 (tpp) cc_final: 0.7126 (tpp) REVERT: B 3998 MET cc_start: 0.8730 (tpp) cc_final: 0.8269 (ttt) REVERT: B 4082 PHE cc_start: 0.5687 (OUTLIER) cc_final: 0.5225 (p90) REVERT: B 4117 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.8181 (t80) REVERT: B 4921 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8370 (tp) REVERT: C 117 HIS cc_start: 0.8420 (OUTLIER) cc_final: 0.7312 (m90) REVERT: C 128 MET cc_start: 0.7969 (mmt) cc_final: 0.7712 (mmt) REVERT: C 152 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.8060 (p0) REVERT: C 245 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6845 (mm) REVERT: C 362 TYR cc_start: 0.7567 (m-80) cc_final: 0.7108 (m-80) REVERT: C 484 ASN cc_start: 0.9125 (OUTLIER) cc_final: 0.8800 (t0) REVERT: C 584 GLU cc_start: 0.7346 (pp20) cc_final: 0.6715 (pp20) REVERT: C 1199 ASP cc_start: 0.8741 (p0) cc_final: 0.8419 (p0) REVERT: C 1641 ASP cc_start: 0.6306 (m-30) cc_final: 0.6084 (m-30) REVERT: C 1897 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8542 (mt) REVERT: C 1903 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8790 (tt) REVERT: C 2174 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7744 (mtp) REVERT: C 2178 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7510 (mm) REVERT: C 2190 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7289 (ptmm) REVERT: C 2198 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.8156 (t80) REVERT: C 2408 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8127 (tt) REVERT: C 2781 MET cc_start: -0.0591 (ptp) cc_final: -0.1495 (mmp) REVERT: C 3045 MET cc_start: 0.5629 (ppp) cc_final: 0.5413 (ppp) REVERT: C 3245 MET cc_start: -0.1478 (mpp) cc_final: -0.1830 (mpp) REVERT: C 3331 MET cc_start: 0.6339 (ppp) cc_final: 0.5421 (tpp) REVERT: C 3672 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7906 (ptp-170) REVERT: C 3718 MET cc_start: 0.7379 (tpp) cc_final: 0.7123 (tpp) REVERT: C 3998 MET cc_start: 0.8721 (tpp) cc_final: 0.8263 (ttt) REVERT: C 4082 PHE cc_start: 0.5583 (OUTLIER) cc_final: 0.5111 (p90) REVERT: C 4117 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.8167 (t80) REVERT: C 4747 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7240 (pmm) REVERT: C 4921 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8394 (tp) REVERT: D 117 HIS cc_start: 0.8419 (OUTLIER) cc_final: 0.7313 (m90) REVERT: D 128 MET cc_start: 0.7962 (mmt) cc_final: 0.7703 (mmt) REVERT: D 152 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.8057 (p0) REVERT: D 245 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6846 (mm) REVERT: D 309 MET cc_start: 0.4995 (mmp) cc_final: 0.4774 (mmt) REVERT: D 362 TYR cc_start: 0.7570 (m-80) cc_final: 0.7109 (m-80) REVERT: D 393 MET cc_start: 0.4177 (mmm) cc_final: 0.3745 (mmt) REVERT: D 484 ASN cc_start: 0.9124 (OUTLIER) cc_final: 0.8801 (t0) REVERT: D 584 GLU cc_start: 0.7350 (pp20) cc_final: 0.6724 (pp20) REVERT: D 629 GLN cc_start: 0.3606 (OUTLIER) cc_final: 0.3294 (tt0) REVERT: D 1199 ASP cc_start: 0.8738 (p0) cc_final: 0.8416 (p0) REVERT: D 1641 ASP cc_start: 0.6296 (m-30) cc_final: 0.6076 (m-30) REVERT: D 1897 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8543 (mt) REVERT: D 2174 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7756 (mtp) REVERT: D 2178 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7508 (mm) REVERT: D 2190 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7282 (ptmm) REVERT: D 2198 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.8153 (t80) REVERT: D 2587 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8135 (mt) REVERT: D 2781 MET cc_start: -0.0581 (ptp) cc_final: -0.1491 (mmp) REVERT: D 3045 MET cc_start: 0.5433 (ppp) cc_final: 0.5222 (ppp) REVERT: D 3245 MET cc_start: -0.1493 (mpp) cc_final: -0.1848 (mpp) REVERT: D 3331 MET cc_start: 0.6342 (ppp) cc_final: 0.5423 (tpp) REVERT: D 3672 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7907 (ptp-170) REVERT: D 3718 MET cc_start: 0.7384 (tpp) cc_final: 0.7124 (tpp) REVERT: D 3998 MET cc_start: 0.8718 (tpp) cc_final: 0.8265 (ttt) REVERT: D 4057 TYR cc_start: 0.8361 (t80) cc_final: 0.7819 (m-80) REVERT: D 4082 PHE cc_start: 0.5553 (OUTLIER) cc_final: 0.5076 (p90) REVERT: D 4117 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.8168 (t80) REVERT: D 4747 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7243 (pmm) REVERT: D 4921 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8391 (tp) REVERT: E 6 GLU cc_start: 0.8094 (mp0) cc_final: 0.7861 (mp0) REVERT: E 26 HIS cc_start: 0.7618 (OUTLIER) cc_final: 0.7356 (t-90) REVERT: E 50 ARG cc_start: 0.7843 (ptm-80) cc_final: 0.7594 (tmm160) REVERT: F 6 GLU cc_start: 0.8050 (mp0) cc_final: 0.7817 (mp0) REVERT: F 26 HIS cc_start: 0.7908 (OUTLIER) cc_final: 0.7261 (t-90) REVERT: F 50 ARG cc_start: 0.7793 (ptm-80) cc_final: 0.7541 (tmm160) REVERT: G 26 HIS cc_start: 0.7611 (OUTLIER) cc_final: 0.7355 (t-90) REVERT: G 50 ARG cc_start: 0.7846 (ptm-80) cc_final: 0.7598 (tmm160) REVERT: H 6 GLU cc_start: 0.8015 (mp0) cc_final: 0.7759 (mp0) REVERT: H 26 HIS cc_start: 0.7553 (OUTLIER) cc_final: 0.7338 (t-90) outliers start: 679 outliers final: 367 residues processed: 1631 average time/residue: 0.9967 time to fit residues: 2947.7433 Evaluate side-chains 1406 residues out of total 14384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 429 poor density : 977 time to evaluate : 10.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 484 ASN Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 517 VAL Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 670 TYR Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 716 ASN Chi-restraints excluded: chain A residue 785 ASP Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1007 TRP Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1202 ILE Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1457 PHE Chi-restraints excluded: chain A residue 1467 VAL Chi-restraints excluded: chain A residue 1507 GLU Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1595 VAL Chi-restraints excluded: chain A residue 1609 VAL Chi-restraints excluded: chain A residue 1658 THR Chi-restraints excluded: chain A residue 1774 ASN Chi-restraints excluded: chain A residue 1783 PHE Chi-restraints excluded: chain A residue 1787 ILE Chi-restraints excluded: chain A residue 1814 THR Chi-restraints excluded: chain A residue 1818 LEU Chi-restraints excluded: chain A residue 1819 PHE Chi-restraints excluded: chain A residue 1829 LEU Chi-restraints excluded: chain A residue 1897 LEU Chi-restraints excluded: chain A residue 1917 VAL Chi-restraints excluded: chain A residue 1932 VAL Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2035 VAL Chi-restraints excluded: chain A residue 2060 LEU Chi-restraints excluded: chain A residue 2064 THR Chi-restraints excluded: chain A residue 2112 VAL Chi-restraints excluded: chain A residue 2116 ILE Chi-restraints excluded: chain A residue 2145 LEU Chi-restraints excluded: chain A residue 2150 ASN Chi-restraints excluded: chain A residue 2164 LEU Chi-restraints excluded: chain A residue 2174 MET Chi-restraints excluded: chain A residue 2178 LEU Chi-restraints excluded: chain A residue 2190 LYS Chi-restraints excluded: chain A residue 2192 VAL Chi-restraints excluded: chain A residue 2195 CYS Chi-restraints excluded: chain A residue 2198 PHE Chi-restraints excluded: chain A residue 2202 PHE Chi-restraints excluded: chain A residue 2220 LEU Chi-restraints excluded: chain A residue 2260 ASP Chi-restraints excluded: chain A residue 2265 VAL Chi-restraints excluded: chain A residue 2280 VAL Chi-restraints excluded: chain A residue 2305 VAL Chi-restraints excluded: chain A residue 2308 ASN Chi-restraints excluded: chain A residue 2342 LEU Chi-restraints excluded: chain A residue 2383 MET Chi-restraints excluded: chain A residue 2405 MET Chi-restraints excluded: chain A residue 2408 ILE Chi-restraints excluded: chain A residue 2523 VAL Chi-restraints excluded: chain A residue 2675 LEU Chi-restraints excluded: chain A residue 2682 SER Chi-restraints excluded: chain A residue 3067 LEU Chi-restraints excluded: chain A residue 3262 MET Chi-restraints excluded: chain A residue 3624 GLU Chi-restraints excluded: chain A residue 3672 ARG Chi-restraints excluded: chain A residue 3772 VAL Chi-restraints excluded: chain A residue 3786 VAL Chi-restraints excluded: chain A residue 3934 LEU Chi-restraints excluded: chain A residue 3970 LEU Chi-restraints excluded: chain A residue 3989 VAL Chi-restraints excluded: chain A residue 4054 HIS Chi-restraints excluded: chain A residue 4117 PHE Chi-restraints excluded: chain A residue 4135 ILE Chi-restraints excluded: chain A residue 4515 LEU Chi-restraints excluded: chain A residue 4594 VAL Chi-restraints excluded: chain A residue 4709 LEU Chi-restraints excluded: chain A residue 4711 VAL Chi-restraints excluded: chain A residue 4713 PHE Chi-restraints excluded: chain A residue 4714 THR Chi-restraints excluded: chain A residue 4767 VAL Chi-restraints excluded: chain A residue 4781 THR Chi-restraints excluded: chain A residue 4800 THR Chi-restraints excluded: chain A residue 4807 ASP Chi-restraints excluded: chain A residue 4830 ILE Chi-restraints excluded: chain A residue 4879 VAL Chi-restraints excluded: chain A residue 4921 LEU Chi-restraints excluded: chain A residue 4933 THR Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 670 TYR Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 716 ASN Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 961 VAL Chi-restraints excluded: chain B residue 1007 TRP Chi-restraints excluded: chain B residue 1161 VAL Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1251 LEU Chi-restraints excluded: chain B residue 1304 LEU Chi-restraints excluded: chain B residue 1430 VAL Chi-restraints excluded: chain B residue 1457 PHE Chi-restraints excluded: chain B residue 1467 VAL Chi-restraints excluded: chain B residue 1507 GLU Chi-restraints excluded: chain B residue 1511 VAL Chi-restraints excluded: chain B residue 1534 VAL Chi-restraints excluded: chain B residue 1595 VAL Chi-restraints excluded: chain B residue 1609 VAL Chi-restraints excluded: chain B residue 1658 THR Chi-restraints excluded: chain B residue 1721 MET Chi-restraints excluded: chain B residue 1774 ASN Chi-restraints excluded: chain B residue 1783 PHE Chi-restraints excluded: chain B residue 1787 ILE Chi-restraints excluded: chain B residue 1814 THR Chi-restraints excluded: chain B residue 1818 LEU Chi-restraints excluded: chain B residue 1819 PHE Chi-restraints excluded: chain B residue 1829 LEU Chi-restraints excluded: chain B residue 1897 LEU Chi-restraints excluded: chain B residue 1917 VAL Chi-restraints excluded: chain B residue 1932 VAL Chi-restraints excluded: chain B residue 1991 ILE Chi-restraints excluded: chain B residue 2035 VAL Chi-restraints excluded: chain B residue 2060 LEU Chi-restraints excluded: chain B residue 2064 THR Chi-restraints excluded: chain B residue 2112 VAL Chi-restraints excluded: chain B residue 2116 ILE Chi-restraints excluded: chain B residue 2145 LEU Chi-restraints excluded: chain B residue 2150 ASN Chi-restraints excluded: chain B residue 2164 LEU Chi-restraints excluded: chain B residue 2174 MET Chi-restraints excluded: chain B residue 2178 LEU Chi-restraints excluded: chain B residue 2190 LYS Chi-restraints excluded: chain B residue 2192 VAL Chi-restraints excluded: chain B residue 2195 CYS Chi-restraints excluded: chain B residue 2198 PHE Chi-restraints excluded: chain B residue 2202 PHE Chi-restraints excluded: chain B residue 2220 LEU Chi-restraints excluded: chain B residue 2260 ASP Chi-restraints excluded: chain B residue 2265 VAL Chi-restraints excluded: chain B residue 2280 VAL Chi-restraints excluded: chain B residue 2305 VAL Chi-restraints excluded: chain B residue 2308 ASN Chi-restraints excluded: chain B residue 2342 LEU Chi-restraints excluded: chain B residue 2383 MET Chi-restraints excluded: chain B residue 2405 MET Chi-restraints excluded: chain B residue 2408 ILE Chi-restraints excluded: chain B residue 2523 VAL Chi-restraints excluded: chain B residue 2675 LEU Chi-restraints excluded: chain B residue 2682 SER Chi-restraints excluded: chain B residue 3067 LEU Chi-restraints excluded: chain B residue 3262 MET Chi-restraints excluded: chain B residue 3624 GLU Chi-restraints excluded: chain B residue 3672 ARG Chi-restraints excluded: chain B residue 3772 VAL Chi-restraints excluded: chain B residue 3786 VAL Chi-restraints excluded: chain B residue 3829 LEU Chi-restraints excluded: chain B residue 3934 LEU Chi-restraints excluded: chain B residue 3970 LEU Chi-restraints excluded: chain B residue 3989 VAL Chi-restraints excluded: chain B residue 4054 HIS Chi-restraints excluded: chain B residue 4082 PHE Chi-restraints excluded: chain B residue 4117 PHE Chi-restraints excluded: chain B residue 4135 ILE Chi-restraints excluded: chain B residue 4515 LEU Chi-restraints excluded: chain B residue 4594 VAL Chi-restraints excluded: chain B residue 4709 LEU Chi-restraints excluded: chain B residue 4711 VAL Chi-restraints excluded: chain B residue 4713 PHE Chi-restraints excluded: chain B residue 4714 THR Chi-restraints excluded: chain B residue 4767 VAL Chi-restraints excluded: chain B residue 4781 THR Chi-restraints excluded: chain B residue 4800 THR Chi-restraints excluded: chain B residue 4807 ASP Chi-restraints excluded: chain B residue 4830 ILE Chi-restraints excluded: chain B residue 4879 VAL Chi-restraints excluded: chain B residue 4921 LEU Chi-restraints excluded: chain B residue 4933 THR Chi-restraints excluded: chain C residue 117 HIS Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 484 ASN Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 670 TYR Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 716 ASN Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1007 TRP Chi-restraints excluded: chain C residue 1161 VAL Chi-restraints excluded: chain C residue 1202 ILE Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1304 LEU Chi-restraints excluded: chain C residue 1430 VAL Chi-restraints excluded: chain C residue 1457 PHE Chi-restraints excluded: chain C residue 1467 VAL Chi-restraints excluded: chain C residue 1507 GLU Chi-restraints excluded: chain C residue 1511 VAL Chi-restraints excluded: chain C residue 1534 VAL Chi-restraints excluded: chain C residue 1595 VAL Chi-restraints excluded: chain C residue 1609 VAL Chi-restraints excluded: chain C residue 1658 THR Chi-restraints excluded: chain C residue 1774 ASN Chi-restraints excluded: chain C residue 1783 PHE Chi-restraints excluded: chain C residue 1787 ILE Chi-restraints excluded: chain C residue 1814 THR Chi-restraints excluded: chain C residue 1818 LEU Chi-restraints excluded: chain C residue 1819 PHE Chi-restraints excluded: chain C residue 1829 LEU Chi-restraints excluded: chain C residue 1897 LEU Chi-restraints excluded: chain C residue 1903 LEU Chi-restraints excluded: chain C residue 1917 VAL Chi-restraints excluded: chain C residue 1932 VAL Chi-restraints excluded: chain C residue 1991 ILE Chi-restraints excluded: chain C residue 2035 VAL Chi-restraints excluded: chain C residue 2060 LEU Chi-restraints excluded: chain C residue 2064 THR Chi-restraints excluded: chain C residue 2112 VAL Chi-restraints excluded: chain C residue 2116 ILE Chi-restraints excluded: chain C residue 2145 LEU Chi-restraints excluded: chain C residue 2150 ASN Chi-restraints excluded: chain C residue 2164 LEU Chi-restraints excluded: chain C residue 2174 MET Chi-restraints excluded: chain C residue 2178 LEU Chi-restraints excluded: chain C residue 2190 LYS Chi-restraints excluded: chain C residue 2192 VAL Chi-restraints excluded: chain C residue 2195 CYS Chi-restraints excluded: chain C residue 2198 PHE Chi-restraints excluded: chain C residue 2202 PHE Chi-restraints excluded: chain C residue 2220 LEU Chi-restraints excluded: chain C residue 2260 ASP Chi-restraints excluded: chain C residue 2265 VAL Chi-restraints excluded: chain C residue 2280 VAL Chi-restraints excluded: chain C residue 2305 VAL Chi-restraints excluded: chain C residue 2308 ASN Chi-restraints excluded: chain C residue 2342 LEU Chi-restraints excluded: chain C residue 2383 MET Chi-restraints excluded: chain C residue 2405 MET Chi-restraints excluded: chain C residue 2408 ILE Chi-restraints excluded: chain C residue 2523 VAL Chi-restraints excluded: chain C residue 2526 LEU Chi-restraints excluded: chain C residue 2675 LEU Chi-restraints excluded: chain C residue 2682 SER Chi-restraints excluded: chain C residue 3067 LEU Chi-restraints excluded: chain C residue 3262 MET Chi-restraints excluded: chain C residue 3624 GLU Chi-restraints excluded: chain C residue 3672 ARG Chi-restraints excluded: chain C residue 3772 VAL Chi-restraints excluded: chain C residue 3786 VAL Chi-restraints excluded: chain C residue 3934 LEU Chi-restraints excluded: chain C residue 3970 LEU Chi-restraints excluded: chain C residue 3989 VAL Chi-restraints excluded: chain C residue 4054 HIS Chi-restraints excluded: chain C residue 4082 PHE Chi-restraints excluded: chain C residue 4117 PHE Chi-restraints excluded: chain C residue 4135 ILE Chi-restraints excluded: chain C residue 4515 LEU Chi-restraints excluded: chain C residue 4594 VAL Chi-restraints excluded: chain C residue 4709 LEU Chi-restraints excluded: chain C residue 4711 VAL Chi-restraints excluded: chain C residue 4713 PHE Chi-restraints excluded: chain C residue 4714 THR Chi-restraints excluded: chain C residue 4747 MET Chi-restraints excluded: chain C residue 4767 VAL Chi-restraints excluded: chain C residue 4781 THR Chi-restraints excluded: chain C residue 4800 THR Chi-restraints excluded: chain C residue 4807 ASP Chi-restraints excluded: chain C residue 4830 ILE Chi-restraints excluded: chain C residue 4879 VAL Chi-restraints excluded: chain C residue 4921 LEU Chi-restraints excluded: chain C residue 4933 THR Chi-restraints excluded: chain D residue 117 HIS Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 629 GLN Chi-restraints excluded: chain D residue 632 ILE Chi-restraints excluded: chain D residue 670 TYR Chi-restraints excluded: chain D residue 679 VAL Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 716 ASN Chi-restraints excluded: chain D residue 785 ASP Chi-restraints excluded: chain D residue 798 ILE Chi-restraints excluded: chain D residue 961 VAL Chi-restraints excluded: chain D residue 1007 TRP Chi-restraints excluded: chain D residue 1161 VAL Chi-restraints excluded: chain D residue 1202 ILE Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1304 LEU Chi-restraints excluded: chain D residue 1430 VAL Chi-restraints excluded: chain D residue 1457 PHE Chi-restraints excluded: chain D residue 1467 VAL Chi-restraints excluded: chain D residue 1507 GLU Chi-restraints excluded: chain D residue 1511 VAL Chi-restraints excluded: chain D residue 1534 VAL Chi-restraints excluded: chain D residue 1595 VAL Chi-restraints excluded: chain D residue 1609 VAL Chi-restraints excluded: chain D residue 1658 THR Chi-restraints excluded: chain D residue 1774 ASN Chi-restraints excluded: chain D residue 1783 PHE Chi-restraints excluded: chain D residue 1787 ILE Chi-restraints excluded: chain D residue 1814 THR Chi-restraints excluded: chain D residue 1818 LEU Chi-restraints excluded: chain D residue 1819 PHE Chi-restraints excluded: chain D residue 1829 LEU Chi-restraints excluded: chain D residue 1897 LEU Chi-restraints excluded: chain D residue 1917 VAL Chi-restraints excluded: chain D residue 1932 VAL Chi-restraints excluded: chain D residue 1991 ILE Chi-restraints excluded: chain D residue 2035 VAL Chi-restraints excluded: chain D residue 2060 LEU Chi-restraints excluded: chain D residue 2064 THR Chi-restraints excluded: chain D residue 2112 VAL Chi-restraints excluded: chain D residue 2116 ILE Chi-restraints excluded: chain D residue 2145 LEU Chi-restraints excluded: chain D residue 2150 ASN Chi-restraints excluded: chain D residue 2164 LEU Chi-restraints excluded: chain D residue 2174 MET Chi-restraints excluded: chain D residue 2178 LEU Chi-restraints excluded: chain D residue 2190 LYS Chi-restraints excluded: chain D residue 2192 VAL Chi-restraints excluded: chain D residue 2195 CYS Chi-restraints excluded: chain D residue 2198 PHE Chi-restraints excluded: chain D residue 2202 PHE Chi-restraints excluded: chain D residue 2220 LEU Chi-restraints excluded: chain D residue 2260 ASP Chi-restraints excluded: chain D residue 2265 VAL Chi-restraints excluded: chain D residue 2280 VAL Chi-restraints excluded: chain D residue 2305 VAL Chi-restraints excluded: chain D residue 2308 ASN Chi-restraints excluded: chain D residue 2342 LEU Chi-restraints excluded: chain D residue 2383 MET Chi-restraints excluded: chain D residue 2405 MET Chi-restraints excluded: chain D residue 2408 ILE Chi-restraints excluded: chain D residue 2523 VAL Chi-restraints excluded: chain D residue 2526 LEU Chi-restraints excluded: chain D residue 2587 LEU Chi-restraints excluded: chain D residue 2675 LEU Chi-restraints excluded: chain D residue 2682 SER Chi-restraints excluded: chain D residue 3067 LEU Chi-restraints excluded: chain D residue 3262 MET Chi-restraints excluded: chain D residue 3624 GLU Chi-restraints excluded: chain D residue 3672 ARG Chi-restraints excluded: chain D residue 3772 VAL Chi-restraints excluded: chain D residue 3786 VAL Chi-restraints excluded: chain D residue 3934 LEU Chi-restraints excluded: chain D residue 3970 LEU Chi-restraints excluded: chain D residue 3989 VAL Chi-restraints excluded: chain D residue 4054 HIS Chi-restraints excluded: chain D residue 4082 PHE Chi-restraints excluded: chain D residue 4117 PHE Chi-restraints excluded: chain D residue 4135 ILE Chi-restraints excluded: chain D residue 4515 LEU Chi-restraints excluded: chain D residue 4594 VAL Chi-restraints excluded: chain D residue 4709 LEU Chi-restraints excluded: chain D residue 4711 VAL Chi-restraints excluded: chain D residue 4713 PHE Chi-restraints excluded: chain D residue 4714 THR Chi-restraints excluded: chain D residue 4747 MET Chi-restraints excluded: chain D residue 4767 VAL Chi-restraints excluded: chain D residue 4781 THR Chi-restraints excluded: chain D residue 4800 THR Chi-restraints excluded: chain D residue 4807 ASP Chi-restraints excluded: chain D residue 4830 ILE Chi-restraints excluded: chain D residue 4879 VAL Chi-restraints excluded: chain D residue 4921 LEU Chi-restraints excluded: chain D residue 4933 THR Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain F residue 15 THR Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 95 ASN Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain H residue 95 ASN Chi-restraints excluded: chain H residue 102 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1640 random chunks: chunk 1474 optimal weight: 50.0000 chunk 1121 optimal weight: 0.9980 chunk 774 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 712 optimal weight: 0.9980 chunk 1001 optimal weight: 0.9990 chunk 1497 optimal weight: 50.0000 chunk 1585 optimal weight: 0.6980 chunk 782 optimal weight: 0.6980 chunk 1419 optimal weight: 7.9990 chunk 427 optimal weight: 3.9990 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 202 HIS ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 GLN A 992 GLN ** A1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1845 GLN ** A2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2157 HIS A2340 ASN ** A2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3617 ASN A3773 GLN A3850 ASN A4628 GLN A4642 ASN A4932 HIS B 202 HIS ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 GLN B 992 GLN B1216 ASN ** B1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1845 GLN ** B2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2157 HIS ** B2223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2340 ASN ** B2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3617 ASN B4628 GLN B4642 ASN B4932 HIS C 202 HIS C 410 HIS ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 669 GLN C 992 GLN ** C1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1845 GLN ** C2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2157 HIS C2340 ASN ** C2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3617 ASN C3773 GLN C3850 ASN C4642 ASN D 202 HIS D 365 HIS D 410 HIS ** D 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 GLN D 992 GLN D1216 ASN ** D1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1845 GLN ** D2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2157 HIS D2340 ASN ** D2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3617 ASN D3773 GLN D3850 ASN D4642 ASN D4932 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 131440 Z= 0.181 Angle : 0.566 9.182 177752 Z= 0.286 Chirality : 0.039 0.194 19688 Planarity : 0.004 0.078 22980 Dihedral : 4.363 47.835 17668 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.20 % Favored : 93.65 % Rotamer: Outliers : 2.92 % Allowed : 17.81 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.07), residues: 16228 helix: 1.60 (0.06), residues: 7420 sheet: -0.70 (0.17), residues: 1032 loop : -2.41 (0.06), residues: 7776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 893 HIS 0.008 0.001 HIS D1267 PHE 0.027 0.001 PHE A1783 TYR 0.031 0.001 TYR B2037 ARG 0.011 0.000 ARG D2197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32456 Ramachandran restraints generated. 16228 Oldfield, 0 Emsley, 16228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32456 Ramachandran restraints generated. 16228 Oldfield, 0 Emsley, 16228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1460 residues out of total 14384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 400 poor density : 1060 time to evaluate : 10.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.5012 (mmp) cc_final: 0.4774 (mmt) REVERT: A 362 TYR cc_start: 0.7658 (m-80) cc_final: 0.7214 (m-80) REVERT: A 419 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8055 (tp) REVERT: A 494 MET cc_start: 0.0349 (OUTLIER) cc_final: -0.0148 (mtt) REVERT: A 678 MET cc_start: 0.7773 (tpp) cc_final: 0.7468 (tpp) REVERT: A 789 PHE cc_start: 0.5250 (OUTLIER) cc_final: 0.5048 (p90) REVERT: A 935 MET cc_start: 0.5895 (tmm) cc_final: 0.4523 (ptt) REVERT: A 1199 ASP cc_start: 0.8624 (p0) cc_final: 0.8351 (p0) REVERT: A 1641 ASP cc_start: 0.6308 (m-30) cc_final: 0.6061 (m-30) REVERT: A 2174 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7771 (mtp) REVERT: A 2190 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.6867 (ptmm) REVERT: A 2233 MET cc_start: 0.8301 (mmm) cc_final: 0.8074 (mmm) REVERT: A 2247 MET cc_start: 0.8548 (tpt) cc_final: 0.8256 (tpt) REVERT: A 2388 MET cc_start: 0.5723 (ppp) cc_final: 0.5507 (ppp) REVERT: A 2408 ILE cc_start: 0.8275 (mm) cc_final: 0.8057 (tt) REVERT: A 2781 MET cc_start: -0.0078 (ptp) cc_final: -0.0817 (mmp) REVERT: A 3245 MET cc_start: -0.1661 (mpp) cc_final: -0.1970 (mpp) REVERT: A 3331 MET cc_start: 0.6342 (ppp) cc_final: 0.5424 (tpp) REVERT: A 3998 MET cc_start: 0.8478 (tpp) cc_final: 0.8175 (ttt) REVERT: A 4862 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.6455 (mp10) REVERT: B 362 TYR cc_start: 0.7589 (m-80) cc_final: 0.7091 (m-80) REVERT: B 419 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8047 (tp) REVERT: B 494 MET cc_start: 0.0342 (OUTLIER) cc_final: -0.0156 (mtt) REVERT: B 935 MET cc_start: 0.5807 (tmm) cc_final: 0.4592 (ptt) REVERT: B 981 MET cc_start: 0.1067 (ppp) cc_final: 0.0062 (ptp) REVERT: B 1199 ASP cc_start: 0.8622 (p0) cc_final: 0.8383 (p0) REVERT: B 1641 ASP cc_start: 0.6311 (m-30) cc_final: 0.6037 (m-30) REVERT: B 2174 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7754 (mtp) REVERT: B 2190 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.6934 (ptmm) REVERT: B 2233 MET cc_start: 0.8287 (mmm) cc_final: 0.8056 (mmm) REVERT: B 2247 MET cc_start: 0.8546 (tpt) cc_final: 0.8253 (tpt) REVERT: B 2388 MET cc_start: 0.5762 (ppp) cc_final: 0.5543 (ppp) REVERT: B 2408 ILE cc_start: 0.8257 (mm) cc_final: 0.8034 (tt) REVERT: B 2781 MET cc_start: -0.0078 (ptp) cc_final: -0.0823 (mmp) REVERT: B 3240 MET cc_start: 0.8048 (mmm) cc_final: 0.7574 (tmm) REVERT: B 3245 MET cc_start: -0.1524 (mpp) cc_final: -0.1897 (mpp) REVERT: B 3331 MET cc_start: 0.6306 (ppp) cc_final: 0.5443 (tpp) REVERT: B 3718 MET cc_start: 0.7137 (tpp) cc_final: 0.6920 (tpp) REVERT: B 3998 MET cc_start: 0.8482 (tpp) cc_final: 0.8165 (ttt) REVERT: B 4082 PHE cc_start: 0.5731 (OUTLIER) cc_final: 0.4401 (p90) REVERT: B 4862 GLN cc_start: 0.7867 (OUTLIER) cc_final: 0.6441 (mp10) REVERT: C 309 MET cc_start: 0.5027 (mmp) cc_final: 0.4792 (mmt) REVERT: C 362 TYR cc_start: 0.7608 (m-80) cc_final: 0.7176 (m-80) REVERT: C 419 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.7941 (tp) REVERT: C 494 MET cc_start: 0.0342 (OUTLIER) cc_final: -0.0154 (mtt) REVERT: C 678 MET cc_start: 0.7772 (tpp) cc_final: 0.7469 (tpp) REVERT: C 789 PHE cc_start: 0.5275 (OUTLIER) cc_final: 0.5074 (p90) REVERT: C 935 MET cc_start: 0.5697 (tmm) cc_final: 0.4477 (ptt) REVERT: C 1199 ASP cc_start: 0.8620 (p0) cc_final: 0.8344 (p0) REVERT: C 1290 PHE cc_start: 0.4054 (m-10) cc_final: 0.3851 (m-10) REVERT: C 1641 ASP cc_start: 0.6317 (m-30) cc_final: 0.6064 (m-30) REVERT: C 2174 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7754 (mtp) REVERT: C 2190 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.6932 (ptmm) REVERT: C 2233 MET cc_start: 0.8336 (mmm) cc_final: 0.8104 (mmm) REVERT: C 2247 MET cc_start: 0.8537 (tpt) cc_final: 0.8238 (tpt) REVERT: C 2388 MET cc_start: 0.5736 (ppp) cc_final: 0.5518 (ppp) REVERT: C 2408 ILE cc_start: 0.8274 (mm) cc_final: 0.8058 (tt) REVERT: C 2781 MET cc_start: -0.0125 (ptp) cc_final: -0.0870 (mmp) REVERT: C 3240 MET cc_start: 0.8069 (mmm) cc_final: 0.7542 (tmm) REVERT: C 3245 MET cc_start: -0.1619 (mpp) cc_final: -0.1921 (mpp) REVERT: C 3331 MET cc_start: 0.6333 (ppp) cc_final: 0.5420 (tpp) REVERT: C 3718 MET cc_start: 0.7154 (tpp) cc_final: 0.6853 (tpp) REVERT: C 3998 MET cc_start: 0.8476 (tpp) cc_final: 0.8171 (ttt) REVERT: C 4082 PHE cc_start: 0.5656 (OUTLIER) cc_final: 0.4361 (p90) REVERT: C 4747 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.6674 (pmm) REVERT: C 4862 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.6449 (mp10) REVERT: D 362 TYR cc_start: 0.7614 (m-80) cc_final: 0.7179 (m-80) REVERT: D 419 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.7943 (tp) REVERT: D 494 MET cc_start: 0.0340 (OUTLIER) cc_final: -0.0162 (mtt) REVERT: D 678 MET cc_start: 0.7779 (tpp) cc_final: 0.7471 (tpp) REVERT: D 789 PHE cc_start: 0.5272 (OUTLIER) cc_final: 0.5072 (p90) REVERT: D 935 MET cc_start: 0.5900 (tmm) cc_final: 0.4528 (ptt) REVERT: D 1199 ASP cc_start: 0.8618 (p0) cc_final: 0.8314 (p0) REVERT: D 1290 PHE cc_start: 0.4055 (m-10) cc_final: 0.3850 (m-10) REVERT: D 1641 ASP cc_start: 0.6317 (m-30) cc_final: 0.6081 (m-30) REVERT: D 2174 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7769 (mtp) REVERT: D 2190 LYS cc_start: 0.7584 (OUTLIER) cc_final: 0.6921 (ptmm) REVERT: D 2233 MET cc_start: 0.8325 (mmm) cc_final: 0.8081 (mmm) REVERT: D 2388 MET cc_start: 0.5760 (ppp) cc_final: 0.5543 (ppp) REVERT: D 2408 ILE cc_start: 0.8254 (mm) cc_final: 0.8037 (tt) REVERT: D 2587 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8183 (mt) REVERT: D 2781 MET cc_start: -0.0065 (ptp) cc_final: -0.0846 (mmp) REVERT: D 3240 MET cc_start: 0.8072 (mmm) cc_final: 0.7539 (tmm) REVERT: D 3245 MET cc_start: -0.1635 (mpp) cc_final: -0.1940 (mpp) REVERT: D 3331 MET cc_start: 0.6348 (ppp) cc_final: 0.5466 (tpp) REVERT: D 3718 MET cc_start: 0.7154 (tpp) cc_final: 0.6877 (tpp) REVERT: D 3998 MET cc_start: 0.8475 (tpp) cc_final: 0.8163 (ttt) REVERT: D 4747 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6686 (pmm) REVERT: D 4862 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.6437 (mp10) REVERT: E 6 GLU cc_start: 0.7997 (mp0) cc_final: 0.7739 (mp0) REVERT: E 26 HIS cc_start: 0.7790 (OUTLIER) cc_final: 0.7298 (t-90) REVERT: F 6 GLU cc_start: 0.8001 (mp0) cc_final: 0.7751 (mp0) REVERT: F 26 HIS cc_start: 0.7731 (OUTLIER) cc_final: 0.7252 (t-90) REVERT: G 26 HIS cc_start: 0.7781 (OUTLIER) cc_final: 0.7284 (t-90) REVERT: H 26 HIS cc_start: 0.7782 (OUTLIER) cc_final: 0.7290 (t-90) outliers start: 400 outliers final: 231 residues processed: 1376 average time/residue: 1.0088 time to fit residues: 2509.6666 Evaluate side-chains 1259 residues out of total 14384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 996 time to evaluate : 9.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 670 TYR Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 789 PHE Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 1007 TRP Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1202 ILE Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1457 PHE Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1722 MET Chi-restraints excluded: chain A residue 1783 PHE Chi-restraints excluded: chain A residue 1787 ILE Chi-restraints excluded: chain A residue 1818 LEU Chi-restraints excluded: chain A residue 1819 PHE Chi-restraints excluded: chain A residue 1932 VAL Chi-restraints excluded: chain A residue 1952 MET Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2060 LEU Chi-restraints excluded: chain A residue 2091 TYR Chi-restraints excluded: chain A residue 2114 ASP Chi-restraints excluded: chain A residue 2174 MET Chi-restraints excluded: chain A residue 2190 LYS Chi-restraints excluded: chain A residue 2202 PHE Chi-restraints excluded: chain A residue 2250 ASN Chi-restraints excluded: chain A residue 2260 ASP Chi-restraints excluded: chain A residue 2383 MET Chi-restraints excluded: chain A residue 2416 ILE Chi-restraints excluded: chain A residue 2472 ASP Chi-restraints excluded: chain A residue 2483 LEU Chi-restraints excluded: chain A residue 2595 VAL Chi-restraints excluded: chain A residue 2682 SER Chi-restraints excluded: chain A residue 3200 VAL Chi-restraints excluded: chain A residue 3262 MET Chi-restraints excluded: chain A residue 3616 VAL Chi-restraints excluded: chain A residue 3786 VAL Chi-restraints excluded: chain A residue 3829 LEU Chi-restraints excluded: chain A residue 3846 CYS Chi-restraints excluded: chain A residue 3857 LEU Chi-restraints excluded: chain A residue 3934 LEU Chi-restraints excluded: chain A residue 3985 LEU Chi-restraints excluded: chain A residue 3989 VAL Chi-restraints excluded: chain A residue 4054 HIS Chi-restraints excluded: chain A residue 4514 ILE Chi-restraints excluded: chain A residue 4515 LEU Chi-restraints excluded: chain A residue 4556 VAL Chi-restraints excluded: chain A residue 4709 LEU Chi-restraints excluded: chain A residue 4713 PHE Chi-restraints excluded: chain A residue 4830 ILE Chi-restraints excluded: chain A residue 4862 GLN Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 419 ILE Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 630 HIS Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 670 TYR Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 1007 TRP Chi-restraints excluded: chain B residue 1166 VAL Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1297 THR Chi-restraints excluded: chain B residue 1304 LEU Chi-restraints excluded: chain B residue 1457 PHE Chi-restraints excluded: chain B residue 1511 VAL Chi-restraints excluded: chain B residue 1544 VAL Chi-restraints excluded: chain B residue 1783 PHE Chi-restraints excluded: chain B residue 1787 ILE Chi-restraints excluded: chain B residue 1818 LEU Chi-restraints excluded: chain B residue 1819 PHE Chi-restraints excluded: chain B residue 1952 MET Chi-restraints excluded: chain B residue 1991 ILE Chi-restraints excluded: chain B residue 2060 LEU Chi-restraints excluded: chain B residue 2091 TYR Chi-restraints excluded: chain B residue 2114 ASP Chi-restraints excluded: chain B residue 2174 MET Chi-restraints excluded: chain B residue 2190 LYS Chi-restraints excluded: chain B residue 2202 PHE Chi-restraints excluded: chain B residue 2250 ASN Chi-restraints excluded: chain B residue 2260 ASP Chi-restraints excluded: chain B residue 2383 MET Chi-restraints excluded: chain B residue 2416 ILE Chi-restraints excluded: chain B residue 2472 ASP Chi-restraints excluded: chain B residue 2483 LEU Chi-restraints excluded: chain B residue 2595 VAL Chi-restraints excluded: chain B residue 2682 SER Chi-restraints excluded: chain B residue 3200 VAL Chi-restraints excluded: chain B residue 3262 MET Chi-restraints excluded: chain B residue 3616 VAL Chi-restraints excluded: chain B residue 3786 VAL Chi-restraints excluded: chain B residue 3846 CYS Chi-restraints excluded: chain B residue 3857 LEU Chi-restraints excluded: chain B residue 3934 LEU Chi-restraints excluded: chain B residue 3985 LEU Chi-restraints excluded: chain B residue 3989 VAL Chi-restraints excluded: chain B residue 4054 HIS Chi-restraints excluded: chain B residue 4082 PHE Chi-restraints excluded: chain B residue 4514 ILE Chi-restraints excluded: chain B residue 4515 LEU Chi-restraints excluded: chain B residue 4556 VAL Chi-restraints excluded: chain B residue 4709 LEU Chi-restraints excluded: chain B residue 4713 PHE Chi-restraints excluded: chain B residue 4830 ILE Chi-restraints excluded: chain B residue 4862 GLN Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 424 PHE Chi-restraints excluded: chain C residue 494 MET Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 630 HIS Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 670 TYR Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 789 PHE Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 1007 TRP Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1202 ILE Chi-restraints excluded: chain C residue 1297 THR Chi-restraints excluded: chain C residue 1304 LEU Chi-restraints excluded: chain C residue 1457 PHE Chi-restraints excluded: chain C residue 1511 VAL Chi-restraints excluded: chain C residue 1544 VAL Chi-restraints excluded: chain C residue 1722 MET Chi-restraints excluded: chain C residue 1768 SER Chi-restraints excluded: chain C residue 1783 PHE Chi-restraints excluded: chain C residue 1818 LEU Chi-restraints excluded: chain C residue 1819 PHE Chi-restraints excluded: chain C residue 1952 MET Chi-restraints excluded: chain C residue 1991 ILE Chi-restraints excluded: chain C residue 2060 LEU Chi-restraints excluded: chain C residue 2091 TYR Chi-restraints excluded: chain C residue 2114 ASP Chi-restraints excluded: chain C residue 2174 MET Chi-restraints excluded: chain C residue 2190 LYS Chi-restraints excluded: chain C residue 2202 PHE Chi-restraints excluded: chain C residue 2250 ASN Chi-restraints excluded: chain C residue 2260 ASP Chi-restraints excluded: chain C residue 2383 MET Chi-restraints excluded: chain C residue 2416 ILE Chi-restraints excluded: chain C residue 2472 ASP Chi-restraints excluded: chain C residue 2483 LEU Chi-restraints excluded: chain C residue 2595 VAL Chi-restraints excluded: chain C residue 2682 SER Chi-restraints excluded: chain C residue 3200 VAL Chi-restraints excluded: chain C residue 3262 MET Chi-restraints excluded: chain C residue 3616 VAL Chi-restraints excluded: chain C residue 3786 VAL Chi-restraints excluded: chain C residue 3829 LEU Chi-restraints excluded: chain C residue 3846 CYS Chi-restraints excluded: chain C residue 3857 LEU Chi-restraints excluded: chain C residue 3934 LEU Chi-restraints excluded: chain C residue 3985 LEU Chi-restraints excluded: chain C residue 3989 VAL Chi-restraints excluded: chain C residue 4054 HIS Chi-restraints excluded: chain C residue 4082 PHE Chi-restraints excluded: chain C residue 4514 ILE Chi-restraints excluded: chain C residue 4515 LEU Chi-restraints excluded: chain C residue 4556 VAL Chi-restraints excluded: chain C residue 4709 LEU Chi-restraints excluded: chain C residue 4713 PHE Chi-restraints excluded: chain C residue 4747 MET Chi-restraints excluded: chain C residue 4830 ILE Chi-restraints excluded: chain C residue 4862 GLN Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 424 PHE Chi-restraints excluded: chain D residue 494 MET Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 630 HIS Chi-restraints excluded: chain D residue 632 ILE Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 670 TYR Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 789 PHE Chi-restraints excluded: chain D residue 798 ILE Chi-restraints excluded: chain D residue 1007 TRP Chi-restraints excluded: chain D residue 1166 VAL Chi-restraints excluded: chain D residue 1202 ILE Chi-restraints excluded: chain D residue 1297 THR Chi-restraints excluded: chain D residue 1304 LEU Chi-restraints excluded: chain D residue 1457 PHE Chi-restraints excluded: chain D residue 1511 VAL Chi-restraints excluded: chain D residue 1544 VAL Chi-restraints excluded: chain D residue 1600 MET Chi-restraints excluded: chain D residue 1722 MET Chi-restraints excluded: chain D residue 1783 PHE Chi-restraints excluded: chain D residue 1787 ILE Chi-restraints excluded: chain D residue 1818 LEU Chi-restraints excluded: chain D residue 1819 PHE Chi-restraints excluded: chain D residue 1952 MET Chi-restraints excluded: chain D residue 1991 ILE Chi-restraints excluded: chain D residue 2060 LEU Chi-restraints excluded: chain D residue 2091 TYR Chi-restraints excluded: chain D residue 2114 ASP Chi-restraints excluded: chain D residue 2174 MET Chi-restraints excluded: chain D residue 2190 LYS Chi-restraints excluded: chain D residue 2202 PHE Chi-restraints excluded: chain D residue 2250 ASN Chi-restraints excluded: chain D residue 2260 ASP Chi-restraints excluded: chain D residue 2280 VAL Chi-restraints excluded: chain D residue 2383 MET Chi-restraints excluded: chain D residue 2416 ILE Chi-restraints excluded: chain D residue 2472 ASP Chi-restraints excluded: chain D residue 2483 LEU Chi-restraints excluded: chain D residue 2587 LEU Chi-restraints excluded: chain D residue 2595 VAL Chi-restraints excluded: chain D residue 2682 SER Chi-restraints excluded: chain D residue 3200 VAL Chi-restraints excluded: chain D residue 3262 MET Chi-restraints excluded: chain D residue 3616 VAL Chi-restraints excluded: chain D residue 3786 VAL Chi-restraints excluded: chain D residue 3829 LEU Chi-restraints excluded: chain D residue 3846 CYS Chi-restraints excluded: chain D residue 3857 LEU Chi-restraints excluded: chain D residue 3934 LEU Chi-restraints excluded: chain D residue 3985 LEU Chi-restraints excluded: chain D residue 3989 VAL Chi-restraints excluded: chain D residue 4054 HIS Chi-restraints excluded: chain D residue 4514 ILE Chi-restraints excluded: chain D residue 4515 LEU Chi-restraints excluded: chain D residue 4556 VAL Chi-restraints excluded: chain D residue 4709 LEU Chi-restraints excluded: chain D residue 4713 PHE Chi-restraints excluded: chain D residue 4747 MET Chi-restraints excluded: chain D residue 4830 ILE Chi-restraints excluded: chain D residue 4862 GLN Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 38 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1640 random chunks: chunk 1320 optimal weight: 9.9990 chunk 899 optimal weight: 30.0000 chunk 23 optimal weight: 0.2980 chunk 1180 optimal weight: 1.9990 chunk 654 optimal weight: 40.0000 chunk 1352 optimal weight: 4.9990 chunk 1095 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 809 optimal weight: 10.0000 chunk 1422 optimal weight: 10.0000 chunk 400 optimal weight: 10.0000 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2340 ASN ** A2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3773 GLN ** B 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1216 ASN ** B1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2340 ASN ** B2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 410 HIS ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2340 ASN ** C2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3773 GLN ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 HIS ** D 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1216 ASN ** D1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2340 ASN ** D2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3773 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 131440 Z= 0.337 Angle : 0.618 9.614 177752 Z= 0.312 Chirality : 0.041 0.240 19688 Planarity : 0.004 0.071 22980 Dihedral : 4.361 49.648 17668 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.77 % Favored : 92.08 % Rotamer: Outliers : 3.69 % Allowed : 17.75 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.07), residues: 16228 helix: 1.64 (0.06), residues: 7420 sheet: -0.82 (0.17), residues: 1044 loop : -2.44 (0.06), residues: 7764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 893 HIS 0.018 0.001 HIS D1267 PHE 0.025 0.002 PHE B4845 TYR 0.020 0.001 TYR D4938 ARG 0.009 0.000 ARG B2197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32456 Ramachandran restraints generated. 16228 Oldfield, 0 Emsley, 16228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32456 Ramachandran restraints generated. 16228 Oldfield, 0 Emsley, 16228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1549 residues out of total 14384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 504 poor density : 1045 time to evaluate : 10.752 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 152 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8232 (p0) REVERT: A 245 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6648 (mm) REVERT: A 362 TYR cc_start: 0.7720 (m-80) cc_final: 0.7261 (m-80) REVERT: A 420 ARG cc_start: 0.7653 (ppt170) cc_final: 0.7316 (ppt170) REVERT: A 474 ASP cc_start: 0.8529 (t70) cc_final: 0.8113 (t0) REVERT: A 484 ASN cc_start: 0.9151 (OUTLIER) cc_final: 0.8857 (t0) REVERT: A 494 MET cc_start: 0.0848 (OUTLIER) cc_final: 0.0351 (mtt) REVERT: A 617 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8519 (mp) REVERT: A 629 GLN cc_start: 0.3886 (OUTLIER) cc_final: 0.3443 (tt0) REVERT: A 1199 ASP cc_start: 0.8687 (p0) cc_final: 0.8417 (p0) REVERT: A 1251 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7298 (pp) REVERT: A 2174 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7922 (mtp) REVERT: A 2190 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.7061 (ptmm) REVERT: A 2247 MET cc_start: 0.8625 (tpt) cc_final: 0.8368 (tpt) REVERT: A 2781 MET cc_start: -0.0110 (ptp) cc_final: -0.0851 (mmp) REVERT: A 3240 MET cc_start: 0.8032 (mmm) cc_final: 0.7501 (tmm) REVERT: A 3331 MET cc_start: 0.6318 (ppp) cc_final: 0.5418 (tpp) REVERT: A 3998 MET cc_start: 0.8528 (tpp) cc_final: 0.8193 (ttt) REVERT: A 4024 ASP cc_start: 0.3958 (OUTLIER) cc_final: 0.3559 (p0) REVERT: A 4082 PHE cc_start: 0.5692 (OUTLIER) cc_final: 0.4317 (p90) REVERT: A 4811 CYS cc_start: 0.7525 (OUTLIER) cc_final: 0.6697 (t) REVERT: A 4862 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.6585 (mp10) REVERT: B 152 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8237 (p0) REVERT: B 245 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6632 (mm) REVERT: B 362 TYR cc_start: 0.7549 (m-80) cc_final: 0.7080 (m-80) REVERT: B 420 ARG cc_start: 0.7658 (ppt170) cc_final: 0.7310 (ppt170) REVERT: B 474 ASP cc_start: 0.8437 (t70) cc_final: 0.8148 (t0) REVERT: B 484 ASN cc_start: 0.9149 (OUTLIER) cc_final: 0.8858 (t0) REVERT: B 494 MET cc_start: 0.0831 (OUTLIER) cc_final: 0.0142 (mtt) REVERT: B 629 GLN cc_start: 0.3914 (OUTLIER) cc_final: 0.3559 (tt0) REVERT: B 981 MET cc_start: 0.0903 (ppp) cc_final: -0.0068 (ptp) REVERT: B 1174 MET cc_start: 0.5583 (ptp) cc_final: 0.4946 (ppp) REVERT: B 1194 ASP cc_start: 0.6942 (t0) cc_final: 0.6664 (t0) REVERT: B 1199 ASP cc_start: 0.8714 (p0) cc_final: 0.8424 (p0) REVERT: B 1251 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7206 (pp) REVERT: B 2174 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7930 (mtp) REVERT: B 2190 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7059 (ptmm) REVERT: B 2247 MET cc_start: 0.8626 (tpt) cc_final: 0.8366 (tpt) REVERT: B 2781 MET cc_start: -0.0107 (ptp) cc_final: -0.0855 (mmp) REVERT: B 3240 MET cc_start: 0.8009 (mmm) cc_final: 0.7525 (tmm) REVERT: B 3331 MET cc_start: 0.6295 (ppp) cc_final: 0.5439 (tpp) REVERT: B 3624 GLU cc_start: 0.4885 (OUTLIER) cc_final: 0.4647 (mt-10) REVERT: B 3718 MET cc_start: 0.7347 (tpp) cc_final: 0.7055 (tpp) REVERT: B 3998 MET cc_start: 0.8542 (tpp) cc_final: 0.8211 (ttt) REVERT: B 4024 ASP cc_start: 0.4179 (OUTLIER) cc_final: 0.3896 (p0) REVERT: B 4082 PHE cc_start: 0.5662 (OUTLIER) cc_final: 0.4330 (p90) REVERT: B 4490 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8203 (mp) REVERT: B 4811 CYS cc_start: 0.7546 (OUTLIER) cc_final: 0.6795 (t) REVERT: B 4862 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.6575 (mp10) REVERT: C 152 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8231 (p0) REVERT: C 245 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6629 (mm) REVERT: C 309 MET cc_start: 0.5133 (mmp) cc_final: 0.4909 (mmt) REVERT: C 362 TYR cc_start: 0.7592 (m-80) cc_final: 0.7129 (m-80) REVERT: C 420 ARG cc_start: 0.7660 (ppt170) cc_final: 0.7312 (ppt170) REVERT: C 474 ASP cc_start: 0.8438 (t70) cc_final: 0.8145 (t0) REVERT: C 484 ASN cc_start: 0.9162 (OUTLIER) cc_final: 0.8872 (t0) REVERT: C 494 MET cc_start: 0.0840 (OUTLIER) cc_final: 0.0370 (mtt) REVERT: C 535 GLU cc_start: 0.6964 (tt0) cc_final: 0.6613 (mm-30) REVERT: C 629 GLN cc_start: 0.3878 (OUTLIER) cc_final: 0.3442 (tt0) REVERT: C 651 HIS cc_start: 0.6329 (OUTLIER) cc_final: 0.5795 (m-70) REVERT: C 789 PHE cc_start: 0.5713 (OUTLIER) cc_final: 0.5511 (p90) REVERT: C 1199 ASP cc_start: 0.8685 (p0) cc_final: 0.8410 (p0) REVERT: C 1251 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7193 (pp) REVERT: C 2174 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7921 (mtp) REVERT: C 2190 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7064 (ptmm) REVERT: C 2247 MET cc_start: 0.8614 (tpt) cc_final: 0.8352 (tpt) REVERT: C 2781 MET cc_start: -0.0098 (ptp) cc_final: -0.0859 (mmp) REVERT: C 3331 MET cc_start: 0.6320 (ppp) cc_final: 0.5418 (tpp) REVERT: C 3718 MET cc_start: 0.7207 (tpp) cc_final: 0.6952 (tpp) REVERT: C 3998 MET cc_start: 0.8532 (tpp) cc_final: 0.8196 (ttt) REVERT: C 4024 ASP cc_start: 0.3980 (OUTLIER) cc_final: 0.3657 (p0) REVERT: C 4082 PHE cc_start: 0.5591 (OUTLIER) cc_final: 0.4281 (p90) REVERT: C 4747 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6741 (pmm) REVERT: C 4811 CYS cc_start: 0.7520 (OUTLIER) cc_final: 0.6690 (t) REVERT: C 4862 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.6580 (mp10) REVERT: D 152 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8226 (p0) REVERT: D 245 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6646 (mm) REVERT: D 362 TYR cc_start: 0.7648 (m-80) cc_final: 0.7196 (m-80) REVERT: D 420 ARG cc_start: 0.7670 (ppt170) cc_final: 0.7323 (ppt170) REVERT: D 474 ASP cc_start: 0.8433 (t70) cc_final: 0.8150 (t0) REVERT: D 484 ASN cc_start: 0.9161 (OUTLIER) cc_final: 0.8871 (t0) REVERT: D 494 MET cc_start: 0.0838 (OUTLIER) cc_final: 0.0367 (mtt) REVERT: D 535 GLU cc_start: 0.6965 (tt0) cc_final: 0.6614 (mm-30) REVERT: D 617 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8495 (mp) REVERT: D 651 HIS cc_start: 0.6330 (OUTLIER) cc_final: 0.5794 (m-70) REVERT: D 789 PHE cc_start: 0.5710 (OUTLIER) cc_final: 0.5510 (p90) REVERT: D 1199 ASP cc_start: 0.8684 (p0) cc_final: 0.8406 (p0) REVERT: D 1216 ASN cc_start: 0.5788 (OUTLIER) cc_final: 0.5044 (t0) REVERT: D 1251 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7190 (pp) REVERT: D 1762 MET cc_start: 0.8166 (ttp) cc_final: 0.7952 (ttp) REVERT: D 2174 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7921 (mtp) REVERT: D 2190 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7048 (ptmm) REVERT: D 2247 MET cc_start: 0.8591 (tpt) cc_final: 0.8325 (tpt) REVERT: D 2781 MET cc_start: -0.0093 (ptp) cc_final: -0.0856 (mmp) REVERT: D 3331 MET cc_start: 0.6334 (ppp) cc_final: 0.5465 (tpp) REVERT: D 3718 MET cc_start: 0.7202 (tpp) cc_final: 0.6947 (tpp) REVERT: D 3998 MET cc_start: 0.8524 (tpp) cc_final: 0.8192 (ttt) REVERT: D 4024 ASP cc_start: 0.3979 (OUTLIER) cc_final: 0.3659 (p0) REVERT: D 4082 PHE cc_start: 0.5571 (OUTLIER) cc_final: 0.4269 (p90) REVERT: D 4747 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.6729 (pmm) REVERT: D 4811 CYS cc_start: 0.7520 (OUTLIER) cc_final: 0.6690 (t) REVERT: D 4862 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.6573 (mp10) REVERT: E 6 GLU cc_start: 0.8035 (mp0) cc_final: 0.7743 (mp0) REVERT: E 26 HIS cc_start: 0.8009 (OUTLIER) cc_final: 0.7393 (t-90) REVERT: F 6 GLU cc_start: 0.8060 (mp0) cc_final: 0.7784 (mp0) REVERT: F 26 HIS cc_start: 0.7901 (OUTLIER) cc_final: 0.7497 (t-90) REVERT: G 26 HIS cc_start: 0.8010 (OUTLIER) cc_final: 0.7387 (t-90) REVERT: H 26 HIS cc_start: 0.7979 (OUTLIER) cc_final: 0.7352 (t-90) outliers start: 504 outliers final: 304 residues processed: 1446 average time/residue: 1.0289 time to fit residues: 2689.4793 Evaluate side-chains 1356 residues out of total 14384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 366 poor density : 990 time to evaluate : 10.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 484 ASN Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 670 TYR Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 716 ASN Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 1007 TRP Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1202 ILE Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1457 PHE Chi-restraints excluded: chain A residue 1467 VAL Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1722 MET Chi-restraints excluded: chain A residue 1783 PHE Chi-restraints excluded: chain A residue 1787 ILE Chi-restraints excluded: chain A residue 1814 THR Chi-restraints excluded: chain A residue 1818 LEU Chi-restraints excluded: chain A residue 1819 PHE Chi-restraints excluded: chain A residue 1828 THR Chi-restraints excluded: chain A residue 1932 VAL Chi-restraints excluded: chain A residue 1952 MET Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2060 LEU Chi-restraints excluded: chain A residue 2091 TYR Chi-restraints excluded: chain A residue 2129 LEU Chi-restraints excluded: chain A residue 2150 ASN Chi-restraints excluded: chain A residue 2174 MET Chi-restraints excluded: chain A residue 2190 LYS Chi-restraints excluded: chain A residue 2250 ASN Chi-restraints excluded: chain A residue 2260 ASP Chi-restraints excluded: chain A residue 2280 VAL Chi-restraints excluded: chain A residue 2308 ASN Chi-restraints excluded: chain A residue 2342 LEU Chi-restraints excluded: chain A residue 2383 MET Chi-restraints excluded: chain A residue 2405 MET Chi-restraints excluded: chain A residue 2416 ILE Chi-restraints excluded: chain A residue 2472 ASP Chi-restraints excluded: chain A residue 2483 LEU Chi-restraints excluded: chain A residue 2583 MET Chi-restraints excluded: chain A residue 2595 VAL Chi-restraints excluded: chain A residue 2682 SER Chi-restraints excluded: chain A residue 3200 VAL Chi-restraints excluded: chain A residue 3262 MET Chi-restraints excluded: chain A residue 3616 VAL Chi-restraints excluded: chain A residue 3782 GLU Chi-restraints excluded: chain A residue 3786 VAL Chi-restraints excluded: chain A residue 3829 LEU Chi-restraints excluded: chain A residue 3846 CYS Chi-restraints excluded: chain A residue 3934 LEU Chi-restraints excluded: chain A residue 3958 SER Chi-restraints excluded: chain A residue 3970 LEU Chi-restraints excluded: chain A residue 3985 LEU Chi-restraints excluded: chain A residue 3989 VAL Chi-restraints excluded: chain A residue 4024 ASP Chi-restraints excluded: chain A residue 4054 HIS Chi-restraints excluded: chain A residue 4082 PHE Chi-restraints excluded: chain A residue 4108 MET Chi-restraints excluded: chain A residue 4155 SER Chi-restraints excluded: chain A residue 4172 ILE Chi-restraints excluded: chain A residue 4515 LEU Chi-restraints excluded: chain A residue 4556 VAL Chi-restraints excluded: chain A residue 4594 VAL Chi-restraints excluded: chain A residue 4659 PHE Chi-restraints excluded: chain A residue 4709 LEU Chi-restraints excluded: chain A residue 4713 PHE Chi-restraints excluded: chain A residue 4800 THR Chi-restraints excluded: chain A residue 4807 ASP Chi-restraints excluded: chain A residue 4811 CYS Chi-restraints excluded: chain A residue 4813 MET Chi-restraints excluded: chain A residue 4830 ILE Chi-restraints excluded: chain A residue 4862 GLN Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 629 GLN Chi-restraints excluded: chain B residue 630 HIS Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 670 TYR Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 716 ASN Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 1007 TRP Chi-restraints excluded: chain B residue 1166 VAL Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1216 ASN Chi-restraints excluded: chain B residue 1251 LEU Chi-restraints excluded: chain B residue 1297 THR Chi-restraints excluded: chain B residue 1457 PHE Chi-restraints excluded: chain B residue 1467 VAL Chi-restraints excluded: chain B residue 1511 VAL Chi-restraints excluded: chain B residue 1534 VAL Chi-restraints excluded: chain B residue 1600 MET Chi-restraints excluded: chain B residue 1783 PHE Chi-restraints excluded: chain B residue 1787 ILE Chi-restraints excluded: chain B residue 1814 THR Chi-restraints excluded: chain B residue 1818 LEU Chi-restraints excluded: chain B residue 1819 PHE Chi-restraints excluded: chain B residue 1991 ILE Chi-restraints excluded: chain B residue 2060 LEU Chi-restraints excluded: chain B residue 2091 TYR Chi-restraints excluded: chain B residue 2129 LEU Chi-restraints excluded: chain B residue 2150 ASN Chi-restraints excluded: chain B residue 2174 MET Chi-restraints excluded: chain B residue 2190 LYS Chi-restraints excluded: chain B residue 2250 ASN Chi-restraints excluded: chain B residue 2260 ASP Chi-restraints excluded: chain B residue 2280 VAL Chi-restraints excluded: chain B residue 2308 ASN Chi-restraints excluded: chain B residue 2342 LEU Chi-restraints excluded: chain B residue 2383 MET Chi-restraints excluded: chain B residue 2416 ILE Chi-restraints excluded: chain B residue 2472 ASP Chi-restraints excluded: chain B residue 2483 LEU Chi-restraints excluded: chain B residue 2583 MET Chi-restraints excluded: chain B residue 2595 VAL Chi-restraints excluded: chain B residue 2682 SER Chi-restraints excluded: chain B residue 3200 VAL Chi-restraints excluded: chain B residue 3262 MET Chi-restraints excluded: chain B residue 3616 VAL Chi-restraints excluded: chain B residue 3624 GLU Chi-restraints excluded: chain B residue 3782 GLU Chi-restraints excluded: chain B residue 3786 VAL Chi-restraints excluded: chain B residue 3829 LEU Chi-restraints excluded: chain B residue 3846 CYS Chi-restraints excluded: chain B residue 3934 LEU Chi-restraints excluded: chain B residue 3958 SER Chi-restraints excluded: chain B residue 3970 LEU Chi-restraints excluded: chain B residue 3985 LEU Chi-restraints excluded: chain B residue 3989 VAL Chi-restraints excluded: chain B residue 4024 ASP Chi-restraints excluded: chain B residue 4054 HIS Chi-restraints excluded: chain B residue 4082 PHE Chi-restraints excluded: chain B residue 4172 ILE Chi-restraints excluded: chain B residue 4490 LEU Chi-restraints excluded: chain B residue 4515 LEU Chi-restraints excluded: chain B residue 4556 VAL Chi-restraints excluded: chain B residue 4594 VAL Chi-restraints excluded: chain B residue 4659 PHE Chi-restraints excluded: chain B residue 4709 LEU Chi-restraints excluded: chain B residue 4713 PHE Chi-restraints excluded: chain B residue 4800 THR Chi-restraints excluded: chain B residue 4807 ASP Chi-restraints excluded: chain B residue 4811 CYS Chi-restraints excluded: chain B residue 4813 MET Chi-restraints excluded: chain B residue 4830 ILE Chi-restraints excluded: chain B residue 4862 GLN Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 152 ASP Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 424 PHE Chi-restraints excluded: chain C residue 484 ASN Chi-restraints excluded: chain C residue 494 MET Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 629 GLN Chi-restraints excluded: chain C residue 630 HIS Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 670 TYR Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 789 PHE Chi-restraints excluded: chain C residue 798 ILE Chi-restraints excluded: chain C residue 1007 TRP Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1202 ILE Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1297 THR Chi-restraints excluded: chain C residue 1457 PHE Chi-restraints excluded: chain C residue 1467 VAL Chi-restraints excluded: chain C residue 1511 VAL Chi-restraints excluded: chain C residue 1534 VAL Chi-restraints excluded: chain C residue 1722 MET Chi-restraints excluded: chain C residue 1783 PHE Chi-restraints excluded: chain C residue 1787 ILE Chi-restraints excluded: chain C residue 1814 THR Chi-restraints excluded: chain C residue 1818 LEU Chi-restraints excluded: chain C residue 1819 PHE Chi-restraints excluded: chain C residue 1828 THR Chi-restraints excluded: chain C residue 1903 LEU Chi-restraints excluded: chain C residue 1952 MET Chi-restraints excluded: chain C residue 1991 ILE Chi-restraints excluded: chain C residue 2060 LEU Chi-restraints excluded: chain C residue 2091 TYR Chi-restraints excluded: chain C residue 2129 LEU Chi-restraints excluded: chain C residue 2150 ASN Chi-restraints excluded: chain C residue 2174 MET Chi-restraints excluded: chain C residue 2190 LYS Chi-restraints excluded: chain C residue 2202 PHE Chi-restraints excluded: chain C residue 2250 ASN Chi-restraints excluded: chain C residue 2260 ASP Chi-restraints excluded: chain C residue 2280 VAL Chi-restraints excluded: chain C residue 2308 ASN Chi-restraints excluded: chain C residue 2342 LEU Chi-restraints excluded: chain C residue 2383 MET Chi-restraints excluded: chain C residue 2405 MET Chi-restraints excluded: chain C residue 2416 ILE Chi-restraints excluded: chain C residue 2472 ASP Chi-restraints excluded: chain C residue 2483 LEU Chi-restraints excluded: chain C residue 2595 VAL Chi-restraints excluded: chain C residue 2682 SER Chi-restraints excluded: chain C residue 3200 VAL Chi-restraints excluded: chain C residue 3262 MET Chi-restraints excluded: chain C residue 3616 VAL Chi-restraints excluded: chain C residue 3782 GLU Chi-restraints excluded: chain C residue 3786 VAL Chi-restraints excluded: chain C residue 3829 LEU Chi-restraints excluded: chain C residue 3934 LEU Chi-restraints excluded: chain C residue 3958 SER Chi-restraints excluded: chain C residue 3970 LEU Chi-restraints excluded: chain C residue 3985 LEU Chi-restraints excluded: chain C residue 3989 VAL Chi-restraints excluded: chain C residue 4024 ASP Chi-restraints excluded: chain C residue 4046 ASP Chi-restraints excluded: chain C residue 4054 HIS Chi-restraints excluded: chain C residue 4082 PHE Chi-restraints excluded: chain C residue 4108 MET Chi-restraints excluded: chain C residue 4155 SER Chi-restraints excluded: chain C residue 4172 ILE Chi-restraints excluded: chain C residue 4515 LEU Chi-restraints excluded: chain C residue 4556 VAL Chi-restraints excluded: chain C residue 4594 VAL Chi-restraints excluded: chain C residue 4659 PHE Chi-restraints excluded: chain C residue 4709 LEU Chi-restraints excluded: chain C residue 4713 PHE Chi-restraints excluded: chain C residue 4747 MET Chi-restraints excluded: chain C residue 4800 THR Chi-restraints excluded: chain C residue 4807 ASP Chi-restraints excluded: chain C residue 4811 CYS Chi-restraints excluded: chain C residue 4813 MET Chi-restraints excluded: chain C residue 4830 ILE Chi-restraints excluded: chain C residue 4862 GLN Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 424 PHE Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain D residue 494 MET Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 630 HIS Chi-restraints excluded: chain D residue 632 ILE Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 670 TYR Chi-restraints excluded: chain D residue 679 VAL Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 716 ASN Chi-restraints excluded: chain D residue 789 PHE Chi-restraints excluded: chain D residue 798 ILE Chi-restraints excluded: chain D residue 1007 TRP Chi-restraints excluded: chain D residue 1166 VAL Chi-restraints excluded: chain D residue 1202 ILE Chi-restraints excluded: chain D residue 1216 ASN Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1297 THR Chi-restraints excluded: chain D residue 1457 PHE Chi-restraints excluded: chain D residue 1467 VAL Chi-restraints excluded: chain D residue 1511 VAL Chi-restraints excluded: chain D residue 1534 VAL Chi-restraints excluded: chain D residue 1722 MET Chi-restraints excluded: chain D residue 1783 PHE Chi-restraints excluded: chain D residue 1787 ILE Chi-restraints excluded: chain D residue 1814 THR Chi-restraints excluded: chain D residue 1818 LEU Chi-restraints excluded: chain D residue 1819 PHE Chi-restraints excluded: chain D residue 1829 LEU Chi-restraints excluded: chain D residue 1952 MET Chi-restraints excluded: chain D residue 1991 ILE Chi-restraints excluded: chain D residue 2060 LEU Chi-restraints excluded: chain D residue 2091 TYR Chi-restraints excluded: chain D residue 2129 LEU Chi-restraints excluded: chain D residue 2150 ASN Chi-restraints excluded: chain D residue 2174 MET Chi-restraints excluded: chain D residue 2190 LYS Chi-restraints excluded: chain D residue 2250 ASN Chi-restraints excluded: chain D residue 2260 ASP Chi-restraints excluded: chain D residue 2280 VAL Chi-restraints excluded: chain D residue 2308 ASN Chi-restraints excluded: chain D residue 2342 LEU Chi-restraints excluded: chain D residue 2383 MET Chi-restraints excluded: chain D residue 2416 ILE Chi-restraints excluded: chain D residue 2472 ASP Chi-restraints excluded: chain D residue 2483 LEU Chi-restraints excluded: chain D residue 2583 MET Chi-restraints excluded: chain D residue 2595 VAL Chi-restraints excluded: chain D residue 2682 SER Chi-restraints excluded: chain D residue 3200 VAL Chi-restraints excluded: chain D residue 3262 MET Chi-restraints excluded: chain D residue 3616 VAL Chi-restraints excluded: chain D residue 3782 GLU Chi-restraints excluded: chain D residue 3786 VAL Chi-restraints excluded: chain D residue 3829 LEU Chi-restraints excluded: chain D residue 3934 LEU Chi-restraints excluded: chain D residue 3958 SER Chi-restraints excluded: chain D residue 3970 LEU Chi-restraints excluded: chain D residue 3985 LEU Chi-restraints excluded: chain D residue 3989 VAL Chi-restraints excluded: chain D residue 4024 ASP Chi-restraints excluded: chain D residue 4046 ASP Chi-restraints excluded: chain D residue 4054 HIS Chi-restraints excluded: chain D residue 4082 PHE Chi-restraints excluded: chain D residue 4108 MET Chi-restraints excluded: chain D residue 4155 SER Chi-restraints excluded: chain D residue 4172 ILE Chi-restraints excluded: chain D residue 4515 LEU Chi-restraints excluded: chain D residue 4556 VAL Chi-restraints excluded: chain D residue 4594 VAL Chi-restraints excluded: chain D residue 4659 PHE Chi-restraints excluded: chain D residue 4709 LEU Chi-restraints excluded: chain D residue 4713 PHE Chi-restraints excluded: chain D residue 4747 MET Chi-restraints excluded: chain D residue 4800 THR Chi-restraints excluded: chain D residue 4807 ASP Chi-restraints excluded: chain D residue 4811 CYS Chi-restraints excluded: chain D residue 4813 MET Chi-restraints excluded: chain D residue 4830 ILE Chi-restraints excluded: chain D residue 4862 GLN Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 38 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1640 random chunks: chunk 533 optimal weight: 20.0000 chunk 1427 optimal weight: 4.9990 chunk 313 optimal weight: 0.5980 chunk 930 optimal weight: 7.9990 chunk 391 optimal weight: 0.8980 chunk 1586 optimal weight: 0.6980 chunk 1317 optimal weight: 0.0570 chunk 734 optimal weight: 2.9990 chunk 131 optimal weight: 8.9990 chunk 524 optimal weight: 30.0000 chunk 833 optimal weight: 20.0000 overall best weight: 1.0500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 669 GLN ** A1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2340 ASN ** A2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 GLN B1216 ASN ** B1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2340 ASN ** B2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 669 GLN ** C1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2340 ASN ** C2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4932 HIS ** D 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 GLN D1216 ASN ** D1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2340 ASN ** D2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 131440 Z= 0.169 Angle : 0.546 10.809 177752 Z= 0.272 Chirality : 0.038 0.206 19688 Planarity : 0.004 0.067 22980 Dihedral : 4.115 48.387 17668 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.68 % Favored : 93.20 % Rotamer: Outliers : 3.04 % Allowed : 18.65 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.07), residues: 16228 helix: 1.87 (0.06), residues: 7416 sheet: -0.63 (0.17), residues: 992 loop : -2.36 (0.06), residues: 7820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 893 HIS 0.006 0.001 HIS A2463 PHE 0.023 0.001 PHE B 685 TYR 0.029 0.001 TYR B2037 ARG 0.012 0.000 ARG F 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32456 Ramachandran restraints generated. 16228 Oldfield, 0 Emsley, 16228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32456 Ramachandran restraints generated. 16228 Oldfield, 0 Emsley, 16228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1467 residues out of total 14384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 416 poor density : 1051 time to evaluate : 10.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7193 (tm-30) REVERT: A 245 LEU cc_start: 0.6738 (OUTLIER) cc_final: 0.6408 (mm) REVERT: A 362 TYR cc_start: 0.7729 (m-80) cc_final: 0.7349 (m-80) REVERT: A 484 ASN cc_start: 0.9107 (OUTLIER) cc_final: 0.8802 (t0) REVERT: A 494 MET cc_start: 0.1208 (OUTLIER) cc_final: 0.0572 (mtt) REVERT: A 678 MET cc_start: 0.7831 (tpp) cc_final: 0.7078 (tpt) REVERT: A 895 MET cc_start: 0.5023 (mmp) cc_final: 0.4007 (mtp) REVERT: A 935 MET cc_start: 0.5671 (tmm) cc_final: 0.4359 (ptt) REVERT: A 1199 ASP cc_start: 0.8646 (p0) cc_final: 0.8414 (p0) REVERT: A 1730 MET cc_start: 0.7252 (mmm) cc_final: 0.7042 (mmt) REVERT: A 2174 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7907 (mtp) REVERT: A 2190 LYS cc_start: 0.7232 (OUTLIER) cc_final: 0.6617 (ptmm) REVERT: A 2247 MET cc_start: 0.8557 (tpt) cc_final: 0.8300 (tpt) REVERT: A 2579 LEU cc_start: 0.7610 (pp) cc_final: 0.7363 (pt) REVERT: A 2781 MET cc_start: -0.0172 (ptp) cc_final: -0.0878 (mmp) REVERT: A 3045 MET cc_start: 0.5443 (ppp) cc_final: 0.5186 (ppp) REVERT: A 3240 MET cc_start: 0.8066 (mmm) cc_final: 0.7532 (tmm) REVERT: A 3245 MET cc_start: -0.1553 (mmm) cc_final: -0.2289 (mpp) REVERT: A 3331 MET cc_start: 0.6301 (ppp) cc_final: 0.5424 (tpp) REVERT: A 3661 ASP cc_start: 0.4955 (OUTLIER) cc_final: 0.4490 (m-30) REVERT: A 3998 MET cc_start: 0.8470 (tpp) cc_final: 0.8201 (ttt) REVERT: A 4024 ASP cc_start: 0.4070 (OUTLIER) cc_final: 0.3817 (p0) REVERT: A 4082 PHE cc_start: 0.5675 (OUTLIER) cc_final: 0.4382 (p90) REVERT: A 4862 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.6421 (mp10) REVERT: A 4948 TRP cc_start: 0.8137 (m-10) cc_final: 0.7641 (m-10) REVERT: B 156 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7126 (tm-30) REVERT: B 362 TYR cc_start: 0.7621 (m-80) cc_final: 0.7179 (m-80) REVERT: B 484 ASN cc_start: 0.9098 (OUTLIER) cc_final: 0.8807 (t0) REVERT: B 494 MET cc_start: 0.1130 (OUTLIER) cc_final: 0.0502 (mtt) REVERT: B 651 HIS cc_start: 0.6235 (OUTLIER) cc_final: 0.5728 (m-70) REVERT: B 935 MET cc_start: 0.5682 (tmm) cc_final: 0.4451 (ptt) REVERT: B 981 MET cc_start: 0.0938 (ppp) cc_final: -0.0086 (ptp) REVERT: B 1174 MET cc_start: 0.5587 (ptp) cc_final: 0.4991 (ppp) REVERT: B 1199 ASP cc_start: 0.8626 (p0) cc_final: 0.8335 (p0) REVERT: B 2174 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7739 (ttp) REVERT: B 2190 LYS cc_start: 0.7237 (OUTLIER) cc_final: 0.6615 (ptmm) REVERT: B 2247 MET cc_start: 0.8556 (tpt) cc_final: 0.8297 (tpt) REVERT: B 2579 LEU cc_start: 0.7609 (pp) cc_final: 0.7363 (pt) REVERT: B 2781 MET cc_start: -0.0113 (ptp) cc_final: -0.0864 (mmp) REVERT: B 3045 MET cc_start: 0.5256 (ppp) cc_final: 0.5005 (ppp) REVERT: B 3240 MET cc_start: 0.8086 (mmm) cc_final: 0.7599 (tmm) REVERT: B 3331 MET cc_start: 0.6308 (ppp) cc_final: 0.5428 (tpp) REVERT: B 3998 MET cc_start: 0.8474 (tpp) cc_final: 0.8207 (ttt) REVERT: B 4024 ASP cc_start: 0.4097 (OUTLIER) cc_final: 0.3873 (p0) REVERT: B 4082 PHE cc_start: 0.5600 (OUTLIER) cc_final: 0.4282 (p90) REVERT: B 4811 CYS cc_start: 0.7265 (OUTLIER) cc_final: 0.6259 (t) REVERT: B 4862 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.6345 (mp10) REVERT: B 4948 TRP cc_start: 0.8128 (m-10) cc_final: 0.7636 (m-10) REVERT: C 156 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7195 (tm-30) REVERT: C 245 LEU cc_start: 0.6625 (OUTLIER) cc_final: 0.6280 (mm) REVERT: C 362 TYR cc_start: 0.7663 (m-80) cc_final: 0.7231 (m-80) REVERT: C 484 ASN cc_start: 0.9094 (OUTLIER) cc_final: 0.8804 (t0) REVERT: C 494 MET cc_start: 0.1206 (OUTLIER) cc_final: 0.0573 (mtt) REVERT: C 535 GLU cc_start: 0.7161 (tt0) cc_final: 0.6714 (mm-30) REVERT: C 651 HIS cc_start: 0.6330 (OUTLIER) cc_final: 0.5894 (m-70) REVERT: C 678 MET cc_start: 0.7893 (tpp) cc_final: 0.7604 (tpp) REVERT: C 895 MET cc_start: 0.5046 (mmp) cc_final: 0.4033 (mtp) REVERT: C 935 MET cc_start: 0.5708 (tmm) cc_final: 0.4442 (ptt) REVERT: C 1199 ASP cc_start: 0.8644 (p0) cc_final: 0.8388 (p0) REVERT: C 1730 MET cc_start: 0.7244 (mmm) cc_final: 0.7038 (mmt) REVERT: C 2174 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7902 (mtp) REVERT: C 2190 LYS cc_start: 0.7236 (OUTLIER) cc_final: 0.6627 (ptmm) REVERT: C 2233 MET cc_start: 0.8347 (mmm) cc_final: 0.8128 (mmm) REVERT: C 2247 MET cc_start: 0.8544 (tpt) cc_final: 0.8278 (tpt) REVERT: C 2781 MET cc_start: -0.0106 (ptp) cc_final: -0.0843 (mmp) REVERT: C 3240 MET cc_start: 0.8168 (mmm) cc_final: 0.7654 (tmm) REVERT: C 3245 MET cc_start: -0.1521 (mmm) cc_final: -0.2253 (mpp) REVERT: C 3331 MET cc_start: 0.6299 (ppp) cc_final: 0.5414 (tpp) REVERT: C 3661 ASP cc_start: 0.4967 (OUTLIER) cc_final: 0.4501 (m-30) REVERT: C 3718 MET cc_start: 0.7215 (tpp) cc_final: 0.6902 (tpp) REVERT: C 3998 MET cc_start: 0.8472 (tpp) cc_final: 0.8201 (ttt) REVERT: C 4024 ASP cc_start: 0.4062 (OUTLIER) cc_final: 0.3813 (p0) REVERT: C 4082 PHE cc_start: 0.5605 (OUTLIER) cc_final: 0.4336 (p90) REVERT: C 4862 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.6343 (mp10) REVERT: C 4948 TRP cc_start: 0.8138 (m-10) cc_final: 0.7644 (m-10) REVERT: D 156 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7247 (tm-30) REVERT: D 245 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.6286 (mm) REVERT: D 362 TYR cc_start: 0.7668 (m-80) cc_final: 0.7232 (m-80) REVERT: D 484 ASN cc_start: 0.9103 (OUTLIER) cc_final: 0.8805 (t0) REVERT: D 494 MET cc_start: 0.1200 (OUTLIER) cc_final: 0.0564 (mtt) REVERT: D 535 GLU cc_start: 0.7181 (tt0) cc_final: 0.6675 (mm-30) REVERT: D 651 HIS cc_start: 0.6328 (OUTLIER) cc_final: 0.5810 (m-70) REVERT: D 678 MET cc_start: 0.7898 (tpp) cc_final: 0.7609 (tpp) REVERT: D 895 MET cc_start: 0.5050 (mmp) cc_final: 0.4041 (mtp) REVERT: D 935 MET cc_start: 0.5669 (tmm) cc_final: 0.4362 (ptt) REVERT: D 1199 ASP cc_start: 0.8639 (p0) cc_final: 0.8382 (p0) REVERT: D 1605 LEU cc_start: 0.6325 (OUTLIER) cc_final: 0.5892 (mt) REVERT: D 1730 MET cc_start: 0.7198 (mmm) cc_final: 0.6987 (mmt) REVERT: D 2174 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7906 (mtp) REVERT: D 2190 LYS cc_start: 0.7229 (OUTLIER) cc_final: 0.6616 (ptmm) REVERT: D 2247 MET cc_start: 0.8542 (tpt) cc_final: 0.8272 (tpt) REVERT: D 2587 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8217 (mt) REVERT: D 2781 MET cc_start: -0.0153 (ptp) cc_final: -0.0883 (mmp) REVERT: D 3240 MET cc_start: 0.8175 (mmm) cc_final: 0.7658 (tmm) REVERT: D 3245 MET cc_start: -0.1552 (mmm) cc_final: -0.2281 (mpp) REVERT: D 3331 MET cc_start: 0.6303 (ppp) cc_final: 0.5416 (tpp) REVERT: D 3718 MET cc_start: 0.7213 (tpp) cc_final: 0.6928 (tpp) REVERT: D 3998 MET cc_start: 0.8467 (tpp) cc_final: 0.8195 (ttt) REVERT: D 4024 ASP cc_start: 0.4064 (OUTLIER) cc_final: 0.3821 (p0) REVERT: D 4082 PHE cc_start: 0.5618 (OUTLIER) cc_final: 0.4369 (p90) REVERT: D 4862 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.6351 (mp10) REVERT: D 4948 TRP cc_start: 0.8118 (m-10) cc_final: 0.7627 (m-10) REVERT: E 6 GLU cc_start: 0.8083 (mp0) cc_final: 0.7814 (mp0) REVERT: E 26 HIS cc_start: 0.7911 (OUTLIER) cc_final: 0.7274 (t-90) REVERT: F 6 GLU cc_start: 0.8096 (mp0) cc_final: 0.7822 (mp0) REVERT: F 26 HIS cc_start: 0.7998 (OUTLIER) cc_final: 0.7407 (t-90) REVERT: G 6 GLU cc_start: 0.8101 (mp0) cc_final: 0.7715 (mp0) REVERT: G 26 HIS cc_start: 0.7908 (OUTLIER) cc_final: 0.7264 (t-90) REVERT: H 6 GLU cc_start: 0.8140 (mp0) cc_final: 0.7761 (mp0) REVERT: H 26 HIS cc_start: 0.7907 (OUTLIER) cc_final: 0.7269 (t-90) outliers start: 416 outliers final: 258 residues processed: 1369 average time/residue: 0.9721 time to fit residues: 2403.9779 Evaluate side-chains 1313 residues out of total 14384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 1008 time to evaluate : 10.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 484 ASN Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 670 TYR Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 1007 TRP Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1467 VAL Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1722 MET Chi-restraints excluded: chain A residue 1783 PHE Chi-restraints excluded: chain A residue 1787 ILE Chi-restraints excluded: chain A residue 1818 LEU Chi-restraints excluded: chain A residue 1819 PHE Chi-restraints excluded: chain A residue 1952 MET Chi-restraints excluded: chain A residue 1991 ILE Chi-restraints excluded: chain A residue 2060 LEU Chi-restraints excluded: chain A residue 2091 TYR Chi-restraints excluded: chain A residue 2129 LEU Chi-restraints excluded: chain A residue 2174 MET Chi-restraints excluded: chain A residue 2190 LYS Chi-restraints excluded: chain A residue 2250 ASN Chi-restraints excluded: chain A residue 2260 ASP Chi-restraints excluded: chain A residue 2280 VAL Chi-restraints excluded: chain A residue 2308 ASN Chi-restraints excluded: chain A residue 2355 ASP Chi-restraints excluded: chain A residue 2383 MET Chi-restraints excluded: chain A residue 2395 ILE Chi-restraints excluded: chain A residue 2416 ILE Chi-restraints excluded: chain A residue 2472 ASP Chi-restraints excluded: chain A residue 2583 MET Chi-restraints excluded: chain A residue 2595 VAL Chi-restraints excluded: chain A residue 2682 SER Chi-restraints excluded: chain A residue 3200 VAL Chi-restraints excluded: chain A residue 3262 MET Chi-restraints excluded: chain A residue 3616 VAL Chi-restraints excluded: chain A residue 3624 GLU Chi-restraints excluded: chain A residue 3661 ASP Chi-restraints excluded: chain A residue 3782 GLU Chi-restraints excluded: chain A residue 3829 LEU Chi-restraints excluded: chain A residue 3846 CYS Chi-restraints excluded: chain A residue 3934 LEU Chi-restraints excluded: chain A residue 3985 LEU Chi-restraints excluded: chain A residue 3989 VAL Chi-restraints excluded: chain A residue 4011 MET Chi-restraints excluded: chain A residue 4016 PHE Chi-restraints excluded: chain A residue 4024 ASP Chi-restraints excluded: chain A residue 4046 ASP Chi-restraints excluded: chain A residue 4054 HIS Chi-restraints excluded: chain A residue 4082 PHE Chi-restraints excluded: chain A residue 4108 MET Chi-restraints excluded: chain A residue 4556 VAL Chi-restraints excluded: chain A residue 4659 PHE Chi-restraints excluded: chain A residue 4709 LEU Chi-restraints excluded: chain A residue 4713 PHE Chi-restraints excluded: chain A residue 4807 ASP Chi-restraints excluded: chain A residue 4813 MET Chi-restraints excluded: chain A residue 4830 ILE Chi-restraints excluded: chain A residue 4862 GLN Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 630 HIS Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 670 TYR Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 1007 TRP Chi-restraints excluded: chain B residue 1166 VAL Chi-restraints excluded: chain B residue 1297 THR Chi-restraints excluded: chain B residue 1467 VAL Chi-restraints excluded: chain B residue 1511 VAL Chi-restraints excluded: chain B residue 1544 VAL Chi-restraints excluded: chain B residue 1783 PHE Chi-restraints excluded: chain B residue 1787 ILE Chi-restraints excluded: chain B residue 1818 LEU Chi-restraints excluded: chain B residue 1819 PHE Chi-restraints excluded: chain B residue 1952 MET Chi-restraints excluded: chain B residue 1991 ILE Chi-restraints excluded: chain B residue 2060 LEU Chi-restraints excluded: chain B residue 2091 TYR Chi-restraints excluded: chain B residue 2129 LEU Chi-restraints excluded: chain B residue 2174 MET Chi-restraints excluded: chain B residue 2190 LYS Chi-restraints excluded: chain B residue 2250 ASN Chi-restraints excluded: chain B residue 2260 ASP Chi-restraints excluded: chain B residue 2280 VAL Chi-restraints excluded: chain B residue 2308 ASN Chi-restraints excluded: chain B residue 2355 ASP Chi-restraints excluded: chain B residue 2383 MET Chi-restraints excluded: chain B residue 2395 ILE Chi-restraints excluded: chain B residue 2416 ILE Chi-restraints excluded: chain B residue 2472 ASP Chi-restraints excluded: chain B residue 2583 MET Chi-restraints excluded: chain B residue 2595 VAL Chi-restraints excluded: chain B residue 2682 SER Chi-restraints excluded: chain B residue 3200 VAL Chi-restraints excluded: chain B residue 3262 MET Chi-restraints excluded: chain B residue 3616 VAL Chi-restraints excluded: chain B residue 3782 GLU Chi-restraints excluded: chain B residue 3846 CYS Chi-restraints excluded: chain B residue 3934 LEU Chi-restraints excluded: chain B residue 3985 LEU Chi-restraints excluded: chain B residue 3989 VAL Chi-restraints excluded: chain B residue 4016 PHE Chi-restraints excluded: chain B residue 4024 ASP Chi-restraints excluded: chain B residue 4054 HIS Chi-restraints excluded: chain B residue 4082 PHE Chi-restraints excluded: chain B residue 4155 SER Chi-restraints excluded: chain B residue 4556 VAL Chi-restraints excluded: chain B residue 4659 PHE Chi-restraints excluded: chain B residue 4709 LEU Chi-restraints excluded: chain B residue 4713 PHE Chi-restraints excluded: chain B residue 4807 ASP Chi-restraints excluded: chain B residue 4811 CYS Chi-restraints excluded: chain B residue 4813 MET Chi-restraints excluded: chain B residue 4830 ILE Chi-restraints excluded: chain B residue 4862 GLN Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 424 PHE Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 484 ASN Chi-restraints excluded: chain C residue 494 MET Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 630 HIS Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 670 TYR Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 716 ASN Chi-restraints excluded: chain C residue 1007 TRP Chi-restraints excluded: chain C residue 1297 THR Chi-restraints excluded: chain C residue 1467 VAL Chi-restraints excluded: chain C residue 1511 VAL Chi-restraints excluded: chain C residue 1544 VAL Chi-restraints excluded: chain C residue 1722 MET Chi-restraints excluded: chain C residue 1783 PHE Chi-restraints excluded: chain C residue 1818 LEU Chi-restraints excluded: chain C residue 1819 PHE Chi-restraints excluded: chain C residue 1903 LEU Chi-restraints excluded: chain C residue 1952 MET Chi-restraints excluded: chain C residue 1991 ILE Chi-restraints excluded: chain C residue 2060 LEU Chi-restraints excluded: chain C residue 2091 TYR Chi-restraints excluded: chain C residue 2129 LEU Chi-restraints excluded: chain C residue 2164 LEU Chi-restraints excluded: chain C residue 2174 MET Chi-restraints excluded: chain C residue 2190 LYS Chi-restraints excluded: chain C residue 2250 ASN Chi-restraints excluded: chain C residue 2260 ASP Chi-restraints excluded: chain C residue 2280 VAL Chi-restraints excluded: chain C residue 2308 ASN Chi-restraints excluded: chain C residue 2355 ASP Chi-restraints excluded: chain C residue 2383 MET Chi-restraints excluded: chain C residue 2395 ILE Chi-restraints excluded: chain C residue 2416 ILE Chi-restraints excluded: chain C residue 2472 ASP Chi-restraints excluded: chain C residue 2526 LEU Chi-restraints excluded: chain C residue 2583 MET Chi-restraints excluded: chain C residue 2595 VAL Chi-restraints excluded: chain C residue 2682 SER Chi-restraints excluded: chain C residue 3200 VAL Chi-restraints excluded: chain C residue 3262 MET Chi-restraints excluded: chain C residue 3616 VAL Chi-restraints excluded: chain C residue 3624 GLU Chi-restraints excluded: chain C residue 3661 ASP Chi-restraints excluded: chain C residue 3782 GLU Chi-restraints excluded: chain C residue 3829 LEU Chi-restraints excluded: chain C residue 3846 CYS Chi-restraints excluded: chain C residue 3934 LEU Chi-restraints excluded: chain C residue 3985 LEU Chi-restraints excluded: chain C residue 3989 VAL Chi-restraints excluded: chain C residue 4011 MET Chi-restraints excluded: chain C residue 4016 PHE Chi-restraints excluded: chain C residue 4024 ASP Chi-restraints excluded: chain C residue 4054 HIS Chi-restraints excluded: chain C residue 4078 ASP Chi-restraints excluded: chain C residue 4082 PHE Chi-restraints excluded: chain C residue 4108 MET Chi-restraints excluded: chain C residue 4556 VAL Chi-restraints excluded: chain C residue 4659 PHE Chi-restraints excluded: chain C residue 4709 LEU Chi-restraints excluded: chain C residue 4713 PHE Chi-restraints excluded: chain C residue 4807 ASP Chi-restraints excluded: chain C residue 4813 MET Chi-restraints excluded: chain C residue 4830 ILE Chi-restraints excluded: chain C residue 4862 GLN Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain D residue 494 MET Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 630 HIS Chi-restraints excluded: chain D residue 632 ILE Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 670 TYR Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 1007 TRP Chi-restraints excluded: chain D residue 1297 THR Chi-restraints excluded: chain D residue 1467 VAL Chi-restraints excluded: chain D residue 1511 VAL Chi-restraints excluded: chain D residue 1544 VAL Chi-restraints excluded: chain D residue 1605 LEU Chi-restraints excluded: chain D residue 1722 MET Chi-restraints excluded: chain D residue 1783 PHE Chi-restraints excluded: chain D residue 1787 ILE Chi-restraints excluded: chain D residue 1818 LEU Chi-restraints excluded: chain D residue 1819 PHE Chi-restraints excluded: chain D residue 1952 MET Chi-restraints excluded: chain D residue 1991 ILE Chi-restraints excluded: chain D residue 2060 LEU Chi-restraints excluded: chain D residue 2091 TYR Chi-restraints excluded: chain D residue 2129 LEU Chi-restraints excluded: chain D residue 2164 LEU Chi-restraints excluded: chain D residue 2174 MET Chi-restraints excluded: chain D residue 2190 LYS Chi-restraints excluded: chain D residue 2260 ASP Chi-restraints excluded: chain D residue 2280 VAL Chi-restraints excluded: chain D residue 2308 ASN Chi-restraints excluded: chain D residue 2355 ASP Chi-restraints excluded: chain D residue 2383 MET Chi-restraints excluded: chain D residue 2395 ILE Chi-restraints excluded: chain D residue 2416 ILE Chi-restraints excluded: chain D residue 2472 ASP Chi-restraints excluded: chain D residue 2526 LEU Chi-restraints excluded: chain D residue 2583 MET Chi-restraints excluded: chain D residue 2587 LEU Chi-restraints excluded: chain D residue 2595 VAL Chi-restraints excluded: chain D residue 2682 SER Chi-restraints excluded: chain D residue 3200 VAL Chi-restraints excluded: chain D residue 3262 MET Chi-restraints excluded: chain D residue 3469 LEU Chi-restraints excluded: chain D residue 3616 VAL Chi-restraints excluded: chain D residue 3624 GLU Chi-restraints excluded: chain D residue 3782 GLU Chi-restraints excluded: chain D residue 3829 LEU Chi-restraints excluded: chain D residue 3846 CYS Chi-restraints excluded: chain D residue 3934 LEU Chi-restraints excluded: chain D residue 3985 LEU Chi-restraints excluded: chain D residue 3989 VAL Chi-restraints excluded: chain D residue 4011 MET Chi-restraints excluded: chain D residue 4016 PHE Chi-restraints excluded: chain D residue 4024 ASP Chi-restraints excluded: chain D residue 4054 HIS Chi-restraints excluded: chain D residue 4078 ASP Chi-restraints excluded: chain D residue 4082 PHE Chi-restraints excluded: chain D residue 4108 MET Chi-restraints excluded: chain D residue 4556 VAL Chi-restraints excluded: chain D residue 4659 PHE Chi-restraints excluded: chain D residue 4709 LEU Chi-restraints excluded: chain D residue 4713 PHE Chi-restraints excluded: chain D residue 4807 ASP Chi-restraints excluded: chain D residue 4813 MET Chi-restraints excluded: chain D residue 4830 ILE Chi-restraints excluded: chain D residue 4862 GLN Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain H residue 26 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1640 random chunks: chunk 1529 optimal weight: 0.7980 chunk 178 optimal weight: 0.8980 chunk 904 optimal weight: 8.9990 chunk 1158 optimal weight: 2.9990 chunk 897 optimal weight: 50.0000 chunk 1335 optimal weight: 0.0020 chunk 886 optimal weight: 30.0000 chunk 1580 optimal weight: 0.9980 chunk 989 optimal weight: 3.9990 chunk 963 optimal weight: 3.9990 chunk 729 optimal weight: 1.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2340 ASN ** A2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2340 ASN ** B2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2340 ASN ** C2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1216 ASN ** D1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2340 ASN ** D2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 131440 Z= 0.160 Angle : 0.533 10.257 177752 Z= 0.264 Chirality : 0.038 0.205 19688 Planarity : 0.003 0.058 22980 Dihedral : 3.937 47.871 17668 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.96 % Favored : 92.91 % Rotamer: Outliers : 3.06 % Allowed : 19.33 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.07), residues: 16228 helix: 1.98 (0.06), residues: 7408 sheet: -0.49 (0.18), residues: 964 loop : -2.31 (0.07), residues: 7856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 893 HIS 0.008 0.001 HIS A1451 PHE 0.022 0.001 PHE B1450 TYR 0.025 0.001 TYR D4938 ARG 0.008 0.000 ARG B2197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32456 Ramachandran restraints generated. 16228 Oldfield, 0 Emsley, 16228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32456 Ramachandran restraints generated. 16228 Oldfield, 0 Emsley, 16228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1463 residues out of total 14384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 418 poor density : 1045 time to evaluate : 10.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7162 (tm-30) REVERT: A 362 TYR cc_start: 0.7680 (m-80) cc_final: 0.7338 (m-80) REVERT: A 420 ARG cc_start: 0.7638 (ppt170) cc_final: 0.7345 (ppt170) REVERT: A 474 ASP cc_start: 0.8418 (t70) cc_final: 0.8072 (t0) REVERT: A 484 ASN cc_start: 0.8936 (OUTLIER) cc_final: 0.8673 (t0) REVERT: A 494 MET cc_start: 0.1605 (OUTLIER) cc_final: 0.0606 (mtt) REVERT: A 629 GLN cc_start: 0.3931 (OUTLIER) cc_final: 0.3181 (tt0) REVERT: A 678 MET cc_start: 0.7924 (tpp) cc_final: 0.7380 (tpt) REVERT: A 935 MET cc_start: 0.5656 (tmm) cc_final: 0.4371 (ptt) REVERT: A 1199 ASP cc_start: 0.8611 (p0) cc_final: 0.8307 (p0) REVERT: A 2174 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7679 (ttp) REVERT: A 2178 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7550 (mm) REVERT: A 2190 LYS cc_start: 0.7219 (OUTLIER) cc_final: 0.6584 (ptmm) REVERT: A 2247 MET cc_start: 0.8530 (tpt) cc_final: 0.8281 (tpt) REVERT: A 2579 LEU cc_start: 0.7612 (pp) cc_final: 0.7368 (pt) REVERT: A 2781 MET cc_start: -0.0373 (ptp) cc_final: -0.1012 (mmp) REVERT: A 3045 MET cc_start: 0.5399 (ppp) cc_final: 0.5144 (ppp) REVERT: A 3240 MET cc_start: 0.8167 (mmm) cc_final: 0.7645 (tmm) REVERT: A 3331 MET cc_start: 0.6236 (ppp) cc_final: 0.5418 (tpp) REVERT: A 3661 ASP cc_start: 0.5327 (OUTLIER) cc_final: 0.4777 (m-30) REVERT: A 3953 MET cc_start: 0.8052 (mmm) cc_final: 0.7743 (mmm) REVERT: A 3998 MET cc_start: 0.8471 (tpp) cc_final: 0.8222 (ttt) REVERT: A 4024 ASP cc_start: 0.4035 (OUTLIER) cc_final: 0.3764 (p0) REVERT: A 4082 PHE cc_start: 0.5755 (OUTLIER) cc_final: 0.4546 (p90) REVERT: A 4811 CYS cc_start: 0.7355 (OUTLIER) cc_final: 0.6357 (t) REVERT: A 4862 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.6332 (mp10) REVERT: A 4948 TRP cc_start: 0.8116 (m-10) cc_final: 0.7623 (m-10) REVERT: B 156 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7084 (tm-30) REVERT: B 245 LEU cc_start: 0.6596 (OUTLIER) cc_final: 0.6249 (mm) REVERT: B 309 MET cc_start: 0.5085 (mmp) cc_final: 0.4812 (mmt) REVERT: B 362 TYR cc_start: 0.7527 (m-80) cc_final: 0.7090 (m-80) REVERT: B 420 ARG cc_start: 0.7645 (ppt170) cc_final: 0.7351 (ppt170) REVERT: B 484 ASN cc_start: 0.8938 (OUTLIER) cc_final: 0.8680 (t0) REVERT: B 494 MET cc_start: 0.1207 (OUTLIER) cc_final: 0.0498 (mtt) REVERT: B 535 GLU cc_start: 0.6891 (tt0) cc_final: 0.6493 (mm-30) REVERT: B 629 GLN cc_start: 0.3955 (OUTLIER) cc_final: 0.3177 (tt0) REVERT: B 651 HIS cc_start: 0.6182 (OUTLIER) cc_final: 0.5643 (m-70) REVERT: B 895 MET cc_start: 0.4969 (mmp) cc_final: 0.3881 (mtp) REVERT: B 935 MET cc_start: 0.5692 (tmm) cc_final: 0.4429 (ptt) REVERT: B 981 MET cc_start: 0.0780 (ppp) cc_final: -0.0186 (ptp) REVERT: B 1174 MET cc_start: 0.5659 (ptp) cc_final: 0.5093 (ppp) REVERT: B 1199 ASP cc_start: 0.8637 (p0) cc_final: 0.8320 (p0) REVERT: B 1605 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.5941 (mt) REVERT: B 2174 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7715 (ttp) REVERT: B 2178 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7550 (mm) REVERT: B 2190 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6584 (ptmm) REVERT: B 2247 MET cc_start: 0.8529 (tpt) cc_final: 0.8277 (tpt) REVERT: B 2579 LEU cc_start: 0.7612 (pp) cc_final: 0.7380 (pt) REVERT: B 2781 MET cc_start: -0.0167 (ptp) cc_final: -0.0905 (mmp) REVERT: B 3045 MET cc_start: 0.5190 (ppp) cc_final: 0.4947 (ppp) REVERT: B 3240 MET cc_start: 0.8064 (mmm) cc_final: 0.7615 (tmm) REVERT: B 3331 MET cc_start: 0.6291 (ppp) cc_final: 0.5410 (tpp) REVERT: B 3661 ASP cc_start: 0.5212 (OUTLIER) cc_final: 0.4648 (m-30) REVERT: B 3953 MET cc_start: 0.8022 (mmm) cc_final: 0.7719 (mmm) REVERT: B 3998 MET cc_start: 0.8474 (tpp) cc_final: 0.8222 (ttt) REVERT: B 4024 ASP cc_start: 0.4062 (OUTLIER) cc_final: 0.3818 (p0) REVERT: B 4811 CYS cc_start: 0.7332 (OUTLIER) cc_final: 0.6345 (t) REVERT: B 4862 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.6405 (mp10) REVERT: B 4948 TRP cc_start: 0.8113 (m-10) cc_final: 0.7628 (m-10) REVERT: C 156 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7160 (tm-30) REVERT: C 245 LEU cc_start: 0.6615 (OUTLIER) cc_final: 0.6262 (mm) REVERT: C 362 TYR cc_start: 0.7656 (m-80) cc_final: 0.7257 (m-80) REVERT: C 420 ARG cc_start: 0.7540 (ppt170) cc_final: 0.7247 (ppt170) REVERT: C 484 ASN cc_start: 0.8969 (OUTLIER) cc_final: 0.8703 (t0) REVERT: C 494 MET cc_start: 0.1601 (OUTLIER) cc_final: 0.0600 (mtt) REVERT: C 629 GLN cc_start: 0.3910 (OUTLIER) cc_final: 0.3174 (tt0) REVERT: C 651 HIS cc_start: 0.6341 (OUTLIER) cc_final: 0.5818 (m-70) REVERT: C 678 MET cc_start: 0.7990 (tpp) cc_final: 0.7418 (tpt) REVERT: C 935 MET cc_start: 0.5702 (tmm) cc_final: 0.4455 (ptt) REVERT: C 1199 ASP cc_start: 0.8607 (p0) cc_final: 0.8295 (p0) REVERT: C 1605 LEU cc_start: 0.6395 (OUTLIER) cc_final: 0.5927 (mt) REVERT: C 2174 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7703 (ttp) REVERT: C 2178 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7548 (mm) REVERT: C 2190 LYS cc_start: 0.7224 (OUTLIER) cc_final: 0.6591 (ptmm) REVERT: C 2247 MET cc_start: 0.8514 (tpt) cc_final: 0.8258 (tpt) REVERT: C 2604 MET cc_start: 0.7267 (mmp) cc_final: 0.6866 (mtm) REVERT: C 2781 MET cc_start: -0.0161 (ptp) cc_final: -0.0882 (mmp) REVERT: C 3240 MET cc_start: 0.8164 (mmm) cc_final: 0.7657 (tmm) REVERT: C 3331 MET cc_start: 0.6231 (ppp) cc_final: 0.5406 (tpp) REVERT: C 3661 ASP cc_start: 0.5337 (OUTLIER) cc_final: 0.4783 (m-30) REVERT: C 3718 MET cc_start: 0.7207 (tpp) cc_final: 0.6917 (tpp) REVERT: C 3953 MET cc_start: 0.8030 (mmm) cc_final: 0.7723 (mmm) REVERT: C 3998 MET cc_start: 0.8473 (tpp) cc_final: 0.8219 (ttt) REVERT: C 4024 ASP cc_start: 0.4026 (OUTLIER) cc_final: 0.3765 (p0) REVERT: C 4811 CYS cc_start: 0.7346 (OUTLIER) cc_final: 0.6352 (t) REVERT: C 4862 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.6326 (mp10) REVERT: C 4948 TRP cc_start: 0.8121 (m-10) cc_final: 0.7626 (m-10) REVERT: D 156 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7164 (tm-30) REVERT: D 245 LEU cc_start: 0.6625 (OUTLIER) cc_final: 0.6280 (mm) REVERT: D 362 TYR cc_start: 0.7659 (m-80) cc_final: 0.7258 (m-80) REVERT: D 420 ARG cc_start: 0.7553 (ppt170) cc_final: 0.7259 (ppt170) REVERT: D 484 ASN cc_start: 0.8971 (OUTLIER) cc_final: 0.8704 (t0) REVERT: D 494 MET cc_start: 0.1724 (OUTLIER) cc_final: 0.0717 (mtt) REVERT: D 651 HIS cc_start: 0.6332 (OUTLIER) cc_final: 0.5787 (m-70) REVERT: D 678 MET cc_start: 0.8023 (tpp) cc_final: 0.7465 (tpt) REVERT: D 935 MET cc_start: 0.5655 (tmm) cc_final: 0.4373 (ptt) REVERT: D 1199 ASP cc_start: 0.8607 (p0) cc_final: 0.8290 (p0) REVERT: D 1605 LEU cc_start: 0.6351 (OUTLIER) cc_final: 0.5915 (mt) REVERT: D 2174 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7672 (ttp) REVERT: D 2178 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7552 (mm) REVERT: D 2190 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6586 (ptmm) REVERT: D 2233 MET cc_start: 0.8144 (mmm) cc_final: 0.7939 (mmm) REVERT: D 2247 MET cc_start: 0.8516 (tpt) cc_final: 0.8251 (tpt) REVERT: D 2587 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8234 (mt) REVERT: D 2781 MET cc_start: -0.0150 (ptp) cc_final: -0.0879 (mmp) REVERT: D 3240 MET cc_start: 0.8170 (mmm) cc_final: 0.7660 (tmm) REVERT: D 3331 MET cc_start: 0.6237 (ppp) cc_final: 0.5411 (tpp) REVERT: D 3661 ASP cc_start: 0.5303 (OUTLIER) cc_final: 0.4764 (m-30) REVERT: D 3718 MET cc_start: 0.7203 (tpp) cc_final: 0.6911 (tpp) REVERT: D 3953 MET cc_start: 0.8034 (mmm) cc_final: 0.7722 (mmm) REVERT: D 3998 MET cc_start: 0.8464 (tpp) cc_final: 0.8206 (ttt) REVERT: D 4024 ASP cc_start: 0.4038 (OUTLIER) cc_final: 0.3741 (p0) REVERT: D 4082 PHE cc_start: 0.5592 (OUTLIER) cc_final: 0.4378 (p90) REVERT: D 4811 CYS cc_start: 0.7374 (OUTLIER) cc_final: 0.6387 (t) REVERT: D 4862 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.6333 (mp10) REVERT: D 4948 TRP cc_start: 0.8093 (m-10) cc_final: 0.7596 (m-10) REVERT: E 6 GLU cc_start: 0.8087 (mp0) cc_final: 0.7826 (mp0) REVERT: E 26 HIS cc_start: 0.8011 (OUTLIER) cc_final: 0.7339 (t-90) REVERT: F 6 GLU cc_start: 0.8068 (mp0) cc_final: 0.7790 (mp0) REVERT: F 26 HIS cc_start: 0.8064 (OUTLIER) cc_final: 0.7527 (t-90) REVERT: G 6 GLU cc_start: 0.8089 (mp0) cc_final: 0.7715 (mp0) REVERT: G 26 HIS cc_start: 0.8010 (OUTLIER) cc_final: 0.7331 (t-90) REVERT: H 6 GLU cc_start: 0.8136 (mp0) cc_final: 0.7765 (mp0) REVERT: H 26 HIS cc_start: 0.7994 (OUTLIER) cc_final: 0.7379 (t-90) outliers start: 418 outliers final: 277 residues processed: 1371 average time/residue: 1.0427 time to fit residues: 2593.3672 Evaluate side-chains 1343 residues out of total 14384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 336 poor density : 1007 time to evaluate : 9.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 484 ASN Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 670 TYR Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1007 TRP Chi-restraints excluded: chain A residue 1143 GLN Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1202 ILE Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1467 VAL Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1722 MET Chi-restraints excluded: chain A residue 1783 PHE Chi-restraints excluded: chain A residue 1787 ILE Chi-restraints excluded: chain A residue 1818 LEU Chi-restraints excluded: chain A residue 1819 PHE Chi-restraints excluded: chain A residue 1952 MET 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 2091 TYR Chi-restraints excluded: chain A residue 2129 LEU Chi-restraints excluded: chain A residue 2145 LEU Chi-restraints excluded: chain A residue 2174 MET Chi-restraints excluded: chain A residue 2178 LEU Chi-restraints excluded: chain A residue 2190 LYS Chi-restraints excluded: chain A residue 2260 ASP Chi-restraints excluded: chain A residue 2280 VAL Chi-restraints excluded: chain A residue 2308 ASN Chi-restraints excluded: chain A residue 2355 ASP Chi-restraints excluded: chain A residue 2383 MET Chi-restraints excluded: chain A residue 2395 ILE Chi-restraints excluded: chain A residue 2526 LEU Chi-restraints excluded: chain A residue 2583 MET Chi-restraints excluded: chain A residue 2595 VAL Chi-restraints excluded: chain A residue 2682 SER Chi-restraints excluded: chain A residue 3200 VAL Chi-restraints excluded: chain A residue 3262 MET Chi-restraints excluded: chain A residue 3469 LEU Chi-restraints excluded: chain A residue 3616 VAL Chi-restraints excluded: chain A residue 3624 GLU Chi-restraints excluded: chain A residue 3661 ASP Chi-restraints excluded: chain A residue 3782 GLU Chi-restraints excluded: chain A residue 3829 LEU Chi-restraints excluded: chain A residue 3846 CYS Chi-restraints excluded: chain A residue 3934 LEU Chi-restraints excluded: chain A residue 3985 LEU Chi-restraints excluded: chain A residue 3989 VAL Chi-restraints excluded: chain A residue 4011 MET Chi-restraints excluded: chain A residue 4024 ASP Chi-restraints excluded: chain A residue 4046 ASP Chi-restraints excluded: chain A residue 4054 HIS Chi-restraints excluded: chain A residue 4082 PHE Chi-restraints excluded: chain A residue 4108 MET Chi-restraints excluded: chain A residue 4155 SER Chi-restraints excluded: chain A residue 4556 VAL Chi-restraints excluded: chain A residue 4659 PHE Chi-restraints excluded: chain A residue 4713 PHE Chi-restraints excluded: chain A residue 4807 ASP Chi-restraints excluded: chain A residue 4811 CYS Chi-restraints excluded: chain A residue 4813 MET Chi-restraints excluded: chain A residue 4830 ILE Chi-restraints excluded: chain A residue 4862 GLN Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 629 GLN Chi-restraints excluded: chain B residue 630 HIS Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 670 TYR Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 961 VAL Chi-restraints excluded: chain B residue 1007 TRP Chi-restraints excluded: chain B residue 1143 GLN Chi-restraints excluded: chain B residue 1166 VAL Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1297 THR Chi-restraints excluded: chain B residue 1304 LEU Chi-restraints excluded: chain B residue 1467 VAL Chi-restraints excluded: chain B residue 1511 VAL Chi-restraints excluded: chain B residue 1544 VAL Chi-restraints excluded: chain B residue 1605 LEU Chi-restraints excluded: chain B residue 1722 MET Chi-restraints excluded: chain B residue 1783 PHE Chi-restraints excluded: chain B residue 1787 ILE Chi-restraints excluded: chain B residue 1818 LEU Chi-restraints excluded: chain B residue 1819 PHE Chi-restraints excluded: chain B residue 1828 THR Chi-restraints excluded: chain B residue 1917 VAL Chi-restraints excluded: chain B residue 1952 MET 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 2091 TYR Chi-restraints excluded: chain B residue 2129 LEU Chi-restraints excluded: chain B residue 2145 LEU Chi-restraints excluded: chain B residue 2174 MET Chi-restraints excluded: chain B residue 2178 LEU Chi-restraints excluded: chain B residue 2190 LYS Chi-restraints excluded: chain B residue 2260 ASP Chi-restraints excluded: chain B residue 2280 VAL Chi-restraints excluded: chain B residue 2308 ASN Chi-restraints excluded: chain B residue 2355 ASP Chi-restraints excluded: chain B residue 2383 MET Chi-restraints excluded: chain B residue 2395 ILE Chi-restraints excluded: chain B residue 2526 LEU Chi-restraints excluded: chain B residue 2583 MET Chi-restraints excluded: chain B residue 2595 VAL Chi-restraints excluded: chain B residue 2682 SER Chi-restraints excluded: chain B residue 3200 VAL Chi-restraints excluded: chain B residue 3262 MET Chi-restraints excluded: chain B residue 3469 LEU Chi-restraints excluded: chain B residue 3616 VAL Chi-restraints excluded: chain B residue 3661 ASP Chi-restraints excluded: chain B residue 3782 GLU Chi-restraints excluded: chain B residue 3846 CYS Chi-restraints excluded: chain B residue 3934 LEU Chi-restraints excluded: chain B residue 3985 LEU Chi-restraints excluded: chain B residue 3989 VAL Chi-restraints excluded: chain B residue 4016 PHE Chi-restraints excluded: chain B residue 4024 ASP Chi-restraints excluded: chain B residue 4046 ASP Chi-restraints excluded: chain B residue 4054 HIS Chi-restraints excluded: chain B residue 4108 MET Chi-restraints excluded: chain B residue 4155 SER Chi-restraints excluded: chain B residue 4556 VAL Chi-restraints excluded: chain B residue 4659 PHE Chi-restraints excluded: chain B residue 4713 PHE Chi-restraints excluded: chain B residue 4800 THR Chi-restraints excluded: chain B residue 4807 ASP Chi-restraints excluded: chain B residue 4811 CYS Chi-restraints excluded: chain B residue 4813 MET Chi-restraints excluded: chain B residue 4830 ILE Chi-restraints excluded: chain B residue 4862 GLN Chi-restraints excluded: chain B residue 4882 ASP Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 424 PHE Chi-restraints excluded: chain C residue 484 ASN Chi-restraints excluded: chain C residue 494 MET Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 629 GLN Chi-restraints excluded: chain C residue 630 HIS Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 670 TYR Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 716 ASN Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1007 TRP Chi-restraints excluded: chain C residue 1143 GLN Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1202 ILE Chi-restraints excluded: chain C residue 1297 THR Chi-restraints excluded: chain C residue 1467 VAL Chi-restraints excluded: chain C residue 1511 VAL Chi-restraints excluded: chain C residue 1544 VAL Chi-restraints excluded: chain C residue 1605 LEU Chi-restraints excluded: chain C residue 1722 MET Chi-restraints excluded: chain C residue 1783 PHE Chi-restraints excluded: chain C residue 1818 LEU Chi-restraints excluded: chain C residue 1819 PHE Chi-restraints excluded: chain C residue 1903 LEU Chi-restraints excluded: chain C residue 1952 MET 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 2091 TYR Chi-restraints excluded: chain C residue 2129 LEU Chi-restraints excluded: chain C residue 2145 LEU Chi-restraints excluded: chain C residue 2174 MET Chi-restraints excluded: chain C residue 2178 LEU Chi-restraints excluded: chain C residue 2190 LYS Chi-restraints excluded: chain C residue 2260 ASP Chi-restraints excluded: chain C residue 2280 VAL Chi-restraints excluded: chain C residue 2308 ASN Chi-restraints excluded: chain C residue 2355 ASP Chi-restraints excluded: chain C residue 2383 MET Chi-restraints excluded: chain C residue 2395 ILE Chi-restraints excluded: chain C residue 2526 LEU Chi-restraints excluded: chain C residue 2583 MET Chi-restraints excluded: chain C residue 2595 VAL Chi-restraints excluded: chain C residue 3200 VAL Chi-restraints excluded: chain C residue 3262 MET Chi-restraints excluded: chain C residue 3469 LEU Chi-restraints excluded: chain C residue 3616 VAL Chi-restraints excluded: chain C residue 3624 GLU Chi-restraints excluded: chain C residue 3661 ASP Chi-restraints excluded: chain C residue 3782 GLU Chi-restraints excluded: chain C residue 3829 LEU Chi-restraints excluded: chain C residue 3846 CYS Chi-restraints excluded: chain C residue 3934 LEU Chi-restraints excluded: chain C residue 3985 LEU Chi-restraints excluded: chain C residue 3989 VAL Chi-restraints excluded: chain C residue 4011 MET Chi-restraints excluded: chain C residue 4016 PHE Chi-restraints excluded: chain C residue 4024 ASP Chi-restraints excluded: chain C residue 4054 HIS Chi-restraints excluded: chain C residue 4108 MET Chi-restraints excluded: chain C residue 4155 SER Chi-restraints excluded: chain C residue 4556 VAL Chi-restraints excluded: chain C residue 4659 PHE Chi-restraints excluded: chain C residue 4713 PHE Chi-restraints excluded: chain C residue 4807 ASP Chi-restraints excluded: chain C residue 4811 CYS Chi-restraints excluded: chain C residue 4813 MET Chi-restraints excluded: chain C residue 4830 ILE Chi-restraints excluded: chain C residue 4862 GLN Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 424 PHE Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain D residue 494 MET Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 630 HIS Chi-restraints excluded: chain D residue 632 ILE Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 670 TYR Chi-restraints excluded: chain D residue 679 VAL Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 961 VAL Chi-restraints excluded: chain D residue 1007 TRP Chi-restraints excluded: chain D residue 1143 GLN Chi-restraints excluded: chain D residue 1166 VAL Chi-restraints excluded: chain D residue 1202 ILE Chi-restraints excluded: chain D residue 1297 THR Chi-restraints excluded: chain D residue 1467 VAL Chi-restraints excluded: chain D residue 1511 VAL Chi-restraints excluded: chain D residue 1544 VAL Chi-restraints excluded: chain D residue 1605 LEU Chi-restraints excluded: chain D residue 1722 MET Chi-restraints excluded: chain D residue 1783 PHE Chi-restraints excluded: chain D residue 1787 ILE Chi-restraints excluded: chain D residue 1818 LEU Chi-restraints excluded: chain D residue 1819 PHE Chi-restraints excluded: chain D residue 1828 THR Chi-restraints excluded: chain D residue 1952 MET Chi-restraints excluded: chain D residue 1957 THR Chi-restraints excluded: chain D residue 1991 ILE Chi-restraints excluded: chain D residue 2060 LEU Chi-restraints excluded: chain D residue 2091 TYR Chi-restraints excluded: chain D residue 2129 LEU Chi-restraints excluded: chain D residue 2145 LEU Chi-restraints excluded: chain D residue 2174 MET Chi-restraints excluded: chain D residue 2178 LEU Chi-restraints excluded: chain D residue 2190 LYS Chi-restraints excluded: chain D residue 2250 ASN Chi-restraints excluded: chain D residue 2260 ASP Chi-restraints excluded: chain D residue 2280 VAL Chi-restraints excluded: chain D residue 2308 ASN Chi-restraints excluded: chain D residue 2355 ASP Chi-restraints excluded: chain D residue 2383 MET Chi-restraints excluded: chain D residue 2395 ILE Chi-restraints excluded: chain D residue 2472 ASP Chi-restraints excluded: chain D residue 2526 LEU Chi-restraints excluded: chain D residue 2583 MET Chi-restraints excluded: chain D residue 2587 LEU Chi-restraints excluded: chain D residue 2595 VAL Chi-restraints excluded: chain D residue 2682 SER Chi-restraints excluded: chain D residue 3200 VAL Chi-restraints excluded: chain D residue 3262 MET Chi-restraints excluded: chain D residue 3616 VAL Chi-restraints excluded: chain D residue 3624 GLU Chi-restraints excluded: chain D residue 3661 ASP Chi-restraints excluded: chain D residue 3782 GLU Chi-restraints excluded: chain D residue 3829 LEU Chi-restraints excluded: chain D residue 3846 CYS Chi-restraints excluded: chain D residue 3934 LEU Chi-restraints excluded: chain D residue 3985 LEU Chi-restraints excluded: chain D residue 3989 VAL Chi-restraints excluded: chain D residue 4011 MET Chi-restraints excluded: chain D residue 4016 PHE Chi-restraints excluded: chain D residue 4024 ASP Chi-restraints excluded: chain D residue 4054 HIS Chi-restraints excluded: chain D residue 4082 PHE Chi-restraints excluded: chain D residue 4108 MET Chi-restraints excluded: chain D residue 4155 SER Chi-restraints excluded: chain D residue 4556 VAL Chi-restraints excluded: chain D residue 4659 PHE Chi-restraints excluded: chain D residue 4713 PHE Chi-restraints excluded: chain D residue 4800 THR Chi-restraints excluded: chain D residue 4807 ASP Chi-restraints excluded: chain D residue 4811 CYS Chi-restraints excluded: chain D residue 4813 MET Chi-restraints excluded: chain D residue 4830 ILE Chi-restraints excluded: chain D residue 4862 GLN Chi-restraints excluded: chain D residue 4882 ASP Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 38 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1640 random chunks: chunk 977 optimal weight: 10.0000 chunk 631 optimal weight: 20.0000 chunk 944 optimal weight: 9.9990 chunk 476 optimal weight: 6.9990 chunk 310 optimal weight: 6.9990 chunk 306 optimal weight: 0.9980 chunk 1004 optimal weight: 0.7980 chunk 1076 optimal weight: 0.0980 chunk 781 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 1242 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1675 HIS ** A2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2340 ASN ** A2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1675 HIS ** B2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2340 ASN ** B2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3665 GLN ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1675 HIS ** C2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2340 ASN ** C2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1216 ASN ** D1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1675 HIS ** D2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2340 ASN ** D2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 ASN F 95 ASN G 95 ASN H 95 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 131440 Z= 0.173 Angle : 0.540 10.673 177752 Z= 0.267 Chirality : 0.038 0.225 19688 Planarity : 0.003 0.053 22980 Dihedral : 3.905 48.237 17668 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.69 % Favored : 93.19 % Rotamer: Outliers : 2.87 % Allowed : 19.95 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.07), residues: 16228 helix: 2.03 (0.06), residues: 7380 sheet: -0.44 (0.18), residues: 964 loop : -2.31 (0.06), residues: 7884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 893 HIS 0.008 0.001 HIS C1451 PHE 0.024 0.001 PHE C1450 TYR 0.032 0.001 TYR B2037 ARG 0.007 0.000 ARG B2197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32456 Ramachandran restraints generated. 16228 Oldfield, 0 Emsley, 16228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32456 Ramachandran restraints generated. 16228 Oldfield, 0 Emsley, 16228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1425 residues out of total 14384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 393 poor density : 1032 time to evaluate : 10.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 245 LEU cc_start: 0.6570 (OUTLIER) cc_final: 0.6220 (mm) REVERT: A 309 MET cc_start: 0.5093 (mmp) cc_final: 0.4838 (mmt) REVERT: A 362 TYR cc_start: 0.7643 (m-80) cc_final: 0.7294 (m-80) REVERT: A 420 ARG cc_start: 0.7629 (ppt170) cc_final: 0.7336 (ppt170) REVERT: A 494 MET cc_start: 0.2006 (OUTLIER) cc_final: 0.0699 (mtt) REVERT: A 629 GLN cc_start: 0.4091 (OUTLIER) cc_final: 0.3299 (tt0) REVERT: A 678 MET cc_start: 0.7934 (tpp) cc_final: 0.7398 (tpt) REVERT: A 895 MET cc_start: 0.4983 (mmp) cc_final: 0.3843 (mtm) REVERT: A 935 MET cc_start: 0.5725 (tmm) cc_final: 0.4521 (ptt) REVERT: A 981 MET cc_start: 0.1345 (ppp) cc_final: 0.0453 (ptm) REVERT: A 1199 ASP cc_start: 0.8609 (p0) cc_final: 0.8295 (p0) REVERT: A 2174 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7735 (ttp) REVERT: A 2190 LYS cc_start: 0.7166 (OUTLIER) cc_final: 0.6621 (ptmm) REVERT: A 2579 LEU cc_start: 0.7598 (pp) cc_final: 0.7368 (pt) REVERT: A 2604 MET cc_start: 0.7340 (mmp) cc_final: 0.6933 (mpp) REVERT: A 2781 MET cc_start: -0.0366 (ptp) cc_final: -0.1040 (mmp) REVERT: A 3045 MET cc_start: 0.5333 (ppp) cc_final: 0.5096 (ppp) REVERT: A 3240 MET cc_start: 0.8212 (mmm) cc_final: 0.7716 (tmm) REVERT: A 3245 MET cc_start: -0.1165 (mmm) cc_final: -0.1420 (mpp) REVERT: A 3331 MET cc_start: 0.6248 (ppp) cc_final: 0.5452 (tpp) REVERT: A 3661 ASP cc_start: 0.5336 (OUTLIER) cc_final: 0.4764 (m-30) REVERT: A 3953 MET cc_start: 0.8126 (mmm) cc_final: 0.7668 (mmm) REVERT: A 3998 MET cc_start: 0.8484 (tpp) cc_final: 0.8229 (ttt) REVERT: A 4024 ASP cc_start: 0.4006 (OUTLIER) cc_final: 0.3626 (p0) REVERT: A 4082 PHE cc_start: 0.5775 (OUTLIER) cc_final: 0.4562 (p90) REVERT: A 4811 CYS cc_start: 0.7367 (OUTLIER) cc_final: 0.6358 (t) REVERT: A 4862 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.6315 (mp10) REVERT: A 4948 TRP cc_start: 0.8121 (m-10) cc_final: 0.7639 (m-10) REVERT: B 245 LEU cc_start: 0.6580 (OUTLIER) cc_final: 0.6231 (mm) REVERT: B 309 MET cc_start: 0.5279 (mmp) cc_final: 0.5039 (mmt) REVERT: B 362 TYR cc_start: 0.7548 (m-80) cc_final: 0.7134 (m-80) REVERT: B 420 ARG cc_start: 0.7502 (ppt170) cc_final: 0.7252 (ppt170) REVERT: B 474 ASP cc_start: 0.8280 (t70) cc_final: 0.8010 (t0) REVERT: B 494 MET cc_start: 0.1622 (OUTLIER) cc_final: 0.0708 (mtt) REVERT: B 535 GLU cc_start: 0.7046 (tt0) cc_final: 0.6582 (mm-30) REVERT: B 629 GLN cc_start: 0.4125 (OUTLIER) cc_final: 0.3318 (tt0) REVERT: B 651 HIS cc_start: 0.6242 (OUTLIER) cc_final: 0.5661 (m-70) REVERT: B 678 MET cc_start: 0.7448 (tpp) cc_final: 0.6706 (tpt) REVERT: B 935 MET cc_start: 0.5716 (tmm) cc_final: 0.4502 (ptt) REVERT: B 981 MET cc_start: 0.0844 (ppp) cc_final: -0.0119 (ptp) REVERT: B 1174 MET cc_start: 0.5662 (ptp) cc_final: 0.5178 (ppp) REVERT: B 1199 ASP cc_start: 0.8630 (p0) cc_final: 0.8288 (p0) REVERT: B 1605 LEU cc_start: 0.6507 (OUTLIER) cc_final: 0.6010 (mt) REVERT: B 2174 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7658 (ttp) REVERT: B 2178 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7558 (mm) REVERT: B 2190 LYS cc_start: 0.7169 (OUTLIER) cc_final: 0.6618 (ptmm) REVERT: B 2579 LEU cc_start: 0.7598 (pp) cc_final: 0.7371 (pt) REVERT: B 2604 MET cc_start: 0.7108 (mmp) cc_final: 0.6737 (mpp) REVERT: B 2781 MET cc_start: -0.0367 (ptp) cc_final: -0.1047 (mmp) REVERT: B 3045 MET cc_start: 0.5164 (ppp) cc_final: 0.4927 (ppp) REVERT: B 3245 MET cc_start: -0.0918 (mmm) cc_final: -0.1187 (mpp) REVERT: B 3331 MET cc_start: 0.6187 (ppp) cc_final: 0.5394 (tpp) REVERT: B 3661 ASP cc_start: 0.5264 (OUTLIER) cc_final: 0.4699 (m-30) REVERT: B 3718 MET cc_start: 0.7031 (tpp) cc_final: 0.6793 (tpp) REVERT: B 3998 MET cc_start: 0.8474 (tpp) cc_final: 0.8207 (ttt) REVERT: B 4024 ASP cc_start: 0.4103 (OUTLIER) cc_final: 0.3887 (p0) REVERT: B 4082 PHE cc_start: 0.5448 (OUTLIER) cc_final: 0.4153 (p90) REVERT: B 4811 CYS cc_start: 0.7358 (OUTLIER) cc_final: 0.6347 (t) REVERT: B 4862 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.6306 (mp10) REVERT: B 4948 TRP cc_start: 0.8136 (m-10) cc_final: 0.7651 (m-10) REVERT: C 362 TYR cc_start: 0.7634 (m-80) cc_final: 0.7305 (m-80) REVERT: C 474 ASP cc_start: 0.8284 (t70) cc_final: 0.7954 (t0) REVERT: C 494 MET cc_start: 0.2091 (OUTLIER) cc_final: 0.0771 (mtt) REVERT: C 629 GLN cc_start: 0.4077 (OUTLIER) cc_final: 0.3291 (tt0) REVERT: C 651 HIS cc_start: 0.6308 (OUTLIER) cc_final: 0.5783 (m-70) REVERT: C 895 MET cc_start: 0.5013 (mmp) cc_final: 0.3895 (mtm) REVERT: C 935 MET cc_start: 0.5703 (tmm) cc_final: 0.4498 (ptt) REVERT: C 1199 ASP cc_start: 0.8631 (p0) cc_final: 0.8309 (p0) REVERT: C 1605 LEU cc_start: 0.6499 (OUTLIER) cc_final: 0.6002 (mp) REVERT: C 2174 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7755 (ttp) REVERT: C 2190 LYS cc_start: 0.7173 (OUTLIER) cc_final: 0.6631 (ptmm) REVERT: C 2247 MET cc_start: 0.8509 (tpt) cc_final: 0.8277 (tpt) REVERT: C 2781 MET cc_start: -0.0362 (ptp) cc_final: -0.1054 (mmp) REVERT: C 3240 MET cc_start: 0.8165 (mmm) cc_final: 0.7667 (tmm) REVERT: C 3245 MET cc_start: -0.1136 (mmm) cc_final: -0.1386 (mpp) REVERT: C 3331 MET cc_start: 0.6215 (ppp) cc_final: 0.5403 (tpp) REVERT: C 3661 ASP cc_start: 0.5343 (OUTLIER) cc_final: 0.4782 (m-30) REVERT: C 3718 MET cc_start: 0.7216 (tpp) cc_final: 0.6940 (tpp) REVERT: C 3953 MET cc_start: 0.8093 (mmm) cc_final: 0.7632 (mmm) REVERT: C 3998 MET cc_start: 0.8489 (tpp) cc_final: 0.8230 (ttt) REVERT: C 4024 ASP cc_start: 0.3955 (OUTLIER) cc_final: 0.3626 (p0) REVERT: C 4811 CYS cc_start: 0.7353 (OUTLIER) cc_final: 0.6346 (t) REVERT: C 4862 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.6312 (mp10) REVERT: C 4948 TRP cc_start: 0.8134 (m-10) cc_final: 0.7651 (m-10) REVERT: D 362 TYR cc_start: 0.7642 (m-80) cc_final: 0.7309 (m-80) REVERT: D 474 ASP cc_start: 0.8280 (t70) cc_final: 0.7951 (t0) REVERT: D 494 MET cc_start: 0.1681 (OUTLIER) cc_final: 0.0691 (mtt) REVERT: D 651 HIS cc_start: 0.6299 (OUTLIER) cc_final: 0.5759 (m-70) REVERT: D 895 MET cc_start: 0.4991 (mmp) cc_final: 0.3854 (mtm) REVERT: D 935 MET cc_start: 0.5683 (tmm) cc_final: 0.4510 (ptt) REVERT: D 981 MET cc_start: 0.0990 (ppp) cc_final: 0.0102 (ptm) REVERT: D 1199 ASP cc_start: 0.8613 (p0) cc_final: 0.8296 (p0) REVERT: D 1605 LEU cc_start: 0.6431 (OUTLIER) cc_final: 0.5947 (mt) REVERT: D 2174 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7651 (ttp) REVERT: D 2178 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7540 (mm) REVERT: D 2190 LYS cc_start: 0.7172 (OUTLIER) cc_final: 0.6625 (ptmm) REVERT: D 2587 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8318 (mt) REVERT: D 2781 MET cc_start: -0.0349 (ptp) cc_final: -0.1048 (mmp) REVERT: D 3240 MET cc_start: 0.8174 (mmm) cc_final: 0.7667 (tmm) REVERT: D 3245 MET cc_start: -0.1142 (mmm) cc_final: -0.1396 (mpp) REVERT: D 3331 MET cc_start: 0.6217 (ppp) cc_final: 0.5404 (tpp) REVERT: D 3661 ASP cc_start: 0.5251 (OUTLIER) cc_final: 0.4727 (m-30) REVERT: D 3718 MET cc_start: 0.7216 (tpp) cc_final: 0.6938 (tpp) REVERT: D 3998 MET cc_start: 0.8467 (tpp) cc_final: 0.8207 (ttt) REVERT: D 4024 ASP cc_start: 0.3940 (OUTLIER) cc_final: 0.3542 (p0) REVERT: D 4082 PHE cc_start: 0.5486 (OUTLIER) cc_final: 0.4296 (p90) REVERT: D 4811 CYS cc_start: 0.7356 (OUTLIER) cc_final: 0.6347 (t) REVERT: D 4862 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.6315 (mp10) REVERT: D 4948 TRP cc_start: 0.8089 (m-10) cc_final: 0.7607 (m-10) REVERT: E 6 GLU cc_start: 0.8083 (mp0) cc_final: 0.7825 (mp0) REVERT: E 26 HIS cc_start: 0.8005 (OUTLIER) cc_final: 0.7292 (t-90) REVERT: F 6 GLU cc_start: 0.8077 (mp0) cc_final: 0.7792 (mp0) REVERT: F 26 HIS cc_start: 0.8057 (OUTLIER) cc_final: 0.7490 (t-90) REVERT: G 6 GLU cc_start: 0.8097 (mp0) cc_final: 0.7729 (mp0) REVERT: G 26 HIS cc_start: 0.8001 (OUTLIER) cc_final: 0.7285 (t-90) REVERT: H 6 GLU cc_start: 0.8119 (mp0) cc_final: 0.7769 (mp0) REVERT: H 26 HIS cc_start: 0.7999 (OUTLIER) cc_final: 0.7285 (t-90) outliers start: 393 outliers final: 295 residues processed: 1329 average time/residue: 0.9727 time to fit residues: 2347.2892 Evaluate side-chains 1346 residues out of total 14384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 344 poor density : 1002 time to evaluate : 10.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 670 TYR Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 731 HIS Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1007 TRP Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1202 ILE Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1467 VAL Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1722 MET Chi-restraints excluded: chain A residue 1783 PHE Chi-restraints excluded: chain A residue 1787 ILE Chi-restraints excluded: chain A residue 1818 LEU Chi-restraints excluded: chain A residue 1819 PHE Chi-restraints excluded: chain A residue 1917 VAL Chi-restraints excluded: chain A residue 1932 VAL Chi-restraints excluded: chain A residue 1952 MET 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 2091 TYR Chi-restraints excluded: chain A residue 2129 LEU Chi-restraints excluded: chain A residue 2145 LEU Chi-restraints excluded: chain A residue 2174 MET Chi-restraints excluded: chain A residue 2190 LYS Chi-restraints excluded: chain A residue 2250 ASN Chi-restraints excluded: chain A residue 2260 ASP Chi-restraints excluded: chain A residue 2280 VAL Chi-restraints excluded: chain A residue 2308 ASN Chi-restraints excluded: chain A residue 2355 ASP Chi-restraints excluded: chain A residue 2383 MET Chi-restraints excluded: chain A residue 2395 ILE Chi-restraints excluded: chain A residue 2472 ASP Chi-restraints excluded: chain A residue 2583 MET Chi-restraints excluded: chain A residue 2595 VAL Chi-restraints excluded: chain A residue 2682 SER Chi-restraints excluded: chain A residue 3200 VAL Chi-restraints excluded: chain A residue 3262 MET Chi-restraints excluded: chain A residue 3469 LEU Chi-restraints excluded: chain A residue 3616 VAL Chi-restraints excluded: chain A residue 3624 GLU Chi-restraints excluded: chain A residue 3661 ASP Chi-restraints excluded: chain A residue 3782 GLU Chi-restraints excluded: chain A residue 3829 LEU Chi-restraints excluded: chain A residue 3846 CYS Chi-restraints excluded: chain A residue 3934 LEU Chi-restraints excluded: chain A residue 3985 LEU Chi-restraints excluded: chain A residue 3989 VAL Chi-restraints excluded: chain A residue 4011 MET Chi-restraints excluded: chain A residue 4016 PHE Chi-restraints excluded: chain A residue 4024 ASP Chi-restraints excluded: chain A residue 4046 ASP Chi-restraints excluded: chain A residue 4054 HIS Chi-restraints excluded: chain A residue 4082 PHE Chi-restraints excluded: chain A residue 4108 MET Chi-restraints excluded: chain A residue 4155 SER Chi-restraints excluded: chain A residue 4556 VAL Chi-restraints excluded: chain A residue 4659 PHE Chi-restraints excluded: chain A residue 4709 LEU Chi-restraints excluded: chain A residue 4713 PHE Chi-restraints excluded: chain A residue 4800 THR Chi-restraints excluded: chain A residue 4807 ASP Chi-restraints excluded: chain A residue 4811 CYS Chi-restraints excluded: chain A residue 4813 MET Chi-restraints excluded: chain A residue 4830 ILE Chi-restraints excluded: chain A residue 4862 GLN Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 629 GLN Chi-restraints excluded: chain B residue 630 HIS Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 670 TYR Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 961 VAL Chi-restraints excluded: chain B residue 1007 TRP Chi-restraints excluded: chain B residue 1166 VAL Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1297 THR Chi-restraints excluded: chain B residue 1467 VAL Chi-restraints excluded: chain B residue 1511 VAL Chi-restraints excluded: chain B residue 1605 LEU Chi-restraints excluded: chain B residue 1722 MET Chi-restraints excluded: chain B residue 1783 PHE Chi-restraints excluded: chain B residue 1818 LEU Chi-restraints excluded: chain B residue 1819 PHE Chi-restraints excluded: chain B residue 1828 THR Chi-restraints excluded: chain B residue 1917 VAL Chi-restraints excluded: chain B residue 1952 MET 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 2091 TYR Chi-restraints excluded: chain B residue 2129 LEU Chi-restraints excluded: chain B residue 2145 LEU Chi-restraints excluded: chain B residue 2174 MET Chi-restraints excluded: chain B residue 2178 LEU Chi-restraints excluded: chain B residue 2190 LYS Chi-restraints excluded: chain B residue 2250 ASN Chi-restraints excluded: chain B residue 2260 ASP Chi-restraints excluded: chain B residue 2280 VAL Chi-restraints excluded: chain B residue 2308 ASN Chi-restraints excluded: chain B residue 2355 ASP Chi-restraints excluded: chain B residue 2395 ILE Chi-restraints excluded: chain B residue 2472 ASP Chi-restraints excluded: chain B residue 2583 MET Chi-restraints excluded: chain B residue 2595 VAL Chi-restraints excluded: chain B residue 2682 SER Chi-restraints excluded: chain B residue 3200 VAL Chi-restraints excluded: chain B residue 3262 MET Chi-restraints excluded: chain B residue 3469 LEU Chi-restraints excluded: chain B residue 3616 VAL Chi-restraints excluded: chain B residue 3661 ASP Chi-restraints excluded: chain B residue 3782 GLU Chi-restraints excluded: chain B residue 3934 LEU Chi-restraints excluded: chain B residue 3985 LEU Chi-restraints excluded: chain B residue 3989 VAL Chi-restraints excluded: chain B residue 4011 MET Chi-restraints excluded: chain B residue 4016 PHE Chi-restraints excluded: chain B residue 4024 ASP Chi-restraints excluded: chain B residue 4046 ASP Chi-restraints excluded: chain B residue 4054 HIS Chi-restraints excluded: chain B residue 4082 PHE Chi-restraints excluded: chain B residue 4108 MET Chi-restraints excluded: chain B residue 4155 SER Chi-restraints excluded: chain B residue 4556 VAL Chi-restraints excluded: chain B residue 4594 VAL Chi-restraints excluded: chain B residue 4659 PHE Chi-restraints excluded: chain B residue 4709 LEU Chi-restraints excluded: chain B residue 4713 PHE Chi-restraints excluded: chain B residue 4800 THR Chi-restraints excluded: chain B residue 4807 ASP Chi-restraints excluded: chain B residue 4811 CYS Chi-restraints excluded: chain B residue 4813 MET Chi-restraints excluded: chain B residue 4830 ILE Chi-restraints excluded: chain B residue 4862 GLN Chi-restraints excluded: chain B residue 4882 ASP Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 494 MET Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 629 GLN Chi-restraints excluded: chain C residue 630 HIS Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 670 TYR Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 716 ASN Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1007 TRP Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1202 ILE Chi-restraints excluded: chain C residue 1297 THR Chi-restraints excluded: chain C residue 1304 LEU Chi-restraints excluded: chain C residue 1467 VAL Chi-restraints excluded: chain C residue 1511 VAL Chi-restraints excluded: chain C residue 1544 VAL Chi-restraints excluded: chain C residue 1605 LEU Chi-restraints excluded: chain C residue 1658 THR Chi-restraints excluded: chain C residue 1722 MET Chi-restraints excluded: chain C residue 1783 PHE Chi-restraints excluded: chain C residue 1818 LEU Chi-restraints excluded: chain C residue 1819 PHE Chi-restraints excluded: chain C residue 1917 VAL Chi-restraints excluded: chain C residue 1952 MET 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 2091 TYR Chi-restraints excluded: chain C residue 2129 LEU Chi-restraints excluded: chain C residue 2145 LEU Chi-restraints excluded: chain C residue 2164 LEU Chi-restraints excluded: chain C residue 2174 MET Chi-restraints excluded: chain C residue 2190 LYS Chi-restraints excluded: chain C residue 2250 ASN Chi-restraints excluded: chain C residue 2260 ASP Chi-restraints excluded: chain C residue 2280 VAL Chi-restraints excluded: chain C residue 2308 ASN Chi-restraints excluded: chain C residue 2355 ASP Chi-restraints excluded: chain C residue 2395 ILE Chi-restraints excluded: chain C residue 2472 ASP Chi-restraints excluded: chain C residue 2526 LEU Chi-restraints excluded: chain C residue 2583 MET Chi-restraints excluded: chain C residue 2595 VAL Chi-restraints excluded: chain C residue 2682 SER Chi-restraints excluded: chain C residue 3200 VAL Chi-restraints excluded: chain C residue 3262 MET Chi-restraints excluded: chain C residue 3469 LEU Chi-restraints excluded: chain C residue 3616 VAL Chi-restraints excluded: chain C residue 3624 GLU Chi-restraints excluded: chain C residue 3661 ASP Chi-restraints excluded: chain C residue 3782 GLU Chi-restraints excluded: chain C residue 3829 LEU Chi-restraints excluded: chain C residue 3846 CYS Chi-restraints excluded: chain C residue 3934 LEU Chi-restraints excluded: chain C residue 3985 LEU Chi-restraints excluded: chain C residue 3989 VAL Chi-restraints excluded: chain C residue 4011 MET Chi-restraints excluded: chain C residue 4016 PHE Chi-restraints excluded: chain C residue 4024 ASP Chi-restraints excluded: chain C residue 4046 ASP Chi-restraints excluded: chain C residue 4054 HIS Chi-restraints excluded: chain C residue 4108 MET Chi-restraints excluded: chain C residue 4155 SER Chi-restraints excluded: chain C residue 4556 VAL Chi-restraints excluded: chain C residue 4659 PHE Chi-restraints excluded: chain C residue 4709 LEU Chi-restraints excluded: chain C residue 4713 PHE Chi-restraints excluded: chain C residue 4800 THR Chi-restraints excluded: chain C residue 4807 ASP Chi-restraints excluded: chain C residue 4811 CYS Chi-restraints excluded: chain C residue 4813 MET Chi-restraints excluded: chain C residue 4862 GLN Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 424 PHE Chi-restraints excluded: chain D residue 494 MET Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 630 HIS Chi-restraints excluded: chain D residue 632 ILE Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 670 TYR Chi-restraints excluded: chain D residue 679 VAL Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 961 VAL Chi-restraints excluded: chain D residue 1007 TRP Chi-restraints excluded: chain D residue 1166 VAL Chi-restraints excluded: chain D residue 1202 ILE Chi-restraints excluded: chain D residue 1297 THR Chi-restraints excluded: chain D residue 1304 LEU Chi-restraints excluded: chain D residue 1467 VAL Chi-restraints excluded: chain D residue 1511 VAL Chi-restraints excluded: chain D residue 1544 VAL Chi-restraints excluded: chain D residue 1605 LEU Chi-restraints excluded: chain D residue 1722 MET Chi-restraints excluded: chain D residue 1783 PHE Chi-restraints excluded: chain D residue 1787 ILE Chi-restraints excluded: chain D residue 1818 LEU Chi-restraints excluded: chain D residue 1819 PHE Chi-restraints excluded: chain D residue 1828 THR Chi-restraints excluded: chain D residue 1917 VAL Chi-restraints excluded: chain D residue 1952 MET Chi-restraints excluded: chain D residue 1957 THR Chi-restraints excluded: chain D residue 1991 ILE Chi-restraints excluded: chain D residue 2060 LEU Chi-restraints excluded: chain D residue 2091 TYR Chi-restraints excluded: chain D residue 2129 LEU Chi-restraints excluded: chain D residue 2145 LEU Chi-restraints excluded: chain D residue 2164 LEU Chi-restraints excluded: chain D residue 2174 MET Chi-restraints excluded: chain D residue 2178 LEU Chi-restraints excluded: chain D residue 2190 LYS Chi-restraints excluded: chain D residue 2250 ASN Chi-restraints excluded: chain D residue 2260 ASP Chi-restraints excluded: chain D residue 2280 VAL Chi-restraints excluded: chain D residue 2308 ASN Chi-restraints excluded: chain D residue 2355 ASP Chi-restraints excluded: chain D residue 2395 ILE Chi-restraints excluded: chain D residue 2405 MET Chi-restraints excluded: chain D residue 2526 LEU Chi-restraints excluded: chain D residue 2583 MET Chi-restraints excluded: chain D residue 2587 LEU Chi-restraints excluded: chain D residue 2595 VAL Chi-restraints excluded: chain D residue 2682 SER Chi-restraints excluded: chain D residue 3200 VAL Chi-restraints excluded: chain D residue 3262 MET Chi-restraints excluded: chain D residue 3469 LEU Chi-restraints excluded: chain D residue 3616 VAL Chi-restraints excluded: chain D residue 3624 GLU Chi-restraints excluded: chain D residue 3661 ASP Chi-restraints excluded: chain D residue 3782 GLU Chi-restraints excluded: chain D residue 3829 LEU Chi-restraints excluded: chain D residue 3846 CYS Chi-restraints excluded: chain D residue 3934 LEU Chi-restraints excluded: chain D residue 3985 LEU Chi-restraints excluded: chain D residue 3989 VAL Chi-restraints excluded: chain D residue 4011 MET Chi-restraints excluded: chain D residue 4016 PHE Chi-restraints excluded: chain D residue 4024 ASP Chi-restraints excluded: chain D residue 4046 ASP Chi-restraints excluded: chain D residue 4054 HIS Chi-restraints excluded: chain D residue 4082 PHE Chi-restraints excluded: chain D residue 4108 MET Chi-restraints excluded: chain D residue 4155 SER Chi-restraints excluded: chain D residue 4556 VAL Chi-restraints excluded: chain D residue 4659 PHE Chi-restraints excluded: chain D residue 4709 LEU Chi-restraints excluded: chain D residue 4713 PHE Chi-restraints excluded: chain D residue 4800 THR Chi-restraints excluded: chain D residue 4807 ASP Chi-restraints excluded: chain D residue 4811 CYS Chi-restraints excluded: chain D residue 4813 MET Chi-restraints excluded: chain D residue 4862 GLN Chi-restraints excluded: chain D residue 4882 ASP Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 38 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1640 random chunks: chunk 1437 optimal weight: 40.0000 chunk 1514 optimal weight: 2.9990 chunk 1381 optimal weight: 4.9990 chunk 1473 optimal weight: 50.0000 chunk 1513 optimal weight: 0.9980 chunk 886 optimal weight: 30.0000 chunk 641 optimal weight: 40.0000 chunk 1156 optimal weight: 0.9990 chunk 452 optimal weight: 5.9990 chunk 1331 optimal weight: 0.0370 chunk 1393 optimal weight: 1.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2340 ASN ** A2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1216 ASN ** B1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2340 ASN ** B2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1440 ASN ** C1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2340 ASN ** C2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1216 ASN ** D1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2340 ASN ** D2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 131440 Z= 0.191 Angle : 0.554 11.423 177752 Z= 0.273 Chirality : 0.038 0.211 19688 Planarity : 0.003 0.057 22980 Dihedral : 3.903 48.772 17668 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.07 % Favored : 92.80 % Rotamer: Outliers : 2.99 % Allowed : 20.02 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.07), residues: 16228 helix: 2.07 (0.06), residues: 7380 sheet: -0.63 (0.17), residues: 1044 loop : -2.32 (0.07), residues: 7804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 893 HIS 0.022 0.001 HIS C1267 PHE 0.020 0.001 PHE B 789 TYR 0.026 0.001 TYR D4938 ARG 0.009 0.000 ARG B1114 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32456 Ramachandran restraints generated. 16228 Oldfield, 0 Emsley, 16228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32456 Ramachandran restraints generated. 16228 Oldfield, 0 Emsley, 16228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1447 residues out of total 14384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 409 poor density : 1038 time to evaluate : 10.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 LEU cc_start: 0.6606 (OUTLIER) cc_final: 0.6249 (mm) REVERT: A 309 MET cc_start: 0.5247 (mmp) cc_final: 0.4996 (mmt) REVERT: A 362 TYR cc_start: 0.7627 (m-80) cc_final: 0.7269 (m-80) REVERT: A 474 ASP cc_start: 0.8444 (t70) cc_final: 0.8004 (t0) REVERT: A 494 MET cc_start: 0.2268 (OUTLIER) cc_final: 0.0950 (mtt) REVERT: A 629 GLN cc_start: 0.4183 (OUTLIER) cc_final: 0.3400 (tt0) REVERT: A 935 MET cc_start: 0.5683 (tmm) cc_final: 0.4522 (ptt) REVERT: A 981 MET cc_start: 0.0952 (ppp) cc_final: 0.0076 (ptm) REVERT: A 1199 ASP cc_start: 0.8646 (p0) cc_final: 0.8323 (p0) REVERT: A 2174 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7642 (ttp) REVERT: A 2178 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7547 (mm) REVERT: A 2190 LYS cc_start: 0.7205 (OUTLIER) cc_final: 0.6634 (ptmm) REVERT: A 2579 LEU cc_start: 0.7615 (pp) cc_final: 0.7389 (pt) REVERT: A 2604 MET cc_start: 0.7432 (mmp) cc_final: 0.7016 (mtm) REVERT: A 2687 MET cc_start: 0.5684 (mmm) cc_final: 0.5427 (mmp) REVERT: A 2781 MET cc_start: -0.0360 (ptp) cc_final: -0.1031 (mmp) REVERT: A 3045 MET cc_start: 0.5422 (ppp) cc_final: 0.5199 (ppp) REVERT: A 3331 MET cc_start: 0.6239 (ppp) cc_final: 0.5441 (tpp) REVERT: A 3629 GLU cc_start: 0.6768 (tt0) cc_final: 0.6398 (tp30) REVERT: A 3661 ASP cc_start: 0.5342 (OUTLIER) cc_final: 0.4788 (m-30) REVERT: A 3998 MET cc_start: 0.8485 (tpp) cc_final: 0.8179 (ttt) REVERT: A 4024 ASP cc_start: 0.4030 (OUTLIER) cc_final: 0.3643 (p0) REVERT: A 4082 PHE cc_start: 0.5630 (OUTLIER) cc_final: 0.4410 (p90) REVERT: A 4811 CYS cc_start: 0.7427 (OUTLIER) cc_final: 0.6748 (t) REVERT: A 4862 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.6334 (mp10) REVERT: A 4948 TRP cc_start: 0.8138 (m-10) cc_final: 0.7662 (m-10) REVERT: B 245 LEU cc_start: 0.6594 (OUTLIER) cc_final: 0.6226 (mm) REVERT: B 309 MET cc_start: 0.5409 (mmp) cc_final: 0.5185 (mmt) REVERT: B 362 TYR cc_start: 0.7534 (m-80) cc_final: 0.7101 (m-80) REVERT: B 474 ASP cc_start: 0.8285 (t70) cc_final: 0.7961 (t0) REVERT: B 494 MET cc_start: 0.1629 (OUTLIER) cc_final: 0.0638 (mtt) REVERT: B 535 GLU cc_start: 0.7028 (tt0) cc_final: 0.6584 (mm-30) REVERT: B 629 GLN cc_start: 0.4197 (OUTLIER) cc_final: 0.3378 (tt0) REVERT: B 651 HIS cc_start: 0.6262 (OUTLIER) cc_final: 0.5671 (m-70) REVERT: B 895 MET cc_start: 0.5031 (mmp) cc_final: 0.3877 (mtm) REVERT: B 935 MET cc_start: 0.5555 (tmm) cc_final: 0.4479 (ptt) REVERT: B 981 MET cc_start: 0.0845 (ppp) cc_final: -0.0111 (ptp) REVERT: B 1174 MET cc_start: 0.5661 (ptp) cc_final: 0.5194 (ppp) REVERT: B 1199 ASP cc_start: 0.8689 (p0) cc_final: 0.8375 (p0) REVERT: B 1605 LEU cc_start: 0.6562 (OUTLIER) cc_final: 0.6048 (mp) REVERT: B 2174 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7631 (ttp) REVERT: B 2178 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7546 (mm) REVERT: B 2190 LYS cc_start: 0.7208 (OUTLIER) cc_final: 0.6635 (ptmm) REVERT: B 2579 LEU cc_start: 0.7614 (pp) cc_final: 0.7386 (pt) REVERT: B 2604 MET cc_start: 0.7380 (mmp) cc_final: 0.6950 (mtm) REVERT: B 2781 MET cc_start: -0.0363 (ptp) cc_final: -0.1040 (mmp) REVERT: B 3045 MET cc_start: 0.5114 (ppp) cc_final: 0.4884 (ppp) REVERT: B 3331 MET cc_start: 0.6176 (ppp) cc_final: 0.5377 (tpp) REVERT: B 3629 GLU cc_start: 0.6764 (tt0) cc_final: 0.6396 (tp30) REVERT: B 3661 ASP cc_start: 0.5312 (OUTLIER) cc_final: 0.4793 (m-30) REVERT: B 3718 MET cc_start: 0.7065 (tpp) cc_final: 0.6821 (tpp) REVERT: B 3953 MET cc_start: 0.8104 (mmm) cc_final: 0.7658 (mmm) REVERT: B 3998 MET cc_start: 0.8493 (tpp) cc_final: 0.8185 (ttt) REVERT: B 4024 ASP cc_start: 0.4040 (OUTLIER) cc_final: 0.3653 (p0) REVERT: B 4082 PHE cc_start: 0.5483 (OUTLIER) cc_final: 0.4092 (p90) REVERT: B 4811 CYS cc_start: 0.7417 (OUTLIER) cc_final: 0.6734 (t) REVERT: B 4862 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.6327 (mp10) REVERT: B 4948 TRP cc_start: 0.8142 (m-10) cc_final: 0.7663 (m-10) REVERT: C 245 LEU cc_start: 0.6589 (OUTLIER) cc_final: 0.6238 (mm) REVERT: C 309 MET cc_start: 0.5097 (mmp) cc_final: 0.4840 (mmt) REVERT: C 362 TYR cc_start: 0.7618 (m-80) cc_final: 0.7283 (m-80) REVERT: C 474 ASP cc_start: 0.8265 (t70) cc_final: 0.7969 (t0) REVERT: C 494 MET cc_start: 0.2141 (OUTLIER) cc_final: 0.0747 (mtt) REVERT: C 629 GLN cc_start: 0.4170 (OUTLIER) cc_final: 0.3391 (tt0) REVERT: C 651 HIS cc_start: 0.6324 (OUTLIER) cc_final: 0.5793 (m-70) REVERT: C 895 MET cc_start: 0.5172 (mmp) cc_final: 0.4073 (mtp) REVERT: C 935 MET cc_start: 0.5698 (tmm) cc_final: 0.4511 (ptt) REVERT: C 981 MET cc_start: 0.0952 (ppp) cc_final: 0.0056 (ptm) REVERT: C 1199 ASP cc_start: 0.8645 (p0) cc_final: 0.8319 (p0) REVERT: C 1605 LEU cc_start: 0.6567 (OUTLIER) cc_final: 0.6065 (mp) REVERT: C 2174 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7635 (ttp) REVERT: C 2178 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7543 (mm) REVERT: C 2190 LYS cc_start: 0.7230 (OUTLIER) cc_final: 0.6648 (ptmm) REVERT: C 2233 MET cc_start: 0.8318 (mmm) cc_final: 0.8013 (mmm) REVERT: C 2781 MET cc_start: -0.0356 (ptp) cc_final: -0.1048 (mmp) REVERT: C 3331 MET cc_start: 0.6208 (ppp) cc_final: 0.5394 (tpp) REVERT: C 3629 GLU cc_start: 0.6772 (tt0) cc_final: 0.6399 (tp30) REVERT: C 3661 ASP cc_start: 0.5345 (OUTLIER) cc_final: 0.4798 (m-30) REVERT: C 3718 MET cc_start: 0.7227 (tpp) cc_final: 0.6937 (tpp) REVERT: C 3953 MET cc_start: 0.8103 (mmm) cc_final: 0.7626 (mmm) REVERT: C 3998 MET cc_start: 0.8484 (tpp) cc_final: 0.8181 (ttt) REVERT: C 4024 ASP cc_start: 0.4011 (OUTLIER) cc_final: 0.3563 (p0) REVERT: C 4082 PHE cc_start: 0.5428 (OUTLIER) cc_final: 0.4162 (p90) REVERT: C 4811 CYS cc_start: 0.7415 (OUTLIER) cc_final: 0.6735 (t) REVERT: C 4862 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.6329 (mp10) REVERT: C 4948 TRP cc_start: 0.8136 (m-10) cc_final: 0.7663 (m-10) REVERT: D 245 LEU cc_start: 0.6604 (OUTLIER) cc_final: 0.6256 (mm) REVERT: D 309 MET cc_start: 0.5070 (mmp) cc_final: 0.4821 (mmt) REVERT: D 362 TYR cc_start: 0.7628 (m-80) cc_final: 0.7287 (m-80) REVERT: D 474 ASP cc_start: 0.8261 (t70) cc_final: 0.7968 (t0) REVERT: D 494 MET cc_start: 0.2135 (OUTLIER) cc_final: 0.0740 (mtt) REVERT: D 651 HIS cc_start: 0.6318 (OUTLIER) cc_final: 0.5770 (m-70) REVERT: D 895 MET cc_start: 0.5187 (mmp) cc_final: 0.4088 (mtp) REVERT: D 935 MET cc_start: 0.5674 (tmm) cc_final: 0.4520 (ptt) REVERT: D 981 MET cc_start: 0.0943 (ppp) cc_final: 0.0051 (ptm) REVERT: D 1199 ASP cc_start: 0.8656 (p0) cc_final: 0.8340 (p0) REVERT: D 1605 LEU cc_start: 0.6543 (OUTLIER) cc_final: 0.6041 (mt) REVERT: D 2174 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7633 (ttp) REVERT: D 2178 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7555 (mm) REVERT: D 2190 LYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6630 (ptmm) REVERT: D 2233 MET cc_start: 0.8326 (mmm) cc_final: 0.8017 (mmm) REVERT: D 2587 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8202 (mt) REVERT: D 2604 MET cc_start: 0.7251 (mmp) cc_final: 0.6678 (mpp) REVERT: D 2781 MET cc_start: -0.0345 (ptp) cc_final: -0.1041 (mmp) REVERT: D 3331 MET cc_start: 0.6213 (ppp) cc_final: 0.5399 (tpp) REVERT: D 3629 GLU cc_start: 0.6771 (tt0) cc_final: 0.6399 (tp30) REVERT: D 3661 ASP cc_start: 0.5268 (OUTLIER) cc_final: 0.4748 (m-30) REVERT: D 3718 MET cc_start: 0.7223 (tpp) cc_final: 0.6933 (tpp) REVERT: D 3953 MET cc_start: 0.8105 (mmm) cc_final: 0.7657 (mmm) REVERT: D 3998 MET cc_start: 0.8467 (tpp) cc_final: 0.8167 (ttt) REVERT: D 4024 ASP cc_start: 0.4014 (OUTLIER) cc_final: 0.3531 (p0) REVERT: D 4082 PHE cc_start: 0.5436 (OUTLIER) cc_final: 0.4200 (p90) REVERT: D 4811 CYS cc_start: 0.7417 (OUTLIER) cc_final: 0.6738 (t) REVERT: D 4862 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.6337 (mp10) REVERT: D 4948 TRP cc_start: 0.8119 (m-10) cc_final: 0.7634 (m-10) REVERT: E 6 GLU cc_start: 0.8088 (mp0) cc_final: 0.7820 (mp0) REVERT: E 26 HIS cc_start: 0.8047 (OUTLIER) cc_final: 0.7356 (t-90) REVERT: F 6 GLU cc_start: 0.8062 (mp0) cc_final: 0.7793 (mp0) REVERT: F 26 HIS cc_start: 0.8087 (OUTLIER) cc_final: 0.7540 (t-90) REVERT: G 6 GLU cc_start: 0.8094 (mp0) cc_final: 0.7730 (mp0) REVERT: G 26 HIS cc_start: 0.8042 (OUTLIER) cc_final: 0.7313 (t-90) REVERT: H 6 GLU cc_start: 0.8114 (mp0) cc_final: 0.7757 (mp0) REVERT: H 26 HIS cc_start: 0.8047 (OUTLIER) cc_final: 0.7360 (t-90) outliers start: 409 outliers final: 312 residues processed: 1345 average time/residue: 0.9893 time to fit residues: 2409.1289 Evaluate side-chains 1371 residues out of total 14384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 366 poor density : 1005 time to evaluate : 10.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 670 TYR Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1007 TRP Chi-restraints excluded: chain A residue 1143 GLN Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1202 ILE Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1467 VAL Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1658 THR Chi-restraints excluded: chain A residue 1722 MET Chi-restraints excluded: chain A residue 1783 PHE Chi-restraints excluded: chain A residue 1818 LEU Chi-restraints excluded: chain A residue 1819 PHE Chi-restraints excluded: chain A residue 1917 VAL Chi-restraints excluded: chain A residue 1932 VAL 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 2091 TYR Chi-restraints excluded: chain A residue 2129 LEU Chi-restraints excluded: chain A residue 2145 LEU Chi-restraints excluded: chain A residue 2161 MET Chi-restraints excluded: chain A residue 2174 MET Chi-restraints excluded: chain A residue 2178 LEU Chi-restraints excluded: chain A residue 2190 LYS Chi-restraints excluded: chain A residue 2250 ASN Chi-restraints excluded: chain A residue 2260 ASP Chi-restraints excluded: chain A residue 2280 VAL Chi-restraints excluded: chain A residue 2308 ASN Chi-restraints excluded: chain A residue 2355 ASP Chi-restraints excluded: chain A residue 2395 ILE Chi-restraints excluded: chain A residue 2472 ASP Chi-restraints excluded: chain A residue 2483 LEU Chi-restraints excluded: chain A residue 2583 MET Chi-restraints excluded: chain A residue 2595 VAL Chi-restraints excluded: chain A residue 2682 SER Chi-restraints excluded: chain A residue 3200 VAL Chi-restraints excluded: chain A residue 3262 MET Chi-restraints excluded: chain A residue 3469 LEU Chi-restraints excluded: chain A residue 3616 VAL Chi-restraints excluded: chain A residue 3624 GLU Chi-restraints excluded: chain A residue 3661 ASP Chi-restraints excluded: chain A residue 3782 GLU Chi-restraints excluded: chain A residue 3829 LEU Chi-restraints excluded: chain A residue 3846 CYS Chi-restraints excluded: chain A residue 3934 LEU Chi-restraints excluded: chain A residue 3985 LEU Chi-restraints excluded: chain A residue 3989 VAL Chi-restraints excluded: chain A residue 4011 MET Chi-restraints excluded: chain A residue 4016 PHE Chi-restraints excluded: chain A residue 4024 ASP Chi-restraints excluded: chain A residue 4046 ASP Chi-restraints excluded: chain A residue 4054 HIS Chi-restraints excluded: chain A residue 4082 PHE Chi-restraints excluded: chain A residue 4108 MET Chi-restraints excluded: chain A residue 4155 SER Chi-restraints excluded: chain A residue 4556 VAL Chi-restraints excluded: chain A residue 4659 PHE Chi-restraints excluded: chain A residue 4709 LEU Chi-restraints excluded: chain A residue 4713 PHE Chi-restraints excluded: chain A residue 4800 THR Chi-restraints excluded: chain A residue 4807 ASP Chi-restraints excluded: chain A residue 4811 CYS Chi-restraints excluded: chain A residue 4813 MET Chi-restraints excluded: chain A residue 4830 ILE Chi-restraints excluded: chain A residue 4862 GLN Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 629 GLN Chi-restraints excluded: chain B residue 630 HIS Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 670 TYR Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 716 ASN Chi-restraints excluded: chain B residue 798 ILE Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 961 VAL Chi-restraints excluded: chain B residue 1007 TRP Chi-restraints excluded: chain B residue 1143 GLN Chi-restraints excluded: chain B residue 1166 VAL Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1297 THR Chi-restraints excluded: chain B residue 1304 LEU Chi-restraints excluded: chain B residue 1467 VAL Chi-restraints excluded: chain B residue 1511 VAL Chi-restraints excluded: chain B residue 1605 LEU Chi-restraints excluded: chain B residue 1722 MET Chi-restraints excluded: chain B residue 1783 PHE Chi-restraints excluded: chain B residue 1818 LEU Chi-restraints excluded: chain B residue 1819 PHE Chi-restraints excluded: chain B residue 1828 THR Chi-restraints excluded: chain B residue 1917 VAL Chi-restraints excluded: chain B residue 1952 MET 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 2091 TYR Chi-restraints excluded: chain B residue 2129 LEU Chi-restraints excluded: chain B residue 2145 LEU Chi-restraints excluded: chain B residue 2164 LEU Chi-restraints excluded: chain B residue 2174 MET Chi-restraints excluded: chain B residue 2178 LEU Chi-restraints excluded: chain B residue 2190 LYS Chi-restraints excluded: chain B residue 2250 ASN Chi-restraints excluded: chain B residue 2260 ASP Chi-restraints excluded: chain B residue 2280 VAL Chi-restraints excluded: chain B residue 2308 ASN Chi-restraints excluded: chain B residue 2324 ILE Chi-restraints excluded: chain B residue 2355 ASP Chi-restraints excluded: chain B residue 2395 ILE Chi-restraints excluded: chain B residue 2416 ILE Chi-restraints excluded: chain B residue 2472 ASP Chi-restraints excluded: chain B residue 2583 MET Chi-restraints excluded: chain B residue 2595 VAL Chi-restraints excluded: chain B residue 2682 SER Chi-restraints excluded: chain B residue 3200 VAL Chi-restraints excluded: chain B residue 3262 MET Chi-restraints excluded: chain B residue 3469 LEU Chi-restraints excluded: chain B residue 3616 VAL Chi-restraints excluded: chain B residue 3661 ASP Chi-restraints excluded: chain B residue 3782 GLU Chi-restraints excluded: chain B residue 3934 LEU Chi-restraints excluded: chain B residue 3985 LEU Chi-restraints excluded: chain B residue 3989 VAL Chi-restraints excluded: chain B residue 4011 MET Chi-restraints excluded: chain B residue 4016 PHE Chi-restraints excluded: chain B residue 4024 ASP Chi-restraints excluded: chain B residue 4046 ASP Chi-restraints excluded: chain B residue 4054 HIS Chi-restraints excluded: chain B residue 4082 PHE Chi-restraints excluded: chain B residue 4108 MET Chi-restraints excluded: chain B residue 4155 SER Chi-restraints excluded: chain B residue 4556 VAL Chi-restraints excluded: chain B residue 4594 VAL Chi-restraints excluded: chain B residue 4659 PHE Chi-restraints excluded: chain B residue 4709 LEU Chi-restraints excluded: chain B residue 4713 PHE Chi-restraints excluded: chain B residue 4800 THR Chi-restraints excluded: chain B residue 4807 ASP Chi-restraints excluded: chain B residue 4811 CYS Chi-restraints excluded: chain B residue 4813 MET Chi-restraints excluded: chain B residue 4830 ILE Chi-restraints excluded: chain B residue 4862 GLN Chi-restraints excluded: chain B residue 4882 ASP Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 424 PHE Chi-restraints excluded: chain C residue 494 MET Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 629 GLN Chi-restraints excluded: chain C residue 630 HIS Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 670 TYR Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 716 ASN Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1007 TRP Chi-restraints excluded: chain C residue 1143 GLN Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1202 ILE Chi-restraints excluded: chain C residue 1297 THR Chi-restraints excluded: chain C residue 1304 LEU Chi-restraints excluded: chain C residue 1467 VAL Chi-restraints excluded: chain C residue 1511 VAL Chi-restraints excluded: chain C residue 1544 VAL Chi-restraints excluded: chain C residue 1605 LEU Chi-restraints excluded: chain C residue 1658 THR Chi-restraints excluded: chain C residue 1722 MET Chi-restraints excluded: chain C residue 1783 PHE Chi-restraints excluded: chain C residue 1818 LEU Chi-restraints excluded: chain C residue 1819 PHE Chi-restraints excluded: chain C residue 1903 LEU Chi-restraints excluded: chain C residue 1917 VAL 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 2091 TYR Chi-restraints excluded: chain C residue 2129 LEU Chi-restraints excluded: chain C residue 2145 LEU Chi-restraints excluded: chain C residue 2161 MET Chi-restraints excluded: chain C residue 2164 LEU Chi-restraints excluded: chain C residue 2174 MET Chi-restraints excluded: chain C residue 2178 LEU Chi-restraints excluded: chain C residue 2190 LYS Chi-restraints excluded: chain C residue 2250 ASN Chi-restraints excluded: chain C residue 2260 ASP Chi-restraints excluded: chain C residue 2280 VAL Chi-restraints excluded: chain C residue 2308 ASN Chi-restraints excluded: chain C residue 2324 ILE Chi-restraints excluded: chain C residue 2355 ASP Chi-restraints excluded: chain C residue 2395 ILE Chi-restraints excluded: chain C residue 2472 ASP Chi-restraints excluded: chain C residue 2526 LEU Chi-restraints excluded: chain C residue 2583 MET Chi-restraints excluded: chain C residue 2595 VAL Chi-restraints excluded: chain C residue 2682 SER Chi-restraints excluded: chain C residue 3200 VAL Chi-restraints excluded: chain C residue 3262 MET Chi-restraints excluded: chain C residue 3469 LEU Chi-restraints excluded: chain C residue 3616 VAL Chi-restraints excluded: chain C residue 3624 GLU Chi-restraints excluded: chain C residue 3661 ASP Chi-restraints excluded: chain C residue 3782 GLU Chi-restraints excluded: chain C residue 3829 LEU Chi-restraints excluded: chain C residue 3846 CYS Chi-restraints excluded: chain C residue 3934 LEU Chi-restraints excluded: chain C residue 3985 LEU Chi-restraints excluded: chain C residue 3989 VAL Chi-restraints excluded: chain C residue 4011 MET Chi-restraints excluded: chain C residue 4016 PHE Chi-restraints excluded: chain C residue 4024 ASP Chi-restraints excluded: chain C residue 4046 ASP Chi-restraints excluded: chain C residue 4054 HIS Chi-restraints excluded: chain C residue 4082 PHE Chi-restraints excluded: chain C residue 4108 MET Chi-restraints excluded: chain C residue 4155 SER Chi-restraints excluded: chain C residue 4556 VAL Chi-restraints excluded: chain C residue 4659 PHE Chi-restraints excluded: chain C residue 4709 LEU Chi-restraints excluded: chain C residue 4713 PHE Chi-restraints excluded: chain C residue 4800 THR Chi-restraints excluded: chain C residue 4807 ASP Chi-restraints excluded: chain C residue 4811 CYS Chi-restraints excluded: chain C residue 4813 MET Chi-restraints excluded: chain C residue 4830 ILE Chi-restraints excluded: chain C residue 4862 GLN Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 424 PHE Chi-restraints excluded: chain D residue 494 MET Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 630 HIS Chi-restraints excluded: chain D residue 632 ILE Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 670 TYR Chi-restraints excluded: chain D residue 679 VAL Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 1007 TRP Chi-restraints excluded: chain D residue 1143 GLN Chi-restraints excluded: chain D residue 1166 VAL Chi-restraints excluded: chain D residue 1202 ILE Chi-restraints excluded: chain D residue 1216 ASN Chi-restraints excluded: chain D residue 1297 THR Chi-restraints excluded: chain D residue 1467 VAL Chi-restraints excluded: chain D residue 1511 VAL Chi-restraints excluded: chain D residue 1544 VAL Chi-restraints excluded: chain D residue 1605 LEU Chi-restraints excluded: chain D residue 1722 MET Chi-restraints excluded: chain D residue 1783 PHE Chi-restraints excluded: chain D residue 1787 ILE Chi-restraints excluded: chain D residue 1818 LEU Chi-restraints excluded: chain D residue 1819 PHE Chi-restraints excluded: chain D residue 1828 THR Chi-restraints excluded: chain D residue 1917 VAL Chi-restraints excluded: chain D residue 1957 THR Chi-restraints excluded: chain D residue 1991 ILE Chi-restraints excluded: chain D residue 2060 LEU Chi-restraints excluded: chain D residue 2085 VAL Chi-restraints excluded: chain D residue 2091 TYR Chi-restraints excluded: chain D residue 2129 LEU Chi-restraints excluded: chain D residue 2145 LEU Chi-restraints excluded: chain D residue 2161 MET Chi-restraints excluded: chain D residue 2164 LEU Chi-restraints excluded: chain D residue 2174 MET Chi-restraints excluded: chain D residue 2178 LEU Chi-restraints excluded: chain D residue 2190 LYS Chi-restraints excluded: chain D residue 2250 ASN Chi-restraints excluded: chain D residue 2260 ASP Chi-restraints excluded: chain D residue 2280 VAL Chi-restraints excluded: chain D residue 2308 ASN Chi-restraints excluded: chain D residue 2355 ASP Chi-restraints excluded: chain D residue 2395 ILE Chi-restraints excluded: chain D residue 2405 MET Chi-restraints excluded: chain D residue 2526 LEU Chi-restraints excluded: chain D residue 2583 MET Chi-restraints excluded: chain D residue 2587 LEU Chi-restraints excluded: chain D residue 2595 VAL Chi-restraints excluded: chain D residue 2682 SER Chi-restraints excluded: chain D residue 3200 VAL Chi-restraints excluded: chain D residue 3262 MET Chi-restraints excluded: chain D residue 3469 LEU Chi-restraints excluded: chain D residue 3616 VAL Chi-restraints excluded: chain D residue 3624 GLU Chi-restraints excluded: chain D residue 3661 ASP Chi-restraints excluded: chain D residue 3782 GLU Chi-restraints excluded: chain D residue 3829 LEU Chi-restraints excluded: chain D residue 3846 CYS Chi-restraints excluded: chain D residue 3934 LEU Chi-restraints excluded: chain D residue 3985 LEU Chi-restraints excluded: chain D residue 3989 VAL Chi-restraints excluded: chain D residue 4016 PHE Chi-restraints excluded: chain D residue 4024 ASP Chi-restraints excluded: chain D residue 4046 ASP Chi-restraints excluded: chain D residue 4054 HIS Chi-restraints excluded: chain D residue 4082 PHE Chi-restraints excluded: chain D residue 4108 MET Chi-restraints excluded: chain D residue 4155 SER Chi-restraints excluded: chain D residue 4556 VAL Chi-restraints excluded: chain D residue 4659 PHE Chi-restraints excluded: chain D residue 4709 LEU Chi-restraints excluded: chain D residue 4713 PHE Chi-restraints excluded: chain D residue 4800 THR Chi-restraints excluded: chain D residue 4807 ASP Chi-restraints excluded: chain D residue 4811 CYS Chi-restraints excluded: chain D residue 4813 MET Chi-restraints excluded: chain D residue 4830 ILE Chi-restraints excluded: chain D residue 4862 GLN Chi-restraints excluded: chain D residue 4882 ASP Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 38 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1640 random chunks: chunk 1467 optimal weight: 0.8980 chunk 967 optimal weight: 1.9990 chunk 1557 optimal weight: 7.9990 chunk 950 optimal weight: 0.9980 chunk 738 optimal weight: 6.9990 chunk 1082 optimal weight: 6.9990 chunk 1633 optimal weight: 5.9990 chunk 1503 optimal weight: 0.2980 chunk 1301 optimal weight: 20.0000 chunk 135 optimal weight: 6.9990 chunk 1004 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2340 ASN ** A2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1216 ASN ** B1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2340 ASN ** B2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1440 ASN ** C1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2340 ASN ** C2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1216 ASN ** D1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2340 ASN ** D2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 131440 Z= 0.166 Angle : 0.557 12.984 177752 Z= 0.273 Chirality : 0.038 0.214 19688 Planarity : 0.003 0.053 22980 Dihedral : 3.883 48.707 17668 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.72 % Favored : 93.16 % Rotamer: Outliers : 2.71 % Allowed : 20.34 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.07), residues: 16228 helix: 2.09 (0.06), residues: 7400 sheet: -0.47 (0.17), residues: 1044 loop : -2.32 (0.07), residues: 7784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP C1145 HIS 0.016 0.001 HIS C1267 PHE 0.041 0.001 PHE D1217 TYR 0.039 0.001 TYR B4079 ARG 0.014 0.000 ARG C1114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 32456 Ramachandran restraints generated. 16228 Oldfield, 0 Emsley, 16228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 32456 Ramachandran restraints generated. 16228 Oldfield, 0 Emsley, 16228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1410 residues out of total 14384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 371 poor density : 1039 time to evaluate : 10.564 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 42 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7792 (t80) REVERT: A 245 LEU cc_start: 0.6522 (OUTLIER) cc_final: 0.6162 (mm) REVERT: A 309 MET cc_start: 0.5260 (mmp) cc_final: 0.5001 (mmt) REVERT: A 362 TYR cc_start: 0.7508 (m-80) cc_final: 0.7153 (m-80) REVERT: A 494 MET cc_start: 0.2248 (OUTLIER) cc_final: 0.0986 (mtt) REVERT: A 629 GLN cc_start: 0.3963 (OUTLIER) cc_final: 0.3211 (tt0) REVERT: A 678 MET cc_start: 0.7605 (tpp) cc_final: 0.7290 (tpt) REVERT: A 895 MET cc_start: 0.5357 (mmp) cc_final: 0.4346 (mtm) REVERT: A 935 MET cc_start: 0.5681 (tmm) cc_final: 0.4507 (ptt) REVERT: A 981 MET cc_start: 0.0947 (ppp) cc_final: 0.0070 (ptm) REVERT: A 1199 ASP cc_start: 0.8635 (p0) cc_final: 0.8290 (p0) REVERT: A 2174 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7574 (ttp) REVERT: A 2178 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7541 (mm) REVERT: A 2190 LYS cc_start: 0.7164 (OUTLIER) cc_final: 0.6552 (ptmm) REVERT: A 2579 LEU cc_start: 0.7555 (pp) cc_final: 0.7317 (pt) REVERT: A 2604 MET cc_start: 0.7441 (mmp) cc_final: 0.7054 (mtm) REVERT: A 2687 MET cc_start: 0.5668 (mmm) cc_final: 0.5413 (mmp) REVERT: A 2781 MET cc_start: -0.0393 (ptp) cc_final: -0.1055 (mmp) REVERT: A 3045 MET cc_start: 0.5421 (ppp) cc_final: 0.5195 (ppp) REVERT: A 3331 MET cc_start: 0.6233 (ppp) cc_final: 0.5437 (tpp) REVERT: A 3629 GLU cc_start: 0.6734 (tt0) cc_final: 0.6410 (tp30) REVERT: A 3661 ASP cc_start: 0.5375 (OUTLIER) cc_final: 0.4823 (m-30) REVERT: A 3953 MET cc_start: 0.8135 (mmm) cc_final: 0.7587 (mmm) REVERT: A 3998 MET cc_start: 0.8505 (tpp) cc_final: 0.8223 (ttt) REVERT: A 4024 ASP cc_start: 0.4001 (OUTLIER) cc_final: 0.3612 (p0) REVERT: A 4082 PHE cc_start: 0.5624 (OUTLIER) cc_final: 0.4411 (p90) REVERT: A 4808 MET cc_start: 0.7894 (tpp) cc_final: 0.7614 (tpp) REVERT: A 4811 CYS cc_start: 0.7294 (OUTLIER) cc_final: 0.6409 (t) REVERT: A 4862 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.6317 (mp10) REVERT: A 4948 TRP cc_start: 0.8123 (m-10) cc_final: 0.7654 (m-10) REVERT: B 245 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.6152 (mm) REVERT: B 309 MET cc_start: 0.5411 (mmp) cc_final: 0.5182 (mmt) REVERT: B 362 TYR cc_start: 0.7388 (m-80) cc_final: 0.7051 (m-80) REVERT: B 474 ASP cc_start: 0.8251 (t70) cc_final: 0.7960 (t0) REVERT: B 494 MET cc_start: 0.2111 (OUTLIER) cc_final: 0.0760 (mtt) REVERT: B 629 GLN cc_start: 0.3979 (OUTLIER) cc_final: 0.3187 (tt0) REVERT: B 651 HIS cc_start: 0.6234 (OUTLIER) cc_final: 0.5655 (m-70) REVERT: B 678 MET cc_start: 0.7587 (tpp) cc_final: 0.6896 (tpt) REVERT: B 895 MET cc_start: 0.4898 (mmp) cc_final: 0.3827 (mtp) REVERT: B 935 MET cc_start: 0.5549 (tmm) cc_final: 0.4486 (ptt) REVERT: B 981 MET cc_start: 0.0845 (ppp) cc_final: 0.0196 (ptm) REVERT: B 1174 MET cc_start: 0.5565 (ptp) cc_final: 0.5137 (ppp) REVERT: B 1199 ASP cc_start: 0.8669 (p0) cc_final: 0.8343 (p0) REVERT: B 1605 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.5954 (mp) REVERT: B 2174 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7597 (ttp) REVERT: B 2178 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7549 (mm) REVERT: B 2190 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6598 (ptmm) REVERT: B 2579 LEU cc_start: 0.7556 (pp) cc_final: 0.7315 (pt) REVERT: B 2604 MET cc_start: 0.7443 (mmp) cc_final: 0.7053 (mtm) REVERT: B 2781 MET cc_start: -0.0394 (ptp) cc_final: -0.1064 (mmp) REVERT: B 3045 MET cc_start: 0.5265 (ppp) cc_final: 0.5050 (ppp) REVERT: B 3331 MET cc_start: 0.6172 (ppp) cc_final: 0.5374 (tpp) REVERT: B 3629 GLU cc_start: 0.6723 (tt0) cc_final: 0.6401 (tp30) REVERT: B 3661 ASP cc_start: 0.5228 (OUTLIER) cc_final: 0.4695 (m-30) REVERT: B 3718 MET cc_start: 0.7134 (tpp) cc_final: 0.6768 (tpp) REVERT: B 3953 MET cc_start: 0.8118 (mmm) cc_final: 0.7572 (mmm) REVERT: B 3998 MET cc_start: 0.8499 (tpp) cc_final: 0.8213 (ttt) REVERT: B 4024 ASP cc_start: 0.4083 (OUTLIER) cc_final: 0.3811 (p0) REVERT: B 4808 MET cc_start: 0.7906 (tpp) cc_final: 0.7618 (tpp) REVERT: B 4811 CYS cc_start: 0.7348 (OUTLIER) cc_final: 0.6728 (t) REVERT: B 4862 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.6326 (mp10) REVERT: B 4948 TRP cc_start: 0.8128 (m-10) cc_final: 0.7652 (m-10) REVERT: C 245 LEU cc_start: 0.6549 (OUTLIER) cc_final: 0.6192 (mm) REVERT: C 309 MET cc_start: 0.5203 (mmp) cc_final: 0.4928 (mmt) REVERT: C 362 TYR cc_start: 0.7561 (m-80) cc_final: 0.7218 (m-80) REVERT: C 474 ASP cc_start: 0.8257 (t70) cc_final: 0.7962 (t0) REVERT: C 494 MET cc_start: 0.2264 (OUTLIER) cc_final: 0.0949 (mtt) REVERT: C 629 GLN cc_start: 0.4136 (OUTLIER) cc_final: 0.3321 (tt0) REVERT: C 651 HIS cc_start: 0.6298 (OUTLIER) cc_final: 0.5781 (m-70) REVERT: C 895 MET cc_start: 0.5332 (mmp) cc_final: 0.4075 (mtp) REVERT: C 935 MET cc_start: 0.5543 (tmm) cc_final: 0.4481 (ptt) REVERT: C 981 MET cc_start: 0.0943 (ppp) cc_final: 0.0053 (ptm) REVERT: C 1199 ASP cc_start: 0.8631 (p0) cc_final: 0.8289 (p0) REVERT: C 1605 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.5962 (mp) REVERT: C 2174 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7854 (ttm) REVERT: C 2178 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7496 (mm) REVERT: C 2190 LYS cc_start: 0.7168 (OUTLIER) cc_final: 0.6541 (ptmm) REVERT: C 2233 MET cc_start: 0.8253 (mmm) cc_final: 0.7957 (mmm) REVERT: C 2781 MET cc_start: -0.0353 (ptp) cc_final: -0.1039 (mmp) REVERT: C 3331 MET cc_start: 0.6200 (ppp) cc_final: 0.5390 (tpp) REVERT: C 3629 GLU cc_start: 0.6732 (tt0) cc_final: 0.6406 (tp30) REVERT: C 3661 ASP cc_start: 0.5282 (OUTLIER) cc_final: 0.4749 (m-30) REVERT: C 3718 MET cc_start: 0.7210 (tpp) cc_final: 0.6927 (tpp) REVERT: C 3998 MET cc_start: 0.8493 (tpp) cc_final: 0.8203 (ttt) REVERT: C 4024 ASP cc_start: 0.3990 (OUTLIER) cc_final: 0.3593 (p0) REVERT: C 4082 PHE cc_start: 0.5320 (OUTLIER) cc_final: 0.4115 (p90) REVERT: C 4808 MET cc_start: 0.7902 (tpp) cc_final: 0.7621 (tpp) REVERT: C 4811 CYS cc_start: 0.7279 (OUTLIER) cc_final: 0.6395 (t) REVERT: C 4862 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.6368 (mp10) REVERT: C 4948 TRP cc_start: 0.8121 (m-10) cc_final: 0.7653 (m-10) REVERT: D 245 LEU cc_start: 0.6561 (OUTLIER) cc_final: 0.6211 (mm) REVERT: D 309 MET cc_start: 0.5181 (mmp) cc_final: 0.4907 (mmt) REVERT: D 362 TYR cc_start: 0.7562 (m-80) cc_final: 0.7216 (m-80) REVERT: D 474 ASP cc_start: 0.8253 (t70) cc_final: 0.7961 (t0) REVERT: D 494 MET cc_start: 0.2263 (OUTLIER) cc_final: 0.0956 (mtt) REVERT: D 651 HIS cc_start: 0.6292 (OUTLIER) cc_final: 0.5759 (m-70) REVERT: D 779 PHE cc_start: 0.5983 (t80) cc_final: 0.5698 (t80) REVERT: D 895 MET cc_start: 0.5097 (mmp) cc_final: 0.3910 (mtp) REVERT: D 935 MET cc_start: 0.5668 (tmm) cc_final: 0.4529 (ptt) REVERT: D 981 MET cc_start: 0.0935 (ppp) cc_final: 0.0049 (ptm) REVERT: D 1199 ASP cc_start: 0.8641 (p0) cc_final: 0.8318 (p0) REVERT: D 1605 LEU cc_start: 0.6461 (OUTLIER) cc_final: 0.5948 (mp) REVERT: D 2174 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7585 (ttp) REVERT: D 2178 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7539 (mm) REVERT: D 2190 LYS cc_start: 0.7144 (OUTLIER) cc_final: 0.6574 (ptmm) REVERT: D 2233 MET cc_start: 0.8264 (mmm) cc_final: 0.7963 (mmm) REVERT: D 2587 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8201 (mt) REVERT: D 2604 MET cc_start: 0.7153 (mmp) cc_final: 0.6742 (mpp) REVERT: D 2781 MET cc_start: -0.0346 (ptp) cc_final: -0.1036 (mmp) REVERT: D 3331 MET cc_start: 0.6208 (ppp) cc_final: 0.5394 (tpp) REVERT: D 3629 GLU cc_start: 0.6731 (tt0) cc_final: 0.6404 (tp30) REVERT: D 3661 ASP cc_start: 0.5199 (OUTLIER) cc_final: 0.4669 (m-30) REVERT: D 3718 MET cc_start: 0.7207 (tpp) cc_final: 0.6924 (tpp) REVERT: D 3998 MET cc_start: 0.8489 (tpp) cc_final: 0.8216 (ttt) REVERT: D 4024 ASP cc_start: 0.3993 (OUTLIER) cc_final: 0.3594 (p0) REVERT: D 4082 PHE cc_start: 0.5269 (OUTLIER) cc_final: 0.4076 (p90) REVERT: D 4808 MET cc_start: 0.7899 (tpp) cc_final: 0.7620 (tpp) REVERT: D 4811 CYS cc_start: 0.7281 (OUTLIER) cc_final: 0.6405 (t) REVERT: D 4862 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.6376 (mp10) REVERT: D 4948 TRP cc_start: 0.8100 (m-10) cc_final: 0.7620 (m-10) REVERT: E 6 GLU cc_start: 0.8080 (mp0) cc_final: 0.7816 (mp0) REVERT: E 26 HIS cc_start: 0.8025 (OUTLIER) cc_final: 0.7298 (t-90) REVERT: F 6 GLU cc_start: 0.8059 (mp0) cc_final: 0.7790 (mp0) REVERT: F 26 HIS cc_start: 0.8094 (OUTLIER) cc_final: 0.7583 (t-90) REVERT: G 6 GLU cc_start: 0.8087 (mp0) cc_final: 0.7727 (mp0) REVERT: G 26 HIS cc_start: 0.8000 (OUTLIER) cc_final: 0.7288 (t-90) REVERT: H 6 GLU cc_start: 0.8104 (mp0) cc_final: 0.7748 (mp0) REVERT: H 26 HIS cc_start: 0.8027 (OUTLIER) cc_final: 0.7298 (t-90) outliers start: 371 outliers final: 292 residues processed: 1319 average time/residue: 0.9787 time to fit residues: 2329.6385 Evaluate side-chains 1369 residues out of total 14384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 346 poor density : 1023 time to evaluate : 10.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 629 GLN Chi-restraints excluded: chain A residue 630 HIS Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 670 TYR Chi-restraints excluded: chain A residue 682 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1007 TRP Chi-restraints excluded: chain A residue 1143 GLN Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1202 ILE Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1467 VAL Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1658 THR Chi-restraints excluded: chain A residue 1722 MET Chi-restraints excluded: chain A residue 1783 PHE Chi-restraints excluded: chain A residue 1818 LEU Chi-restraints excluded: chain A residue 1819 PHE Chi-restraints excluded: chain A residue 1917 VAL Chi-restraints excluded: chain A residue 1932 VAL 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 2091 TYR Chi-restraints excluded: chain A residue 2129 LEU Chi-restraints excluded: chain A residue 2145 LEU Chi-restraints excluded: chain A residue 2174 MET Chi-restraints excluded: chain A residue 2178 LEU Chi-restraints excluded: chain A residue 2190 LYS Chi-restraints excluded: chain A residue 2250 ASN Chi-restraints excluded: chain A residue 2260 ASP Chi-restraints excluded: chain A residue 2280 VAL Chi-restraints excluded: chain A residue 2308 ASN Chi-restraints excluded: chain A residue 2355 ASP Chi-restraints excluded: chain A residue 2395 ILE Chi-restraints excluded: chain A residue 2472 ASP Chi-restraints excluded: chain A residue 2483 LEU Chi-restraints excluded: chain A residue 2583 MET Chi-restraints excluded: chain A residue 2595 VAL Chi-restraints excluded: chain A residue 2682 SER Chi-restraints excluded: chain A residue 3200 VAL Chi-restraints excluded: chain A residue 3262 MET Chi-restraints excluded: chain A residue 3469 LEU Chi-restraints excluded: chain A residue 3616 VAL Chi-restraints excluded: chain A residue 3624 GLU Chi-restraints excluded: chain A residue 3661 ASP Chi-restraints excluded: chain A residue 3782 GLU Chi-restraints excluded: chain A residue 3829 LEU Chi-restraints excluded: chain A residue 3846 CYS Chi-restraints excluded: chain A residue 3985 LEU Chi-restraints excluded: chain A residue 3989 VAL Chi-restraints excluded: chain A residue 4011 MET Chi-restraints excluded: chain A residue 4016 PHE Chi-restraints excluded: chain A residue 4024 ASP Chi-restraints excluded: chain A residue 4046 ASP Chi-restraints excluded: chain A residue 4054 HIS Chi-restraints excluded: chain A residue 4082 PHE Chi-restraints excluded: chain A residue 4108 MET Chi-restraints excluded: chain A residue 4155 SER Chi-restraints excluded: chain A residue 4556 VAL Chi-restraints excluded: chain A residue 4659 PHE Chi-restraints excluded: chain A residue 4709 LEU Chi-restraints excluded: chain A residue 4713 PHE Chi-restraints excluded: chain A residue 4800 THR Chi-restraints excluded: chain A residue 4807 ASP Chi-restraints excluded: chain A residue 4811 CYS Chi-restraints excluded: chain A residue 4813 MET Chi-restraints excluded: chain A residue 4830 ILE Chi-restraints excluded: chain A residue 4862 GLN Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 147 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 571 ILE Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 629 GLN Chi-restraints excluded: chain B residue 630 HIS Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 651 HIS Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 670 TYR Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 682 THR Chi-restraints excluded: chain B residue 800 VAL Chi-restraints excluded: chain B residue 961 VAL Chi-restraints excluded: chain B residue 1007 TRP Chi-restraints excluded: chain B residue 1166 VAL Chi-restraints excluded: chain B residue 1202 ILE Chi-restraints excluded: chain B residue 1216 ASN Chi-restraints excluded: chain B residue 1297 THR Chi-restraints excluded: chain B residue 1304 LEU Chi-restraints excluded: chain B residue 1467 VAL Chi-restraints excluded: chain B residue 1511 VAL Chi-restraints excluded: chain B residue 1605 LEU Chi-restraints excluded: chain B residue 1722 MET Chi-restraints excluded: chain B residue 1783 PHE Chi-restraints excluded: chain B residue 1818 LEU Chi-restraints excluded: chain B residue 1819 PHE Chi-restraints excluded: chain B residue 1828 THR Chi-restraints excluded: chain B residue 1952 MET 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 2091 TYR Chi-restraints excluded: chain B residue 2129 LEU Chi-restraints excluded: chain B residue 2145 LEU Chi-restraints excluded: chain B residue 2161 MET Chi-restraints excluded: chain B residue 2164 LEU Chi-restraints excluded: chain B residue 2174 MET Chi-restraints excluded: chain B residue 2178 LEU Chi-restraints excluded: chain B residue 2190 LYS Chi-restraints excluded: chain B residue 2250 ASN Chi-restraints excluded: chain B residue 2260 ASP Chi-restraints excluded: chain B residue 2280 VAL Chi-restraints excluded: chain B residue 2308 ASN Chi-restraints excluded: chain B residue 2324 ILE Chi-restraints excluded: chain B residue 2355 ASP Chi-restraints excluded: chain B residue 2395 ILE Chi-restraints excluded: chain B residue 2472 ASP Chi-restraints excluded: chain B residue 2583 MET Chi-restraints excluded: chain B residue 2595 VAL Chi-restraints excluded: chain B residue 2682 SER Chi-restraints excluded: chain B residue 3200 VAL Chi-restraints excluded: chain B residue 3262 MET Chi-restraints excluded: chain B residue 3469 LEU Chi-restraints excluded: chain B residue 3616 VAL Chi-restraints excluded: chain B residue 3661 ASP Chi-restraints excluded: chain B residue 3782 GLU Chi-restraints excluded: chain B residue 3846 CYS Chi-restraints excluded: chain B residue 3985 LEU Chi-restraints excluded: chain B residue 3989 VAL Chi-restraints excluded: chain B residue 4011 MET Chi-restraints excluded: chain B residue 4016 PHE Chi-restraints excluded: chain B residue 4024 ASP Chi-restraints excluded: chain B residue 4046 ASP Chi-restraints excluded: chain B residue 4054 HIS Chi-restraints excluded: chain B residue 4108 MET Chi-restraints excluded: chain B residue 4155 SER Chi-restraints excluded: chain B residue 4556 VAL Chi-restraints excluded: chain B residue 4659 PHE Chi-restraints excluded: chain B residue 4709 LEU Chi-restraints excluded: chain B residue 4713 PHE Chi-restraints excluded: chain B residue 4800 THR Chi-restraints excluded: chain B residue 4807 ASP Chi-restraints excluded: chain B residue 4811 CYS Chi-restraints excluded: chain B residue 4813 MET Chi-restraints excluded: chain B residue 4830 ILE Chi-restraints excluded: chain B residue 4862 GLN Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 494 MET Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 571 ILE Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 629 GLN Chi-restraints excluded: chain C residue 630 HIS Chi-restraints excluded: chain C residue 632 ILE Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 670 TYR Chi-restraints excluded: chain C residue 679 VAL Chi-restraints excluded: chain C residue 682 THR Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 716 ASN Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1007 TRP Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1202 ILE Chi-restraints excluded: chain C residue 1297 THR Chi-restraints excluded: chain C residue 1304 LEU Chi-restraints excluded: chain C residue 1467 VAL Chi-restraints excluded: chain C residue 1511 VAL Chi-restraints excluded: chain C residue 1605 LEU Chi-restraints excluded: chain C residue 1722 MET Chi-restraints excluded: chain C residue 1783 PHE Chi-restraints excluded: chain C residue 1818 LEU Chi-restraints excluded: chain C residue 1819 PHE Chi-restraints excluded: chain C residue 1917 VAL 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 2091 TYR Chi-restraints excluded: chain C residue 2129 LEU Chi-restraints excluded: chain C residue 2145 LEU Chi-restraints excluded: chain C residue 2161 MET Chi-restraints excluded: chain C residue 2164 LEU Chi-restraints excluded: chain C residue 2174 MET Chi-restraints excluded: chain C residue 2178 LEU Chi-restraints excluded: chain C residue 2190 LYS Chi-restraints excluded: chain C residue 2250 ASN Chi-restraints excluded: chain C residue 2260 ASP Chi-restraints excluded: chain C residue 2280 VAL Chi-restraints excluded: chain C residue 2308 ASN Chi-restraints excluded: chain C residue 2324 ILE Chi-restraints excluded: chain C residue 2355 ASP Chi-restraints excluded: chain C residue 2395 ILE Chi-restraints excluded: chain C residue 2425 LEU Chi-restraints excluded: chain C residue 2472 ASP Chi-restraints excluded: chain C residue 2526 LEU Chi-restraints excluded: chain C residue 2583 MET Chi-restraints excluded: chain C residue 2595 VAL Chi-restraints excluded: chain C residue 2682 SER Chi-restraints excluded: chain C residue 3200 VAL Chi-restraints excluded: chain C residue 3262 MET Chi-restraints excluded: chain C residue 3469 LEU Chi-restraints excluded: chain C residue 3616 VAL Chi-restraints excluded: chain C residue 3624 GLU Chi-restraints excluded: chain C residue 3661 ASP Chi-restraints excluded: chain C residue 3782 GLU Chi-restraints excluded: chain C residue 3829 LEU Chi-restraints excluded: chain C residue 3846 CYS Chi-restraints excluded: chain C residue 3985 LEU Chi-restraints excluded: chain C residue 3989 VAL Chi-restraints excluded: chain C residue 4016 PHE Chi-restraints excluded: chain C residue 4024 ASP Chi-restraints excluded: chain C residue 4046 ASP Chi-restraints excluded: chain C residue 4054 HIS Chi-restraints excluded: chain C residue 4082 PHE Chi-restraints excluded: chain C residue 4108 MET Chi-restraints excluded: chain C residue 4155 SER Chi-restraints excluded: chain C residue 4556 VAL Chi-restraints excluded: chain C residue 4659 PHE Chi-restraints excluded: chain C residue 4709 LEU Chi-restraints excluded: chain C residue 4713 PHE Chi-restraints excluded: chain C residue 4800 THR Chi-restraints excluded: chain C residue 4807 ASP Chi-restraints excluded: chain C residue 4811 CYS Chi-restraints excluded: chain C residue 4813 MET Chi-restraints excluded: chain C residue 4830 ILE Chi-restraints excluded: chain C residue 4862 GLN Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 424 PHE Chi-restraints excluded: chain D residue 494 MET Chi-restraints excluded: chain D residue 541 ILE Chi-restraints excluded: chain D residue 571 ILE Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 630 HIS Chi-restraints excluded: chain D residue 632 ILE Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 670 TYR Chi-restraints excluded: chain D residue 679 VAL Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 1007 TRP Chi-restraints excluded: chain D residue 1166 VAL Chi-restraints excluded: chain D residue 1202 ILE Chi-restraints excluded: chain D residue 1216 ASN Chi-restraints excluded: chain D residue 1297 THR Chi-restraints excluded: chain D residue 1467 VAL Chi-restraints excluded: chain D residue 1511 VAL Chi-restraints excluded: chain D residue 1605 LEU Chi-restraints excluded: chain D residue 1658 THR Chi-restraints excluded: chain D residue 1722 MET Chi-restraints excluded: chain D residue 1783 PHE Chi-restraints excluded: chain D residue 1818 LEU Chi-restraints excluded: chain D residue 1819 PHE Chi-restraints excluded: chain D residue 1828 THR Chi-restraints excluded: chain D residue 1917 VAL Chi-restraints excluded: chain D residue 1957 THR Chi-restraints excluded: chain D residue 1991 ILE Chi-restraints excluded: chain D residue 2060 LEU Chi-restraints excluded: chain D residue 2085 VAL Chi-restraints excluded: chain D residue 2091 TYR Chi-restraints excluded: chain D residue 2129 LEU Chi-restraints excluded: chain D residue 2145 LEU Chi-restraints excluded: chain D residue 2161 MET Chi-restraints excluded: chain D residue 2164 LEU Chi-restraints excluded: chain D residue 2174 MET Chi-restraints excluded: chain D residue 2178 LEU Chi-restraints excluded: chain D residue 2190 LYS Chi-restraints excluded: chain D residue 2250 ASN Chi-restraints excluded: chain D residue 2260 ASP Chi-restraints excluded: chain D residue 2280 VAL Chi-restraints excluded: chain D residue 2308 ASN Chi-restraints excluded: chain D residue 2355 ASP Chi-restraints excluded: chain D residue 2395 ILE Chi-restraints excluded: chain D residue 2472 ASP Chi-restraints excluded: chain D residue 2483 LEU Chi-restraints excluded: chain D residue 2526 LEU Chi-restraints excluded: chain D residue 2583 MET Chi-restraints excluded: chain D residue 2587 LEU Chi-restraints excluded: chain D residue 2595 VAL Chi-restraints excluded: chain D residue 2682 SER Chi-restraints excluded: chain D residue 3200 VAL Chi-restraints excluded: chain D residue 3262 MET Chi-restraints excluded: chain D residue 3469 LEU Chi-restraints excluded: chain D residue 3616 VAL Chi-restraints excluded: chain D residue 3624 GLU Chi-restraints excluded: chain D residue 3661 ASP Chi-restraints excluded: chain D residue 3782 GLU Chi-restraints excluded: chain D residue 3829 LEU Chi-restraints excluded: chain D residue 3846 CYS Chi-restraints excluded: chain D residue 3985 LEU Chi-restraints excluded: chain D residue 3989 VAL Chi-restraints excluded: chain D residue 4011 MET Chi-restraints excluded: chain D residue 4016 PHE Chi-restraints excluded: chain D residue 4024 ASP Chi-restraints excluded: chain D residue 4046 ASP Chi-restraints excluded: chain D residue 4054 HIS Chi-restraints excluded: chain D residue 4082 PHE Chi-restraints excluded: chain D residue 4108 MET Chi-restraints excluded: chain D residue 4155 SER Chi-restraints excluded: chain D residue 4556 VAL Chi-restraints excluded: chain D residue 4659 PHE Chi-restraints excluded: chain D residue 4709 LEU Chi-restraints excluded: chain D residue 4713 PHE Chi-restraints excluded: chain D residue 4800 THR Chi-restraints excluded: chain D residue 4807 ASP Chi-restraints excluded: chain D residue 4811 CYS Chi-restraints excluded: chain D residue 4813 MET Chi-restraints excluded: chain D residue 4830 ILE Chi-restraints excluded: chain D residue 4862 GLN Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 38 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1640 random chunks: chunk 797 optimal weight: 4.9990 chunk 1033 optimal weight: 7.9990 chunk 1385 optimal weight: 3.9990 chunk 398 optimal weight: 1.9990 chunk 1199 optimal weight: 0.5980 chunk 192 optimal weight: 6.9990 chunk 361 optimal weight: 3.9990 chunk 1303 optimal weight: 20.0000 chunk 545 optimal weight: 0.5980 chunk 1338 optimal weight: 5.9990 chunk 164 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2340 ASN ** A2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2340 ASN ** B2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1440 ASN ** C1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2340 ASN ** C2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2090 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2340 ASN ** D2849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.187775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.143627 restraints weight = 298675.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.141090 restraints weight = 169544.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.140945 restraints weight = 143521.736| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4032 r_free = 0.4032 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4031 r_free = 0.4031 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.4031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 131440 Z= 0.205 Angle : 0.565 12.040 177752 Z= 0.277 Chirality : 0.038 0.207 19688 Planarity : 0.004 0.127 22980 Dihedral : 3.886 48.989 17668 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.03 % Favored : 92.85 % Rotamer: Outliers : 2.76 % Allowed : 20.22 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.07), residues: 16228 helix: 2.10 (0.06), residues: 7392 sheet: -0.48 (0.17), residues: 1044 loop : -2.32 (0.07), residues: 7792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 893 HIS 0.015 0.001 HIS C1267 PHE 0.028 0.001 PHE D 789 TYR 0.036 0.001 TYR C4079 ARG 0.016 0.000 ARG B 626 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 36614.61 seconds wall clock time: 636 minutes 41.33 seconds (38201.33 seconds total)