Starting phenix.real_space_refine on Sun Mar 17 00:33:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t64_25709/03_2024/7t64_25709.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t64_25709/03_2024/7t64_25709.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t64_25709/03_2024/7t64_25709.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t64_25709/03_2024/7t64_25709.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t64_25709/03_2024/7t64_25709.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t64_25709/03_2024/7t64_25709.pdb" } resolution = 4.0 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= 0.006 sd= 0.038 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 836 5.16 5 C 85460 2.51 5 N 22964 2.21 5 O 24932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 623": "OE1" <-> "OE2" Residue "A PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1224": "OE1" <-> "OE2" Residue "A GLU 1285": "OE1" <-> "OE2" Residue "A PHE 1612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1854": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 3415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4065": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4191": "OE1" <-> "OE2" Residue "A PHE 4809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4917": "OD1" <-> "OD2" Residue "B PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 623": "OE1" <-> "OE2" Residue "B PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1224": "OE1" <-> "OE2" Residue "B GLU 1285": "OE1" <-> "OE2" Residue "B PHE 1612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1854": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 3280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 3415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4065": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4191": "OE1" <-> "OE2" Residue "B PHE 4809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 4917": "OD1" <-> "OD2" Residue "C PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 623": "OE1" <-> "OE2" Residue "C PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1224": "OE1" <-> "OE2" Residue "C GLU 1285": "OE1" <-> "OE2" Residue "C PHE 1612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1854": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 3280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 3415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4065": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4191": "OE1" <-> "OE2" Residue "C PHE 4809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 4917": "OD1" <-> "OD2" Residue "D PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 623": "OE1" <-> "OE2" Residue "D PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1224": "OE1" <-> "OE2" Residue "D GLU 1285": "OE1" <-> "OE2" Residue "D PHE 1612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1854": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 3280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 3415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4065": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4191": "OE1" <-> "OE2" Residue "D PHE 4809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 4917": "OD1" <-> "OD2" Residue "E ASP 11": "OD1" <-> "OD2" Residue "E TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 54": "OE1" <-> "OE2" Residue "E TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 11": "OD1" <-> "OD2" Residue "F TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 54": "OE1" <-> "OE2" Residue "F TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 11": "OD1" <-> "OD2" Residue "G TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 54": "OE1" <-> "OE2" Residue "G TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 11": "OD1" <-> "OD2" Residue "H TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 54": "OE1" <-> "OE2" Residue "H TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.39s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 134196 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 32730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4247, 32730 Classifications: {'peptide': 4247} Incomplete info: {'truncation_to_alanine': 276} Link IDs: {'PTRANS': 210, 'TRANS': 4036} Chain breaks: 24 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1172 Unresolved non-hydrogen angles: 1420 Unresolved non-hydrogen dihedrals: 990 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 11, 'TRP:plan': 3, 'ASP:plan': 17, 'PHE:plan': 10, 'GLU:plan': 57, 'ARG:plan': 51} Unresolved non-hydrogen planarities: 748 Chain: "B" Number of atoms: 32730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4247, 32730 Classifications: {'peptide': 4247} Incomplete info: {'truncation_to_alanine': 276} Link IDs: {'PTRANS': 210, 'TRANS': 4036} Chain breaks: 24 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1172 Unresolved non-hydrogen angles: 1420 Unresolved non-hydrogen dihedrals: 990 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 11, 'TRP:plan': 3, 'ASP:plan': 17, 'PHE:plan': 10, 'GLU:plan': 57, 'ARG:plan': 51} Unresolved non-hydrogen planarities: 748 Chain: "C" Number of atoms: 32730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4247, 32730 Classifications: {'peptide': 4247} Incomplete info: {'truncation_to_alanine': 276} Link IDs: {'PTRANS': 210, 'TRANS': 4036} Chain breaks: 24 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1172 Unresolved non-hydrogen angles: 1420 Unresolved non-hydrogen dihedrals: 990 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 11, 'TRP:plan': 3, 'ASP:plan': 17, 'PHE:plan': 10, 'GLU:plan': 57, 'ARG:plan': 51} Unresolved non-hydrogen planarities: 748 Chain: "D" Number of atoms: 32730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4247, 32730 Classifications: {'peptide': 4247} Incomplete info: {'truncation_to_alanine': 276} Link IDs: {'PTRANS': 210, 'TRANS': 4036} Chain breaks: 24 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 1172 Unresolved non-hydrogen angles: 1420 Unresolved non-hydrogen dihedrals: 990 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 11, 'TRP:plan': 3, 'ASP:plan': 17, 'PHE:plan': 10, 'GLU:plan': 57, 'ARG:plan': 51} Unresolved non-hydrogen planarities: 748 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 32060 SG CYS A4958 203.329 190.878 120.997 1.00 34.05 S ATOM 32085 SG CYS A4961 203.257 193.724 118.319 1.00 37.71 S ATOM 64790 SG CYS B4958 180.634 203.316 120.998 1.00 33.20 S ATOM 64815 SG CYS B4961 177.788 203.244 118.320 1.00 37.09 S ATOM 97520 SG CYS C4958 168.188 180.646 120.996 1.00 33.00 S ATOM 97545 SG CYS C4961 168.258 177.800 118.317 1.00 37.35 S ATOM A0NCA SG CYS D4958 190.881 168.198 120.998 1.00 32.92 S ATOM A0NCZ SG CYS D4961 193.727 168.269 118.320 1.00 38.43 S Time building chain proxies: 46.82, per 1000 atoms: 0.35 Number of scatterers: 134196 At special positions: 0 Unit cell: (372.6, 372.6, 212.76, 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 836 16.00 O 24932 8.00 N 22964 7.00 C 85460 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: 33.14 Conformation dependent library (CDL) restraints added in 15.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A6000 " pdb="ZN ZN A6000 " - pdb=" NE2 HIS A4983 " pdb="ZN ZN A6000 " - pdb=" NE2 HIS A4978 " pdb="ZN ZN A6000 " - pdb=" SG CYS A4961 " pdb="ZN ZN A6000 " - pdb=" SG CYS A4958 " pdb=" ZN B6000 " pdb="ZN ZN B6000 " - pdb=" NE2 HIS B4983 " pdb="ZN ZN B6000 " - pdb=" NE2 HIS B4978 " pdb="ZN ZN B6000 " - pdb=" SG CYS B4958 " pdb="ZN ZN B6000 " - pdb=" SG CYS B4961 " pdb=" ZN C6000 " pdb="ZN ZN C6000 " - pdb=" NE2 HIS C4983 " pdb="ZN ZN C6000 " - pdb=" NE2 HIS C4978 " pdb="ZN ZN C6000 " - pdb=" SG CYS C4958 " pdb="ZN ZN C6000 " - pdb=" SG CYS C4961 " pdb=" ZN D6000 " pdb="ZN ZN D6000 " - pdb=" NE2 HIS D4983 " pdb="ZN ZN D6000 " - pdb=" NE2 HIS D4978 " pdb="ZN ZN D6000 " - pdb=" SG CYS D4961 " pdb="ZN ZN D6000 " - pdb=" SG CYS D4958 " Number of angles added : 8 34416 Ramachandran restraints generated. 17208 Oldfield, 0 Emsley, 17208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 32616 Finding SS restraints... Secondary structure from input PDB file: 624 helices and 112 sheets defined 50.7% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 15.30 Creating SS restraints... Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 249 through 253 removed outlier: 4.052A pdb=" N VAL A 252 " --> pdb=" O GLY A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 removed outlier: 3.706A pdb=" N SER A 313 " --> pdb=" O THR A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 421 removed outlier: 4.340A pdb=" N PHE A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 452 Processing helix chain 'A' and resid 460 through 482 removed outlier: 3.649A pdb=" N GLU A 481 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 495 Processing helix chain 'A' and resid 503 through 507 Processing helix chain 'A' and resid 515 through 531 Processing helix chain 'A' and resid 534 through 541 Processing helix chain 'A' and resid 543 through 550 removed outlier: 3.945A pdb=" N VAL A 547 " --> pdb=" O ASN A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 571 Processing helix chain 'A' and resid 579 through 593 removed outlier: 3.850A pdb=" N ILE A 583 " --> pdb=" O GLN A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 removed outlier: 3.772A pdb=" N LEU A 600 " --> pdb=" O ASN A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 625 Processing helix chain 'A' and resid 865 through 890 Processing helix chain 'A' and resid 914 through 934 Processing helix chain 'A' and resid 945 through 949 removed outlier: 3.927A pdb=" N ASP A 948 " --> pdb=" O LYS A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 960 removed outlier: 3.602A pdb=" N MET A 960 " --> pdb=" O LYS A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 1001 Processing helix chain 'A' and resid 1028 through 1048 removed outlier: 3.981A pdb=" N LYS A1032 " --> pdb=" O ASP A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1656 through 1674 Processing helix chain 'A' and resid 1678 through 1689 Processing helix chain 'A' and resid 1690 through 1700 Processing helix chain 'A' and resid 1704 through 1719 Processing helix chain 'A' and resid 1721 through 1729 Processing helix chain 'A' and resid 1739 through 1744 Processing helix chain 'A' and resid 1803 through 1825 Processing helix chain 'A' and resid 1833 through 1852 Proline residue: A1840 - end of helix Processing helix chain 'A' and resid 1856 through 1867 Processing helix chain 'A' and resid 1925 through 1929 Processing helix chain 'A' and resid 1932 through 1983 Processing helix chain 'A' and resid 1989 through 1998 Processing helix chain 'A' and resid 2001 through 2012 removed outlier: 3.670A pdb=" N PHE A2012 " --> pdb=" O MET A2008 " (cutoff:3.500A) Processing helix chain 'A' and resid 2026 through 2042 removed outlier: 3.906A pdb=" N ASP A2030 " --> pdb=" O ASP A2026 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2108 Processing helix chain 'A' and resid 2113 through 2127 Processing helix chain 'A' and resid 2129 through 2138 removed outlier: 3.644A pdb=" N GLU A2133 " --> pdb=" O ASP A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2149 through 2167 Processing helix chain 'A' and resid 2171 through 2184 Processing helix chain 'A' and resid 2195 through 2200 Processing helix chain 'A' and resid 2202 through 2216 Processing helix chain 'A' and resid 2218 through 2224 removed outlier: 3.997A pdb=" N GLU A2222 " --> pdb=" O GLU A2219 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE A2223 " --> pdb=" O THR A2220 " (cutoff:3.500A) Processing helix chain 'A' and resid 2228 through 2243 removed outlier: 3.694A pdb=" N CYS A2232 " --> pdb=" O MET A2228 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER A2243 " --> pdb=" O PHE A2239 " (cutoff:3.500A) Processing helix chain 'A' and resid 2244 through 2263 Processing helix chain 'A' and resid 2271 through 2280 removed outlier: 3.522A pdb=" N VAL A2275 " --> pdb=" O THR A2271 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A2280 " --> pdb=" O ALA A2276 " (cutoff:3.500A) Processing helix chain 'A' and resid 2292 through 2307 Processing helix chain 'A' and resid 2310 through 2317 Processing helix chain 'A' and resid 2324 through 2337 Processing helix chain 'A' and resid 2346 through 2360 removed outlier: 4.023A pdb=" N LYS A2360 " --> pdb=" O LEU A2356 " (cutoff:3.500A) Processing helix chain 'A' and resid 2375 through 2388 Processing helix chain 'A' and resid 2417 through 2436 removed outlier: 3.779A pdb=" N ALA A2421 " --> pdb=" O HIS A2417 " (cutoff:3.500A) Processing helix chain 'A' and resid 2440 through 2445 removed outlier: 3.725A pdb=" N GLN A2444 " --> pdb=" O MET A2440 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A2445 " --> pdb=" O HIS A2441 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2440 through 2445' Processing helix chain 'A' and resid 2448 through 2461 removed outlier: 3.705A pdb=" N VAL A2461 " --> pdb=" O LEU A2457 " (cutoff:3.500A) Processing helix chain 'A' and resid 2465 through 2472 Processing helix chain 'A' and resid 2495 through 2509 removed outlier: 4.253A pdb=" N LYS A2499 " --> pdb=" O VAL A2495 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA A2500 " --> pdb=" O PRO A2496 " (cutoff:3.500A) Processing helix chain 'A' and resid 2514 through 2527 removed outlier: 3.614A pdb=" N LEU A2527 " --> pdb=" O ASP A2523 " (cutoff:3.500A) Processing helix chain 'A' and resid 2529 through 2534 removed outlier: 3.623A pdb=" N ALA A2534 " --> pdb=" O MET A2530 " (cutoff:3.500A) Processing helix chain 'A' and resid 2543 through 2558 removed outlier: 4.378A pdb=" N ALA A2547 " --> pdb=" O THR A2543 " (cutoff:3.500A) Processing helix chain 'A' and resid 2568 through 2581 Processing helix chain 'A' and resid 2587 through 2605 removed outlier: 3.636A pdb=" N ARG A2591 " --> pdb=" O TYR A2587 " (cutoff:3.500A) Processing helix chain 'A' and resid 2610 through 2623 Proline residue: A2616 - end of helix Processing helix chain 'A' and resid 2629 through 2644 Proline residue: A2640 - end of helix Processing helix chain 'A' and resid 2651 through 2671 removed outlier: 4.276A pdb=" N CYS A2656 " --> pdb=" O TRP A2652 " (cutoff:3.500A) Proline residue: A2658 - end of helix Processing helix chain 'A' and resid 2675 through 2682 Processing helix chain 'A' and resid 2748 through 2774 Processing helix chain 'A' and resid 2798 through 2807 removed outlier: 3.916A pdb=" N ILE A2804 " --> pdb=" O LYS A2800 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR A2805 " --> pdb=" O ASP A2801 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TRP A2807 " --> pdb=" O GLU A2803 " (cutoff:3.500A) Processing helix chain 'A' and resid 2809 through 2820 Processing helix chain 'A' and resid 2868 through 2898 Processing helix chain 'A' and resid 2907 through 2911 removed outlier: 3.660A pdb=" N LEU A2911 " --> pdb=" O TYR A2908 " (cutoff:3.500A) Processing helix chain 'A' and resid 2912 through 2930 removed outlier: 4.036A pdb=" N ARG A2920 " --> pdb=" O LYS A2916 " (cutoff:3.500A) Processing helix chain 'A' and resid 2955 through 2972 Processing helix chain 'A' and resid 2994 through 3013 Proline residue: A3004 - end of helix Processing helix chain 'A' and resid 3020 through 3024 Processing helix chain 'A' and resid 3032 through 3051 removed outlier: 3.861A pdb=" N LYS A3036 " --> pdb=" O SER A3032 " (cutoff:3.500A) Processing helix chain 'A' and resid 3060 through 3074 Processing helix chain 'A' and resid 3087 through 3111 removed outlier: 4.259A pdb=" N GLY A3091 " --> pdb=" O ILE A3087 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG A3111 " --> pdb=" O VAL A3107 " (cutoff:3.500A) Processing helix chain 'A' and resid 3128 through 3135 Processing helix chain 'A' and resid 3136 through 3142 Processing helix chain 'A' and resid 3158 through 3174 Processing helix chain 'A' and resid 3187 through 3200 Processing helix chain 'A' and resid 3224 through 3229 Processing helix chain 'A' and resid 3245 through 3260 removed outlier: 4.157A pdb=" N GLY A3260 " --> pdb=" O LEU A3256 " (cutoff:3.500A) Processing helix chain 'A' and resid 3269 through 3286 Proline residue: A3275 - end of helix Proline residue: A3282 - end of helix removed outlier: 4.359A pdb=" N GLU A3286 " --> pdb=" O PRO A3282 " (cutoff:3.500A) Processing helix chain 'A' and resid 3295 through 3300 removed outlier: 3.819A pdb=" N GLY A3299 " --> pdb=" O ALA A3295 " (cutoff:3.500A) Processing helix chain 'A' and resid 3308 through 3326 removed outlier: 3.577A pdb=" N LEU A3312 " --> pdb=" O THR A3308 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN A3326 " --> pdb=" O ILE A3322 " (cutoff:3.500A) Processing helix chain 'A' and resid 3332 through 3342 removed outlier: 4.270A pdb=" N LYS A3336 " --> pdb=" O ALA A3332 " (cutoff:3.500A) Processing helix chain 'A' and resid 3353 through 3381 Proline residue: A3360 - end of helix Processing helix chain 'A' and resid 3384 through 3426 Proline residue: A3410 - end of helix Processing helix chain 'A' and resid 3430 through 3447 Processing helix chain 'A' and resid 3448 through 3463 removed outlier: 3.600A pdb=" N GLU A3463 " --> pdb=" O VAL A3459 " (cutoff:3.500A) Processing helix chain 'A' and resid 3508 through 3518 removed outlier: 4.118A pdb=" N ALA A3512 " --> pdb=" O SER A3508 " (cutoff:3.500A) Processing helix chain 'A' and resid 3519 through 3521 No H-bonds generated for 'chain 'A' and resid 3519 through 3521' Processing helix chain 'A' and resid 3526 through 3542 Processing helix chain 'A' and resid 3545 through 3552 Processing helix chain 'A' and resid 3568 through 3578 removed outlier: 3.628A pdb=" N GLN A3572 " --> pdb=" O SER A3568 " (cutoff:3.500A) Processing helix chain 'A' and resid 3593 through 3611 removed outlier: 4.210A pdb=" N HIS A3611 " --> pdb=" O GLU A3607 " (cutoff:3.500A) Processing helix chain 'A' and resid 3645 through 3659 removed outlier: 3.588A pdb=" N ALA A3649 " --> pdb=" O PRO A3645 " (cutoff:3.500A) Processing helix chain 'A' and resid 3669 through 3679 Processing helix chain 'A' and resid 3699 through 3710 Processing helix chain 'A' and resid 3719 through 3736 Processing helix chain 'A' and resid 3752 through 3757 removed outlier: 3.582A pdb=" N GLU A3757 " --> pdb=" O PHE A3753 " (cutoff:3.500A) Processing helix chain 'A' and resid 3757 through 3770 Processing helix chain 'A' and resid 3771 through 3784 removed outlier: 6.900A pdb=" N GLU A3777 " --> pdb=" O ARG A3773 " (cutoff:3.500A) Processing helix chain 'A' and resid 3791 through 3806 removed outlier: 3.633A pdb=" N SER A3795 " --> pdb=" O GLY A3791 " (cutoff:3.500A) Processing helix chain 'A' and resid 3809 through 3824 Processing helix chain 'A' and resid 3827 through 3838 Processing helix chain 'A' and resid 3843 through 3855 Processing helix chain 'A' and resid 3863 through 3868 removed outlier: 4.312A pdb=" N ARG A3868 " --> pdb=" O THR A3864 " (cutoff:3.500A) Processing helix chain 'A' and resid 3877 through 3892 Processing helix chain 'A' and resid 3898 through 3905 Processing helix chain 'A' and resid 3914 through 3938 removed outlier: 3.734A pdb=" N CYS A3918 " --> pdb=" O ASN A3914 " (cutoff:3.500A) Processing helix chain 'A' and resid 3944 through 3969 Processing helix chain 'A' and resid 3973 through 3982 removed outlier: 3.613A pdb=" N GLN A3977 " --> pdb=" O CYS A3973 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS A3982 " --> pdb=" O GLN A3978 " (cutoff:3.500A) Processing helix chain 'A' and resid 3985 through 4003 Processing helix chain 'A' and resid 4009 through 4032 Processing helix chain 'A' and resid 4038 through 4051 Processing helix chain 'A' and resid 4055 through 4072 Processing helix chain 'A' and resid 4076 through 4081 removed outlier: 4.271A pdb=" N VAL A4081 " --> pdb=" O PHE A4077 " (cutoff:3.500A) Processing helix chain 'A' and resid 4089 through 4100 Processing helix chain 'A' and resid 4104 through 4115 Processing helix chain 'A' and resid 4117 through 4121 Processing helix chain 'A' and resid 4124 through 4130 removed outlier: 3.728A pdb=" N ASN A4130 " --> pdb=" O GLU A4126 " (cutoff:3.500A) Processing helix chain 'A' and resid 4133 through 4154 removed outlier: 3.524A pdb=" N VAL A4154 " --> pdb=" O LEU A4150 " (cutoff:3.500A) Processing helix chain 'A' and resid 4157 through 4167 removed outlier: 4.010A pdb=" N LEU A4166 " --> pdb=" O ASN A4162 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA A4167 " --> pdb=" O PHE A4163 " (cutoff:3.500A) Processing helix chain 'A' and resid 4168 through 4174 removed outlier: 4.017A pdb=" N PHE A4174 " --> pdb=" O ILE A4170 " (cutoff:3.500A) Processing helix chain 'A' and resid 4175 through 4178 removed outlier: 3.921A pdb=" N LEU A4178 " --> pdb=" O ARG A4175 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4175 through 4178' Processing helix chain 'A' and resid 4198 through 4204 Processing helix chain 'A' and resid 4207 through 4224 removed outlier: 3.543A pdb=" N LYS A4211 " --> pdb=" O MET A4207 " (cutoff:3.500A) Processing helix chain 'A' and resid 4229 through 4251 removed outlier: 4.000A pdb=" N LEU A4233 " --> pdb=" O GLU A4229 " (cutoff:3.500A) Processing helix chain 'A' and resid 4541 through 4558 Processing helix chain 'A' and resid 4559 through 4578 Processing helix chain 'A' and resid 4639 through 4665 Processing helix chain 'A' and resid 4665 through 4683 removed outlier: 3.544A pdb=" N VAL A4669 " --> pdb=" O LYS A4665 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A4683 " --> pdb=" O ARG A4679 " (cutoff:3.500A) Processing helix chain 'A' and resid 4696 through 4704 Processing helix chain 'A' and resid 4719 through 4728 removed outlier: 3.517A pdb=" N LYS A4723 " --> pdb=" O PHE A4719 " (cutoff:3.500A) Processing helix chain 'A' and resid 4733 through 4742 Processing helix chain 'A' and resid 4745 through 4751 removed outlier: 3.610A pdb=" N GLU A4749 " --> pdb=" O LEU A4745 " (cutoff:3.500A) Processing helix chain 'A' and resid 4766 through 4771 removed outlier: 3.952A pdb=" N SER A4770 " --> pdb=" O THR A4766 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE A4771 " --> pdb=" O TRP A4767 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4766 through 4771' Processing helix chain 'A' and resid 4773 through 4785 Processing helix chain 'A' and resid 4787 through 4803 Processing helix chain 'A' and resid 4809 through 4812 Processing helix chain 'A' and resid 4813 through 4818 Processing helix chain 'A' and resid 4823 through 4833 removed outlier: 4.569A pdb=" N ASN A4833 " --> pdb=" O SER A4829 " (cutoff:3.500A) Processing helix chain 'A' and resid 4833 through 4857 removed outlier: 3.638A pdb=" N LEU A4837 " --> pdb=" O ASN A4833 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A4838 " --> pdb=" O GLY A4834 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASN A4857 " --> pdb=" O VAL A4853 " (cutoff:3.500A) Processing helix chain 'A' and resid 4878 through 4891 Processing helix chain 'A' and resid 4909 through 4956 Processing helix chain 'A' and resid 4966 through 4970 removed outlier: 3.553A pdb=" N ASP A4969 " --> pdb=" O ASP A4966 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR A4970 " --> pdb=" O TYR A4967 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4966 through 4970' Processing helix chain 'A' and resid 4973 through 4982 removed outlier: 3.519A pdb=" N LEU A4980 " --> pdb=" O GLU A4976 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A4982 " --> pdb=" O HIS A4978 " (cutoff:3.500A) Processing helix chain 'A' and resid 4985 through 4997 removed outlier: 3.858A pdb=" N MET A4989 " --> pdb=" O LEU A4985 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN A4997 " --> pdb=" O MET A4993 " (cutoff:3.500A) Processing helix chain 'A' and resid 4999 through 5003 Processing helix chain 'A' and resid 5004 through 5017 Processing helix chain 'A' and resid 5031 through 5036 removed outlier: 4.236A pdb=" N GLN A5035 " --> pdb=" O GLN A5031 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A5036 " --> pdb=" O TYR A5032 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 5031 through 5036' Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 249 through 253 removed outlier: 4.052A pdb=" N VAL B 252 " --> pdb=" O GLY B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.706A pdb=" N SER B 313 " --> pdb=" O THR B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 421 removed outlier: 4.340A pdb=" N PHE B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 452 Processing helix chain 'B' and resid 460 through 482 removed outlier: 3.650A pdb=" N GLU B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 495 Processing helix chain 'B' and resid 503 through 507 Processing helix chain 'B' and resid 515 through 531 Processing helix chain 'B' and resid 534 through 541 Processing helix chain 'B' and resid 543 through 550 removed outlier: 3.946A pdb=" N VAL B 547 " --> pdb=" O ASN B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 571 Processing helix chain 'B' and resid 579 through 593 removed outlier: 3.851A pdb=" N ILE B 583 " --> pdb=" O GLN B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 606 removed outlier: 3.771A pdb=" N LEU B 600 " --> pdb=" O ASN B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 625 Processing helix chain 'B' and resid 865 through 890 Processing helix chain 'B' and resid 914 through 934 Processing helix chain 'B' and resid 945 through 949 removed outlier: 3.927A pdb=" N ASP B 948 " --> pdb=" O LYS B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 960 removed outlier: 3.602A pdb=" N MET B 960 " --> pdb=" O LYS B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 1001 Processing helix chain 'B' and resid 1028 through 1048 removed outlier: 3.981A pdb=" N LYS B1032 " --> pdb=" O ASP B1028 " (cutoff:3.500A) Processing helix chain 'B' and resid 1656 through 1674 Processing helix chain 'B' and resid 1678 through 1689 Processing helix chain 'B' and resid 1690 through 1700 Processing helix chain 'B' and resid 1704 through 1719 Processing helix chain 'B' and resid 1721 through 1729 Processing helix chain 'B' and resid 1739 through 1744 Processing helix chain 'B' and resid 1803 through 1825 Processing helix chain 'B' and resid 1833 through 1852 Proline residue: B1840 - end of helix Processing helix chain 'B' and resid 1856 through 1867 Processing helix chain 'B' and resid 1925 through 1929 Processing helix chain 'B' and resid 1932 through 1983 Processing helix chain 'B' and resid 1989 through 1998 Processing helix chain 'B' and resid 2001 through 2012 removed outlier: 3.670A pdb=" N PHE B2012 " --> pdb=" O MET B2008 " (cutoff:3.500A) Processing helix chain 'B' and resid 2026 through 2042 removed outlier: 3.907A pdb=" N ASP B2030 " --> pdb=" O ASP B2026 " (cutoff:3.500A) Processing helix chain 'B' and resid 2094 through 2108 Processing helix chain 'B' and resid 2113 through 2127 Processing helix chain 'B' and resid 2129 through 2138 removed outlier: 3.644A pdb=" N GLU B2133 " --> pdb=" O ASP B2129 " (cutoff:3.500A) Processing helix chain 'B' and resid 2149 through 2167 Processing helix chain 'B' and resid 2171 through 2184 Processing helix chain 'B' and resid 2195 through 2200 Processing helix chain 'B' and resid 2202 through 2216 Processing helix chain 'B' and resid 2218 through 2224 removed outlier: 3.998A pdb=" N GLU B2222 " --> pdb=" O GLU B2219 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE B2223 " --> pdb=" O THR B2220 " (cutoff:3.500A) Processing helix chain 'B' and resid 2228 through 2243 removed outlier: 3.694A pdb=" N CYS B2232 " --> pdb=" O MET B2228 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER B2243 " --> pdb=" O PHE B2239 " (cutoff:3.500A) Processing helix chain 'B' and resid 2244 through 2263 Processing helix chain 'B' and resid 2271 through 2280 removed outlier: 3.522A pdb=" N VAL B2275 " --> pdb=" O THR B2271 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL B2280 " --> pdb=" O ALA B2276 " (cutoff:3.500A) Processing helix chain 'B' and resid 2292 through 2307 Processing helix chain 'B' and resid 2310 through 2317 Processing helix chain 'B' and resid 2324 through 2337 Processing helix chain 'B' and resid 2346 through 2360 removed outlier: 4.023A pdb=" N LYS B2360 " --> pdb=" O LEU B2356 " (cutoff:3.500A) Processing helix chain 'B' and resid 2375 through 2388 Processing helix chain 'B' and resid 2417 through 2436 removed outlier: 3.779A pdb=" N ALA B2421 " --> pdb=" O HIS B2417 " (cutoff:3.500A) Processing helix chain 'B' and resid 2440 through 2445 removed outlier: 3.725A pdb=" N GLN B2444 " --> pdb=" O MET B2440 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA B2445 " --> pdb=" O HIS B2441 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2440 through 2445' Processing helix chain 'B' and resid 2448 through 2461 removed outlier: 3.705A pdb=" N VAL B2461 " --> pdb=" O LEU B2457 " (cutoff:3.500A) Processing helix chain 'B' and resid 2465 through 2472 Processing helix chain 'B' and resid 2495 through 2509 removed outlier: 4.253A pdb=" N LYS B2499 " --> pdb=" O VAL B2495 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA B2500 " --> pdb=" O PRO B2496 " (cutoff:3.500A) Processing helix chain 'B' and resid 2514 through 2527 removed outlier: 3.613A pdb=" N LEU B2527 " --> pdb=" O ASP B2523 " (cutoff:3.500A) Processing helix chain 'B' and resid 2529 through 2534 removed outlier: 3.624A pdb=" N ALA B2534 " --> pdb=" O MET B2530 " (cutoff:3.500A) Processing helix chain 'B' and resid 2543 through 2558 removed outlier: 4.379A pdb=" N ALA B2547 " --> pdb=" O THR B2543 " (cutoff:3.500A) Processing helix chain 'B' and resid 2568 through 2581 Processing helix chain 'B' and resid 2587 through 2605 removed outlier: 3.635A pdb=" N ARG B2591 " --> pdb=" O TYR B2587 " (cutoff:3.500A) Processing helix chain 'B' and resid 2610 through 2623 Proline residue: B2616 - end of helix Processing helix chain 'B' and resid 2629 through 2644 Proline residue: B2640 - end of helix Processing helix chain 'B' and resid 2651 through 2671 removed outlier: 4.276A pdb=" N CYS B2656 " --> pdb=" O TRP B2652 " (cutoff:3.500A) Proline residue: B2658 - end of helix Processing helix chain 'B' and resid 2675 through 2682 Processing helix chain 'B' and resid 2748 through 2774 Processing helix chain 'B' and resid 2798 through 2807 removed outlier: 3.916A pdb=" N ILE B2804 " --> pdb=" O LYS B2800 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR B2805 " --> pdb=" O ASP B2801 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TRP B2807 " --> pdb=" O GLU B2803 " (cutoff:3.500A) Processing helix chain 'B' and resid 2809 through 2820 Processing helix chain 'B' and resid 2868 through 2898 Processing helix chain 'B' and resid 2907 through 2911 removed outlier: 3.660A pdb=" N LEU B2911 " --> pdb=" O TYR B2908 " (cutoff:3.500A) Processing helix chain 'B' and resid 2912 through 2930 removed outlier: 4.035A pdb=" N ARG B2920 " --> pdb=" O LYS B2916 " (cutoff:3.500A) Processing helix chain 'B' and resid 2955 through 2972 Processing helix chain 'B' and resid 2994 through 3013 Proline residue: B3004 - end of helix Processing helix chain 'B' and resid 3020 through 3024 Processing helix chain 'B' and resid 3032 through 3051 removed outlier: 3.862A pdb=" N LYS B3036 " --> pdb=" O SER B3032 " (cutoff:3.500A) Processing helix chain 'B' and resid 3060 through 3074 Processing helix chain 'B' and resid 3087 through 3111 removed outlier: 4.258A pdb=" N GLY B3091 " --> pdb=" O ILE B3087 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG B3111 " --> pdb=" O VAL B3107 " (cutoff:3.500A) Processing helix chain 'B' and resid 3128 through 3135 Processing helix chain 'B' and resid 3136 through 3142 Processing helix chain 'B' and resid 3158 through 3174 Processing helix chain 'B' and resid 3187 through 3200 Processing helix chain 'B' and resid 3224 through 3229 Processing helix chain 'B' and resid 3245 through 3260 removed outlier: 4.157A pdb=" N GLY B3260 " --> pdb=" O LEU B3256 " (cutoff:3.500A) Processing helix chain 'B' and resid 3269 through 3286 Proline residue: B3275 - end of helix Proline residue: B3282 - end of helix removed outlier: 4.359A pdb=" N GLU B3286 " --> pdb=" O PRO B3282 " (cutoff:3.500A) Processing helix chain 'B' and resid 3295 through 3300 removed outlier: 3.819A pdb=" N GLY B3299 " --> pdb=" O ALA B3295 " (cutoff:3.500A) Processing helix chain 'B' and resid 3308 through 3326 removed outlier: 3.577A pdb=" N LEU B3312 " --> pdb=" O THR B3308 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN B3326 " --> pdb=" O ILE B3322 " (cutoff:3.500A) Processing helix chain 'B' and resid 3332 through 3342 removed outlier: 4.270A pdb=" N LYS B3336 " --> pdb=" O ALA B3332 " (cutoff:3.500A) Processing helix chain 'B' and resid 3353 through 3381 Proline residue: B3360 - end of helix Processing helix chain 'B' and resid 3384 through 3426 Proline residue: B3410 - end of helix Processing helix chain 'B' and resid 3430 through 3447 Processing helix chain 'B' and resid 3448 through 3463 removed outlier: 3.600A pdb=" N GLU B3463 " --> pdb=" O VAL B3459 " (cutoff:3.500A) Processing helix chain 'B' and resid 3508 through 3518 removed outlier: 4.118A pdb=" N ALA B3512 " --> pdb=" O SER B3508 " (cutoff:3.500A) Processing helix chain 'B' and resid 3519 through 3521 No H-bonds generated for 'chain 'B' and resid 3519 through 3521' Processing helix chain 'B' and resid 3526 through 3542 Processing helix chain 'B' and resid 3545 through 3552 Processing helix chain 'B' and resid 3568 through 3578 removed outlier: 3.629A pdb=" N GLN B3572 " --> pdb=" O SER B3568 " (cutoff:3.500A) Processing helix chain 'B' and resid 3593 through 3611 removed outlier: 4.210A pdb=" N HIS B3611 " --> pdb=" O GLU B3607 " (cutoff:3.500A) Processing helix chain 'B' and resid 3645 through 3659 removed outlier: 3.588A pdb=" N ALA B3649 " --> pdb=" O PRO B3645 " (cutoff:3.500A) Processing helix chain 'B' and resid 3669 through 3679 Processing helix chain 'B' and resid 3699 through 3710 Processing helix chain 'B' and resid 3719 through 3736 Processing helix chain 'B' and resid 3752 through 3757 removed outlier: 3.582A pdb=" N GLU B3757 " --> pdb=" O PHE B3753 " (cutoff:3.500A) Processing helix chain 'B' and resid 3757 through 3770 Processing helix chain 'B' and resid 3771 through 3784 removed outlier: 6.901A pdb=" N GLU B3777 " --> pdb=" O ARG B3773 " (cutoff:3.500A) Processing helix chain 'B' and resid 3791 through 3806 removed outlier: 3.633A pdb=" N SER B3795 " --> pdb=" O GLY B3791 " (cutoff:3.500A) Processing helix chain 'B' and resid 3809 through 3824 Processing helix chain 'B' and resid 3827 through 3838 Processing helix chain 'B' and resid 3843 through 3855 Processing helix chain 'B' and resid 3863 through 3868 removed outlier: 4.312A pdb=" N ARG B3868 " --> pdb=" O THR B3864 " (cutoff:3.500A) Processing helix chain 'B' and resid 3877 through 3892 Processing helix chain 'B' and resid 3898 through 3905 Processing helix chain 'B' and resid 3914 through 3938 removed outlier: 3.734A pdb=" N CYS B3918 " --> pdb=" O ASN B3914 " (cutoff:3.500A) Processing helix chain 'B' and resid 3944 through 3969 Processing helix chain 'B' and resid 3973 through 3982 removed outlier: 3.613A pdb=" N GLN B3977 " --> pdb=" O CYS B3973 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS B3982 " --> pdb=" O GLN B3978 " (cutoff:3.500A) Processing helix chain 'B' and resid 3985 through 4003 Processing helix chain 'B' and resid 4009 through 4032 Processing helix chain 'B' and resid 4038 through 4051 Processing helix chain 'B' and resid 4055 through 4072 Processing helix chain 'B' and resid 4076 through 4081 removed outlier: 4.272A pdb=" N VAL B4081 " --> pdb=" O PHE B4077 " (cutoff:3.500A) Processing helix chain 'B' and resid 4089 through 4100 Processing helix chain 'B' and resid 4104 through 4115 Processing helix chain 'B' and resid 4117 through 4121 Processing helix chain 'B' and resid 4124 through 4130 removed outlier: 3.728A pdb=" N ASN B4130 " --> pdb=" O GLU B4126 " (cutoff:3.500A) Processing helix chain 'B' and resid 4133 through 4154 removed outlier: 3.524A pdb=" N VAL B4154 " --> pdb=" O LEU B4150 " (cutoff:3.500A) Processing helix chain 'B' and resid 4157 through 4167 removed outlier: 4.010A pdb=" N LEU B4166 " --> pdb=" O ASN B4162 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA B4167 " --> pdb=" O PHE B4163 " (cutoff:3.500A) Processing helix chain 'B' and resid 4168 through 4174 removed outlier: 4.016A pdb=" N PHE B4174 " --> pdb=" O ILE B4170 " (cutoff:3.500A) Processing helix chain 'B' and resid 4175 through 4178 removed outlier: 3.921A pdb=" N LEU B4178 " --> pdb=" O ARG B4175 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4175 through 4178' Processing helix chain 'B' and resid 4198 through 4204 Processing helix chain 'B' and resid 4207 through 4224 removed outlier: 3.543A pdb=" N LYS B4211 " --> pdb=" O MET B4207 " (cutoff:3.500A) Processing helix chain 'B' and resid 4229 through 4251 removed outlier: 4.000A pdb=" N LEU B4233 " --> pdb=" O GLU B4229 " (cutoff:3.500A) Processing helix chain 'B' and resid 4541 through 4558 Processing helix chain 'B' and resid 4559 through 4578 Processing helix chain 'B' and resid 4639 through 4665 Processing helix chain 'B' and resid 4665 through 4683 removed outlier: 3.544A pdb=" N VAL B4669 " --> pdb=" O LYS B4665 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE B4683 " --> pdb=" O ARG B4679 " (cutoff:3.500A) Processing helix chain 'B' and resid 4696 through 4704 Processing helix chain 'B' and resid 4719 through 4728 removed outlier: 3.516A pdb=" N LYS B4723 " --> pdb=" O PHE B4719 " (cutoff:3.500A) Processing helix chain 'B' and resid 4733 through 4742 Processing helix chain 'B' and resid 4745 through 4751 removed outlier: 3.610A pdb=" N GLU B4749 " --> pdb=" O LEU B4745 " (cutoff:3.500A) Processing helix chain 'B' and resid 4766 through 4771 removed outlier: 3.952A pdb=" N SER B4770 " --> pdb=" O THR B4766 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE B4771 " --> pdb=" O TRP B4767 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4766 through 4771' Processing helix chain 'B' and resid 4773 through 4785 Processing helix chain 'B' and resid 4787 through 4803 Processing helix chain 'B' and resid 4809 through 4812 Processing helix chain 'B' and resid 4813 through 4818 Processing helix chain 'B' and resid 4823 through 4833 removed outlier: 4.569A pdb=" N ASN B4833 " --> pdb=" O SER B4829 " (cutoff:3.500A) Processing helix chain 'B' and resid 4833 through 4857 removed outlier: 3.638A pdb=" N LEU B4837 " --> pdb=" O ASN B4833 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL B4838 " --> pdb=" O GLY B4834 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASN B4857 " --> pdb=" O VAL B4853 " (cutoff:3.500A) Processing helix chain 'B' and resid 4878 through 4891 Processing helix chain 'B' and resid 4909 through 4956 Processing helix chain 'B' and resid 4966 through 4970 removed outlier: 3.552A pdb=" N ASP B4969 " --> pdb=" O ASP B4966 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR B4970 " --> pdb=" O TYR B4967 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4966 through 4970' Processing helix chain 'B' and resid 4973 through 4982 removed outlier: 3.519A pdb=" N LEU B4980 " --> pdb=" O GLU B4976 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU B4982 " --> pdb=" O HIS B4978 " (cutoff:3.500A) Processing helix chain 'B' and resid 4985 through 4997 removed outlier: 3.858A pdb=" N MET B4989 " --> pdb=" O LEU B4985 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN B4997 " --> pdb=" O MET B4993 " (cutoff:3.500A) Processing helix chain 'B' and resid 4999 through 5003 Processing helix chain 'B' and resid 5004 through 5017 Processing helix chain 'B' and resid 5031 through 5036 removed outlier: 4.236A pdb=" N GLN B5035 " --> pdb=" O GLN B5031 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU B5036 " --> pdb=" O TYR B5032 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 5031 through 5036' Processing helix chain 'C' and resid 74 through 84 Processing helix chain 'C' and resid 249 through 253 removed outlier: 4.052A pdb=" N VAL C 252 " --> pdb=" O GLY C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 313 removed outlier: 3.705A pdb=" N SER C 313 " --> pdb=" O THR C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 421 removed outlier: 4.339A pdb=" N PHE C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 452 Processing helix chain 'C' and resid 460 through 482 removed outlier: 3.649A pdb=" N GLU C 481 " --> pdb=" O LEU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 495 Processing helix chain 'C' and resid 503 through 507 Processing helix chain 'C' and resid 515 through 531 Processing helix chain 'C' and resid 534 through 541 Processing helix chain 'C' and resid 543 through 550 removed outlier: 3.945A pdb=" N VAL C 547 " --> pdb=" O ASN C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 571 Processing helix chain 'C' and resid 579 through 593 removed outlier: 3.851A pdb=" N ILE C 583 " --> pdb=" O GLN C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 606 removed outlier: 3.772A pdb=" N LEU C 600 " --> pdb=" O ASN C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 625 Processing helix chain 'C' and resid 865 through 890 Processing helix chain 'C' and resid 914 through 934 Processing helix chain 'C' and resid 945 through 949 removed outlier: 3.926A pdb=" N ASP C 948 " --> pdb=" O LYS C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 960 removed outlier: 3.602A pdb=" N MET C 960 " --> pdb=" O LYS C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 1001 Processing helix chain 'C' and resid 1028 through 1048 removed outlier: 3.980A pdb=" N LYS C1032 " --> pdb=" O ASP C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1656 through 1674 Processing helix chain 'C' and resid 1678 through 1689 Processing helix chain 'C' and resid 1690 through 1700 Processing helix chain 'C' and resid 1704 through 1719 Processing helix chain 'C' and resid 1721 through 1729 Processing helix chain 'C' and resid 1739 through 1744 Processing helix chain 'C' and resid 1803 through 1825 Processing helix chain 'C' and resid 1833 through 1852 Proline residue: C1840 - end of helix Processing helix chain 'C' and resid 1856 through 1867 Processing helix chain 'C' and resid 1925 through 1929 Processing helix chain 'C' and resid 1932 through 1983 Processing helix chain 'C' and resid 1989 through 1998 Processing helix chain 'C' and resid 2001 through 2012 removed outlier: 3.670A pdb=" N PHE C2012 " --> pdb=" O MET C2008 " (cutoff:3.500A) Processing helix chain 'C' and resid 2026 through 2042 removed outlier: 3.907A pdb=" N ASP C2030 " --> pdb=" O ASP C2026 " (cutoff:3.500A) Processing helix chain 'C' and resid 2094 through 2108 Processing helix chain 'C' and resid 2113 through 2127 Processing helix chain 'C' and resid 2129 through 2138 removed outlier: 3.645A pdb=" N GLU C2133 " --> pdb=" O ASP C2129 " (cutoff:3.500A) Processing helix chain 'C' and resid 2149 through 2167 Processing helix chain 'C' and resid 2171 through 2184 Processing helix chain 'C' and resid 2195 through 2200 Processing helix chain 'C' and resid 2202 through 2216 Processing helix chain 'C' and resid 2218 through 2224 removed outlier: 3.998A pdb=" N GLU C2222 " --> pdb=" O GLU C2219 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE C2223 " --> pdb=" O THR C2220 " (cutoff:3.500A) Processing helix chain 'C' and resid 2228 through 2243 removed outlier: 3.694A pdb=" N CYS C2232 " --> pdb=" O MET C2228 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER C2243 " --> pdb=" O PHE C2239 " (cutoff:3.500A) Processing helix chain 'C' and resid 2244 through 2263 Processing helix chain 'C' and resid 2271 through 2280 removed outlier: 3.522A pdb=" N VAL C2275 " --> pdb=" O THR C2271 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL C2280 " --> pdb=" O ALA C2276 " (cutoff:3.500A) Processing helix chain 'C' and resid 2292 through 2307 Processing helix chain 'C' and resid 2310 through 2317 Processing helix chain 'C' and resid 2324 through 2337 Processing helix chain 'C' and resid 2346 through 2360 removed outlier: 4.022A pdb=" N LYS C2360 " --> pdb=" O LEU C2356 " (cutoff:3.500A) Processing helix chain 'C' and resid 2375 through 2388 Processing helix chain 'C' and resid 2417 through 2436 removed outlier: 3.779A pdb=" N ALA C2421 " --> pdb=" O HIS C2417 " (cutoff:3.500A) Processing helix chain 'C' and resid 2440 through 2445 removed outlier: 3.725A pdb=" N GLN C2444 " --> pdb=" O MET C2440 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA C2445 " --> pdb=" O HIS C2441 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2440 through 2445' Processing helix chain 'C' and resid 2448 through 2461 removed outlier: 3.705A pdb=" N VAL C2461 " --> pdb=" O LEU C2457 " (cutoff:3.500A) Processing helix chain 'C' and resid 2465 through 2472 Processing helix chain 'C' and resid 2495 through 2509 removed outlier: 4.253A pdb=" N LYS C2499 " --> pdb=" O VAL C2495 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA C2500 " --> pdb=" O PRO C2496 " (cutoff:3.500A) Processing helix chain 'C' and resid 2514 through 2527 removed outlier: 3.613A pdb=" N LEU C2527 " --> pdb=" O ASP C2523 " (cutoff:3.500A) Processing helix chain 'C' and resid 2529 through 2534 removed outlier: 3.624A pdb=" N ALA C2534 " --> pdb=" O MET C2530 " (cutoff:3.500A) Processing helix chain 'C' and resid 2543 through 2558 removed outlier: 4.378A pdb=" N ALA C2547 " --> pdb=" O THR C2543 " (cutoff:3.500A) Processing helix chain 'C' and resid 2568 through 2581 Processing helix chain 'C' and resid 2587 through 2605 removed outlier: 3.635A pdb=" N ARG C2591 " --> pdb=" O TYR C2587 " (cutoff:3.500A) Processing helix chain 'C' and resid 2610 through 2623 Proline residue: C2616 - end of helix Processing helix chain 'C' and resid 2629 through 2644 Proline residue: C2640 - end of helix Processing helix chain 'C' and resid 2651 through 2671 removed outlier: 4.276A pdb=" N CYS C2656 " --> pdb=" O TRP C2652 " (cutoff:3.500A) Proline residue: C2658 - end of helix Processing helix chain 'C' and resid 2675 through 2682 Processing helix chain 'C' and resid 2748 through 2774 Processing helix chain 'C' and resid 2798 through 2807 removed outlier: 3.916A pdb=" N ILE C2804 " --> pdb=" O LYS C2800 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR C2805 " --> pdb=" O ASP C2801 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TRP C2807 " --> pdb=" O GLU C2803 " (cutoff:3.500A) Processing helix chain 'C' and resid 2809 through 2820 Processing helix chain 'C' and resid 2868 through 2898 Processing helix chain 'C' and resid 2907 through 2911 removed outlier: 3.659A pdb=" N LEU C2911 " --> pdb=" O TYR C2908 " (cutoff:3.500A) Processing helix chain 'C' and resid 2912 through 2930 removed outlier: 4.035A pdb=" N ARG C2920 " --> pdb=" O LYS C2916 " (cutoff:3.500A) Processing helix chain 'C' and resid 2955 through 2972 Processing helix chain 'C' and resid 2994 through 3013 Proline residue: C3004 - end of helix Processing helix chain 'C' and resid 3020 through 3024 Processing helix chain 'C' and resid 3032 through 3051 removed outlier: 3.861A pdb=" N LYS C3036 " --> pdb=" O SER C3032 " (cutoff:3.500A) Processing helix chain 'C' and resid 3060 through 3074 Processing helix chain 'C' and resid 3087 through 3111 removed outlier: 4.259A pdb=" N GLY C3091 " --> pdb=" O ILE C3087 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG C3111 " --> pdb=" O VAL C3107 " (cutoff:3.500A) Processing helix chain 'C' and resid 3128 through 3135 Processing helix chain 'C' and resid 3136 through 3142 Processing helix chain 'C' and resid 3158 through 3174 Processing helix chain 'C' and resid 3187 through 3200 Processing helix chain 'C' and resid 3224 through 3229 Processing helix chain 'C' and resid 3245 through 3260 removed outlier: 4.157A pdb=" N GLY C3260 " --> pdb=" O LEU C3256 " (cutoff:3.500A) Processing helix chain 'C' and resid 3269 through 3286 Proline residue: C3275 - end of helix Proline residue: C3282 - end of helix removed outlier: 4.359A pdb=" N GLU C3286 " --> pdb=" O PRO C3282 " (cutoff:3.500A) Processing helix chain 'C' and resid 3295 through 3300 removed outlier: 3.818A pdb=" N GLY C3299 " --> pdb=" O ALA C3295 " (cutoff:3.500A) Processing helix chain 'C' and resid 3308 through 3326 removed outlier: 3.576A pdb=" N LEU C3312 " --> pdb=" O THR C3308 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN C3326 " --> pdb=" O ILE C3322 " (cutoff:3.500A) Processing helix chain 'C' and resid 3332 through 3342 removed outlier: 4.270A pdb=" N LYS C3336 " --> pdb=" O ALA C3332 " (cutoff:3.500A) Processing helix chain 'C' and resid 3353 through 3381 Proline residue: C3360 - end of helix Processing helix chain 'C' and resid 3384 through 3426 Proline residue: C3410 - end of helix Processing helix chain 'C' and resid 3430 through 3447 Processing helix chain 'C' and resid 3448 through 3463 removed outlier: 3.600A pdb=" N GLU C3463 " --> pdb=" O VAL C3459 " (cutoff:3.500A) Processing helix chain 'C' and resid 3508 through 3518 removed outlier: 4.117A pdb=" N ALA C3512 " --> pdb=" O SER C3508 " (cutoff:3.500A) Processing helix chain 'C' and resid 3519 through 3521 No H-bonds generated for 'chain 'C' and resid 3519 through 3521' Processing helix chain 'C' and resid 3526 through 3542 Processing helix chain 'C' and resid 3545 through 3552 Processing helix chain 'C' and resid 3568 through 3578 removed outlier: 3.629A pdb=" N GLN C3572 " --> pdb=" O SER C3568 " (cutoff:3.500A) Processing helix chain 'C' and resid 3593 through 3611 removed outlier: 4.210A pdb=" N HIS C3611 " --> pdb=" O GLU C3607 " (cutoff:3.500A) Processing helix chain 'C' and resid 3645 through 3659 removed outlier: 3.588A pdb=" N ALA C3649 " --> pdb=" O PRO C3645 " (cutoff:3.500A) Processing helix chain 'C' and resid 3669 through 3679 Processing helix chain 'C' and resid 3699 through 3710 Processing helix chain 'C' and resid 3719 through 3736 Processing helix chain 'C' and resid 3752 through 3757 removed outlier: 3.583A pdb=" N GLU C3757 " --> pdb=" O PHE C3753 " (cutoff:3.500A) Processing helix chain 'C' and resid 3757 through 3770 Processing helix chain 'C' and resid 3771 through 3784 removed outlier: 6.899A pdb=" N GLU C3777 " --> pdb=" O ARG C3773 " (cutoff:3.500A) Processing helix chain 'C' and resid 3791 through 3806 removed outlier: 3.634A pdb=" N SER C3795 " --> pdb=" O GLY C3791 " (cutoff:3.500A) Processing helix chain 'C' and resid 3809 through 3824 Processing helix chain 'C' and resid 3827 through 3838 Processing helix chain 'C' and resid 3843 through 3855 Processing helix chain 'C' and resid 3863 through 3868 removed outlier: 4.312A pdb=" N ARG C3868 " --> pdb=" O THR C3864 " (cutoff:3.500A) Processing helix chain 'C' and resid 3877 through 3892 Processing helix chain 'C' and resid 3898 through 3905 Processing helix chain 'C' and resid 3914 through 3938 removed outlier: 3.735A pdb=" N CYS C3918 " --> pdb=" O ASN C3914 " (cutoff:3.500A) Processing helix chain 'C' and resid 3944 through 3969 Processing helix chain 'C' and resid 3973 through 3982 removed outlier: 3.613A pdb=" N GLN C3977 " --> pdb=" O CYS C3973 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS C3982 " --> pdb=" O GLN C3978 " (cutoff:3.500A) Processing helix chain 'C' and resid 3985 through 4003 Processing helix chain 'C' and resid 4009 through 4032 Processing helix chain 'C' and resid 4038 through 4051 Processing helix chain 'C' and resid 4055 through 4072 Processing helix chain 'C' and resid 4076 through 4081 removed outlier: 4.272A pdb=" N VAL C4081 " --> pdb=" O PHE C4077 " (cutoff:3.500A) Processing helix chain 'C' and resid 4089 through 4100 Processing helix chain 'C' and resid 4104 through 4115 Processing helix chain 'C' and resid 4117 through 4121 Processing helix chain 'C' and resid 4124 through 4130 removed outlier: 3.728A pdb=" N ASN C4130 " --> pdb=" O GLU C4126 " (cutoff:3.500A) Processing helix chain 'C' and resid 4133 through 4154 removed outlier: 3.525A pdb=" N VAL C4154 " --> pdb=" O LEU C4150 " (cutoff:3.500A) Processing helix chain 'C' and resid 4157 through 4167 removed outlier: 4.010A pdb=" N LEU C4166 " --> pdb=" O ASN C4162 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA C4167 " --> pdb=" O PHE C4163 " (cutoff:3.500A) Processing helix chain 'C' and resid 4168 through 4174 removed outlier: 4.016A pdb=" N PHE C4174 " --> pdb=" O ILE C4170 " (cutoff:3.500A) Processing helix chain 'C' and resid 4175 through 4178 removed outlier: 3.922A pdb=" N LEU C4178 " --> pdb=" O ARG C4175 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4175 through 4178' Processing helix chain 'C' and resid 4198 through 4204 Processing helix chain 'C' and resid 4207 through 4224 removed outlier: 3.543A pdb=" N LYS C4211 " --> pdb=" O MET C4207 " (cutoff:3.500A) Processing helix chain 'C' and resid 4229 through 4251 removed outlier: 4.000A pdb=" N LEU C4233 " --> pdb=" O GLU C4229 " (cutoff:3.500A) Processing helix chain 'C' and resid 4541 through 4558 Processing helix chain 'C' and resid 4559 through 4578 Processing helix chain 'C' and resid 4639 through 4665 Processing helix chain 'C' and resid 4665 through 4683 removed outlier: 3.544A pdb=" N VAL C4669 " --> pdb=" O LYS C4665 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE C4683 " --> pdb=" O ARG C4679 " (cutoff:3.500A) Processing helix chain 'C' and resid 4696 through 4704 Processing helix chain 'C' and resid 4719 through 4728 removed outlier: 3.517A pdb=" N LYS C4723 " --> pdb=" O PHE C4719 " (cutoff:3.500A) Processing helix chain 'C' and resid 4733 through 4742 Processing helix chain 'C' and resid 4745 through 4751 removed outlier: 3.611A pdb=" N GLU C4749 " --> pdb=" O LEU C4745 " (cutoff:3.500A) Processing helix chain 'C' and resid 4766 through 4771 removed outlier: 3.952A pdb=" N SER C4770 " --> pdb=" O THR C4766 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE C4771 " --> pdb=" O TRP C4767 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4766 through 4771' Processing helix chain 'C' and resid 4773 through 4785 Processing helix chain 'C' and resid 4787 through 4803 Processing helix chain 'C' and resid 4809 through 4812 Processing helix chain 'C' and resid 4813 through 4818 Processing helix chain 'C' and resid 4823 through 4833 removed outlier: 4.569A pdb=" N ASN C4833 " --> pdb=" O SER C4829 " (cutoff:3.500A) Processing helix chain 'C' and resid 4833 through 4857 removed outlier: 3.639A pdb=" N LEU C4837 " --> pdb=" O ASN C4833 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL C4838 " --> pdb=" O GLY C4834 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASN C4857 " --> pdb=" O VAL C4853 " (cutoff:3.500A) Processing helix chain 'C' and resid 4878 through 4891 Processing helix chain 'C' and resid 4909 through 4956 Processing helix chain 'C' and resid 4966 through 4970 removed outlier: 3.553A pdb=" N ASP C4969 " --> pdb=" O ASP C4966 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR C4970 " --> pdb=" O TYR C4967 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4966 through 4970' Processing helix chain 'C' and resid 4973 through 4982 removed outlier: 3.519A pdb=" N LEU C4980 " --> pdb=" O GLU C4976 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU C4982 " --> pdb=" O HIS C4978 " (cutoff:3.500A) Processing helix chain 'C' and resid 4985 through 4997 removed outlier: 3.858A pdb=" N MET C4989 " --> pdb=" O LEU C4985 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN C4997 " --> pdb=" O MET C4993 " (cutoff:3.500A) Processing helix chain 'C' and resid 4999 through 5003 Processing helix chain 'C' and resid 5004 through 5017 Processing helix chain 'C' and resid 5031 through 5036 removed outlier: 4.237A pdb=" N GLN C5035 " --> pdb=" O GLN C5031 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU C5036 " --> pdb=" O TYR C5032 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 5031 through 5036' Processing helix chain 'D' and resid 74 through 84 Processing helix chain 'D' and resid 249 through 253 removed outlier: 4.052A pdb=" N VAL D 252 " --> pdb=" O GLY D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 313 removed outlier: 3.705A pdb=" N SER D 313 " --> pdb=" O THR D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 421 removed outlier: 4.339A pdb=" N PHE D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 452 Processing helix chain 'D' and resid 460 through 482 removed outlier: 3.650A pdb=" N GLU D 481 " --> pdb=" O LEU D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 495 Processing helix chain 'D' and resid 503 through 507 Processing helix chain 'D' and resid 515 through 531 Processing helix chain 'D' and resid 534 through 541 Processing helix chain 'D' and resid 543 through 550 removed outlier: 3.945A pdb=" N VAL D 547 " --> pdb=" O ASN D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 571 Processing helix chain 'D' and resid 579 through 593 removed outlier: 3.851A pdb=" N ILE D 583 " --> pdb=" O GLN D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 606 removed outlier: 3.771A pdb=" N LEU D 600 " --> pdb=" O ASN D 596 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 625 Processing helix chain 'D' and resid 865 through 890 Processing helix chain 'D' and resid 914 through 934 Processing helix chain 'D' and resid 945 through 949 removed outlier: 3.927A pdb=" N ASP D 948 " --> pdb=" O LYS D 945 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 960 removed outlier: 3.602A pdb=" N MET D 960 " --> pdb=" O LYS D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 979 through 1001 Processing helix chain 'D' and resid 1028 through 1048 removed outlier: 3.980A pdb=" N LYS D1032 " --> pdb=" O ASP D1028 " (cutoff:3.500A) Processing helix chain 'D' and resid 1656 through 1674 Processing helix chain 'D' and resid 1678 through 1689 Processing helix chain 'D' and resid 1690 through 1700 Processing helix chain 'D' and resid 1704 through 1719 Processing helix chain 'D' and resid 1721 through 1729 Processing helix chain 'D' and resid 1739 through 1744 Processing helix chain 'D' and resid 1803 through 1825 Processing helix chain 'D' and resid 1833 through 1852 Proline residue: D1840 - end of helix Processing helix chain 'D' and resid 1856 through 1867 Processing helix chain 'D' and resid 1925 through 1929 Processing helix chain 'D' and resid 1932 through 1983 Processing helix chain 'D' and resid 1989 through 1998 Processing helix chain 'D' and resid 2001 through 2012 removed outlier: 3.669A pdb=" N PHE D2012 " --> pdb=" O MET D2008 " (cutoff:3.500A) Processing helix chain 'D' and resid 2026 through 2042 removed outlier: 3.906A pdb=" N ASP D2030 " --> pdb=" O ASP D2026 " (cutoff:3.500A) Processing helix chain 'D' and resid 2094 through 2108 Processing helix chain 'D' and resid 2113 through 2127 Processing helix chain 'D' and resid 2129 through 2138 removed outlier: 3.645A pdb=" N GLU D2133 " --> pdb=" O ASP D2129 " (cutoff:3.500A) Processing helix chain 'D' and resid 2149 through 2167 Processing helix chain 'D' and resid 2171 through 2184 Processing helix chain 'D' and resid 2195 through 2200 Processing helix chain 'D' and resid 2202 through 2216 Processing helix chain 'D' and resid 2218 through 2224 removed outlier: 3.998A pdb=" N GLU D2222 " --> pdb=" O GLU D2219 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE D2223 " --> pdb=" O THR D2220 " (cutoff:3.500A) Processing helix chain 'D' and resid 2228 through 2243 removed outlier: 3.694A pdb=" N CYS D2232 " --> pdb=" O MET D2228 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER D2243 " --> pdb=" O PHE D2239 " (cutoff:3.500A) Processing helix chain 'D' and resid 2244 through 2263 Processing helix chain 'D' and resid 2271 through 2280 removed outlier: 3.521A pdb=" N VAL D2275 " --> pdb=" O THR D2271 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL D2280 " --> pdb=" O ALA D2276 " (cutoff:3.500A) Processing helix chain 'D' and resid 2292 through 2307 Processing helix chain 'D' and resid 2310 through 2317 Processing helix chain 'D' and resid 2324 through 2337 Processing helix chain 'D' and resid 2346 through 2360 removed outlier: 4.024A pdb=" N LYS D2360 " --> pdb=" O LEU D2356 " (cutoff:3.500A) Processing helix chain 'D' and resid 2375 through 2388 Processing helix chain 'D' and resid 2417 through 2436 removed outlier: 3.778A pdb=" N ALA D2421 " --> pdb=" O HIS D2417 " (cutoff:3.500A) Processing helix chain 'D' and resid 2440 through 2445 removed outlier: 3.725A pdb=" N GLN D2444 " --> pdb=" O MET D2440 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA D2445 " --> pdb=" O HIS D2441 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2440 through 2445' Processing helix chain 'D' and resid 2448 through 2461 removed outlier: 3.705A pdb=" N VAL D2461 " --> pdb=" O LEU D2457 " (cutoff:3.500A) Processing helix chain 'D' and resid 2465 through 2472 Processing helix chain 'D' and resid 2495 through 2509 removed outlier: 4.253A pdb=" N LYS D2499 " --> pdb=" O VAL D2495 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA D2500 " --> pdb=" O PRO D2496 " (cutoff:3.500A) Processing helix chain 'D' and resid 2514 through 2527 removed outlier: 3.613A pdb=" N LEU D2527 " --> pdb=" O ASP D2523 " (cutoff:3.500A) Processing helix chain 'D' and resid 2529 through 2534 removed outlier: 3.624A pdb=" N ALA D2534 " --> pdb=" O MET D2530 " (cutoff:3.500A) Processing helix chain 'D' and resid 2543 through 2558 removed outlier: 4.379A pdb=" N ALA D2547 " --> pdb=" O THR D2543 " (cutoff:3.500A) Processing helix chain 'D' and resid 2568 through 2581 Processing helix chain 'D' and resid 2587 through 2605 removed outlier: 3.635A pdb=" N ARG D2591 " --> pdb=" O TYR D2587 " (cutoff:3.500A) Processing helix chain 'D' and resid 2610 through 2623 Proline residue: D2616 - end of helix Processing helix chain 'D' and resid 2629 through 2644 Proline residue: D2640 - end of helix Processing helix chain 'D' and resid 2651 through 2671 removed outlier: 4.276A pdb=" N CYS D2656 " --> pdb=" O TRP D2652 " (cutoff:3.500A) Proline residue: D2658 - end of helix Processing helix chain 'D' and resid 2675 through 2682 Processing helix chain 'D' and resid 2748 through 2774 Processing helix chain 'D' and resid 2798 through 2807 removed outlier: 3.916A pdb=" N ILE D2804 " --> pdb=" O LYS D2800 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TYR D2805 " --> pdb=" O ASP D2801 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TRP D2807 " --> pdb=" O GLU D2803 " (cutoff:3.500A) Processing helix chain 'D' and resid 2809 through 2820 Processing helix chain 'D' and resid 2868 through 2898 Processing helix chain 'D' and resid 2907 through 2911 removed outlier: 3.659A pdb=" N LEU D2911 " --> pdb=" O TYR D2908 " (cutoff:3.500A) Processing helix chain 'D' and resid 2912 through 2930 removed outlier: 4.035A pdb=" N ARG D2920 " --> pdb=" O LYS D2916 " (cutoff:3.500A) Processing helix chain 'D' and resid 2955 through 2972 Processing helix chain 'D' and resid 2994 through 3013 Proline residue: D3004 - end of helix Processing helix chain 'D' and resid 3020 through 3024 Processing helix chain 'D' and resid 3032 through 3051 removed outlier: 3.861A pdb=" N LYS D3036 " --> pdb=" O SER D3032 " (cutoff:3.500A) Processing helix chain 'D' and resid 3060 through 3074 Processing helix chain 'D' and resid 3087 through 3111 removed outlier: 4.258A pdb=" N GLY D3091 " --> pdb=" O ILE D3087 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG D3111 " --> pdb=" O VAL D3107 " (cutoff:3.500A) Processing helix chain 'D' and resid 3128 through 3135 Processing helix chain 'D' and resid 3136 through 3142 Processing helix chain 'D' and resid 3158 through 3174 Processing helix chain 'D' and resid 3187 through 3200 Processing helix chain 'D' and resid 3224 through 3229 Processing helix chain 'D' and resid 3245 through 3260 removed outlier: 4.158A pdb=" N GLY D3260 " --> pdb=" O LEU D3256 " (cutoff:3.500A) Processing helix chain 'D' and resid 3269 through 3286 Proline residue: D3275 - end of helix Proline residue: D3282 - end of helix removed outlier: 4.358A pdb=" N GLU D3286 " --> pdb=" O PRO D3282 " (cutoff:3.500A) Processing helix chain 'D' and resid 3295 through 3300 removed outlier: 3.819A pdb=" N GLY D3299 " --> pdb=" O ALA D3295 " (cutoff:3.500A) Processing helix chain 'D' and resid 3308 through 3326 removed outlier: 3.577A pdb=" N LEU D3312 " --> pdb=" O THR D3308 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN D3326 " --> pdb=" O ILE D3322 " (cutoff:3.500A) Processing helix chain 'D' and resid 3332 through 3342 removed outlier: 4.270A pdb=" N LYS D3336 " --> pdb=" O ALA D3332 " (cutoff:3.500A) Processing helix chain 'D' and resid 3353 through 3381 Proline residue: D3360 - end of helix Processing helix chain 'D' and resid 3384 through 3426 Proline residue: D3410 - end of helix Processing helix chain 'D' and resid 3430 through 3447 Processing helix chain 'D' and resid 3448 through 3463 removed outlier: 3.600A pdb=" N GLU D3463 " --> pdb=" O VAL D3459 " (cutoff:3.500A) Processing helix chain 'D' and resid 3508 through 3518 removed outlier: 4.118A pdb=" N ALA D3512 " --> pdb=" O SER D3508 " (cutoff:3.500A) Processing helix chain 'D' and resid 3519 through 3521 No H-bonds generated for 'chain 'D' and resid 3519 through 3521' Processing helix chain 'D' and resid 3526 through 3542 Processing helix chain 'D' and resid 3545 through 3552 Processing helix chain 'D' and resid 3568 through 3578 removed outlier: 3.629A pdb=" N GLN D3572 " --> pdb=" O SER D3568 " (cutoff:3.500A) Processing helix chain 'D' and resid 3593 through 3611 removed outlier: 4.210A pdb=" N HIS D3611 " --> pdb=" O GLU D3607 " (cutoff:3.500A) Processing helix chain 'D' and resid 3645 through 3659 removed outlier: 3.588A pdb=" N ALA D3649 " --> pdb=" O PRO D3645 " (cutoff:3.500A) Processing helix chain 'D' and resid 3669 through 3679 Processing helix chain 'D' and resid 3699 through 3710 Processing helix chain 'D' and resid 3719 through 3736 Processing helix chain 'D' and resid 3752 through 3757 removed outlier: 3.582A pdb=" N GLU D3757 " --> pdb=" O PHE D3753 " (cutoff:3.500A) Processing helix chain 'D' and resid 3757 through 3770 Processing helix chain 'D' and resid 3771 through 3784 removed outlier: 6.900A pdb=" N GLU D3777 " --> pdb=" O ARG D3773 " (cutoff:3.500A) Processing helix chain 'D' and resid 3791 through 3806 removed outlier: 3.633A pdb=" N SER D3795 " --> pdb=" O GLY D3791 " (cutoff:3.500A) Processing helix chain 'D' and resid 3809 through 3824 Processing helix chain 'D' and resid 3827 through 3838 Processing helix chain 'D' and resid 3843 through 3855 Processing helix chain 'D' and resid 3863 through 3868 removed outlier: 4.312A pdb=" N ARG D3868 " --> pdb=" O THR D3864 " (cutoff:3.500A) Processing helix chain 'D' and resid 3877 through 3892 Processing helix chain 'D' and resid 3898 through 3905 Processing helix chain 'D' and resid 3914 through 3938 removed outlier: 3.735A pdb=" N CYS D3918 " --> pdb=" O ASN D3914 " (cutoff:3.500A) Processing helix chain 'D' and resid 3944 through 3969 Processing helix chain 'D' and resid 3973 through 3982 removed outlier: 3.613A pdb=" N GLN D3977 " --> pdb=" O CYS D3973 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS D3982 " --> pdb=" O GLN D3978 " (cutoff:3.500A) Processing helix chain 'D' and resid 3985 through 4003 Processing helix chain 'D' and resid 4009 through 4032 Processing helix chain 'D' and resid 4038 through 4051 Processing helix chain 'D' and resid 4055 through 4072 Processing helix chain 'D' and resid 4076 through 4081 removed outlier: 4.271A pdb=" N VAL D4081 " --> pdb=" O PHE D4077 " (cutoff:3.500A) Processing helix chain 'D' and resid 4089 through 4100 Processing helix chain 'D' and resid 4104 through 4115 Processing helix chain 'D' and resid 4117 through 4121 Processing helix chain 'D' and resid 4124 through 4130 removed outlier: 3.728A pdb=" N ASN D4130 " --> pdb=" O GLU D4126 " (cutoff:3.500A) Processing helix chain 'D' and resid 4133 through 4154 removed outlier: 3.525A pdb=" N VAL D4154 " --> pdb=" O LEU D4150 " (cutoff:3.500A) Processing helix chain 'D' and resid 4157 through 4167 removed outlier: 4.010A pdb=" N LEU D4166 " --> pdb=" O ASN D4162 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA D4167 " --> pdb=" O PHE D4163 " (cutoff:3.500A) Processing helix chain 'D' and resid 4168 through 4174 removed outlier: 4.016A pdb=" N PHE D4174 " --> pdb=" O ILE D4170 " (cutoff:3.500A) Processing helix chain 'D' and resid 4175 through 4178 removed outlier: 3.923A pdb=" N LEU D4178 " --> pdb=" O ARG D4175 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4175 through 4178' Processing helix chain 'D' and resid 4198 through 4204 Processing helix chain 'D' and resid 4207 through 4224 removed outlier: 3.542A pdb=" N LYS D4211 " --> pdb=" O MET D4207 " (cutoff:3.500A) Processing helix chain 'D' and resid 4229 through 4251 removed outlier: 3.999A pdb=" N LEU D4233 " --> pdb=" O GLU D4229 " (cutoff:3.500A) Processing helix chain 'D' and resid 4541 through 4558 Processing helix chain 'D' and resid 4559 through 4578 Processing helix chain 'D' and resid 4639 through 4665 Processing helix chain 'D' and resid 4665 through 4683 removed outlier: 3.545A pdb=" N VAL D4669 " --> pdb=" O LYS D4665 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE D4683 " --> pdb=" O ARG D4679 " (cutoff:3.500A) Processing helix chain 'D' and resid 4696 through 4704 Processing helix chain 'D' and resid 4719 through 4728 removed outlier: 3.517A pdb=" N LYS D4723 " --> pdb=" O PHE D4719 " (cutoff:3.500A) Processing helix chain 'D' and resid 4733 through 4742 Processing helix chain 'D' and resid 4745 through 4751 removed outlier: 3.610A pdb=" N GLU D4749 " --> pdb=" O LEU D4745 " (cutoff:3.500A) Processing helix chain 'D' and resid 4766 through 4771 removed outlier: 3.952A pdb=" N SER D4770 " --> pdb=" O THR D4766 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE D4771 " --> pdb=" O TRP D4767 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4766 through 4771' Processing helix chain 'D' and resid 4773 through 4785 Processing helix chain 'D' and resid 4787 through 4803 Processing helix chain 'D' and resid 4809 through 4812 Processing helix chain 'D' and resid 4813 through 4818 Processing helix chain 'D' and resid 4823 through 4833 removed outlier: 4.569A pdb=" N ASN D4833 " --> pdb=" O SER D4829 " (cutoff:3.500A) Processing helix chain 'D' and resid 4833 through 4857 removed outlier: 3.638A pdb=" N LEU D4837 " --> pdb=" O ASN D4833 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL D4838 " --> pdb=" O GLY D4834 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASN D4857 " --> pdb=" O VAL D4853 " (cutoff:3.500A) Processing helix chain 'D' and resid 4878 through 4891 Processing helix chain 'D' and resid 4909 through 4956 Processing helix chain 'D' and resid 4966 through 4970 removed outlier: 3.553A pdb=" N ASP D4969 " --> pdb=" O ASP D4966 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR D4970 " --> pdb=" O TYR D4967 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4966 through 4970' Processing helix chain 'D' and resid 4973 through 4982 removed outlier: 3.519A pdb=" N LEU D4980 " --> pdb=" O GLU D4976 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU D4982 " --> pdb=" O HIS D4978 " (cutoff:3.500A) Processing helix chain 'D' and resid 4985 through 4997 removed outlier: 3.858A pdb=" N MET D4989 " --> pdb=" O LEU D4985 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN D4997 " --> pdb=" O MET D4993 " (cutoff:3.500A) Processing helix chain 'D' and resid 4999 through 5003 Processing helix chain 'D' and resid 5004 through 5017 Processing helix chain 'D' and resid 5031 through 5036 removed outlier: 4.236A pdb=" N GLN D5035 " --> pdb=" O GLN D5031 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU D5036 " --> pdb=" O TYR D5032 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 5031 through 5036' Processing helix chain 'E' and resid 38 through 43 removed outlier: 3.725A pdb=" N ARG E 42 " --> pdb=" O SER E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 65 removed outlier: 4.628A pdb=" N GLN E 65 " --> pdb=" O GLU E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 82 removed outlier: 3.513A pdb=" N TYR E 82 " --> pdb=" O PRO E 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 43 removed outlier: 3.725A pdb=" N ARG F 42 " --> pdb=" O SER F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 65 removed outlier: 4.627A pdb=" N GLN F 65 " --> pdb=" O GLU F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 82 removed outlier: 3.513A pdb=" N TYR F 82 " --> pdb=" O PRO F 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 43 removed outlier: 3.725A pdb=" N ARG G 42 " --> pdb=" O SER G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 65 removed outlier: 4.627A pdb=" N GLN G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 82 removed outlier: 3.513A pdb=" N TYR G 82 " --> pdb=" O PRO G 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 43 removed outlier: 3.725A pdb=" N ARG H 42 " --> pdb=" O SER H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 65 removed outlier: 4.628A pdb=" N GLN H 65 " --> pdb=" O GLU H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 82 removed outlier: 3.513A pdb=" N TYR H 82 " --> pdb=" O PRO H 78 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 36 removed outlier: 4.196A pdb=" N LEU A 33 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A 26 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 36 removed outlier: 4.196A pdb=" N LEU A 33 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A 26 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 21 " --> pdb=" O ASN A 203 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN A 203 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A 23 " --> pdb=" O ASN A 201 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73 removed outlier: 3.525A pdb=" N LEU A 73 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS A 151 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE A 170 " --> pdb=" O HIS A 151 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 120 Processing sheet with id=AA5, first strand: chain 'A' and resid 219 through 220 Processing sheet with id=AA6, first strand: chain 'A' and resid 223 through 224 removed outlier: 3.714A pdb=" N GLU A 229 " --> pdb=" O HIS A 224 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 290 through 293 removed outlier: 3.595A pdb=" N VAL A 300 " --> pdb=" O ALA A 292 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 314 through 317 removed outlier: 3.603A pdb=" N CYS A 315 " --> pdb=" O GLN A 349 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A 349 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 347 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 634 through 639 removed outlier: 4.496A pdb=" N GLN A 634 " --> pdb=" O HIS A1640 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 644 through 645 Processing sheet with id=AB2, first strand: chain 'A' and resid 754 through 758 removed outlier: 4.254A pdb=" N SER A 754 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 745 " --> pdb=" O ARG A 758 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP A 742 " --> pdb=" O VAL A 668 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 668 " --> pdb=" O ASP A 742 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N CYS A 746 " --> pdb=" O PHE A 664 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE A 664 " --> pdb=" O CYS A 746 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU A 748 " --> pdb=" O TRP A 662 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N TRP A 662 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP A 669 " --> pdb=" O LYS A 788 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LYS A 788 " --> pdb=" O ASP A 669 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 684 through 686 Processing sheet with id=AB4, first strand: chain 'A' and resid 715 through 716 removed outlier: 3.676A pdb=" N GLY A 715 " --> pdb=" O TRP A 722 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 767 through 769 Processing sheet with id=AB6, first strand: chain 'A' and resid 839 through 840 removed outlier: 4.044A pdb=" N TRP A1088 " --> pdb=" O ILE A1153 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE A1153 " --> pdb=" O TRP A1088 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 839 through 840 Processing sheet with id=AB8, first strand: chain 'A' and resid 1137 through 1138 removed outlier: 3.927A pdb=" N GLN A1130 " --> pdb=" O ASN A1125 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TRP A1104 " --> pdb=" O TYR A1122 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A1102 " --> pdb=" O PHE A1124 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA A1077 " --> pdb=" O PRO A1190 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A1604 " --> pdb=" O LYS A1240 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1244 through 1245 Processing sheet with id=AC1, first strand: chain 'A' and resid 1255 through 1258 removed outlier: 3.547A pdb=" N ALA A1258 " --> pdb=" O ARG A1271 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1285 through 1287 removed outlier: 3.788A pdb=" N MET A1462 " --> pdb=" O GLU A1285 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1436 through 1438 removed outlier: 4.096A pdb=" N SER A1436 " --> pdb=" O THR A1557 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR A1557 " --> pdb=" O SER A1436 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A1438 " --> pdb=" O LEU A1555 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A1555 " --> pdb=" O ARG A1438 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A1552 " --> pdb=" O LEU A1487 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A1487 " --> pdb=" O VAL A1552 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A1554 " --> pdb=" O SER A1485 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A1485 " --> pdb=" O VAL A1554 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1436 through 1438 removed outlier: 4.096A pdb=" N SER A1436 " --> pdb=" O THR A1557 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR A1557 " --> pdb=" O SER A1436 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A1438 " --> pdb=" O LEU A1555 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A1555 " --> pdb=" O ARG A1438 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1734 through 1736 removed outlier: 3.577A pdb=" N TYR A2142 " --> pdb=" O TYR A1734 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 4181 through 4183 removed outlier: 3.614A pdb=" N ILE A4183 " --> pdb=" O GLU A4191 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A4191 " --> pdb=" O ILE A4183 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 4582 through 4583 removed outlier: 3.605A pdb=" N SER A4583 " --> pdb=" O VAL A4628 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 4957 through 4958 removed outlier: 3.941A pdb=" N CYS A4958 " --> pdb=" O ILE A4963 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ILE A4963 " --> pdb=" O CYS A4958 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 33 through 36 removed outlier: 4.196A pdb=" N LEU B 33 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B 26 " --> pdb=" O LEU B 33 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 33 through 36 removed outlier: 4.196A pdb=" N LEU B 33 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B 26 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 21 " --> pdb=" O ASN B 203 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN B 203 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN B 23 " --> pdb=" O ASN B 201 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 72 through 73 removed outlier: 3.526A pdb=" N LEU B 73 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS B 151 " --> pdb=" O ILE B 170 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE B 170 " --> pdb=" O HIS B 151 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 117 through 120 Processing sheet with id=AD4, first strand: chain 'B' and resid 219 through 220 Processing sheet with id=AD5, first strand: chain 'B' and resid 223 through 224 removed outlier: 3.714A pdb=" N GLU B 229 " --> pdb=" O HIS B 224 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 290 through 293 removed outlier: 3.595A pdb=" N VAL B 300 " --> pdb=" O ALA B 292 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 314 through 317 removed outlier: 3.603A pdb=" N CYS B 315 " --> pdb=" O GLN B 349 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B 349 " --> pdb=" O CYS B 315 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE B 347 " --> pdb=" O ARG B 317 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 634 through 639 removed outlier: 4.495A pdb=" N GLN B 634 " --> pdb=" O HIS B1640 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 644 through 645 Processing sheet with id=AE1, first strand: chain 'B' and resid 754 through 758 removed outlier: 4.255A pdb=" N SER B 754 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER B 745 " --> pdb=" O ARG B 758 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP B 742 " --> pdb=" O VAL B 668 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 668 " --> pdb=" O ASP B 742 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N CYS B 746 " --> pdb=" O PHE B 664 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE B 664 " --> pdb=" O CYS B 746 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU B 748 " --> pdb=" O TRP B 662 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TRP B 662 " --> pdb=" O LEU B 748 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP B 669 " --> pdb=" O LYS B 788 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N LYS B 788 " --> pdb=" O ASP B 669 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 684 through 686 Processing sheet with id=AE3, first strand: chain 'B' and resid 715 through 716 removed outlier: 3.676A pdb=" N GLY B 715 " --> pdb=" O TRP B 722 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 767 through 769 Processing sheet with id=AE5, first strand: chain 'B' and resid 839 through 840 removed outlier: 4.044A pdb=" N TRP B1088 " --> pdb=" O ILE B1153 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE B1153 " --> pdb=" O TRP B1088 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 839 through 840 Processing sheet with id=AE7, first strand: chain 'B' and resid 1137 through 1138 removed outlier: 3.926A pdb=" N GLN B1130 " --> pdb=" O ASN B1125 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TRP B1104 " --> pdb=" O TYR B1122 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL B1102 " --> pdb=" O PHE B1124 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA B1077 " --> pdb=" O PRO B1190 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER B1604 " --> pdb=" O LYS B1240 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 1244 through 1245 Processing sheet with id=AE9, first strand: chain 'B' and resid 1255 through 1258 removed outlier: 3.546A pdb=" N ALA B1258 " --> pdb=" O ARG B1271 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 1285 through 1287 removed outlier: 3.788A pdb=" N MET B1462 " --> pdb=" O GLU B1285 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 1436 through 1438 removed outlier: 4.095A pdb=" N SER B1436 " --> pdb=" O THR B1557 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR B1557 " --> pdb=" O SER B1436 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG B1438 " --> pdb=" O LEU B1555 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU B1555 " --> pdb=" O ARG B1438 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B1552 " --> pdb=" O LEU B1487 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU B1487 " --> pdb=" O VAL B1552 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL B1554 " --> pdb=" O SER B1485 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER B1485 " --> pdb=" O VAL B1554 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 1436 through 1438 removed outlier: 4.095A pdb=" N SER B1436 " --> pdb=" O THR B1557 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR B1557 " --> pdb=" O SER B1436 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG B1438 " --> pdb=" O LEU B1555 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU B1555 " --> pdb=" O ARG B1438 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 1734 through 1736 removed outlier: 3.576A pdb=" N TYR B2142 " --> pdb=" O TYR B1734 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 4181 through 4183 removed outlier: 3.614A pdb=" N ILE B4183 " --> pdb=" O GLU B4191 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B4191 " --> pdb=" O ILE B4183 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 4582 through 4583 removed outlier: 3.605A pdb=" N SER B4583 " --> pdb=" O VAL B4628 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 4957 through 4958 removed outlier: 3.941A pdb=" N CYS B4958 " --> pdb=" O ILE B4963 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ILE B4963 " --> pdb=" O CYS B4958 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'C' and resid 33 through 36 removed outlier: 4.195A pdb=" N LEU C 33 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA C 26 " --> pdb=" O LEU C 33 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 33 through 36 removed outlier: 4.195A pdb=" N LEU C 33 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA C 26 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL C 21 " --> pdb=" O ASN C 203 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN C 203 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN C 23 " --> pdb=" O ASN C 201 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 72 through 73 removed outlier: 3.525A pdb=" N LEU C 73 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS C 151 " --> pdb=" O ILE C 170 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE C 170 " --> pdb=" O HIS C 151 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 117 through 120 Processing sheet with id=AG3, first strand: chain 'C' and resid 219 through 220 Processing sheet with id=AG4, first strand: chain 'C' and resid 223 through 224 removed outlier: 3.714A pdb=" N GLU C 229 " --> pdb=" O HIS C 224 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 290 through 293 removed outlier: 3.596A pdb=" N VAL C 300 " --> pdb=" O ALA C 292 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 314 through 317 removed outlier: 3.603A pdb=" N CYS C 315 " --> pdb=" O GLN C 349 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN C 349 " --> pdb=" O CYS C 315 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE C 347 " --> pdb=" O ARG C 317 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 634 through 639 removed outlier: 4.495A pdb=" N GLN C 634 " --> pdb=" O HIS C1640 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 644 through 645 Processing sheet with id=AG9, first strand: chain 'C' and resid 754 through 758 removed outlier: 4.255A pdb=" N SER C 754 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER C 745 " --> pdb=" O ARG C 758 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP C 742 " --> pdb=" O VAL C 668 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL C 668 " --> pdb=" O ASP C 742 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N CYS C 746 " --> pdb=" O PHE C 664 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE C 664 " --> pdb=" O CYS C 746 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU C 748 " --> pdb=" O TRP C 662 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N TRP C 662 " --> pdb=" O LEU C 748 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP C 669 " --> pdb=" O LYS C 788 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LYS C 788 " --> pdb=" O ASP C 669 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 684 through 686 Processing sheet with id=AH2, first strand: chain 'C' and resid 715 through 716 removed outlier: 3.676A pdb=" N GLY C 715 " --> pdb=" O TRP C 722 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 767 through 769 Processing sheet with id=AH4, first strand: chain 'C' and resid 839 through 840 removed outlier: 4.044A pdb=" N TRP C1088 " --> pdb=" O ILE C1153 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE C1153 " --> pdb=" O TRP C1088 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 839 through 840 Processing sheet with id=AH6, first strand: chain 'C' and resid 1137 through 1138 removed outlier: 3.926A pdb=" N GLN C1130 " --> pdb=" O ASN C1125 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TRP C1104 " --> pdb=" O TYR C1122 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C1102 " --> pdb=" O PHE C1124 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA C1077 " --> pdb=" O PRO C1190 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER C1604 " --> pdb=" O LYS C1240 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'C' and resid 1244 through 1245 Processing sheet with id=AH8, first strand: chain 'C' and resid 1255 through 1258 removed outlier: 3.546A pdb=" N ALA C1258 " --> pdb=" O ARG C1271 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'C' and resid 1285 through 1287 removed outlier: 3.788A pdb=" N MET C1462 " --> pdb=" O GLU C1285 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'C' and resid 1436 through 1438 removed outlier: 4.096A pdb=" N SER C1436 " --> pdb=" O THR C1557 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR C1557 " --> pdb=" O SER C1436 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG C1438 " --> pdb=" O LEU C1555 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C1555 " --> pdb=" O ARG C1438 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL C1552 " --> pdb=" O LEU C1487 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU C1487 " --> pdb=" O VAL C1552 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL C1554 " --> pdb=" O SER C1485 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER C1485 " --> pdb=" O VAL C1554 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'C' and resid 1436 through 1438 removed outlier: 4.096A pdb=" N SER C1436 " --> pdb=" O THR C1557 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR C1557 " --> pdb=" O SER C1436 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG C1438 " --> pdb=" O LEU C1555 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C1555 " --> pdb=" O ARG C1438 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'C' and resid 1734 through 1736 removed outlier: 3.576A pdb=" N TYR C2142 " --> pdb=" O TYR C1734 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'C' and resid 4181 through 4183 removed outlier: 3.614A pdb=" N ILE C4183 " --> pdb=" O GLU C4191 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU C4191 " --> pdb=" O ILE C4183 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'C' and resid 4582 through 4583 removed outlier: 3.605A pdb=" N SER C4583 " --> pdb=" O VAL C4628 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'C' and resid 4957 through 4958 removed outlier: 3.941A pdb=" N CYS C4958 " --> pdb=" O ILE C4963 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ILE C4963 " --> pdb=" O CYS C4958 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'D' and resid 33 through 36 removed outlier: 4.196A pdb=" N LEU D 33 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA D 26 " --> pdb=" O LEU D 33 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'D' and resid 33 through 36 removed outlier: 4.196A pdb=" N LEU D 33 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA D 26 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 21 " --> pdb=" O ASN D 203 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN D 203 " --> pdb=" O VAL D 21 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN D 23 " --> pdb=" O ASN D 201 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'D' and resid 72 through 73 removed outlier: 3.524A pdb=" N LEU D 73 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS D 151 " --> pdb=" O ILE D 170 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE D 170 " --> pdb=" O HIS D 151 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'D' and resid 117 through 120 Processing sheet with id=AJ2, first strand: chain 'D' and resid 219 through 220 Processing sheet with id=AJ3, first strand: chain 'D' and resid 223 through 224 removed outlier: 3.714A pdb=" N GLU D 229 " --> pdb=" O HIS D 224 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'D' and resid 290 through 293 removed outlier: 3.596A pdb=" N VAL D 300 " --> pdb=" O ALA D 292 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'D' and resid 314 through 317 removed outlier: 3.603A pdb=" N CYS D 315 " --> pdb=" O GLN D 349 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN D 349 " --> pdb=" O CYS D 315 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE D 347 " --> pdb=" O ARG D 317 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'D' and resid 634 through 639 removed outlier: 4.495A pdb=" N GLN D 634 " --> pdb=" O HIS D1640 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'D' and resid 644 through 645 Processing sheet with id=AJ8, first strand: chain 'D' and resid 754 through 758 removed outlier: 4.255A pdb=" N SER D 754 " --> pdb=" O ASP D 749 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER D 745 " --> pdb=" O ARG D 758 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP D 742 " --> pdb=" O VAL D 668 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL D 668 " --> pdb=" O ASP D 742 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N CYS D 746 " --> pdb=" O PHE D 664 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE D 664 " --> pdb=" O CYS D 746 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU D 748 " --> pdb=" O TRP D 662 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N TRP D 662 " --> pdb=" O LEU D 748 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP D 669 " --> pdb=" O LYS D 788 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LYS D 788 " --> pdb=" O ASP D 669 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'D' and resid 684 through 686 Processing sheet with id=AK1, first strand: chain 'D' and resid 715 through 716 removed outlier: 3.677A pdb=" N GLY D 715 " --> pdb=" O TRP D 722 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'D' and resid 767 through 769 Processing sheet with id=AK3, first strand: chain 'D' and resid 839 through 840 removed outlier: 4.044A pdb=" N TRP D1088 " --> pdb=" O ILE D1153 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE D1153 " --> pdb=" O TRP D1088 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'D' and resid 839 through 840 Processing sheet with id=AK5, first strand: chain 'D' and resid 1137 through 1138 removed outlier: 3.927A pdb=" N GLN D1130 " --> pdb=" O ASN D1125 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TRP D1104 " --> pdb=" O TYR D1122 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL D1102 " --> pdb=" O PHE D1124 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA D1077 " --> pdb=" O PRO D1190 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER D1604 " --> pdb=" O LYS D1240 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'D' and resid 1244 through 1245 Processing sheet with id=AK7, first strand: chain 'D' and resid 1255 through 1258 removed outlier: 3.546A pdb=" N ALA D1258 " --> pdb=" O ARG D1271 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'D' and resid 1285 through 1287 removed outlier: 3.788A pdb=" N MET D1462 " --> pdb=" O GLU D1285 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'D' and resid 1436 through 1438 removed outlier: 4.096A pdb=" N SER D1436 " --> pdb=" O THR D1557 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR D1557 " --> pdb=" O SER D1436 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG D1438 " --> pdb=" O LEU D1555 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU D1555 " --> pdb=" O ARG D1438 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL D1552 " --> pdb=" O LEU D1487 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU D1487 " --> pdb=" O VAL D1552 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL D1554 " --> pdb=" O SER D1485 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER D1485 " --> pdb=" O VAL D1554 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'D' and resid 1436 through 1438 removed outlier: 4.096A pdb=" N SER D1436 " --> pdb=" O THR D1557 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR D1557 " --> pdb=" O SER D1436 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG D1438 " --> pdb=" O LEU D1555 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU D1555 " --> pdb=" O ARG D1438 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'D' and resid 1734 through 1736 removed outlier: 3.576A pdb=" N TYR D2142 " --> pdb=" O TYR D1734 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'D' and resid 4181 through 4183 removed outlier: 3.613A pdb=" N ILE D4183 " --> pdb=" O GLU D4191 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU D4191 " --> pdb=" O ILE D4183 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'D' and resid 4582 through 4583 removed outlier: 3.605A pdb=" N SER D4583 " --> pdb=" O VAL D4628 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'D' and resid 4957 through 4958 removed outlier: 3.941A pdb=" N CYS D4958 " --> pdb=" O ILE D4963 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ILE D4963 " --> pdb=" O CYS D4958 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL5 Processing sheet with id=AL6, first strand: chain 'E' and resid 21 through 24 Processing sheet with id=AL7, first strand: chain 'E' and resid 28 through 30 removed outlier: 3.594A pdb=" N PHE E 99 " --> pdb=" O LEU E 74 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'F' and resid 21 through 24 Processing sheet with id=AL9, first strand: chain 'F' and resid 28 through 30 removed outlier: 3.594A pdb=" N PHE F 99 " --> pdb=" O LEU F 74 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'G' and resid 21 through 24 Processing sheet with id=AM2, first strand: chain 'G' and resid 28 through 30 removed outlier: 3.594A pdb=" N PHE G 99 " --> pdb=" O LEU G 74 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'H' and resid 21 through 24 Processing sheet with id=AM4, first strand: chain 'H' and resid 28 through 30 removed outlier: 3.595A pdb=" N PHE H 99 " --> pdb=" O LEU H 74 " (cutoff:3.500A) 6396 hydrogen bonds defined for protein. 18636 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: 86.87 Time building geometry restraints manager: 36.96 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: 44463 1.34 - 1.46: 28803 1.46 - 1.58: 62630 1.58 - 1.70: 0 1.70 - 1.82: 1284 Bond restraints: 137180 Sorted by residual: bond pdb=" C THR B 978 " pdb=" N PRO B 979 " ideal model delta sigma weight residual 1.334 1.351 -0.018 8.40e-03 1.42e+04 4.39e+00 bond pdb=" C THR C 978 " pdb=" N PRO C 979 " ideal model delta sigma weight residual 1.334 1.351 -0.017 8.40e-03 1.42e+04 4.08e+00 bond pdb=" C THR D 978 " pdb=" N PRO D 979 " ideal model delta sigma weight residual 1.334 1.350 -0.017 8.40e-03 1.42e+04 3.97e+00 bond pdb=" C THR A 978 " pdb=" N PRO A 979 " ideal model delta sigma weight residual 1.334 1.350 -0.017 8.40e-03 1.42e+04 3.97e+00 bond pdb=" CA GLY B 482 " pdb=" C GLY B 482 " ideal model delta sigma weight residual 1.530 1.511 0.019 1.04e-02 9.25e+03 3.38e+00 ... (remaining 137175 not shown) Histogram of bond angle deviations from ideal: 96.11 - 103.76: 2117 103.76 - 111.41: 58808 111.41 - 119.06: 51987 119.06 - 126.71: 71254 126.71 - 134.36: 2182 Bond angle restraints: 186348 Sorted by residual: angle pdb=" N VAL A 28 " pdb=" CA VAL A 28 " pdb=" C VAL A 28 " ideal model delta sigma weight residual 113.71 108.40 5.31 9.50e-01 1.11e+00 3.12e+01 angle pdb=" N VAL D 28 " pdb=" CA VAL D 28 " pdb=" C VAL D 28 " ideal model delta sigma weight residual 113.71 108.41 5.30 9.50e-01 1.11e+00 3.12e+01 angle pdb=" N VAL C 28 " pdb=" CA VAL C 28 " pdb=" C VAL C 28 " ideal model delta sigma weight residual 113.71 108.41 5.30 9.50e-01 1.11e+00 3.12e+01 angle pdb=" N VAL B 28 " pdb=" CA VAL B 28 " pdb=" C VAL B 28 " ideal model delta sigma weight residual 113.71 108.45 5.26 9.50e-01 1.11e+00 3.07e+01 angle pdb=" N ILE A4816 " pdb=" CA ILE A4816 " pdb=" C ILE A4816 " ideal model delta sigma weight residual 112.96 108.04 4.92 1.00e+00 1.00e+00 2.43e+01 ... (remaining 186343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 73205 17.94 - 35.88: 7299 35.88 - 53.82: 1108 53.82 - 71.77: 296 71.77 - 89.71: 136 Dihedral angle restraints: 82044 sinusoidal: 31592 harmonic: 50452 Sorted by residual: dihedral pdb=" CA PHE B1124 " pdb=" C PHE B1124 " pdb=" N ASN B1125 " pdb=" CA ASN B1125 " ideal model delta harmonic sigma weight residual 180.00 -161.83 -18.17 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA PHE C1124 " pdb=" C PHE C1124 " pdb=" N ASN C1125 " pdb=" CA ASN C1125 " ideal model delta harmonic sigma weight residual -180.00 -161.85 -18.15 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA PHE D1124 " pdb=" C PHE D1124 " pdb=" N ASN D1125 " pdb=" CA ASN D1125 " ideal model delta harmonic sigma weight residual -180.00 -161.87 -18.13 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 82041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 17615 0.054 - 0.109: 3019 0.109 - 0.163: 306 0.163 - 0.218: 8 0.218 - 0.272: 8 Chirality restraints: 20956 Sorted by residual: chirality pdb=" CB VAL A1767 " pdb=" CA VAL A1767 " pdb=" CG1 VAL A1767 " pdb=" CG2 VAL A1767 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CB VAL C1767 " pdb=" CA VAL C1767 " pdb=" CG1 VAL C1767 " pdb=" CG2 VAL C1767 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB VAL B1767 " pdb=" CA VAL B1767 " pdb=" CG1 VAL B1767 " pdb=" CG2 VAL B1767 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 20953 not shown) Planarity restraints: 24244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B1143 " 0.017 2.00e-02 2.50e+03 1.77e-02 7.81e+00 pdb=" CG TRP B1143 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP B1143 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP B1143 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B1143 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B1143 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B1143 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1143 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1143 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B1143 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C1143 " 0.018 2.00e-02 2.50e+03 1.77e-02 7.79e+00 pdb=" CG TRP C1143 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP C1143 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP C1143 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C1143 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C1143 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C1143 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1143 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1143 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP C1143 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1143 " 0.017 2.00e-02 2.50e+03 1.76e-02 7.74e+00 pdb=" CG TRP A1143 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP A1143 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A1143 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A1143 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A1143 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1143 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1143 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1143 " 0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP A1143 " -0.002 2.00e-02 2.50e+03 ... (remaining 24241 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 4587 2.72 - 3.26: 130760 3.26 - 3.81: 214955 3.81 - 4.35: 234815 4.35 - 4.90: 401799 Nonbonded interactions: 986916 Sorted by model distance: nonbonded pdb=" O PHE D 452 " pdb=" OG SER D 528 " model vdw 2.175 2.440 nonbonded pdb=" O PHE B 452 " pdb=" OG SER B 528 " model vdw 2.175 2.440 nonbonded pdb=" O PHE A 452 " pdb=" OG SER A 528 " model vdw 2.175 2.440 nonbonded pdb=" O PHE C 452 " pdb=" OG SER C 528 " model vdw 2.176 2.440 nonbonded pdb=" OG SER A4866 " pdb=" OD2 ASP A4873 " model vdw 2.205 2.440 ... (remaining 986911 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.620 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: 0.080 Extract box with map and model: 20.320 Check model and map are aligned: 1.410 Set scattering table: 0.900 Process input model: 297.150 Find NCS groups from input model: 6.300 Set up NCS constraints: 0.930 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 333.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 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 : 0.002 0.050 137180 Z= 0.165 Angle : 0.641 14.688 186348 Z= 0.319 Chirality : 0.040 0.272 20956 Planarity : 0.003 0.050 24244 Dihedral : 14.828 89.706 49428 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.10 % Favored : 93.51 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -0.38 (0.07), residues: 17208 helix: 1.70 (0.06), residues: 8208 sheet: -0.83 (0.16), residues: 1112 loop : -2.44 (0.07), residues: 7888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP C1143 HIS 0.011 0.001 HIS C3422 PHE 0.038 0.001 PHE B1124 TYR 0.036 0.001 TYR C3968 ARG 0.003 0.000 ARG A4913 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34416 Ramachandran restraints generated. 17208 Oldfield, 0 Emsley, 17208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34416 Ramachandran restraints generated. 17208 Oldfield, 0 Emsley, 17208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 15132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 879 time to evaluate : 11.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 MET cc_start: 0.5304 (mmp) cc_final: 0.4885 (tpp) REVERT: A 649 PHE cc_start: 0.6410 (m-10) cc_final: 0.6196 (m-10) REVERT: A 1585 LYS cc_start: 0.8462 (mmpt) cc_final: 0.8250 (mmmt) REVERT: A 1929 MET cc_start: 0.7526 (ttm) cc_final: 0.7281 (ttm) REVERT: A 4064 MET cc_start: 0.8395 (ppp) cc_final: 0.7855 (ppp) REVERT: A 4969 ASP cc_start: 0.6749 (m-30) cc_final: 0.6490 (m-30) REVERT: B 334 MET cc_start: 0.5202 (mmp) cc_final: 0.4841 (tpp) REVERT: B 1585 LYS cc_start: 0.8454 (mmpt) cc_final: 0.8249 (mmmt) REVERT: B 4064 MET cc_start: 0.8402 (ppp) cc_final: 0.7896 (ppp) REVERT: B 4969 ASP cc_start: 0.6941 (m-30) cc_final: 0.6688 (m-30) REVERT: C 334 MET cc_start: 0.5285 (mmp) cc_final: 0.4851 (tpp) REVERT: C 4064 MET cc_start: 0.8343 (ppp) cc_final: 0.7763 (ppp) REVERT: C 4969 ASP cc_start: 0.6738 (m-30) cc_final: 0.6468 (m-30) REVERT: D 334 MET cc_start: 0.5262 (mmp) cc_final: 0.4858 (tpp) REVERT: D 649 PHE cc_start: 0.6356 (m-10) cc_final: 0.6150 (m-10) REVERT: D 1585 LYS cc_start: 0.8479 (mmpt) cc_final: 0.8264 (mmmt) REVERT: D 1929 MET cc_start: 0.7523 (ttm) cc_final: 0.7283 (ttm) REVERT: D 4064 MET cc_start: 0.8400 (ppp) cc_final: 0.7894 (ppp) REVERT: D 4969 ASP cc_start: 0.6772 (m-30) cc_final: 0.6498 (m-30) outliers start: 0 outliers final: 0 residues processed: 879 average time/residue: 1.0759 time to fit residues: 1737.4251 Evaluate side-chains 714 residues out of total 15132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 714 time to evaluate : 11.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1736 random chunks: chunk 1465 optimal weight: 0.8980 chunk 1315 optimal weight: 9.9990 chunk 730 optimal weight: 50.0000 chunk 449 optimal weight: 40.0000 chunk 887 optimal weight: 4.9990 chunk 702 optimal weight: 50.0000 chunk 1360 optimal weight: 0.4980 chunk 526 optimal weight: 0.0870 chunk 827 optimal weight: 5.9990 chunk 1012 optimal weight: 20.0000 chunk 1576 optimal weight: 6.9990 overall best weight: 2.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1201 HIS A1775 HIS ** A2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2883 HIS A3449 HIS A3994 HIS ** A4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1201 HIS B1775 HIS ** B2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2883 HIS B3449 HIS B3994 HIS ** B4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1201 HIS C1775 HIS ** C2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3449 HIS C3994 HIS ** C4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 399 GLN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1201 HIS D1775 HIS ** D2127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2883 HIS D3449 HIS D3994 HIS ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 137180 Z= 0.184 Angle : 0.535 10.128 186348 Z= 0.263 Chirality : 0.038 0.176 20956 Planarity : 0.003 0.039 24244 Dihedral : 3.082 17.142 18656 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.60 % Favored : 93.03 % Rotamer: Outliers : 0.38 % Allowed : 5.96 % Favored : 93.66 % 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: -0.09 (0.07), residues: 17208 helix: 2.00 (0.06), residues: 8340 sheet: -1.06 (0.15), residues: 1164 loop : -2.40 (0.07), residues: 7704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 882 HIS 0.010 0.001 HIS D3449 PHE 0.024 0.001 PHE B1124 TYR 0.024 0.001 TYR D 920 ARG 0.004 0.000 ARG B4131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34416 Ramachandran restraints generated. 17208 Oldfield, 0 Emsley, 17208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34416 Ramachandran restraints generated. 17208 Oldfield, 0 Emsley, 17208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 15132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 752 time to evaluate : 11.128 Fit side-chains REVERT: A 334 MET cc_start: 0.5570 (mmp) cc_final: 0.4957 (tpp) REVERT: A 1260 MET cc_start: 0.6194 (tpt) cc_final: 0.5956 (tpt) REVERT: A 2228 MET cc_start: 0.7083 (ppp) cc_final: 0.6629 (tmm) REVERT: A 2502 MET cc_start: 0.8031 (mmm) cc_final: 0.7806 (mmm) REVERT: A 3442 PHE cc_start: 0.7696 (m-80) cc_final: 0.7444 (m-10) REVERT: A 3652 MET cc_start: 0.8297 (mmt) cc_final: 0.7862 (mmt) REVERT: A 3758 MET cc_start: 0.7226 (tpt) cc_final: 0.6837 (tpt) REVERT: A 4064 MET cc_start: 0.8425 (ppp) cc_final: 0.8181 (ppp) REVERT: A 4702 ASP cc_start: 0.8379 (t0) cc_final: 0.8158 (t0) REVERT: B 334 MET cc_start: 0.5584 (mmp) cc_final: 0.4971 (tpp) REVERT: B 1260 MET cc_start: 0.6175 (tpt) cc_final: 0.5936 (tpt) REVERT: B 2228 MET cc_start: 0.7101 (ppp) cc_final: 0.6727 (tmm) REVERT: B 2502 MET cc_start: 0.8046 (mmm) cc_final: 0.7822 (mmm) REVERT: B 3442 PHE cc_start: 0.7687 (m-80) cc_final: 0.7448 (m-10) REVERT: B 3652 MET cc_start: 0.8270 (mmt) cc_final: 0.7820 (mmt) REVERT: B 3758 MET cc_start: 0.7200 (tpt) cc_final: 0.6809 (tpt) REVERT: B 4064 MET cc_start: 0.8433 (ppp) cc_final: 0.8213 (ppp) REVERT: B 4702 ASP cc_start: 0.8372 (t0) cc_final: 0.8144 (t0) REVERT: C 334 MET cc_start: 0.5382 (mmp) cc_final: 0.4874 (tpp) REVERT: C 2228 MET cc_start: 0.7123 (ppp) cc_final: 0.6152 (tmm) REVERT: C 2502 MET cc_start: 0.8044 (mmm) cc_final: 0.7816 (mmm) REVERT: C 3652 MET cc_start: 0.8349 (mmt) cc_final: 0.7917 (mmt) REVERT: C 3758 MET cc_start: 0.7157 (tpt) cc_final: 0.6777 (tpt) REVERT: C 4064 MET cc_start: 0.8371 (ppp) cc_final: 0.8111 (ppp) REVERT: D 334 MET cc_start: 0.5522 (mmp) cc_final: 0.4909 (tpp) REVERT: D 1260 MET cc_start: 0.6187 (tpt) cc_final: 0.5972 (tpt) REVERT: D 2228 MET cc_start: 0.7098 (ppp) cc_final: 0.6657 (tmm) REVERT: D 2502 MET cc_start: 0.8061 (mmm) cc_final: 0.7838 (mmm) REVERT: D 3652 MET cc_start: 0.8288 (mmt) cc_final: 0.7841 (mmt) REVERT: D 3758 MET cc_start: 0.7211 (tpt) cc_final: 0.6829 (tpt) REVERT: D 4064 MET cc_start: 0.8433 (ppp) cc_final: 0.8213 (ppp) REVERT: D 4702 ASP cc_start: 0.8399 (t0) cc_final: 0.8178 (t0) outliers start: 53 outliers final: 39 residues processed: 780 average time/residue: 1.0890 time to fit residues: 1569.3403 Evaluate side-chains 737 residues out of total 15132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 698 time to evaluate : 11.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1158 ASN Chi-restraints excluded: chain A residue 1599 MET Chi-restraints excluded: chain A residue 1653 LEU Chi-restraints excluded: chain A residue 3753 PHE Chi-restraints excluded: chain A residue 3816 MET Chi-restraints excluded: chain A residue 3926 LEU Chi-restraints excluded: chain A residue 4782 VAL Chi-restraints excluded: chain A residue 4797 VAL Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain B residue 1158 ASN Chi-restraints excluded: chain B residue 1653 LEU Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 3753 PHE Chi-restraints excluded: chain B residue 3816 MET Chi-restraints excluded: chain B residue 3926 LEU Chi-restraints excluded: chain B residue 4782 VAL Chi-restraints excluded: chain B residue 4797 VAL Chi-restraints excluded: chain B residue 4853 VAL Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1158 ASN Chi-restraints excluded: chain C residue 1599 MET Chi-restraints excluded: chain C residue 1653 LEU Chi-restraints excluded: chain C residue 2610 LEU Chi-restraints excluded: chain C residue 3753 PHE Chi-restraints excluded: chain C residue 3816 MET Chi-restraints excluded: chain C residue 3926 LEU Chi-restraints excluded: chain C residue 4782 VAL Chi-restraints excluded: chain C residue 4797 VAL Chi-restraints excluded: chain C residue 4853 VAL Chi-restraints excluded: chain D residue 1039 LEU Chi-restraints excluded: chain D residue 1158 ASN Chi-restraints excluded: chain D residue 1599 MET Chi-restraints excluded: chain D residue 1653 LEU Chi-restraints excluded: chain D residue 3753 PHE Chi-restraints excluded: chain D residue 3816 MET Chi-restraints excluded: chain D residue 3926 LEU Chi-restraints excluded: chain D residue 4782 VAL Chi-restraints excluded: chain D residue 4797 VAL Chi-restraints excluded: chain D residue 4853 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1736 random chunks: chunk 876 optimal weight: 9.9990 chunk 489 optimal weight: 7.9990 chunk 1312 optimal weight: 0.0670 chunk 1073 optimal weight: 40.0000 chunk 434 optimal weight: 2.9990 chunk 1579 optimal weight: 0.9980 chunk 1706 optimal weight: 30.0000 chunk 1406 optimal weight: 20.0000 chunk 1566 optimal weight: 50.0000 chunk 538 optimal weight: 9.9990 chunk 1266 optimal weight: 0.0870 overall best weight: 2.4300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1003 GLN A2127 GLN A2247 GLN ** A2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3422 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3597 GLN ** A4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1003 GLN B2127 GLN B2247 GLN ** B2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1003 GLN C2127 GLN C2247 GLN ** C2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2883 HIS C3597 GLN ** C4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 399 GLN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1003 GLN D2127 GLN D2247 GLN ** D2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3597 GLN ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 137180 Z= 0.174 Angle : 0.512 8.989 186348 Z= 0.251 Chirality : 0.037 0.146 20956 Planarity : 0.003 0.038 24244 Dihedral : 3.101 15.178 18656 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.61 % Favored : 93.07 % Rotamer: Outliers : 0.85 % Allowed : 8.64 % Favored : 90.51 % 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: 0.06 (0.07), residues: 17208 helix: 2.18 (0.06), residues: 8324 sheet: -1.22 (0.15), residues: 1244 loop : -2.36 (0.07), residues: 7640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A3423 HIS 0.011 0.001 HIS B2621 PHE 0.032 0.001 PHE C3010 TYR 0.025 0.001 TYR B 920 ARG 0.006 0.000 ARG D1584 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34416 Ramachandran restraints generated. 17208 Oldfield, 0 Emsley, 17208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34416 Ramachandran restraints generated. 17208 Oldfield, 0 Emsley, 17208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 15132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 737 time to evaluate : 11.031 Fit side-chains REVERT: A 334 MET cc_start: 0.5487 (mmp) cc_final: 0.5007 (tpp) REVERT: A 2250 MET cc_start: 0.8065 (tpp) cc_final: 0.7772 (tpp) REVERT: A 2340 PHE cc_start: 0.6430 (p90) cc_final: 0.6160 (p90) REVERT: A 2502 MET cc_start: 0.8167 (mmm) cc_final: 0.7927 (mmm) REVERT: A 3409 TYR cc_start: 0.5585 (OUTLIER) cc_final: 0.3784 (m-80) REVERT: A 3517 MET cc_start: 0.3924 (ppp) cc_final: 0.3326 (ppp) REVERT: A 3652 MET cc_start: 0.8340 (mmt) cc_final: 0.8114 (mmt) REVERT: A 3758 MET cc_start: 0.7180 (tpt) cc_final: 0.6817 (tpt) REVERT: A 3999 MET cc_start: 0.9015 (tpp) cc_final: 0.8790 (mmm) REVERT: A 4000 MET cc_start: 0.7739 (mpp) cc_final: 0.7259 (mpp) REVERT: A 4064 MET cc_start: 0.8366 (ppp) cc_final: 0.8145 (ppp) REVERT: A 4702 ASP cc_start: 0.8545 (t0) cc_final: 0.8296 (t0) REVERT: B 334 MET cc_start: 0.5459 (mmp) cc_final: 0.4987 (tpp) REVERT: B 1599 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7916 (ppp) REVERT: B 2250 MET cc_start: 0.8060 (tpp) cc_final: 0.7771 (tpp) REVERT: B 2340 PHE cc_start: 0.6379 (p90) cc_final: 0.6112 (p90) REVERT: B 2502 MET cc_start: 0.8182 (mmm) cc_final: 0.7935 (mmm) REVERT: B 3409 TYR cc_start: 0.5540 (OUTLIER) cc_final: 0.3751 (m-80) REVERT: B 3517 MET cc_start: 0.4182 (ppp) cc_final: 0.3473 (ppp) REVERT: B 3652 MET cc_start: 0.8327 (mmt) cc_final: 0.8100 (mmt) REVERT: B 3758 MET cc_start: 0.7161 (tpt) cc_final: 0.6784 (tpt) REVERT: B 4000 MET cc_start: 0.7767 (mpp) cc_final: 0.7307 (mpp) REVERT: B 4064 MET cc_start: 0.8423 (ppp) cc_final: 0.8185 (ppp) REVERT: B 4702 ASP cc_start: 0.8510 (t0) cc_final: 0.8268 (t0) REVERT: C 334 MET cc_start: 0.5330 (mmp) cc_final: 0.4930 (tpp) REVERT: C 2250 MET cc_start: 0.8074 (tpp) cc_final: 0.7775 (tpp) REVERT: C 2340 PHE cc_start: 0.6439 (p90) cc_final: 0.6172 (p90) REVERT: C 2502 MET cc_start: 0.8178 (mmm) cc_final: 0.7962 (mmm) REVERT: C 3409 TYR cc_start: 0.5522 (OUTLIER) cc_final: 0.3740 (m-80) REVERT: C 3517 MET cc_start: 0.3988 (ppp) cc_final: 0.3469 (ppp) REVERT: C 3652 MET cc_start: 0.8360 (mmt) cc_final: 0.8126 (mmt) REVERT: C 4000 MET cc_start: 0.7787 (mpp) cc_final: 0.7302 (mpp) REVERT: C 4064 MET cc_start: 0.8382 (ppp) cc_final: 0.8179 (ppp) REVERT: C 4702 ASP cc_start: 0.8470 (t0) cc_final: 0.8238 (t0) REVERT: D 334 MET cc_start: 0.5407 (mmp) cc_final: 0.4957 (tpp) REVERT: D 2250 MET cc_start: 0.8077 (tpp) cc_final: 0.7782 (tpp) REVERT: D 2340 PHE cc_start: 0.6413 (p90) cc_final: 0.6151 (p90) REVERT: D 2502 MET cc_start: 0.8178 (mmm) cc_final: 0.7933 (mmm) REVERT: D 3409 TYR cc_start: 0.5484 (OUTLIER) cc_final: 0.3716 (m-80) REVERT: D 3517 MET cc_start: 0.3995 (ppp) cc_final: 0.3401 (ppp) REVERT: D 3652 MET cc_start: 0.8346 (mmt) cc_final: 0.8117 (mmt) REVERT: D 3758 MET cc_start: 0.7164 (tpt) cc_final: 0.6785 (tpt) REVERT: D 3999 MET cc_start: 0.9025 (tpp) cc_final: 0.8799 (mmm) REVERT: D 4000 MET cc_start: 0.7767 (mpp) cc_final: 0.7283 (mpp) REVERT: D 4064 MET cc_start: 0.8425 (ppp) cc_final: 0.8189 (ppp) REVERT: D 4702 ASP cc_start: 0.8477 (t0) cc_final: 0.8232 (t0) outliers start: 119 outliers final: 69 residues processed: 830 average time/residue: 1.0250 time to fit residues: 1562.5780 Evaluate side-chains 762 residues out of total 15132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 688 time to evaluate : 10.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 778 PHE Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1158 ASN Chi-restraints excluded: chain A residue 1453 VAL Chi-restraints excluded: chain A residue 1653 LEU Chi-restraints excluded: chain A residue 1681 VAL Chi-restraints excluded: chain A residue 1685 LEU Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2460 LEU Chi-restraints excluded: chain A residue 2610 LEU Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 3409 TYR Chi-restraints excluded: chain A residue 3816 MET Chi-restraints excluded: chain A residue 3926 LEU Chi-restraints excluded: chain A residue 4782 VAL Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4886 HIS Chi-restraints excluded: chain B residue 778 PHE Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1158 ASN Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1599 MET Chi-restraints excluded: chain B residue 1653 LEU Chi-restraints excluded: chain B residue 1681 VAL Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 2138 LEU Chi-restraints excluded: chain B residue 2460 LEU Chi-restraints excluded: chain B residue 2610 LEU Chi-restraints excluded: chain B residue 2932 MET Chi-restraints excluded: chain B residue 3409 TYR Chi-restraints excluded: chain B residue 3816 MET Chi-restraints excluded: chain B residue 3926 LEU Chi-restraints excluded: chain B residue 4782 VAL Chi-restraints excluded: chain B residue 4797 VAL Chi-restraints excluded: chain B residue 4820 VAL Chi-restraints excluded: chain B residue 4853 VAL Chi-restraints excluded: chain B residue 4886 HIS Chi-restraints excluded: chain C residue 778 PHE Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1158 ASN Chi-restraints excluded: chain C residue 1453 VAL Chi-restraints excluded: chain C residue 1653 LEU Chi-restraints excluded: chain C residue 1681 VAL Chi-restraints excluded: chain C residue 1685 LEU Chi-restraints excluded: chain C residue 2138 LEU Chi-restraints excluded: chain C residue 2460 LEU Chi-restraints excluded: chain C residue 2610 LEU Chi-restraints excluded: chain C residue 2932 MET Chi-restraints excluded: chain C residue 3409 TYR Chi-restraints excluded: chain C residue 3816 MET Chi-restraints excluded: chain C residue 3926 LEU Chi-restraints excluded: chain C residue 4782 VAL Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4853 VAL Chi-restraints excluded: chain C residue 4886 HIS Chi-restraints excluded: chain D residue 778 PHE Chi-restraints excluded: chain D residue 1039 LEU Chi-restraints excluded: chain D residue 1158 ASN Chi-restraints excluded: chain D residue 1453 VAL Chi-restraints excluded: chain D residue 1653 LEU Chi-restraints excluded: chain D residue 1681 VAL Chi-restraints excluded: chain D residue 1685 LEU Chi-restraints excluded: chain D residue 2138 LEU Chi-restraints excluded: chain D residue 2460 LEU Chi-restraints excluded: chain D residue 2610 LEU Chi-restraints excluded: chain D residue 3409 TYR Chi-restraints excluded: chain D residue 3816 MET Chi-restraints excluded: chain D residue 3926 LEU Chi-restraints excluded: chain D residue 4782 VAL Chi-restraints excluded: chain D residue 4797 VAL Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4853 VAL Chi-restraints excluded: chain D residue 4886 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1736 random chunks: chunk 1560 optimal weight: 30.0000 chunk 1187 optimal weight: 50.0000 chunk 819 optimal weight: 9.9990 chunk 174 optimal weight: 9.9990 chunk 753 optimal weight: 10.0000 chunk 1060 optimal weight: 5.9990 chunk 1584 optimal weight: 20.0000 chunk 1678 optimal weight: 2.9990 chunk 828 optimal weight: 4.9990 chunk 1502 optimal weight: 20.0000 chunk 452 optimal weight: 0.0070 overall best weight: 4.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1611 HIS A2035 HIS A2041 HIS ** A2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3851 ASN A3960 GLN ** A4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1611 HIS B2035 HIS B2041 HIS ** B2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3597 GLN ** B3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3851 ASN B3960 GLN ** B4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4650 HIS C 54 ASN ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1611 HIS C2035 HIS C2041 HIS ** C2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3781 GLN C3851 ASN C3960 GLN ** C4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4650 HIS D 54 ASN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1611 HIS D2035 HIS D2041 HIS ** D2204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3851 ASN D3960 GLN ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4650 HIS E 94 ASN F 94 ASN G 94 ASN H 94 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 137180 Z= 0.300 Angle : 0.645 18.896 186348 Z= 0.321 Chirality : 0.040 0.235 20956 Planarity : 0.004 0.049 24244 Dihedral : 3.746 19.866 18656 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.57 % Favored : 91.11 % Rotamer: Outliers : 1.51 % Allowed : 11.58 % Favored : 86.91 % 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: -0.26 (0.07), residues: 17208 helix: 1.88 (0.06), residues: 8292 sheet: -1.38 (0.15), residues: 1244 loop : -2.45 (0.07), residues: 7672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B3423 HIS 0.010 0.001 HIS B3647 PHE 0.026 0.002 PHE A3010 TYR 0.022 0.002 TYR B4795 ARG 0.010 0.001 ARG D4892 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34416 Ramachandran restraints generated. 17208 Oldfield, 0 Emsley, 17208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34416 Ramachandran restraints generated. 17208 Oldfield, 0 Emsley, 17208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 943 residues out of total 15132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 731 time to evaluate : 10.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 MET cc_start: 0.6099 (mmp) cc_final: 0.5664 (tpp) REVERT: A 1599 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8133 (ppp) REVERT: A 2101 MET cc_start: 0.8749 (tmm) cc_final: 0.8436 (tmm) REVERT: A 2250 MET cc_start: 0.8131 (tpp) cc_final: 0.7902 (tpp) REVERT: A 2340 PHE cc_start: 0.6565 (p90) cc_final: 0.6075 (p90) REVERT: A 3409 TYR cc_start: 0.5720 (OUTLIER) cc_final: 0.3795 (m-80) REVERT: A 3517 MET cc_start: 0.4885 (ppp) cc_final: 0.3749 (ppp) REVERT: A 3652 MET cc_start: 0.8331 (mmt) cc_final: 0.8093 (mmt) REVERT: A 3758 MET cc_start: 0.7296 (tpt) cc_final: 0.6892 (tpt) REVERT: A 3899 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.7301 (m-10) REVERT: A 4064 MET cc_start: 0.8303 (ppp) cc_final: 0.7748 (ppp) REVERT: A 4769 MET cc_start: 0.8398 (tpp) cc_final: 0.8081 (tpp) REVERT: A 4849 TYR cc_start: 0.8229 (t80) cc_final: 0.7937 (t80) REVERT: B 334 MET cc_start: 0.6095 (mmp) cc_final: 0.5673 (tpp) REVERT: B 1599 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8214 (ppp) REVERT: B 2101 MET cc_start: 0.8701 (tmm) cc_final: 0.8388 (tmm) REVERT: B 2250 MET cc_start: 0.8152 (tpp) cc_final: 0.7909 (tpp) REVERT: B 2340 PHE cc_start: 0.6523 (p90) cc_final: 0.6043 (p90) REVERT: B 3409 TYR cc_start: 0.5753 (OUTLIER) cc_final: 0.3815 (m-80) REVERT: B 3517 MET cc_start: 0.4896 (ppp) cc_final: 0.3759 (ppp) REVERT: B 3652 MET cc_start: 0.8318 (mmt) cc_final: 0.8077 (mmt) REVERT: B 3758 MET cc_start: 0.7278 (tpt) cc_final: 0.6877 (tpt) REVERT: B 3899 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.7320 (m-10) REVERT: B 4064 MET cc_start: 0.8376 (ppp) cc_final: 0.7824 (ppp) REVERT: B 4769 MET cc_start: 0.8405 (tpp) cc_final: 0.8070 (tpp) REVERT: B 4849 TYR cc_start: 0.8256 (t80) cc_final: 0.7954 (t80) REVERT: B 4989 MET cc_start: 0.8048 (tmm) cc_final: 0.7730 (tmm) REVERT: C 334 MET cc_start: 0.6069 (mmp) cc_final: 0.5590 (tpp) REVERT: C 600 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8481 (mp) REVERT: C 1599 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8157 (ppp) REVERT: C 2101 MET cc_start: 0.8767 (tmm) cc_final: 0.8446 (tmm) REVERT: C 2250 MET cc_start: 0.8119 (tpp) cc_final: 0.7877 (tpp) REVERT: C 2340 PHE cc_start: 0.6568 (p90) cc_final: 0.6080 (p90) REVERT: C 3409 TYR cc_start: 0.5672 (OUTLIER) cc_final: 0.3789 (m-80) REVERT: C 3415 TYR cc_start: 0.5955 (t80) cc_final: 0.5001 (t80) REVERT: C 3442 PHE cc_start: 0.7566 (m-80) cc_final: 0.7315 (m-10) REVERT: C 3517 MET cc_start: 0.5000 (ppp) cc_final: 0.3926 (ppp) REVERT: C 3652 MET cc_start: 0.8358 (mmt) cc_final: 0.8114 (mmt) REVERT: C 3758 MET cc_start: 0.7300 (tpt) cc_final: 0.6893 (tpt) REVERT: C 3899 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.7307 (m-10) REVERT: C 4064 MET cc_start: 0.8318 (ppp) cc_final: 0.7776 (ppp) REVERT: C 4769 MET cc_start: 0.8406 (tpp) cc_final: 0.8078 (tpp) REVERT: C 4849 TYR cc_start: 0.8458 (t80) cc_final: 0.8181 (t80) REVERT: C 4929 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6773 (mp) REVERT: D 334 MET cc_start: 0.6082 (mmp) cc_final: 0.5653 (tpp) REVERT: D 1599 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8121 (ppp) REVERT: D 2101 MET cc_start: 0.8721 (tmm) cc_final: 0.8407 (tmm) REVERT: D 2250 MET cc_start: 0.8136 (tpp) cc_final: 0.7906 (tpp) REVERT: D 2340 PHE cc_start: 0.6565 (p90) cc_final: 0.6079 (p90) REVERT: D 3409 TYR cc_start: 0.5767 (OUTLIER) cc_final: 0.3828 (m-80) REVERT: D 3415 TYR cc_start: 0.5887 (t80) cc_final: 0.4952 (t80) REVERT: D 3517 MET cc_start: 0.4936 (ppp) cc_final: 0.3773 (ppp) REVERT: D 3652 MET cc_start: 0.8334 (mmt) cc_final: 0.8093 (mmt) REVERT: D 3758 MET cc_start: 0.7287 (tpt) cc_final: 0.6885 (tpt) REVERT: D 3899 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.7302 (m-10) REVERT: D 4064 MET cc_start: 0.8302 (ppp) cc_final: 0.7745 (ppp) REVERT: D 4769 MET cc_start: 0.8462 (tpp) cc_final: 0.8114 (tpp) REVERT: D 4849 TYR cc_start: 0.8009 (t80) cc_final: 0.7768 (t80) outliers start: 212 outliers final: 113 residues processed: 914 average time/residue: 0.9916 time to fit residues: 1665.6185 Evaluate side-chains 803 residues out of total 15132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 676 time to evaluate : 11.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 774 ASP Chi-restraints excluded: chain A residue 778 PHE Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1158 ASN Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1514 LEU Chi-restraints excluded: chain A residue 1599 MET Chi-restraints excluded: chain A residue 1650 ILE Chi-restraints excluded: chain A residue 1653 LEU Chi-restraints excluded: chain A residue 1673 VAL Chi-restraints excluded: chain A residue 1685 LEU Chi-restraints excluded: chain A residue 2182 ILE Chi-restraints excluded: chain A residue 2251 PHE Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2461 VAL Chi-restraints excluded: chain A residue 3137 LEU Chi-restraints excluded: chain A residue 3409 TYR Chi-restraints excluded: chain A residue 3647 HIS Chi-restraints excluded: chain A residue 3717 ASP Chi-restraints excluded: chain A residue 3899 PHE Chi-restraints excluded: chain A residue 3926 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4782 VAL Chi-restraints excluded: chain A residue 4814 LEU Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4830 VAL Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4929 LEU Chi-restraints excluded: chain A residue 5018 CYS Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 774 ASP Chi-restraints excluded: chain B residue 778 PHE Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1123 VAL Chi-restraints excluded: chain B residue 1158 ASN Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1514 LEU Chi-restraints excluded: chain B residue 1599 MET Chi-restraints excluded: chain B residue 1650 ILE Chi-restraints excluded: chain B residue 1653 LEU Chi-restraints excluded: chain B residue 1673 VAL Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 2182 ILE Chi-restraints excluded: chain B residue 2251 PHE Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 2461 VAL Chi-restraints excluded: chain B residue 3137 LEU Chi-restraints excluded: chain B residue 3409 TYR Chi-restraints excluded: chain B residue 3647 HIS Chi-restraints excluded: chain B residue 3717 ASP Chi-restraints excluded: chain B residue 3779 VAL Chi-restraints excluded: chain B residue 3899 PHE Chi-restraints excluded: chain B residue 3926 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4782 VAL Chi-restraints excluded: chain B residue 4814 LEU Chi-restraints excluded: chain B residue 4820 VAL Chi-restraints excluded: chain B residue 4830 VAL Chi-restraints excluded: chain B residue 4853 VAL Chi-restraints excluded: chain B residue 4929 LEU Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 774 ASP Chi-restraints excluded: chain C residue 778 PHE Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1123 VAL Chi-restraints excluded: chain C residue 1158 ASN Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1599 MET Chi-restraints excluded: chain C residue 1650 ILE Chi-restraints excluded: chain C residue 1653 LEU Chi-restraints excluded: chain C residue 1673 VAL Chi-restraints excluded: chain C residue 1685 LEU Chi-restraints excluded: chain C residue 2182 ILE Chi-restraints excluded: chain C residue 2251 PHE Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 2461 VAL Chi-restraints excluded: chain C residue 2610 LEU Chi-restraints excluded: chain C residue 2885 THR Chi-restraints excluded: chain C residue 3137 LEU Chi-restraints excluded: chain C residue 3409 TYR Chi-restraints excluded: chain C residue 3647 HIS Chi-restraints excluded: chain C residue 3716 LEU Chi-restraints excluded: chain C residue 3717 ASP Chi-restraints excluded: chain C residue 3899 PHE Chi-restraints excluded: chain C residue 3926 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4782 VAL Chi-restraints excluded: chain C residue 4814 LEU Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4830 VAL Chi-restraints excluded: chain C residue 4853 VAL Chi-restraints excluded: chain C residue 4929 LEU Chi-restraints excluded: chain C residue 5018 CYS Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 774 ASP Chi-restraints excluded: chain D residue 778 PHE Chi-restraints excluded: chain D residue 1039 LEU Chi-restraints excluded: chain D residue 1123 VAL Chi-restraints excluded: chain D residue 1158 ASN Chi-restraints excluded: chain D residue 1168 VAL Chi-restraints excluded: chain D residue 1514 LEU Chi-restraints excluded: chain D residue 1599 MET Chi-restraints excluded: chain D residue 1650 ILE Chi-restraints excluded: chain D residue 1653 LEU Chi-restraints excluded: chain D residue 1673 VAL Chi-restraints excluded: chain D residue 1685 LEU Chi-restraints excluded: chain D residue 2182 ILE Chi-restraints excluded: chain D residue 2251 PHE Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 2461 VAL Chi-restraints excluded: chain D residue 2932 MET Chi-restraints excluded: chain D residue 3137 LEU Chi-restraints excluded: chain D residue 3409 TYR Chi-restraints excluded: chain D residue 3647 HIS Chi-restraints excluded: chain D residue 3717 ASP Chi-restraints excluded: chain D residue 3899 PHE Chi-restraints excluded: chain D residue 3926 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4782 VAL Chi-restraints excluded: chain D residue 4814 LEU Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4830 VAL Chi-restraints excluded: chain D residue 4853 VAL Chi-restraints excluded: chain D residue 4929 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1736 random chunks: chunk 1397 optimal weight: 20.0000 chunk 952 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 1249 optimal weight: 3.9990 chunk 692 optimal weight: 40.0000 chunk 1431 optimal weight: 20.0000 chunk 1159 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 856 optimal weight: 20.0000 chunk 1506 optimal weight: 30.0000 chunk 423 optimal weight: 0.8980 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 HIS ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1296 GLN A1560 ASN ** A1610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1775 HIS A2260 ASN ** A2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2584 HIS A3418 ASN ** A3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3851 ASN A4094 GLN ** A4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 HIS ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 HIS ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1296 GLN B1560 ASN ** B1610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1775 HIS B2204 HIS ** B2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3781 GLN B3851 ASN B4094 GLN ** B4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1296 GLN C1560 ASN C1610 ASN C1775 HIS ** C2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3851 ASN C4094 GLN ** C4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 760 ASN ** D1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1296 GLN D1560 ASN D1610 ASN D1775 HIS D2260 ASN ** D2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3851 ASN D4094 GLN ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 137180 Z= 0.369 Angle : 0.667 11.267 186348 Z= 0.334 Chirality : 0.041 0.282 20956 Planarity : 0.004 0.056 24244 Dihedral : 4.135 22.381 18656 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.86 % Favored : 90.84 % Rotamer: Outliers : 2.15 % Allowed : 13.73 % Favored : 84.12 % 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: -0.47 (0.07), residues: 17208 helix: 1.69 (0.06), residues: 8288 sheet: -1.51 (0.15), residues: 1296 loop : -2.53 (0.07), residues: 7624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B3423 HIS 0.009 0.001 HIS B3647 PHE 0.033 0.002 PHE C3010 TYR 0.018 0.002 TYR B 920 ARG 0.008 0.001 ARG B2163 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34416 Ramachandran restraints generated. 17208 Oldfield, 0 Emsley, 17208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34416 Ramachandran restraints generated. 17208 Oldfield, 0 Emsley, 17208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 996 residues out of total 15132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 694 time to evaluate : 11.109 Fit side-chains REVERT: A 334 MET cc_start: 0.6576 (mmp) cc_final: 0.6145 (tpp) REVERT: A 1601 MET cc_start: 0.8384 (mmm) cc_final: 0.7533 (mmt) REVERT: A 1648 MET cc_start: 0.8229 (tpp) cc_final: 0.8018 (tpp) REVERT: A 1713 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.7637 (t70) REVERT: A 1851 MET cc_start: 0.9005 (tpp) cc_final: 0.8735 (mmm) REVERT: A 2101 MET cc_start: 0.8710 (tmm) cc_final: 0.8433 (tmm) REVERT: A 2198 MET cc_start: 0.9491 (mpp) cc_final: 0.9168 (mpp) REVERT: A 2228 MET cc_start: 0.7803 (ppp) cc_final: 0.7362 (tmm) REVERT: A 2340 PHE cc_start: 0.6630 (p90) cc_final: 0.6053 (p90) REVERT: A 2502 MET cc_start: 0.8245 (mmm) cc_final: 0.7966 (mmm) REVERT: A 3409 TYR cc_start: 0.5396 (OUTLIER) cc_final: 0.3359 (m-80) REVERT: A 3442 PHE cc_start: 0.7767 (m-80) cc_final: 0.7558 (m-10) REVERT: A 3517 MET cc_start: 0.5020 (ppp) cc_final: 0.3575 (ppp) REVERT: A 3899 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.7329 (m-10) REVERT: A 3955 MET cc_start: 0.8093 (mtp) cc_final: 0.7702 (mtm) REVERT: A 3999 MET cc_start: 0.9200 (tpp) cc_final: 0.8970 (tpp) REVERT: A 4000 MET cc_start: 0.8040 (mpp) cc_final: 0.7788 (mpp) REVERT: A 4064 MET cc_start: 0.8210 (ppp) cc_final: 0.7651 (ppp) REVERT: A 4989 MET cc_start: 0.8105 (tmm) cc_final: 0.7792 (tmm) REVERT: B 334 MET cc_start: 0.6538 (mmp) cc_final: 0.6130 (tpp) REVERT: B 1599 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8024 (ppp) REVERT: B 1601 MET cc_start: 0.8372 (mmm) cc_final: 0.7590 (mmt) REVERT: B 1648 MET cc_start: 0.8229 (tpp) cc_final: 0.8026 (tpp) REVERT: B 1713 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.7654 (t70) REVERT: B 1851 MET cc_start: 0.9004 (tpp) cc_final: 0.8743 (mmm) REVERT: B 2101 MET cc_start: 0.8682 (tmm) cc_final: 0.8404 (tmm) REVERT: B 2198 MET cc_start: 0.9485 (mpp) cc_final: 0.9051 (mpp) REVERT: B 2228 MET cc_start: 0.7809 (ppp) cc_final: 0.7383 (tmm) REVERT: B 2250 MET cc_start: 0.8207 (tpp) cc_final: 0.7949 (tpp) REVERT: B 2340 PHE cc_start: 0.6586 (p90) cc_final: 0.6007 (p90) REVERT: B 2502 MET cc_start: 0.8263 (mmm) cc_final: 0.7996 (mmm) REVERT: B 3277 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7353 (pp) REVERT: B 3409 TYR cc_start: 0.5444 (OUTLIER) cc_final: 0.3440 (m-80) REVERT: B 3415 TYR cc_start: 0.6801 (t80) cc_final: 0.5627 (t80) REVERT: B 3517 MET cc_start: 0.5181 (ppp) cc_final: 0.3959 (ppp) REVERT: B 3652 MET cc_start: 0.8303 (mmt) cc_final: 0.8103 (mmt) REVERT: B 3758 MET cc_start: 0.7310 (tpt) cc_final: 0.6909 (tpt) REVERT: B 3899 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.7340 (m-10) REVERT: B 3955 MET cc_start: 0.8077 (mtp) cc_final: 0.7681 (mtm) REVERT: B 4064 MET cc_start: 0.8198 (ppp) cc_final: 0.7620 (ppp) REVERT: B 4989 MET cc_start: 0.8110 (tmm) cc_final: 0.7822 (tmm) REVERT: C 334 MET cc_start: 0.6526 (mmp) cc_final: 0.6123 (tpp) REVERT: C 667 MET cc_start: 0.5237 (tmm) cc_final: 0.4890 (tmm) REVERT: C 1601 MET cc_start: 0.8443 (mmm) cc_final: 0.7582 (mmt) REVERT: C 1648 MET cc_start: 0.8243 (tpp) cc_final: 0.8030 (tpp) REVERT: C 1713 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.7657 (t70) REVERT: C 1851 MET cc_start: 0.9012 (tpp) cc_final: 0.8744 (mmm) REVERT: C 2101 MET cc_start: 0.8696 (tmm) cc_final: 0.8422 (tmm) REVERT: C 2198 MET cc_start: 0.9498 (mpp) cc_final: 0.9169 (mpp) REVERT: C 2228 MET cc_start: 0.7906 (ppp) cc_final: 0.7540 (tmm) REVERT: C 2340 PHE cc_start: 0.6606 (p90) cc_final: 0.6022 (p90) REVERT: C 2502 MET cc_start: 0.8292 (mmm) cc_final: 0.8013 (mmm) REVERT: C 3409 TYR cc_start: 0.5375 (OUTLIER) cc_final: 0.3471 (m-80) REVERT: C 3415 TYR cc_start: 0.5532 (t80) cc_final: 0.4983 (t80) REVERT: C 3517 MET cc_start: 0.5051 (ppp) cc_final: 0.3881 (ppp) REVERT: C 3652 MET cc_start: 0.8335 (mmt) cc_final: 0.8131 (mmt) REVERT: C 3899 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.7336 (m-10) REVERT: C 3955 MET cc_start: 0.8087 (mtp) cc_final: 0.7694 (mtm) REVERT: C 4000 MET cc_start: 0.8085 (mpp) cc_final: 0.7843 (mpp) REVERT: C 4064 MET cc_start: 0.8221 (ppp) cc_final: 0.7654 (ppp) REVERT: C 4989 MET cc_start: 0.8106 (tmm) cc_final: 0.7784 (tmm) REVERT: D 334 MET cc_start: 0.6540 (mmp) cc_final: 0.6123 (tpp) REVERT: D 1601 MET cc_start: 0.8385 (mmm) cc_final: 0.7550 (mmt) REVERT: D 1648 MET cc_start: 0.8236 (tpp) cc_final: 0.8025 (tpp) REVERT: D 1713 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.7636 (t70) REVERT: D 2101 MET cc_start: 0.8694 (tmm) cc_final: 0.8416 (tmm) REVERT: D 2198 MET cc_start: 0.9491 (mpp) cc_final: 0.9168 (mpp) REVERT: D 2228 MET cc_start: 0.7819 (ppp) cc_final: 0.7374 (tmm) REVERT: D 2340 PHE cc_start: 0.6605 (p90) cc_final: 0.6030 (p90) REVERT: D 2502 MET cc_start: 0.8319 (mmm) cc_final: 0.8032 (mmm) REVERT: D 3277 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7367 (pp) REVERT: D 3409 TYR cc_start: 0.5452 (OUTLIER) cc_final: 0.3441 (m-80) REVERT: D 3415 TYR cc_start: 0.5505 (t80) cc_final: 0.4963 (t80) REVERT: D 3517 MET cc_start: 0.4996 (ppp) cc_final: 0.3935 (ppp) REVERT: D 3899 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.7324 (m-10) REVERT: D 3955 MET cc_start: 0.8080 (mtp) cc_final: 0.7693 (mtm) REVERT: D 3999 MET cc_start: 0.9187 (tpp) cc_final: 0.8953 (tpp) REVERT: D 4000 MET cc_start: 0.8039 (mpp) cc_final: 0.7792 (mpp) REVERT: D 4064 MET cc_start: 0.8225 (ppp) cc_final: 0.7667 (ppp) REVERT: D 4989 MET cc_start: 0.8080 (tmm) cc_final: 0.7768 (tmm) outliers start: 302 outliers final: 182 residues processed: 968 average time/residue: 1.0399 time to fit residues: 1858.6983 Evaluate side-chains 855 residues out of total 15132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 658 time to evaluate : 11.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 478 PHE Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 778 PHE Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1158 ASN Chi-restraints excluded: chain A residue 1453 VAL Chi-restraints excluded: chain A residue 1599 MET Chi-restraints excluded: chain A residue 1653 LEU Chi-restraints excluded: chain A residue 1681 VAL Chi-restraints excluded: chain A residue 1685 LEU Chi-restraints excluded: chain A residue 1688 HIS Chi-restraints excluded: chain A residue 1713 ASP Chi-restraints excluded: chain A residue 1858 ASP Chi-restraints excluded: chain A residue 1939 MET Chi-restraints excluded: chain A residue 2134 LEU Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2203 MET Chi-restraints excluded: chain A residue 2251 PHE Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2610 LEU Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 2959 PHE Chi-restraints excluded: chain A residue 3409 TYR Chi-restraints excluded: chain A residue 3666 ASP Chi-restraints excluded: chain A residue 3698 LEU Chi-restraints excluded: chain A residue 3717 ASP Chi-restraints excluded: chain A residue 3832 ILE Chi-restraints excluded: chain A residue 3899 PHE Chi-restraints excluded: chain A residue 3926 LEU Chi-restraints excluded: chain A residue 3965 LEU Chi-restraints excluded: chain A residue 4030 LEU Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4648 LEU Chi-restraints excluded: chain A residue 4657 CYS Chi-restraints excluded: chain A residue 4686 LEU Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4782 VAL Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4827 LEU Chi-restraints excluded: chain A residue 4852 THR Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4877 ASP Chi-restraints excluded: chain A residue 4880 MET Chi-restraints excluded: chain A residue 4929 LEU Chi-restraints excluded: chain A residue 5018 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 478 PHE Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 778 PHE Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1123 VAL Chi-restraints excluded: chain B residue 1158 ASN Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1599 MET Chi-restraints excluded: chain B residue 1653 LEU Chi-restraints excluded: chain B residue 1681 VAL Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 1688 HIS Chi-restraints excluded: chain B residue 1713 ASP Chi-restraints excluded: chain B residue 1858 ASP Chi-restraints excluded: chain B residue 1939 MET Chi-restraints excluded: chain B residue 2134 LEU Chi-restraints excluded: chain B residue 2138 LEU Chi-restraints excluded: chain B residue 2203 MET Chi-restraints excluded: chain B residue 2251 PHE Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 2610 LEU Chi-restraints excluded: chain B residue 2932 MET Chi-restraints excluded: chain B residue 2959 PHE Chi-restraints excluded: chain B residue 3277 LEU Chi-restraints excluded: chain B residue 3409 TYR Chi-restraints excluded: chain B residue 3666 ASP Chi-restraints excluded: chain B residue 3698 LEU Chi-restraints excluded: chain B residue 3717 ASP Chi-restraints excluded: chain B residue 3832 ILE Chi-restraints excluded: chain B residue 3899 PHE Chi-restraints excluded: chain B residue 3926 LEU Chi-restraints excluded: chain B residue 3965 LEU Chi-restraints excluded: chain B residue 4030 LEU Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4648 LEU Chi-restraints excluded: chain B residue 4686 LEU Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4782 VAL Chi-restraints excluded: chain B residue 4820 VAL Chi-restraints excluded: chain B residue 4827 LEU Chi-restraints excluded: chain B residue 4852 THR Chi-restraints excluded: chain B residue 4853 VAL Chi-restraints excluded: chain B residue 4877 ASP Chi-restraints excluded: chain B residue 4880 MET Chi-restraints excluded: chain B residue 4929 LEU Chi-restraints excluded: chain B residue 5018 CYS Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 478 PHE Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 778 PHE Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1123 VAL Chi-restraints excluded: chain C residue 1158 ASN Chi-restraints excluded: chain C residue 1453 VAL Chi-restraints excluded: chain C residue 1599 MET Chi-restraints excluded: chain C residue 1653 LEU Chi-restraints excluded: chain C residue 1681 VAL Chi-restraints excluded: chain C residue 1685 LEU Chi-restraints excluded: chain C residue 1688 HIS Chi-restraints excluded: chain C residue 1713 ASP Chi-restraints excluded: chain C residue 1858 ASP Chi-restraints excluded: chain C residue 1939 MET Chi-restraints excluded: chain C residue 2134 LEU Chi-restraints excluded: chain C residue 2138 LEU Chi-restraints excluded: chain C residue 2203 MET Chi-restraints excluded: chain C residue 2251 PHE Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 2610 LEU Chi-restraints excluded: chain C residue 2932 MET Chi-restraints excluded: chain C residue 3409 TYR Chi-restraints excluded: chain C residue 3666 ASP Chi-restraints excluded: chain C residue 3698 LEU Chi-restraints excluded: chain C residue 3717 ASP Chi-restraints excluded: chain C residue 3832 ILE Chi-restraints excluded: chain C residue 3899 PHE Chi-restraints excluded: chain C residue 3926 LEU Chi-restraints excluded: chain C residue 3965 LEU Chi-restraints excluded: chain C residue 4030 LEU Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4648 LEU Chi-restraints excluded: chain C residue 4686 LEU Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4782 VAL Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4827 LEU Chi-restraints excluded: chain C residue 4852 THR Chi-restraints excluded: chain C residue 4853 VAL Chi-restraints excluded: chain C residue 4877 ASP Chi-restraints excluded: chain C residue 4880 MET Chi-restraints excluded: chain C residue 4929 LEU Chi-restraints excluded: chain C residue 5018 CYS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 478 PHE Chi-restraints excluded: chain D residue 648 ILE Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 778 PHE Chi-restraints excluded: chain D residue 1039 LEU Chi-restraints excluded: chain D residue 1123 VAL Chi-restraints excluded: chain D residue 1158 ASN Chi-restraints excluded: chain D residue 1453 VAL Chi-restraints excluded: chain D residue 1599 MET Chi-restraints excluded: chain D residue 1653 LEU Chi-restraints excluded: chain D residue 1681 VAL Chi-restraints excluded: chain D residue 1685 LEU Chi-restraints excluded: chain D residue 1688 HIS Chi-restraints excluded: chain D residue 1713 ASP Chi-restraints excluded: chain D residue 1858 ASP Chi-restraints excluded: chain D residue 1939 MET Chi-restraints excluded: chain D residue 2134 LEU Chi-restraints excluded: chain D residue 2138 LEU Chi-restraints excluded: chain D residue 2203 MET Chi-restraints excluded: chain D residue 2251 PHE Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 2610 LEU Chi-restraints excluded: chain D residue 2932 MET Chi-restraints excluded: chain D residue 2959 PHE Chi-restraints excluded: chain D residue 3277 LEU Chi-restraints excluded: chain D residue 3409 TYR Chi-restraints excluded: chain D residue 3666 ASP Chi-restraints excluded: chain D residue 3698 LEU Chi-restraints excluded: chain D residue 3717 ASP Chi-restraints excluded: chain D residue 3832 ILE Chi-restraints excluded: chain D residue 3899 PHE Chi-restraints excluded: chain D residue 3926 LEU Chi-restraints excluded: chain D residue 3965 LEU Chi-restraints excluded: chain D residue 4030 LEU Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4648 LEU Chi-restraints excluded: chain D residue 4686 LEU Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4782 VAL Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4827 LEU Chi-restraints excluded: chain D residue 4852 THR Chi-restraints excluded: chain D residue 4853 VAL Chi-restraints excluded: chain D residue 4877 ASP Chi-restraints excluded: chain D residue 4880 MET Chi-restraints excluded: chain D residue 4929 LEU Chi-restraints excluded: chain D residue 5018 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1736 random chunks: chunk 564 optimal weight: 6.9990 chunk 1511 optimal weight: 0.7980 chunk 331 optimal weight: 2.9990 chunk 985 optimal weight: 0.5980 chunk 414 optimal weight: 0.5980 chunk 1679 optimal weight: 2.9990 chunk 1394 optimal weight: 2.9990 chunk 777 optimal weight: 10.0000 chunk 139 optimal weight: 20.0000 chunk 555 optimal weight: 4.9990 chunk 881 optimal weight: 30.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 ASN ** A1460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1610 ASN ** A2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3781 GLN A3851 ASN ** A4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4754 ASN ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 ASN ** B1460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3851 ASN ** B4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 502 HIS ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3419 ASN C3851 ASN ** C4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 HIS ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3419 ASN D3781 GLN D3851 ASN ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 137180 Z= 0.162 Angle : 0.540 10.010 186348 Z= 0.266 Chirality : 0.038 0.204 20956 Planarity : 0.003 0.048 24244 Dihedral : 3.738 23.108 18656 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.41 % Favored : 92.29 % Rotamer: Outliers : 1.49 % Allowed : 15.21 % Favored : 83.30 % 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: -0.13 (0.07), residues: 17208 helix: 2.05 (0.06), residues: 8300 sheet: -1.46 (0.15), residues: 1176 loop : -2.42 (0.07), residues: 7732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP D3285 HIS 0.006 0.001 HIS A3422 PHE 0.015 0.001 PHE B1238 TYR 0.043 0.001 TYR B3968 ARG 0.005 0.000 ARG D4892 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34416 Ramachandran restraints generated. 17208 Oldfield, 0 Emsley, 17208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34416 Ramachandran restraints generated. 17208 Oldfield, 0 Emsley, 17208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 15132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 687 time to evaluate : 11.420 Fit side-chains REVERT: A 334 MET cc_start: 0.6432 (mmp) cc_final: 0.6099 (tpp) REVERT: A 667 MET cc_start: 0.5053 (tmm) cc_final: 0.4656 (tmm) REVERT: A 1648 MET cc_start: 0.8180 (tpp) cc_final: 0.7800 (tpp) REVERT: A 1851 MET cc_start: 0.8897 (tpp) cc_final: 0.8552 (mmm) REVERT: A 2101 MET cc_start: 0.8657 (tmm) cc_final: 0.8438 (tmm) REVERT: A 2198 MET cc_start: 0.9455 (mpp) cc_final: 0.8918 (mpp) REVERT: A 2228 MET cc_start: 0.7912 (ppp) cc_final: 0.7472 (tmm) REVERT: A 2250 MET cc_start: 0.8135 (tpp) cc_final: 0.7761 (tpp) REVERT: A 2340 PHE cc_start: 0.6690 (p90) cc_final: 0.6071 (p90) REVERT: A 2502 MET cc_start: 0.8236 (mmm) cc_final: 0.7916 (mmm) REVERT: A 3409 TYR cc_start: 0.5322 (OUTLIER) cc_final: 0.3292 (m-80) REVERT: A 3517 MET cc_start: 0.5215 (ppp) cc_final: 0.3956 (ppp) REVERT: A 3652 MET cc_start: 0.8341 (mmt) cc_final: 0.7744 (mmt) REVERT: A 3793 MET cc_start: 0.8632 (mmm) cc_final: 0.8270 (tpp) REVERT: A 3899 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.7279 (m-10) REVERT: A 4000 MET cc_start: 0.7972 (mpp) cc_final: 0.7621 (mpp) REVERT: A 4064 MET cc_start: 0.8167 (ppp) cc_final: 0.7602 (ppp) REVERT: A 4849 TYR cc_start: 0.8028 (t80) cc_final: 0.7712 (t80) REVERT: A 4989 MET cc_start: 0.8035 (tmm) cc_final: 0.7729 (tmm) REVERT: B 334 MET cc_start: 0.6437 (mmp) cc_final: 0.6114 (tpp) REVERT: B 667 MET cc_start: 0.5071 (tmm) cc_final: 0.4670 (tmm) REVERT: B 1599 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8106 (ppp) REVERT: B 1648 MET cc_start: 0.8178 (tpp) cc_final: 0.7803 (tpp) REVERT: B 1851 MET cc_start: 0.8892 (tpp) cc_final: 0.8553 (mmm) REVERT: B 2198 MET cc_start: 0.9429 (mpp) cc_final: 0.8876 (mpp) REVERT: B 2228 MET cc_start: 0.7920 (ppp) cc_final: 0.7482 (tmm) REVERT: B 2340 PHE cc_start: 0.6606 (p90) cc_final: 0.5987 (p90) REVERT: B 2502 MET cc_start: 0.8247 (mmm) cc_final: 0.7929 (mmm) REVERT: B 3409 TYR cc_start: 0.5375 (OUTLIER) cc_final: 0.3389 (m-80) REVERT: B 3415 TYR cc_start: 0.6765 (OUTLIER) cc_final: 0.5470 (t80) REVERT: B 3517 MET cc_start: 0.5225 (ppp) cc_final: 0.4948 (ppp) REVERT: B 3652 MET cc_start: 0.8250 (mmt) cc_final: 0.7988 (mmt) REVERT: B 3758 MET cc_start: 0.7087 (tpt) cc_final: 0.6772 (tpt) REVERT: B 3793 MET cc_start: 0.8688 (mmm) cc_final: 0.8428 (tpp) REVERT: B 3899 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.7291 (m-10) REVERT: B 4064 MET cc_start: 0.8142 (ppp) cc_final: 0.7570 (ppp) REVERT: B 4795 TYR cc_start: 0.8600 (t80) cc_final: 0.8111 (t80) REVERT: B 4849 TYR cc_start: 0.8054 (t80) cc_final: 0.7754 (t80) REVERT: B 4880 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7560 (tmm) REVERT: B 4886 HIS cc_start: 0.8701 (OUTLIER) cc_final: 0.6994 (m170) REVERT: B 4989 MET cc_start: 0.8041 (tmm) cc_final: 0.7782 (tmm) REVERT: C 334 MET cc_start: 0.6416 (mmp) cc_final: 0.6069 (tpp) REVERT: C 600 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8275 (mp) REVERT: C 1648 MET cc_start: 0.8177 (tpp) cc_final: 0.7792 (tpp) REVERT: C 1851 MET cc_start: 0.8899 (tpp) cc_final: 0.8555 (mmm) REVERT: C 2101 MET cc_start: 0.8651 (tmm) cc_final: 0.8451 (tmm) REVERT: C 2198 MET cc_start: 0.9460 (mpp) cc_final: 0.8911 (mpp) REVERT: C 2250 MET cc_start: 0.8144 (tpp) cc_final: 0.7761 (tpp) REVERT: C 2340 PHE cc_start: 0.6650 (p90) cc_final: 0.6025 (p90) REVERT: C 2502 MET cc_start: 0.8233 (mmm) cc_final: 0.7909 (mmm) REVERT: C 3409 TYR cc_start: 0.5321 (OUTLIER) cc_final: 0.3408 (m-80) REVERT: C 3415 TYR cc_start: 0.5549 (t80) cc_final: 0.4999 (t80) REVERT: C 3517 MET cc_start: 0.5295 (ppp) cc_final: 0.5001 (ppp) REVERT: C 3652 MET cc_start: 0.8281 (mmt) cc_final: 0.8021 (mmt) REVERT: C 3793 MET cc_start: 0.8679 (mmm) cc_final: 0.8424 (tpp) REVERT: C 3899 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.7264 (m-10) REVERT: C 4000 MET cc_start: 0.8007 (mpp) cc_final: 0.7652 (mpp) REVERT: C 4064 MET cc_start: 0.8172 (ppp) cc_final: 0.7605 (ppp) REVERT: C 4849 TYR cc_start: 0.8329 (t80) cc_final: 0.8084 (t80) REVERT: C 4886 HIS cc_start: 0.8742 (OUTLIER) cc_final: 0.6954 (m170) REVERT: C 4989 MET cc_start: 0.8039 (tmm) cc_final: 0.7729 (tmm) REVERT: D 334 MET cc_start: 0.6432 (mmp) cc_final: 0.6093 (tpp) REVERT: D 667 MET cc_start: 0.5057 (tmm) cc_final: 0.4663 (tmm) REVERT: D 1648 MET cc_start: 0.8179 (tpp) cc_final: 0.7797 (tpp) REVERT: D 1851 MET cc_start: 0.8905 (tpp) cc_final: 0.8556 (mmm) REVERT: D 2101 MET cc_start: 0.8647 (tmm) cc_final: 0.8445 (tmm) REVERT: D 2198 MET cc_start: 0.9452 (mpp) cc_final: 0.8924 (mpp) REVERT: D 2228 MET cc_start: 0.7863 (ppp) cc_final: 0.7413 (tmm) REVERT: D 2250 MET cc_start: 0.8177 (tpp) cc_final: 0.7815 (tpp) REVERT: D 2340 PHE cc_start: 0.6656 (p90) cc_final: 0.6035 (p90) REVERT: D 2356 LEU cc_start: 0.8951 (mt) cc_final: 0.8720 (mp) REVERT: D 2502 MET cc_start: 0.8240 (mmm) cc_final: 0.7909 (mmm) REVERT: D 3409 TYR cc_start: 0.5356 (OUTLIER) cc_final: 0.3353 (m-80) REVERT: D 3415 TYR cc_start: 0.5520 (t80) cc_final: 0.4981 (t80) REVERT: D 3517 MET cc_start: 0.5273 (ppp) cc_final: 0.5023 (ppp) REVERT: D 3652 MET cc_start: 0.8343 (mmt) cc_final: 0.7749 (mmt) REVERT: D 3793 MET cc_start: 0.8670 (mmm) cc_final: 0.8405 (tpp) REVERT: D 3899 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.7274 (m-10) REVERT: D 4000 MET cc_start: 0.7977 (mpp) cc_final: 0.7623 (mpp) REVERT: D 4064 MET cc_start: 0.8180 (ppp) cc_final: 0.7617 (ppp) REVERT: D 4795 TYR cc_start: 0.8553 (t80) cc_final: 0.8064 (t80) REVERT: D 4849 TYR cc_start: 0.7832 (t80) cc_final: 0.7530 (t80) REVERT: D 4880 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7672 (tmm) REVERT: D 4887 MET cc_start: 0.7576 (tpt) cc_final: 0.7352 (tpt) REVERT: D 4989 MET cc_start: 0.7992 (tmm) cc_final: 0.7728 (tmm) outliers start: 209 outliers final: 121 residues processed: 877 average time/residue: 1.0487 time to fit residues: 1698.6253 Evaluate side-chains 802 residues out of total 15132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 666 time to evaluate : 13.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 778 PHE Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1158 ASN Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1453 VAL Chi-restraints excluded: chain A residue 1560 ASN Chi-restraints excluded: chain A residue 1650 ILE Chi-restraints excluded: chain A residue 1653 LEU Chi-restraints excluded: chain A residue 1681 VAL Chi-restraints excluded: chain A residue 1685 LEU Chi-restraints excluded: chain A residue 1858 ASP Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2203 MET Chi-restraints excluded: chain A residue 2461 VAL Chi-restraints excluded: chain A residue 2959 PHE Chi-restraints excluded: chain A residue 3409 TYR Chi-restraints excluded: chain A residue 3647 HIS Chi-restraints excluded: chain A residue 3717 ASP Chi-restraints excluded: chain A residue 3899 PHE Chi-restraints excluded: chain A residue 3926 LEU Chi-restraints excluded: chain A residue 4150 LEU Chi-restraints excluded: chain A residue 4154 VAL Chi-restraints excluded: chain A residue 4571 PHE Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4782 VAL Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4886 HIS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 778 PHE Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1158 ASN Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1514 LEU Chi-restraints excluded: chain B residue 1560 ASN Chi-restraints excluded: chain B residue 1599 MET Chi-restraints excluded: chain B residue 1650 ILE Chi-restraints excluded: chain B residue 1653 LEU Chi-restraints excluded: chain B residue 1681 VAL Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 1858 ASP Chi-restraints excluded: chain B residue 2138 LEU Chi-restraints excluded: chain B residue 2203 MET Chi-restraints excluded: chain B residue 2461 VAL Chi-restraints excluded: chain B residue 2932 MET Chi-restraints excluded: chain B residue 2959 PHE Chi-restraints excluded: chain B residue 3409 TYR Chi-restraints excluded: chain B residue 3415 TYR Chi-restraints excluded: chain B residue 3647 HIS Chi-restraints excluded: chain B residue 3698 LEU Chi-restraints excluded: chain B residue 3717 ASP Chi-restraints excluded: chain B residue 3899 PHE Chi-restraints excluded: chain B residue 3926 LEU Chi-restraints excluded: chain B residue 4150 LEU Chi-restraints excluded: chain B residue 4154 VAL Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4657 CYS Chi-restraints excluded: chain B residue 4853 VAL Chi-restraints excluded: chain B residue 4880 MET Chi-restraints excluded: chain B residue 4881 THR Chi-restraints excluded: chain B residue 4886 HIS Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 778 PHE Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1158 ASN Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1453 VAL Chi-restraints excluded: chain C residue 1560 ASN Chi-restraints excluded: chain C residue 1599 MET Chi-restraints excluded: chain C residue 1650 ILE Chi-restraints excluded: chain C residue 1653 LEU Chi-restraints excluded: chain C residue 1681 VAL Chi-restraints excluded: chain C residue 1685 LEU Chi-restraints excluded: chain C residue 1858 ASP Chi-restraints excluded: chain C residue 1939 MET Chi-restraints excluded: chain C residue 2138 LEU Chi-restraints excluded: chain C residue 2203 MET Chi-restraints excluded: chain C residue 2251 PHE Chi-restraints excluded: chain C residue 2461 VAL Chi-restraints excluded: chain C residue 2932 MET Chi-restraints excluded: chain C residue 2959 PHE Chi-restraints excluded: chain C residue 3409 TYR Chi-restraints excluded: chain C residue 3647 HIS Chi-restraints excluded: chain C residue 3666 ASP Chi-restraints excluded: chain C residue 3717 ASP Chi-restraints excluded: chain C residue 3899 PHE Chi-restraints excluded: chain C residue 3926 LEU Chi-restraints excluded: chain C residue 4150 LEU Chi-restraints excluded: chain C residue 4154 VAL Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4657 CYS Chi-restraints excluded: chain C residue 4782 VAL Chi-restraints excluded: chain C residue 4853 VAL Chi-restraints excluded: chain C residue 4881 THR Chi-restraints excluded: chain C residue 4886 HIS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 748 LEU Chi-restraints excluded: chain D residue 778 PHE Chi-restraints excluded: chain D residue 1039 LEU Chi-restraints excluded: chain D residue 1158 ASN Chi-restraints excluded: chain D residue 1168 VAL Chi-restraints excluded: chain D residue 1453 VAL Chi-restraints excluded: chain D residue 1560 ASN Chi-restraints excluded: chain D residue 1650 ILE Chi-restraints excluded: chain D residue 1653 LEU Chi-restraints excluded: chain D residue 1681 VAL Chi-restraints excluded: chain D residue 1685 LEU Chi-restraints excluded: chain D residue 1858 ASP Chi-restraints excluded: chain D residue 2138 LEU Chi-restraints excluded: chain D residue 2203 MET Chi-restraints excluded: chain D residue 2461 VAL Chi-restraints excluded: chain D residue 2932 MET Chi-restraints excluded: chain D residue 2959 PHE Chi-restraints excluded: chain D residue 3409 TYR Chi-restraints excluded: chain D residue 3647 HIS Chi-restraints excluded: chain D residue 3666 ASP Chi-restraints excluded: chain D residue 3698 LEU Chi-restraints excluded: chain D residue 3717 ASP Chi-restraints excluded: chain D residue 3899 PHE Chi-restraints excluded: chain D residue 3926 LEU Chi-restraints excluded: chain D residue 4150 LEU Chi-restraints excluded: chain D residue 4154 VAL Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4657 CYS Chi-restraints excluded: chain D residue 4853 VAL Chi-restraints excluded: chain D residue 4880 MET Chi-restraints excluded: chain D residue 4881 THR Chi-restraints excluded: chain D residue 4886 HIS Chi-restraints excluded: chain D residue 5020 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1736 random chunks: chunk 1619 optimal weight: 0.2980 chunk 189 optimal weight: 8.9990 chunk 956 optimal weight: 20.0000 chunk 1226 optimal weight: 20.0000 chunk 950 optimal weight: 20.0000 chunk 1413 optimal weight: 0.0020 chunk 937 optimal weight: 20.0000 chunk 1673 optimal weight: 4.9990 chunk 1047 optimal weight: 8.9990 chunk 1020 optimal weight: 9.9990 chunk 772 optimal weight: 7.9990 overall best weight: 4.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2204 HIS ** A2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3851 ASN ** A4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3851 ASN ** B4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN ** C1558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2204 HIS ** C2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3419 ASN C3851 ASN ** C4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2204 HIS ** D2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3419 ASN D3851 ASN ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 137180 Z= 0.274 Angle : 0.610 11.682 186348 Z= 0.300 Chirality : 0.039 0.160 20956 Planarity : 0.004 0.046 24244 Dihedral : 3.847 20.475 18656 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.27 % Favored : 90.45 % Rotamer: Outliers : 1.95 % Allowed : 15.19 % Favored : 82.86 % 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: -0.25 (0.07), residues: 17208 helix: 1.92 (0.06), residues: 8352 sheet: -1.66 (0.14), residues: 1372 loop : -2.45 (0.07), residues: 7484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B3285 HIS 0.014 0.001 HIS C 993 PHE 0.018 0.002 PHE C1782 TYR 0.048 0.002 TYR B1024 ARG 0.008 0.000 ARG D4892 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34416 Ramachandran restraints generated. 17208 Oldfield, 0 Emsley, 17208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34416 Ramachandran restraints generated. 17208 Oldfield, 0 Emsley, 17208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 15132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 674 time to evaluate : 11.059 Fit side-chains REVERT: A 334 MET cc_start: 0.6466 (mmp) cc_final: 0.6086 (tpp) REVERT: A 443 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9053 (tt) REVERT: A 1648 MET cc_start: 0.8231 (tpp) cc_final: 0.8001 (tpp) REVERT: A 1851 MET cc_start: 0.9050 (tpp) cc_final: 0.8795 (mmm) REVERT: A 2101 MET cc_start: 0.8709 (tmm) cc_final: 0.8456 (tmm) REVERT: A 2198 MET cc_start: 0.9500 (mpp) cc_final: 0.9075 (mpp) REVERT: A 2228 MET cc_start: 0.7960 (ppp) cc_final: 0.7541 (tmm) REVERT: A 2250 MET cc_start: 0.8197 (tpp) cc_final: 0.7830 (tpp) REVERT: A 2340 PHE cc_start: 0.6733 (p90) cc_final: 0.6026 (p90) REVERT: A 2502 MET cc_start: 0.8514 (mmm) cc_final: 0.8197 (mmm) REVERT: A 3409 TYR cc_start: 0.5407 (OUTLIER) cc_final: 0.3441 (m-80) REVERT: A 3517 MET cc_start: 0.5390 (ppp) cc_final: 0.4576 (ppp) REVERT: A 3523 ASN cc_start: 0.5688 (m110) cc_final: 0.4865 (t0) REVERT: A 3652 MET cc_start: 0.8284 (mmt) cc_final: 0.8045 (mmt) REVERT: A 3758 MET cc_start: 0.7238 (tpt) cc_final: 0.6889 (tpt) REVERT: A 3899 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.7339 (m-10) REVERT: A 4000 MET cc_start: 0.8050 (mpp) cc_final: 0.7802 (mpp) REVERT: A 4064 MET cc_start: 0.8170 (ppp) cc_final: 0.7639 (ppp) REVERT: A 4880 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7755 (tmm) REVERT: A 4989 MET cc_start: 0.8106 (tmm) cc_final: 0.7791 (tmm) REVERT: B 334 MET cc_start: 0.6468 (mmp) cc_final: 0.6096 (tpp) REVERT: B 443 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9066 (tt) REVERT: B 1648 MET cc_start: 0.8228 (tpp) cc_final: 0.8006 (tpp) REVERT: B 1851 MET cc_start: 0.9045 (tpp) cc_final: 0.8798 (mmm) REVERT: B 2198 MET cc_start: 0.9494 (mpp) cc_final: 0.9072 (mpp) REVERT: B 2228 MET cc_start: 0.7971 (ppp) cc_final: 0.7555 (tmm) REVERT: B 2340 PHE cc_start: 0.6688 (p90) cc_final: 0.5991 (p90) REVERT: B 2502 MET cc_start: 0.8520 (mmm) cc_final: 0.8206 (mmm) REVERT: B 3409 TYR cc_start: 0.5466 (OUTLIER) cc_final: 0.3514 (m-80) REVERT: B 3415 TYR cc_start: 0.6668 (OUTLIER) cc_final: 0.5488 (t80) REVERT: B 3517 MET cc_start: 0.5368 (ppp) cc_final: 0.5088 (ppp) REVERT: B 3523 ASN cc_start: 0.5651 (m110) cc_final: 0.4855 (t0) REVERT: B 3652 MET cc_start: 0.8262 (mmt) cc_final: 0.7995 (mmt) REVERT: B 3758 MET cc_start: 0.7222 (tpt) cc_final: 0.6882 (tpt) REVERT: B 3899 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.7352 (m-10) REVERT: B 3955 MET cc_start: 0.7903 (mtp) cc_final: 0.7678 (mtm) REVERT: B 4064 MET cc_start: 0.8169 (ppp) cc_final: 0.7626 (ppp) REVERT: B 4880 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7661 (tmm) REVERT: B 4989 MET cc_start: 0.8088 (tmm) cc_final: 0.7817 (tmm) REVERT: B 5020 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7617 (m-30) REVERT: C 334 MET cc_start: 0.6452 (mmp) cc_final: 0.6087 (tpp) REVERT: C 443 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9064 (tt) REVERT: C 600 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8404 (mp) REVERT: C 667 MET cc_start: 0.5144 (tmm) cc_final: 0.4800 (tmm) REVERT: C 1648 MET cc_start: 0.8241 (tpp) cc_final: 0.8006 (tpp) REVERT: C 1851 MET cc_start: 0.9055 (tpp) cc_final: 0.8803 (mmm) REVERT: C 2101 MET cc_start: 0.8720 (tmm) cc_final: 0.8487 (tmm) REVERT: C 2198 MET cc_start: 0.9500 (mpp) cc_final: 0.9061 (mpp) REVERT: C 2250 MET cc_start: 0.8195 (tpp) cc_final: 0.7827 (tpp) REVERT: C 2340 PHE cc_start: 0.6704 (p90) cc_final: 0.5997 (p90) REVERT: C 2502 MET cc_start: 0.8579 (mmm) cc_final: 0.8276 (mmm) REVERT: C 3409 TYR cc_start: 0.5497 (OUTLIER) cc_final: 0.3514 (m-80) REVERT: C 3415 TYR cc_start: 0.5398 (t80) cc_final: 0.4935 (t80) REVERT: C 3517 MET cc_start: 0.5646 (ppp) cc_final: 0.5359 (ppp) REVERT: C 3523 ASN cc_start: 0.5657 (m110) cc_final: 0.4877 (t0) REVERT: C 3652 MET cc_start: 0.8289 (mmt) cc_final: 0.8025 (mmt) REVERT: C 3758 MET cc_start: 0.7240 (tpt) cc_final: 0.6887 (tpt) REVERT: C 3899 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.7352 (m-10) REVERT: C 4000 MET cc_start: 0.8082 (mpp) cc_final: 0.7804 (mpp) REVERT: C 4064 MET cc_start: 0.8176 (ppp) cc_final: 0.7645 (ppp) REVERT: C 4880 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.7081 (tmm) REVERT: C 4989 MET cc_start: 0.8103 (tmm) cc_final: 0.7785 (tmm) REVERT: D 334 MET cc_start: 0.6465 (mmp) cc_final: 0.6083 (tpp) REVERT: D 443 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9063 (tt) REVERT: D 1648 MET cc_start: 0.8231 (tpp) cc_final: 0.8003 (tpp) REVERT: D 1851 MET cc_start: 0.9059 (tpp) cc_final: 0.8800 (mmm) REVERT: D 2101 MET cc_start: 0.8724 (tmm) cc_final: 0.8490 (tmm) REVERT: D 2198 MET cc_start: 0.9498 (mpp) cc_final: 0.9073 (mpp) REVERT: D 2228 MET cc_start: 0.7976 (ppp) cc_final: 0.7551 (tmm) REVERT: D 2250 MET cc_start: 0.8191 (tpp) cc_final: 0.7835 (tpp) REVERT: D 2340 PHE cc_start: 0.6710 (p90) cc_final: 0.6010 (p90) REVERT: D 2356 LEU cc_start: 0.8980 (mt) cc_final: 0.8750 (mp) REVERT: D 2502 MET cc_start: 0.8579 (mmm) cc_final: 0.8273 (mmm) REVERT: D 3409 TYR cc_start: 0.5476 (OUTLIER) cc_final: 0.3505 (m-80) REVERT: D 3415 TYR cc_start: 0.5479 (t80) cc_final: 0.4996 (t80) REVERT: D 3517 MET cc_start: 0.5554 (ppp) cc_final: 0.5319 (ppp) REVERT: D 3523 ASN cc_start: 0.5673 (m110) cc_final: 0.4876 (t0) REVERT: D 3652 MET cc_start: 0.8282 (mmt) cc_final: 0.8045 (mmt) REVERT: D 3758 MET cc_start: 0.7239 (tpt) cc_final: 0.6897 (tpt) REVERT: D 3899 PHE cc_start: 0.8613 (OUTLIER) cc_final: 0.7333 (m-10) REVERT: D 3955 MET cc_start: 0.7890 (mtp) cc_final: 0.7678 (mtm) REVERT: D 4000 MET cc_start: 0.8059 (mpp) cc_final: 0.7803 (mpp) REVERT: D 4064 MET cc_start: 0.8179 (ppp) cc_final: 0.7640 (ppp) REVERT: D 4849 TYR cc_start: 0.7981 (t80) cc_final: 0.7487 (t80) REVERT: D 4880 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7829 (tmm) REVERT: D 4887 MET cc_start: 0.7576 (tpt) cc_final: 0.7332 (tpt) REVERT: D 4989 MET cc_start: 0.8095 (tmm) cc_final: 0.7800 (tmm) REVERT: D 5020 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7613 (m-30) outliers start: 274 outliers final: 192 residues processed: 913 average time/residue: 1.0186 time to fit residues: 1719.9810 Evaluate side-chains 884 residues out of total 15132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 672 time to evaluate : 11.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 778 PHE Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1158 ASN Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1453 VAL Chi-restraints excluded: chain A residue 1514 LEU Chi-restraints excluded: chain A residue 1560 ASN Chi-restraints excluded: chain A residue 1575 LEU Chi-restraints excluded: chain A residue 1599 MET Chi-restraints excluded: chain A residue 1650 ILE Chi-restraints excluded: chain A residue 1653 LEU Chi-restraints excluded: chain A residue 1673 VAL Chi-restraints excluded: chain A residue 1681 VAL Chi-restraints excluded: chain A residue 1685 LEU Chi-restraints excluded: chain A residue 1715 LEU Chi-restraints excluded: chain A residue 1858 ASP Chi-restraints excluded: chain A residue 1939 MET Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2182 ILE Chi-restraints excluded: chain A residue 2203 MET Chi-restraints excluded: chain A residue 2251 PHE Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2356 LEU Chi-restraints excluded: chain A residue 2461 VAL Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 2959 PHE Chi-restraints excluded: chain A residue 3409 TYR Chi-restraints excluded: chain A residue 3647 HIS Chi-restraints excluded: chain A residue 3666 ASP Chi-restraints excluded: chain A residue 3698 LEU Chi-restraints excluded: chain A residue 3717 ASP Chi-restraints excluded: chain A residue 3899 PHE Chi-restraints excluded: chain A residue 3926 LEU Chi-restraints excluded: chain A residue 4150 LEU Chi-restraints excluded: chain A residue 4154 VAL Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4657 CYS Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4782 VAL Chi-restraints excluded: chain A residue 4814 LEU Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4830 VAL Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4877 ASP Chi-restraints excluded: chain A residue 4880 MET Chi-restraints excluded: chain A residue 4881 THR Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 4931 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 778 PHE Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1158 ASN Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1514 LEU Chi-restraints excluded: chain B residue 1560 ASN Chi-restraints excluded: chain B residue 1575 LEU Chi-restraints excluded: chain B residue 1599 MET Chi-restraints excluded: chain B residue 1650 ILE Chi-restraints excluded: chain B residue 1653 LEU Chi-restraints excluded: chain B residue 1673 VAL Chi-restraints excluded: chain B residue 1681 VAL Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 1715 LEU Chi-restraints excluded: chain B residue 1858 ASP Chi-restraints excluded: chain B residue 2138 LEU Chi-restraints excluded: chain B residue 2182 ILE Chi-restraints excluded: chain B residue 2203 MET Chi-restraints excluded: chain B residue 2251 PHE Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 2356 LEU Chi-restraints excluded: chain B residue 2461 VAL Chi-restraints excluded: chain B residue 2932 MET Chi-restraints excluded: chain B residue 2959 PHE Chi-restraints excluded: chain B residue 3409 TYR Chi-restraints excluded: chain B residue 3415 TYR Chi-restraints excluded: chain B residue 3647 HIS Chi-restraints excluded: chain B residue 3666 ASP Chi-restraints excluded: chain B residue 3698 LEU Chi-restraints excluded: chain B residue 3717 ASP Chi-restraints excluded: chain B residue 3899 PHE Chi-restraints excluded: chain B residue 3926 LEU Chi-restraints excluded: chain B residue 4150 LEU Chi-restraints excluded: chain B residue 4154 VAL Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4657 CYS Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4782 VAL Chi-restraints excluded: chain B residue 4814 LEU Chi-restraints excluded: chain B residue 4820 VAL Chi-restraints excluded: chain B residue 4830 VAL Chi-restraints excluded: chain B residue 4853 VAL Chi-restraints excluded: chain B residue 4877 ASP Chi-restraints excluded: chain B residue 4880 MET Chi-restraints excluded: chain B residue 4881 THR Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4931 ILE Chi-restraints excluded: chain B residue 5020 ASP Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 778 PHE Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1158 ASN Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1453 VAL Chi-restraints excluded: chain C residue 1560 ASN Chi-restraints excluded: chain C residue 1575 LEU Chi-restraints excluded: chain C residue 1650 ILE Chi-restraints excluded: chain C residue 1653 LEU Chi-restraints excluded: chain C residue 1673 VAL Chi-restraints excluded: chain C residue 1681 VAL Chi-restraints excluded: chain C residue 1685 LEU Chi-restraints excluded: chain C residue 1715 LEU Chi-restraints excluded: chain C residue 1858 ASP Chi-restraints excluded: chain C residue 1939 MET Chi-restraints excluded: chain C residue 2138 LEU Chi-restraints excluded: chain C residue 2203 MET Chi-restraints excluded: chain C residue 2251 PHE Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 2461 VAL Chi-restraints excluded: chain C residue 2932 MET Chi-restraints excluded: chain C residue 3409 TYR Chi-restraints excluded: chain C residue 3647 HIS Chi-restraints excluded: chain C residue 3666 ASP Chi-restraints excluded: chain C residue 3698 LEU Chi-restraints excluded: chain C residue 3717 ASP Chi-restraints excluded: chain C residue 3899 PHE Chi-restraints excluded: chain C residue 3926 LEU Chi-restraints excluded: chain C residue 3965 LEU Chi-restraints excluded: chain C residue 4150 LEU Chi-restraints excluded: chain C residue 4154 VAL Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4657 CYS Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4782 VAL Chi-restraints excluded: chain C residue 4814 LEU Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4830 VAL Chi-restraints excluded: chain C residue 4853 VAL Chi-restraints excluded: chain C residue 4877 ASP Chi-restraints excluded: chain C residue 4880 MET Chi-restraints excluded: chain C residue 4881 THR Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 4931 ILE Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 778 PHE Chi-restraints excluded: chain D residue 1039 LEU Chi-restraints excluded: chain D residue 1158 ASN Chi-restraints excluded: chain D residue 1168 VAL Chi-restraints excluded: chain D residue 1453 VAL Chi-restraints excluded: chain D residue 1514 LEU Chi-restraints excluded: chain D residue 1560 ASN Chi-restraints excluded: chain D residue 1575 LEU Chi-restraints excluded: chain D residue 1599 MET Chi-restraints excluded: chain D residue 1650 ILE Chi-restraints excluded: chain D residue 1653 LEU Chi-restraints excluded: chain D residue 1673 VAL Chi-restraints excluded: chain D residue 1681 VAL Chi-restraints excluded: chain D residue 1685 LEU Chi-restraints excluded: chain D residue 1715 LEU Chi-restraints excluded: chain D residue 1858 ASP Chi-restraints excluded: chain D residue 1939 MET Chi-restraints excluded: chain D residue 2138 LEU Chi-restraints excluded: chain D residue 2182 ILE Chi-restraints excluded: chain D residue 2203 MET Chi-restraints excluded: chain D residue 2251 PHE Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 2461 VAL Chi-restraints excluded: chain D residue 2932 MET Chi-restraints excluded: chain D residue 2959 PHE Chi-restraints excluded: chain D residue 3409 TYR Chi-restraints excluded: chain D residue 3647 HIS Chi-restraints excluded: chain D residue 3666 ASP Chi-restraints excluded: chain D residue 3698 LEU Chi-restraints excluded: chain D residue 3717 ASP Chi-restraints excluded: chain D residue 3899 PHE Chi-restraints excluded: chain D residue 3926 LEU Chi-restraints excluded: chain D residue 4016 LEU Chi-restraints excluded: chain D residue 4150 LEU Chi-restraints excluded: chain D residue 4154 VAL Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4657 CYS Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4782 VAL Chi-restraints excluded: chain D residue 4814 LEU Chi-restraints excluded: chain D residue 4830 VAL Chi-restraints excluded: chain D residue 4853 VAL Chi-restraints excluded: chain D residue 4877 ASP Chi-restraints excluded: chain D residue 4880 MET Chi-restraints excluded: chain D residue 4881 THR Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4931 ILE Chi-restraints excluded: chain D residue 5020 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1736 random chunks: chunk 1035 optimal weight: 4.9990 chunk 668 optimal weight: 9.9990 chunk 999 optimal weight: 5.9990 chunk 504 optimal weight: 8.9990 chunk 328 optimal weight: 5.9990 chunk 324 optimal weight: 10.0000 chunk 1063 optimal weight: 0.3980 chunk 1139 optimal weight: 7.9990 chunk 827 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 1315 optimal weight: 9.9990 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3851 ASN ** A4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1610 ASN ** B1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3851 ASN ** B4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4754 ASN ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3851 ASN ** C4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4754 ASN ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3851 ASN ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4754 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 137180 Z= 0.188 Angle : 0.560 11.275 186348 Z= 0.272 Chirality : 0.038 0.146 20956 Planarity : 0.003 0.045 24244 Dihedral : 3.734 23.972 18656 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.67 % Favored : 92.05 % Rotamer: Outliers : 1.90 % Allowed : 15.54 % Favored : 82.56 % 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: 17208 helix: 2.03 (0.06), residues: 8348 sheet: -1.75 (0.14), residues: 1292 loop : -2.42 (0.07), residues: 7568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 882 HIS 0.008 0.001 HIS A2621 PHE 0.018 0.001 PHE C 649 TYR 0.033 0.001 TYR B3968 ARG 0.006 0.000 ARG D4892 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34416 Ramachandran restraints generated. 17208 Oldfield, 0 Emsley, 17208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34416 Ramachandran restraints generated. 17208 Oldfield, 0 Emsley, 17208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 949 residues out of total 15132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 683 time to evaluate : 11.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 MET cc_start: 0.6411 (mmp) cc_final: 0.6187 (tpp) REVERT: A 443 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9017 (tt) REVERT: A 667 MET cc_start: 0.5036 (tmm) cc_final: 0.4701 (tmm) REVERT: A 1648 MET cc_start: 0.8207 (tpp) cc_final: 0.7937 (tpp) REVERT: A 1713 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7505 (t70) REVERT: A 1851 MET cc_start: 0.8975 (tpp) cc_final: 0.8681 (mmm) REVERT: A 2101 MET cc_start: 0.8670 (tmm) cc_final: 0.8441 (tmm) REVERT: A 2198 MET cc_start: 0.9477 (mpp) cc_final: 0.9044 (mpp) REVERT: A 2228 MET cc_start: 0.7866 (ppp) cc_final: 0.7467 (tmm) REVERT: A 2250 MET cc_start: 0.8130 (tpp) cc_final: 0.7874 (tpp) REVERT: A 2340 PHE cc_start: 0.6735 (p90) cc_final: 0.5977 (p90) REVERT: A 2502 MET cc_start: 0.8536 (mmm) cc_final: 0.8223 (mmm) REVERT: A 3409 TYR cc_start: 0.5424 (OUTLIER) cc_final: 0.3446 (m-80) REVERT: A 3517 MET cc_start: 0.5499 (ppp) cc_final: 0.5113 (ppp) REVERT: A 3523 ASN cc_start: 0.5571 (m110) cc_final: 0.4741 (t0) REVERT: A 3604 TYR cc_start: 0.7042 (t80) cc_final: 0.6798 (t80) REVERT: A 3652 MET cc_start: 0.8333 (mmt) cc_final: 0.8104 (mmt) REVERT: A 3758 MET cc_start: 0.7134 (tpt) cc_final: 0.6806 (tpt) REVERT: A 3899 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.7297 (m-10) REVERT: A 4001 MET cc_start: 0.8048 (mmp) cc_final: 0.7691 (tpp) REVERT: A 4064 MET cc_start: 0.8130 (ppp) cc_final: 0.7557 (ppp) REVERT: A 4184 MET cc_start: 0.8888 (tpp) cc_final: 0.8684 (tpp) REVERT: A 4849 TYR cc_start: 0.8162 (t80) cc_final: 0.7587 (t80) REVERT: A 4880 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7609 (tmm) REVERT: A 4989 MET cc_start: 0.8053 (tmm) cc_final: 0.7760 (tmm) REVERT: B 334 MET cc_start: 0.6426 (mmp) cc_final: 0.6207 (tpp) REVERT: B 443 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9014 (tt) REVERT: B 667 MET cc_start: 0.5114 (tmm) cc_final: 0.4773 (tmm) REVERT: B 979 PRO cc_start: 0.7993 (Cg_exo) cc_final: 0.7788 (Cg_endo) REVERT: B 1648 MET cc_start: 0.8202 (tpp) cc_final: 0.7937 (tpp) REVERT: B 1713 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7527 (t70) REVERT: B 1851 MET cc_start: 0.8963 (tpp) cc_final: 0.8691 (mmm) REVERT: B 2128 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.7907 (m-10) REVERT: B 2198 MET cc_start: 0.9482 (mpp) cc_final: 0.9049 (mpp) REVERT: B 2228 MET cc_start: 0.7868 (ppp) cc_final: 0.7471 (tmm) REVERT: B 2340 PHE cc_start: 0.6686 (p90) cc_final: 0.5929 (p90) REVERT: B 2502 MET cc_start: 0.8543 (mmm) cc_final: 0.8229 (mmm) REVERT: B 3409 TYR cc_start: 0.5482 (OUTLIER) cc_final: 0.3492 (m-80) REVERT: B 3415 TYR cc_start: 0.6684 (OUTLIER) cc_final: 0.5556 (t80) REVERT: B 3523 ASN cc_start: 0.5676 (m110) cc_final: 0.4808 (t0) REVERT: B 3604 TYR cc_start: 0.7096 (t80) cc_final: 0.6860 (t80) REVERT: B 3652 MET cc_start: 0.8288 (mmt) cc_final: 0.7981 (mmt) REVERT: B 3758 MET cc_start: 0.7117 (tpt) cc_final: 0.6798 (tpt) REVERT: B 3899 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.7291 (m-10) REVERT: B 4064 MET cc_start: 0.8118 (ppp) cc_final: 0.7524 (ppp) REVERT: B 4849 TYR cc_start: 0.8188 (t80) cc_final: 0.7562 (t80) REVERT: B 4880 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7514 (tmm) REVERT: B 4989 MET cc_start: 0.8028 (tmm) cc_final: 0.7793 (tmm) REVERT: C 334 MET cc_start: 0.6402 (mmp) cc_final: 0.6151 (tpp) REVERT: C 600 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8292 (mp) REVERT: C 667 MET cc_start: 0.5096 (tmm) cc_final: 0.4731 (tmm) REVERT: C 979 PRO cc_start: 0.7938 (Cg_exo) cc_final: 0.7735 (Cg_endo) REVERT: C 1648 MET cc_start: 0.8191 (tpp) cc_final: 0.7908 (tpp) REVERT: C 1713 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7530 (t70) REVERT: C 1851 MET cc_start: 0.8976 (tpp) cc_final: 0.8686 (mmm) REVERT: C 2198 MET cc_start: 0.9474 (mpp) cc_final: 0.9032 (mpp) REVERT: C 2250 MET cc_start: 0.8095 (tpp) cc_final: 0.7868 (tpp) REVERT: C 2340 PHE cc_start: 0.6716 (p90) cc_final: 0.5961 (p90) REVERT: C 2502 MET cc_start: 0.8585 (mmm) cc_final: 0.8283 (mmm) REVERT: C 3409 TYR cc_start: 0.5509 (OUTLIER) cc_final: 0.3503 (m-80) REVERT: C 3415 TYR cc_start: 0.5461 (t80) cc_final: 0.5002 (t80) REVERT: C 3523 ASN cc_start: 0.5557 (m110) cc_final: 0.4722 (t0) REVERT: C 3652 MET cc_start: 0.8319 (mmt) cc_final: 0.8011 (mmt) REVERT: C 3758 MET cc_start: 0.7131 (tpt) cc_final: 0.6803 (tpt) REVERT: C 3899 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.7308 (m-10) REVERT: C 4064 MET cc_start: 0.8133 (ppp) cc_final: 0.7558 (ppp) REVERT: C 4184 MET cc_start: 0.8890 (tpp) cc_final: 0.8686 (tpp) REVERT: C 4849 TYR cc_start: 0.8443 (t80) cc_final: 0.7928 (t80) REVERT: C 4880 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.6958 (tmm) REVERT: C 4989 MET cc_start: 0.8053 (tmm) cc_final: 0.7750 (tmm) REVERT: D 334 MET cc_start: 0.6413 (mmp) cc_final: 0.6183 (tpp) REVERT: D 443 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9025 (tt) REVERT: D 667 MET cc_start: 0.5050 (tmm) cc_final: 0.4716 (tmm) REVERT: D 1648 MET cc_start: 0.8210 (tpp) cc_final: 0.7940 (tpp) REVERT: D 1713 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7520 (t70) REVERT: D 1851 MET cc_start: 0.8984 (tpp) cc_final: 0.8688 (mmm) REVERT: D 2101 MET cc_start: 0.8650 (tmm) cc_final: 0.8435 (tmm) REVERT: D 2198 MET cc_start: 0.9475 (mpp) cc_final: 0.9046 (mpp) REVERT: D 2228 MET cc_start: 0.7884 (ppp) cc_final: 0.7476 (tmm) REVERT: D 2250 MET cc_start: 0.8095 (tpp) cc_final: 0.7866 (tpp) REVERT: D 2340 PHE cc_start: 0.6711 (p90) cc_final: 0.5950 (p90) REVERT: D 2356 LEU cc_start: 0.8951 (mt) cc_final: 0.8710 (mp) REVERT: D 2502 MET cc_start: 0.8597 (mmm) cc_final: 0.8289 (mmm) REVERT: D 3409 TYR cc_start: 0.5488 (OUTLIER) cc_final: 0.3496 (m-80) REVERT: D 3415 TYR cc_start: 0.5494 (t80) cc_final: 0.5049 (t80) REVERT: D 3517 MET cc_start: 0.5598 (ppp) cc_final: 0.5370 (ppp) REVERT: D 3523 ASN cc_start: 0.5657 (m110) cc_final: 0.4766 (t0) REVERT: D 3652 MET cc_start: 0.8333 (mmt) cc_final: 0.8105 (mmt) REVERT: D 3758 MET cc_start: 0.7133 (tpt) cc_final: 0.6811 (tpt) REVERT: D 3899 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.7293 (m-10) REVERT: D 4001 MET cc_start: 0.8034 (mmp) cc_final: 0.7666 (tpp) REVERT: D 4064 MET cc_start: 0.8141 (ppp) cc_final: 0.7571 (ppp) REVERT: D 4184 MET cc_start: 0.8882 (tpp) cc_final: 0.8681 (tpp) REVERT: D 4849 TYR cc_start: 0.7867 (t80) cc_final: 0.7657 (t80) REVERT: D 4880 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7697 (tmm) REVERT: D 4887 MET cc_start: 0.7490 (tpt) cc_final: 0.7283 (tpt) REVERT: D 4989 MET cc_start: 0.8066 (tmm) cc_final: 0.7784 (tmm) REVERT: E 29 MET cc_start: 0.7657 (tpt) cc_final: 0.7449 (tpt) REVERT: F 29 MET cc_start: 0.7659 (tpt) cc_final: 0.7454 (tpt) REVERT: H 29 MET cc_start: 0.7661 (tpt) cc_final: 0.7455 (tpt) outliers start: 266 outliers final: 206 residues processed: 914 average time/residue: 0.9897 time to fit residues: 1669.7729 Evaluate side-chains 895 residues out of total 15132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 667 time to evaluate : 11.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 778 PHE Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1158 ASN Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1453 VAL Chi-restraints excluded: chain A residue 1514 LEU Chi-restraints excluded: chain A residue 1560 ASN Chi-restraints excluded: chain A residue 1650 ILE Chi-restraints excluded: chain A residue 1653 LEU Chi-restraints excluded: chain A residue 1673 VAL Chi-restraints excluded: chain A residue 1681 VAL Chi-restraints excluded: chain A residue 1685 LEU Chi-restraints excluded: chain A residue 1713 ASP Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 1858 ASP Chi-restraints excluded: chain A residue 1939 MET Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2182 ILE Chi-restraints excluded: chain A residue 2203 MET Chi-restraints excluded: chain A residue 2251 PHE Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2356 LEU Chi-restraints excluded: chain A residue 2461 VAL Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 2959 PHE Chi-restraints excluded: chain A residue 3269 VAL Chi-restraints excluded: chain A residue 3409 TYR Chi-restraints excluded: chain A residue 3647 HIS Chi-restraints excluded: chain A residue 3666 ASP Chi-restraints excluded: chain A residue 3698 LEU Chi-restraints excluded: chain A residue 3717 ASP Chi-restraints excluded: chain A residue 3899 PHE Chi-restraints excluded: chain A residue 3926 LEU Chi-restraints excluded: chain A residue 3965 LEU Chi-restraints excluded: chain A residue 4150 LEU Chi-restraints excluded: chain A residue 4154 VAL Chi-restraints excluded: chain A residue 4571 PHE Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4648 LEU Chi-restraints excluded: chain A residue 4657 CYS Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4782 VAL Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4827 LEU Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4877 ASP Chi-restraints excluded: chain A residue 4880 MET Chi-restraints excluded: chain A residue 4881 THR Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 5018 CYS Chi-restraints excluded: chain A residue 5020 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 778 PHE Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1123 VAL Chi-restraints excluded: chain B residue 1158 ASN Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1514 LEU Chi-restraints excluded: chain B residue 1560 ASN Chi-restraints excluded: chain B residue 1650 ILE Chi-restraints excluded: chain B residue 1653 LEU Chi-restraints excluded: chain B residue 1673 VAL Chi-restraints excluded: chain B residue 1681 VAL Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 1713 ASP Chi-restraints excluded: chain B residue 1841 VAL Chi-restraints excluded: chain B residue 1858 ASP Chi-restraints excluded: chain B residue 2128 TYR Chi-restraints excluded: chain B residue 2138 LEU Chi-restraints excluded: chain B residue 2182 ILE Chi-restraints excluded: chain B residue 2203 MET Chi-restraints excluded: chain B residue 2211 MET Chi-restraints excluded: chain B residue 2251 PHE Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 2356 LEU Chi-restraints excluded: chain B residue 2461 VAL Chi-restraints excluded: chain B residue 2932 MET Chi-restraints excluded: chain B residue 2959 PHE Chi-restraints excluded: chain B residue 3409 TYR Chi-restraints excluded: chain B residue 3415 TYR Chi-restraints excluded: chain B residue 3666 ASP Chi-restraints excluded: chain B residue 3698 LEU Chi-restraints excluded: chain B residue 3717 ASP Chi-restraints excluded: chain B residue 3721 LEU Chi-restraints excluded: chain B residue 3899 PHE Chi-restraints excluded: chain B residue 3926 LEU Chi-restraints excluded: chain B residue 3965 LEU Chi-restraints excluded: chain B residue 4150 LEU Chi-restraints excluded: chain B residue 4154 VAL Chi-restraints excluded: chain B residue 4571 PHE Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4648 LEU Chi-restraints excluded: chain B residue 4657 CYS Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4782 VAL Chi-restraints excluded: chain B residue 4820 VAL Chi-restraints excluded: chain B residue 4827 LEU Chi-restraints excluded: chain B residue 4853 VAL Chi-restraints excluded: chain B residue 4877 ASP Chi-restraints excluded: chain B residue 4880 MET Chi-restraints excluded: chain B residue 4881 THR Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4993 MET Chi-restraints excluded: chain B residue 5020 ASP Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 778 PHE Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1158 ASN Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1453 VAL Chi-restraints excluded: chain C residue 1560 ASN Chi-restraints excluded: chain C residue 1650 ILE Chi-restraints excluded: chain C residue 1653 LEU Chi-restraints excluded: chain C residue 1673 VAL Chi-restraints excluded: chain C residue 1681 VAL Chi-restraints excluded: chain C residue 1685 LEU Chi-restraints excluded: chain C residue 1713 ASP Chi-restraints excluded: chain C residue 1841 VAL Chi-restraints excluded: chain C residue 1858 ASP Chi-restraints excluded: chain C residue 1939 MET Chi-restraints excluded: chain C residue 2138 LEU Chi-restraints excluded: chain C residue 2203 MET Chi-restraints excluded: chain C residue 2251 PHE Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 2461 VAL Chi-restraints excluded: chain C residue 2932 MET Chi-restraints excluded: chain C residue 3409 TYR Chi-restraints excluded: chain C residue 3666 ASP Chi-restraints excluded: chain C residue 3698 LEU Chi-restraints excluded: chain C residue 3717 ASP Chi-restraints excluded: chain C residue 3899 PHE Chi-restraints excluded: chain C residue 3926 LEU Chi-restraints excluded: chain C residue 4150 LEU Chi-restraints excluded: chain C residue 4154 VAL Chi-restraints excluded: chain C residue 4571 PHE Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4648 LEU Chi-restraints excluded: chain C residue 4657 CYS Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4782 VAL Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4827 LEU Chi-restraints excluded: chain C residue 4853 VAL Chi-restraints excluded: chain C residue 4877 ASP Chi-restraints excluded: chain C residue 4880 MET Chi-restraints excluded: chain C residue 4881 THR Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 5018 CYS Chi-restraints excluded: chain C residue 5020 ASP Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 575 LEU Chi-restraints excluded: chain D residue 778 PHE Chi-restraints excluded: chain D residue 1039 LEU Chi-restraints excluded: chain D residue 1123 VAL Chi-restraints excluded: chain D residue 1158 ASN Chi-restraints excluded: chain D residue 1168 VAL Chi-restraints excluded: chain D residue 1453 VAL Chi-restraints excluded: chain D residue 1514 LEU Chi-restraints excluded: chain D residue 1560 ASN Chi-restraints excluded: chain D residue 1650 ILE Chi-restraints excluded: chain D residue 1653 LEU Chi-restraints excluded: chain D residue 1673 VAL Chi-restraints excluded: chain D residue 1681 VAL Chi-restraints excluded: chain D residue 1685 LEU Chi-restraints excluded: chain D residue 1713 ASP Chi-restraints excluded: chain D residue 1841 VAL Chi-restraints excluded: chain D residue 1858 ASP Chi-restraints excluded: chain D residue 1939 MET Chi-restraints excluded: chain D residue 2138 LEU Chi-restraints excluded: chain D residue 2182 ILE Chi-restraints excluded: chain D residue 2203 MET Chi-restraints excluded: chain D residue 2251 PHE Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 2461 VAL Chi-restraints excluded: chain D residue 2932 MET Chi-restraints excluded: chain D residue 2959 PHE Chi-restraints excluded: chain D residue 3269 VAL Chi-restraints excluded: chain D residue 3409 TYR Chi-restraints excluded: chain D residue 3666 ASP Chi-restraints excluded: chain D residue 3698 LEU Chi-restraints excluded: chain D residue 3717 ASP Chi-restraints excluded: chain D residue 3899 PHE Chi-restraints excluded: chain D residue 3926 LEU Chi-restraints excluded: chain D residue 3965 LEU Chi-restraints excluded: chain D residue 4016 LEU Chi-restraints excluded: chain D residue 4150 LEU Chi-restraints excluded: chain D residue 4154 VAL Chi-restraints excluded: chain D residue 4571 PHE Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4648 LEU Chi-restraints excluded: chain D residue 4657 CYS Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4782 VAL Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4827 LEU Chi-restraints excluded: chain D residue 4853 VAL Chi-restraints excluded: chain D residue 4877 ASP Chi-restraints excluded: chain D residue 4880 MET Chi-restraints excluded: chain D residue 4881 THR Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4993 MET Chi-restraints excluded: chain D residue 5020 ASP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 96 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1736 random chunks: chunk 1522 optimal weight: 3.9990 chunk 1602 optimal weight: 0.8980 chunk 1462 optimal weight: 5.9990 chunk 1559 optimal weight: 30.0000 chunk 938 optimal weight: 5.9990 chunk 679 optimal weight: 4.9990 chunk 1224 optimal weight: 0.8980 chunk 478 optimal weight: 6.9990 chunk 1408 optimal weight: 10.0000 chunk 1474 optimal weight: 0.6980 chunk 1553 optimal weight: 40.0000 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3851 ASN ** A4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3851 ASN ** B4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3851 ASN ** C4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3851 ASN ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 137180 Z= 0.177 Angle : 0.560 12.391 186348 Z= 0.270 Chirality : 0.038 0.146 20956 Planarity : 0.003 0.043 24244 Dihedral : 3.654 22.254 18656 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.23 % Favored : 91.49 % Rotamer: Outliers : 1.87 % Allowed : 15.90 % Favored : 82.24 % 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: -0.10 (0.07), residues: 17208 helix: 2.08 (0.06), residues: 8352 sheet: -1.66 (0.14), residues: 1300 loop : -2.41 (0.07), residues: 7556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 882 HIS 0.008 0.001 HIS A2621 PHE 0.016 0.001 PHE D 649 TYR 0.038 0.001 TYR D3968 ARG 0.005 0.000 ARG D4892 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34416 Ramachandran restraints generated. 17208 Oldfield, 0 Emsley, 17208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34416 Ramachandran restraints generated. 17208 Oldfield, 0 Emsley, 17208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 938 residues out of total 15132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 676 time to evaluate : 11.134 Fit side-chains revert: symmetry clash REVERT: A 667 MET cc_start: 0.5063 (tmm) cc_final: 0.4721 (tmm) REVERT: A 1648 MET cc_start: 0.8155 (tpp) cc_final: 0.7860 (tpp) REVERT: A 1713 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7507 (t70) REVERT: A 1851 MET cc_start: 0.8966 (tpp) cc_final: 0.8670 (mmm) REVERT: A 2101 MET cc_start: 0.8646 (tmm) cc_final: 0.8419 (tmm) REVERT: A 2128 TYR cc_start: 0.8692 (OUTLIER) cc_final: 0.7876 (m-10) REVERT: A 2198 MET cc_start: 0.9447 (mpp) cc_final: 0.9068 (mpp) REVERT: A 2228 MET cc_start: 0.7912 (ppp) cc_final: 0.7560 (tmm) REVERT: A 2250 MET cc_start: 0.8094 (tpp) cc_final: 0.7879 (tpp) REVERT: A 2340 PHE cc_start: 0.6720 (p90) cc_final: 0.5955 (p90) REVERT: A 2502 MET cc_start: 0.8590 (mmm) cc_final: 0.8315 (mmm) REVERT: A 3409 TYR cc_start: 0.5476 (OUTLIER) cc_final: 0.3448 (m-80) REVERT: A 3517 MET cc_start: 0.5714 (ppp) cc_final: 0.5481 (ppp) REVERT: A 3523 ASN cc_start: 0.5620 (m110) cc_final: 0.4728 (t0) REVERT: A 3604 TYR cc_start: 0.7035 (t80) cc_final: 0.6806 (t80) REVERT: A 3652 MET cc_start: 0.8353 (mmt) cc_final: 0.8090 (mmt) REVERT: A 3758 MET cc_start: 0.7107 (tpt) cc_final: 0.6787 (tpt) REVERT: A 3899 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.7246 (m-10) REVERT: A 4001 MET cc_start: 0.8021 (mmp) cc_final: 0.7686 (tpp) REVERT: A 4064 MET cc_start: 0.8137 (ppp) cc_final: 0.7608 (ppp) REVERT: A 4849 TYR cc_start: 0.8140 (t80) cc_final: 0.7551 (t80) REVERT: A 4880 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7619 (tmm) REVERT: A 4989 MET cc_start: 0.8046 (tmm) cc_final: 0.7761 (tmm) REVERT: B 443 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.9014 (tt) REVERT: B 667 MET cc_start: 0.5069 (tmm) cc_final: 0.4729 (tmm) REVERT: B 1648 MET cc_start: 0.8150 (tpp) cc_final: 0.7860 (tpp) REVERT: B 1713 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7527 (t70) REVERT: B 1851 MET cc_start: 0.8961 (tpp) cc_final: 0.8676 (mmm) REVERT: B 2128 TYR cc_start: 0.8676 (OUTLIER) cc_final: 0.7862 (m-10) REVERT: B 2198 MET cc_start: 0.9452 (mpp) cc_final: 0.9075 (mpp) REVERT: B 2228 MET cc_start: 0.7907 (ppp) cc_final: 0.7558 (tmm) REVERT: B 2340 PHE cc_start: 0.6667 (p90) cc_final: 0.5911 (p90) REVERT: B 2502 MET cc_start: 0.8625 (mmm) cc_final: 0.8357 (mmm) REVERT: B 3409 TYR cc_start: 0.5514 (OUTLIER) cc_final: 0.3504 (m-80) REVERT: B 3415 TYR cc_start: 0.6681 (OUTLIER) cc_final: 0.5574 (t80) REVERT: B 3523 ASN cc_start: 0.5632 (m110) cc_final: 0.4729 (t0) REVERT: B 3604 TYR cc_start: 0.7075 (t80) cc_final: 0.6847 (t80) REVERT: B 3652 MET cc_start: 0.8272 (mmt) cc_final: 0.7923 (mmt) REVERT: B 3758 MET cc_start: 0.7091 (tpt) cc_final: 0.6780 (tpt) REVERT: B 3899 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.7254 (m-10) REVERT: B 4064 MET cc_start: 0.8138 (ppp) cc_final: 0.7603 (ppp) REVERT: B 4849 TYR cc_start: 0.8134 (t80) cc_final: 0.7558 (t80) REVERT: B 4880 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7605 (tmm) REVERT: B 4989 MET cc_start: 0.8050 (tmm) cc_final: 0.7821 (tmm) REVERT: C 600 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8249 (mp) REVERT: C 1648 MET cc_start: 0.8150 (tpp) cc_final: 0.7852 (tpp) REVERT: C 1713 ASP cc_start: 0.8186 (OUTLIER) cc_final: 0.7533 (t70) REVERT: C 1851 MET cc_start: 0.8976 (tpp) cc_final: 0.8674 (mmm) REVERT: C 2198 MET cc_start: 0.9446 (mpp) cc_final: 0.9054 (mpp) REVERT: C 2250 MET cc_start: 0.8088 (tpp) cc_final: 0.7887 (tpp) REVERT: C 2340 PHE cc_start: 0.6701 (p90) cc_final: 0.5933 (p90) REVERT: C 2502 MET cc_start: 0.8623 (mmm) cc_final: 0.8373 (mmm) REVERT: C 3409 TYR cc_start: 0.5546 (OUTLIER) cc_final: 0.3510 (m-80) REVERT: C 3415 TYR cc_start: 0.5502 (t80) cc_final: 0.5060 (t80) REVERT: C 3523 ASN cc_start: 0.5595 (m110) cc_final: 0.4727 (t0) REVERT: C 3604 TYR cc_start: 0.7041 (t80) cc_final: 0.6838 (t80) REVERT: C 3652 MET cc_start: 0.8295 (mmt) cc_final: 0.7971 (mmt) REVERT: C 3758 MET cc_start: 0.7104 (tpt) cc_final: 0.6790 (tpt) REVERT: C 3899 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.7256 (m-10) REVERT: C 4000 MET cc_start: 0.8001 (mpp) cc_final: 0.7670 (mtm) REVERT: C 4001 MET cc_start: 0.8040 (mmp) cc_final: 0.7717 (tpp) REVERT: C 4064 MET cc_start: 0.8141 (ppp) cc_final: 0.7611 (ppp) REVERT: C 4849 TYR cc_start: 0.8445 (t80) cc_final: 0.8167 (t80) REVERT: C 4880 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.6984 (tmm) REVERT: C 4989 MET cc_start: 0.8041 (tmm) cc_final: 0.7751 (tmm) REVERT: D 667 MET cc_start: 0.5078 (tmm) cc_final: 0.4740 (tmm) REVERT: D 1648 MET cc_start: 0.8156 (tpp) cc_final: 0.7861 (tpp) REVERT: D 1713 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7525 (t70) REVERT: D 1851 MET cc_start: 0.8973 (tpp) cc_final: 0.8675 (mmm) REVERT: D 2128 TYR cc_start: 0.8674 (OUTLIER) cc_final: 0.7836 (m-10) REVERT: D 2198 MET cc_start: 0.9446 (mpp) cc_final: 0.9069 (mpp) REVERT: D 2228 MET cc_start: 0.7955 (ppp) cc_final: 0.7607 (tmm) REVERT: D 2340 PHE cc_start: 0.6693 (p90) cc_final: 0.5926 (p90) REVERT: D 2356 LEU cc_start: 0.8948 (mt) cc_final: 0.8678 (mp) REVERT: D 2502 MET cc_start: 0.8637 (mmm) cc_final: 0.8359 (mmm) REVERT: D 3409 TYR cc_start: 0.5529 (OUTLIER) cc_final: 0.3508 (m-80) REVERT: D 3415 TYR cc_start: 0.5604 (t80) cc_final: 0.5146 (t80) REVERT: D 3523 ASN cc_start: 0.5612 (m110) cc_final: 0.4731 (t0) REVERT: D 3652 MET cc_start: 0.8346 (mmt) cc_final: 0.8084 (mmt) REVERT: D 3758 MET cc_start: 0.7104 (tpt) cc_final: 0.6796 (tpt) REVERT: D 3899 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.7238 (m-10) REVERT: D 4001 MET cc_start: 0.7955 (mmp) cc_final: 0.7599 (tpp) REVERT: D 4064 MET cc_start: 0.8147 (ppp) cc_final: 0.7630 (ppp) REVERT: D 4849 TYR cc_start: 0.7859 (t80) cc_final: 0.7369 (t80) REVERT: D 4880 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7756 (tmm) REVERT: D 4989 MET cc_start: 0.8077 (tmm) cc_final: 0.7806 (tmm) outliers start: 262 outliers final: 196 residues processed: 909 average time/residue: 1.0343 time to fit residues: 1740.3589 Evaluate side-chains 890 residues out of total 15132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 672 time to evaluate : 11.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 778 PHE Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1158 ASN Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1453 VAL Chi-restraints excluded: chain A residue 1514 LEU Chi-restraints excluded: chain A residue 1560 ASN Chi-restraints excluded: chain A residue 1599 MET Chi-restraints excluded: chain A residue 1650 ILE Chi-restraints excluded: chain A residue 1653 LEU Chi-restraints excluded: chain A residue 1673 VAL Chi-restraints excluded: chain A residue 1681 VAL Chi-restraints excluded: chain A residue 1685 LEU Chi-restraints excluded: chain A residue 1713 ASP Chi-restraints excluded: chain A residue 1858 ASP Chi-restraints excluded: chain A residue 1939 MET Chi-restraints excluded: chain A residue 2011 HIS Chi-restraints excluded: chain A residue 2128 TYR Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2182 ILE Chi-restraints excluded: chain A residue 2251 PHE Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2356 LEU Chi-restraints excluded: chain A residue 2461 VAL Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 2959 PHE Chi-restraints excluded: chain A residue 3409 TYR Chi-restraints excluded: chain A residue 3666 ASP Chi-restraints excluded: chain A residue 3698 LEU Chi-restraints excluded: chain A residue 3717 ASP Chi-restraints excluded: chain A residue 3899 PHE Chi-restraints excluded: chain A residue 3915 ILE Chi-restraints excluded: chain A residue 3926 LEU Chi-restraints excluded: chain A residue 3965 LEU Chi-restraints excluded: chain A residue 4150 LEU Chi-restraints excluded: chain A residue 4154 VAL Chi-restraints excluded: chain A residue 4571 PHE Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4648 LEU Chi-restraints excluded: chain A residue 4657 CYS Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4782 VAL Chi-restraints excluded: chain A residue 4827 LEU Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4877 ASP Chi-restraints excluded: chain A residue 4880 MET Chi-restraints excluded: chain A residue 4881 THR Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 5018 CYS Chi-restraints excluded: chain A residue 5020 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 778 PHE Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1123 VAL Chi-restraints excluded: chain B residue 1158 ASN Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1514 LEU Chi-restraints excluded: chain B residue 1560 ASN Chi-restraints excluded: chain B residue 1650 ILE Chi-restraints excluded: chain B residue 1653 LEU Chi-restraints excluded: chain B residue 1673 VAL Chi-restraints excluded: chain B residue 1681 VAL Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 1713 ASP Chi-restraints excluded: chain B residue 1858 ASP Chi-restraints excluded: chain B residue 2128 TYR Chi-restraints excluded: chain B residue 2138 LEU Chi-restraints excluded: chain B residue 2182 ILE Chi-restraints excluded: chain B residue 2211 MET Chi-restraints excluded: chain B residue 2251 PHE Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 2356 LEU Chi-restraints excluded: chain B residue 2461 VAL Chi-restraints excluded: chain B residue 2932 MET Chi-restraints excluded: chain B residue 2959 PHE Chi-restraints excluded: chain B residue 3409 TYR Chi-restraints excluded: chain B residue 3415 TYR Chi-restraints excluded: chain B residue 3666 ASP Chi-restraints excluded: chain B residue 3698 LEU Chi-restraints excluded: chain B residue 3717 ASP Chi-restraints excluded: chain B residue 3721 LEU Chi-restraints excluded: chain B residue 3899 PHE Chi-restraints excluded: chain B residue 3915 ILE Chi-restraints excluded: chain B residue 3926 LEU Chi-restraints excluded: chain B residue 3965 LEU Chi-restraints excluded: chain B residue 4150 LEU Chi-restraints excluded: chain B residue 4154 VAL Chi-restraints excluded: chain B residue 4571 PHE Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4657 CYS Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4782 VAL Chi-restraints excluded: chain B residue 4827 LEU Chi-restraints excluded: chain B residue 4853 VAL Chi-restraints excluded: chain B residue 4877 ASP Chi-restraints excluded: chain B residue 4880 MET Chi-restraints excluded: chain B residue 4881 THR Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4993 MET Chi-restraints excluded: chain B residue 5020 ASP Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 778 PHE Chi-restraints excluded: chain C residue 1123 VAL Chi-restraints excluded: chain C residue 1158 ASN Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1453 VAL Chi-restraints excluded: chain C residue 1560 ASN Chi-restraints excluded: chain C residue 1575 LEU Chi-restraints excluded: chain C residue 1650 ILE Chi-restraints excluded: chain C residue 1653 LEU Chi-restraints excluded: chain C residue 1673 VAL Chi-restraints excluded: chain C residue 1681 VAL Chi-restraints excluded: chain C residue 1685 LEU Chi-restraints excluded: chain C residue 1713 ASP Chi-restraints excluded: chain C residue 1841 VAL Chi-restraints excluded: chain C residue 1858 ASP Chi-restraints excluded: chain C residue 1939 MET Chi-restraints excluded: chain C residue 2138 LEU Chi-restraints excluded: chain C residue 2251 PHE Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 2461 VAL Chi-restraints excluded: chain C residue 2932 MET Chi-restraints excluded: chain C residue 3409 TYR Chi-restraints excluded: chain C residue 3666 ASP Chi-restraints excluded: chain C residue 3698 LEU Chi-restraints excluded: chain C residue 3717 ASP Chi-restraints excluded: chain C residue 3899 PHE Chi-restraints excluded: chain C residue 3915 ILE Chi-restraints excluded: chain C residue 3926 LEU Chi-restraints excluded: chain C residue 4150 LEU Chi-restraints excluded: chain C residue 4154 VAL Chi-restraints excluded: chain C residue 4571 PHE Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4648 LEU Chi-restraints excluded: chain C residue 4657 CYS Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4782 VAL Chi-restraints excluded: chain C residue 4827 LEU Chi-restraints excluded: chain C residue 4853 VAL Chi-restraints excluded: chain C residue 4877 ASP Chi-restraints excluded: chain C residue 4880 MET Chi-restraints excluded: chain C residue 4881 THR Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 5018 CYS Chi-restraints excluded: chain C residue 5020 ASP Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 778 PHE Chi-restraints excluded: chain D residue 1039 LEU Chi-restraints excluded: chain D residue 1123 VAL Chi-restraints excluded: chain D residue 1158 ASN Chi-restraints excluded: chain D residue 1168 VAL Chi-restraints excluded: chain D residue 1453 VAL Chi-restraints excluded: chain D residue 1514 LEU Chi-restraints excluded: chain D residue 1560 ASN Chi-restraints excluded: chain D residue 1575 LEU Chi-restraints excluded: chain D residue 1650 ILE Chi-restraints excluded: chain D residue 1653 LEU Chi-restraints excluded: chain D residue 1673 VAL Chi-restraints excluded: chain D residue 1681 VAL Chi-restraints excluded: chain D residue 1685 LEU Chi-restraints excluded: chain D residue 1713 ASP Chi-restraints excluded: chain D residue 1841 VAL Chi-restraints excluded: chain D residue 1858 ASP Chi-restraints excluded: chain D residue 1939 MET Chi-restraints excluded: chain D residue 2128 TYR Chi-restraints excluded: chain D residue 2138 LEU Chi-restraints excluded: chain D residue 2182 ILE Chi-restraints excluded: chain D residue 2251 PHE Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 2461 VAL Chi-restraints excluded: chain D residue 2932 MET Chi-restraints excluded: chain D residue 2959 PHE Chi-restraints excluded: chain D residue 3409 TYR Chi-restraints excluded: chain D residue 3666 ASP Chi-restraints excluded: chain D residue 3698 LEU Chi-restraints excluded: chain D residue 3717 ASP Chi-restraints excluded: chain D residue 3721 LEU Chi-restraints excluded: chain D residue 3899 PHE Chi-restraints excluded: chain D residue 3915 ILE Chi-restraints excluded: chain D residue 3926 LEU Chi-restraints excluded: chain D residue 3965 LEU Chi-restraints excluded: chain D residue 4150 LEU Chi-restraints excluded: chain D residue 4154 VAL Chi-restraints excluded: chain D residue 4571 PHE Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4657 CYS Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4782 VAL Chi-restraints excluded: chain D residue 4827 LEU Chi-restraints excluded: chain D residue 4853 VAL Chi-restraints excluded: chain D residue 4877 ASP Chi-restraints excluded: chain D residue 4880 MET Chi-restraints excluded: chain D residue 4881 THR Chi-restraints excluded: chain D residue 4886 HIS Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4993 MET Chi-restraints excluded: chain D residue 5020 ASP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1736 random chunks: chunk 1023 optimal weight: 20.0000 chunk 1648 optimal weight: 0.6980 chunk 1006 optimal weight: 9.9990 chunk 782 optimal weight: 10.0000 chunk 1146 optimal weight: 30.0000 chunk 1729 optimal weight: 10.0000 chunk 1591 optimal weight: 2.9990 chunk 1377 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 1063 optimal weight: 0.0040 chunk 844 optimal weight: 2.9990 overall best weight: 2.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3851 ASN ** A4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3851 ASN ** B4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3851 ASN ** C4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3851 ASN ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 137180 Z= 0.187 Angle : 0.577 13.824 186348 Z= 0.276 Chirality : 0.038 0.430 20956 Planarity : 0.003 0.043 24244 Dihedral : 3.639 23.359 18656 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.90 % Favored : 91.82 % Rotamer: Outliers : 1.74 % Allowed : 16.13 % Favored : 82.13 % 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: -0.09 (0.07), residues: 17208 helix: 2.09 (0.06), residues: 8356 sheet: -1.64 (0.14), residues: 1300 loop : -2.42 (0.07), residues: 7552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 882 HIS 0.008 0.001 HIS A2621 PHE 0.022 0.001 PHE C 649 TYR 0.042 0.001 TYR D3968 ARG 0.005 0.000 ARG D4892 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34416 Ramachandran restraints generated. 17208 Oldfield, 0 Emsley, 17208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34416 Ramachandran restraints generated. 17208 Oldfield, 0 Emsley, 17208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 927 residues out of total 15132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 683 time to evaluate : 11.208 Fit side-chains revert: symmetry clash REVERT: A 667 MET cc_start: 0.5022 (tmm) cc_final: 0.4681 (tmm) REVERT: A 1648 MET cc_start: 0.8148 (tpp) cc_final: 0.7867 (tpp) REVERT: A 1713 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7499 (t70) REVERT: A 2101 MET cc_start: 0.8649 (tmm) cc_final: 0.8421 (tmm) REVERT: A 2128 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.7869 (m-10) REVERT: A 2198 MET cc_start: 0.9435 (mpp) cc_final: 0.9057 (mpp) REVERT: A 2250 MET cc_start: 0.8110 (tpp) cc_final: 0.7881 (tpp) REVERT: A 2340 PHE cc_start: 0.6724 (p90) cc_final: 0.5963 (p90) REVERT: A 2502 MET cc_start: 0.8637 (mmm) cc_final: 0.8387 (mmm) REVERT: A 3409 TYR cc_start: 0.5544 (OUTLIER) cc_final: 0.3476 (m-80) REVERT: A 3523 ASN cc_start: 0.5636 (m110) cc_final: 0.4684 (t0) REVERT: A 3604 TYR cc_start: 0.7034 (t80) cc_final: 0.6809 (t80) REVERT: A 3652 MET cc_start: 0.8350 (mmt) cc_final: 0.8078 (mmt) REVERT: A 3758 MET cc_start: 0.7112 (tpt) cc_final: 0.6793 (tpt) REVERT: A 3899 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.7209 (m-10) REVERT: A 4000 MET cc_start: 0.7978 (mpp) cc_final: 0.7674 (mtm) REVERT: A 4001 MET cc_start: 0.8056 (mmp) cc_final: 0.7746 (tpp) REVERT: A 4064 MET cc_start: 0.8134 (ppp) cc_final: 0.7580 (ppp) REVERT: A 4849 TYR cc_start: 0.8136 (t80) cc_final: 0.7535 (t80) REVERT: A 4880 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7629 (tmm) REVERT: A 4989 MET cc_start: 0.8067 (tmm) cc_final: 0.7777 (tmm) REVERT: B 667 MET cc_start: 0.5040 (tmm) cc_final: 0.4696 (tmm) REVERT: B 1648 MET cc_start: 0.8146 (tpp) cc_final: 0.7868 (tpp) REVERT: B 1713 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7521 (t70) REVERT: B 2101 MET cc_start: 0.8486 (tmm) cc_final: 0.8277 (tmm) REVERT: B 2128 TYR cc_start: 0.8637 (OUTLIER) cc_final: 0.7756 (m-10) REVERT: B 2198 MET cc_start: 0.9441 (mpp) cc_final: 0.9064 (mpp) REVERT: B 2228 MET cc_start: 0.7883 (ppp) cc_final: 0.7542 (tmm) REVERT: B 2340 PHE cc_start: 0.6674 (p90) cc_final: 0.5911 (p90) REVERT: B 2502 MET cc_start: 0.8643 (mmm) cc_final: 0.8392 (mmm) REVERT: B 3409 TYR cc_start: 0.5580 (OUTLIER) cc_final: 0.3531 (m-80) REVERT: B 3415 TYR cc_start: 0.6684 (OUTLIER) cc_final: 0.5594 (t80) REVERT: B 3523 ASN cc_start: 0.5675 (m110) cc_final: 0.4724 (t0) REVERT: B 3604 TYR cc_start: 0.7131 (t80) cc_final: 0.6909 (t80) REVERT: B 3652 MET cc_start: 0.8264 (mmt) cc_final: 0.7902 (mmt) REVERT: B 3758 MET cc_start: 0.7100 (tpt) cc_final: 0.6791 (tpt) REVERT: B 3899 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.7190 (m-10) REVERT: B 3955 MET cc_start: 0.8090 (mtp) cc_final: 0.7696 (mtm) REVERT: B 4064 MET cc_start: 0.8117 (ppp) cc_final: 0.7551 (ppp) REVERT: B 4849 TYR cc_start: 0.8163 (t80) cc_final: 0.7563 (t80) REVERT: B 4880 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7612 (tmm) REVERT: B 4989 MET cc_start: 0.8051 (tmm) cc_final: 0.7824 (tmm) REVERT: C 600 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8261 (mp) REVERT: C 667 MET cc_start: 0.5035 (tmm) cc_final: 0.4654 (tmm) REVERT: C 1648 MET cc_start: 0.8146 (tpp) cc_final: 0.7864 (tpp) REVERT: C 1713 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7525 (t70) REVERT: C 2198 MET cc_start: 0.9435 (mpp) cc_final: 0.9044 (mpp) REVERT: C 2250 MET cc_start: 0.8110 (tpp) cc_final: 0.7909 (tpp) REVERT: C 2340 PHE cc_start: 0.6704 (p90) cc_final: 0.5928 (p90) REVERT: C 2502 MET cc_start: 0.8648 (mmm) cc_final: 0.8406 (mmm) REVERT: C 3409 TYR cc_start: 0.5546 (OUTLIER) cc_final: 0.3500 (m-80) REVERT: C 3415 TYR cc_start: 0.5577 (t80) cc_final: 0.5163 (t80) REVERT: C 3523 ASN cc_start: 0.5661 (m110) cc_final: 0.4753 (t0) REVERT: C 3604 TYR cc_start: 0.7043 (t80) cc_final: 0.6789 (t80) REVERT: C 3652 MET cc_start: 0.8295 (mmt) cc_final: 0.7937 (mmt) REVERT: C 3758 MET cc_start: 0.7110 (tpt) cc_final: 0.6794 (tpt) REVERT: C 3899 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.7194 (m-10) REVERT: C 4000 MET cc_start: 0.7958 (mpp) cc_final: 0.7633 (mtm) REVERT: C 4001 MET cc_start: 0.8049 (mmp) cc_final: 0.7737 (tpp) REVERT: C 4064 MET cc_start: 0.8137 (ppp) cc_final: 0.7585 (ppp) REVERT: C 4849 TYR cc_start: 0.8425 (t80) cc_final: 0.8150 (t80) REVERT: C 4880 MET cc_start: 0.7420 (OUTLIER) cc_final: 0.6995 (tmm) REVERT: C 4989 MET cc_start: 0.8061 (tmm) cc_final: 0.7765 (tmm) REVERT: D 667 MET cc_start: 0.5038 (tmm) cc_final: 0.4699 (tmm) REVERT: D 1648 MET cc_start: 0.8152 (tpp) cc_final: 0.7872 (tpp) REVERT: D 1713 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7517 (t70) REVERT: D 2128 TYR cc_start: 0.8633 (OUTLIER) cc_final: 0.7750 (m-10) REVERT: D 2198 MET cc_start: 0.9436 (mpp) cc_final: 0.9062 (mpp) REVERT: D 2250 MET cc_start: 0.8052 (tpp) cc_final: 0.7800 (tpp) REVERT: D 2340 PHE cc_start: 0.6703 (p90) cc_final: 0.5941 (p90) REVERT: D 2356 LEU cc_start: 0.8946 (mt) cc_final: 0.8672 (mp) REVERT: D 2502 MET cc_start: 0.8655 (mmm) cc_final: 0.8396 (mmm) REVERT: D 3409 TYR cc_start: 0.5594 (OUTLIER) cc_final: 0.3533 (m-80) REVERT: D 3415 TYR cc_start: 0.5592 (t80) cc_final: 0.5143 (t80) REVERT: D 3523 ASN cc_start: 0.5664 (m110) cc_final: 0.4725 (t0) REVERT: D 3652 MET cc_start: 0.8348 (mmt) cc_final: 0.8080 (mmt) REVERT: D 3758 MET cc_start: 0.7108 (tpt) cc_final: 0.6797 (tpt) REVERT: D 3899 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.7203 (m-10) REVERT: D 4001 MET cc_start: 0.7973 (mmp) cc_final: 0.7588 (tpp) REVERT: D 4064 MET cc_start: 0.8152 (ppp) cc_final: 0.7600 (ppp) REVERT: D 4849 TYR cc_start: 0.7863 (t80) cc_final: 0.7358 (t80) REVERT: D 4880 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7761 (tmm) REVERT: D 4989 MET cc_start: 0.8090 (tmm) cc_final: 0.7819 (tmm) outliers start: 244 outliers final: 208 residues processed: 902 average time/residue: 1.0348 time to fit residues: 1727.3936 Evaluate side-chains 900 residues out of total 15132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 671 time to evaluate : 10.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 778 PHE Chi-restraints excluded: chain A residue 1039 LEU Chi-restraints excluded: chain A residue 1123 VAL Chi-restraints excluded: chain A residue 1158 ASN Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1453 VAL Chi-restraints excluded: chain A residue 1514 LEU Chi-restraints excluded: chain A residue 1560 ASN Chi-restraints excluded: chain A residue 1575 LEU Chi-restraints excluded: chain A residue 1599 MET Chi-restraints excluded: chain A residue 1650 ILE Chi-restraints excluded: chain A residue 1653 LEU Chi-restraints excluded: chain A residue 1673 VAL Chi-restraints excluded: chain A residue 1681 VAL Chi-restraints excluded: chain A residue 1685 LEU Chi-restraints excluded: chain A residue 1713 ASP Chi-restraints excluded: chain A residue 1841 VAL Chi-restraints excluded: chain A residue 1858 ASP Chi-restraints excluded: chain A residue 1939 MET Chi-restraints excluded: chain A residue 2011 HIS Chi-restraints excluded: chain A residue 2128 TYR Chi-restraints excluded: chain A residue 2138 LEU Chi-restraints excluded: chain A residue 2182 ILE Chi-restraints excluded: chain A residue 2203 MET Chi-restraints excluded: chain A residue 2251 PHE Chi-restraints excluded: chain A residue 2294 ASP Chi-restraints excluded: chain A residue 2356 LEU Chi-restraints excluded: chain A residue 2461 VAL Chi-restraints excluded: chain A residue 2932 MET Chi-restraints excluded: chain A residue 3409 TYR Chi-restraints excluded: chain A residue 3666 ASP Chi-restraints excluded: chain A residue 3698 LEU Chi-restraints excluded: chain A residue 3717 ASP Chi-restraints excluded: chain A residue 3899 PHE Chi-restraints excluded: chain A residue 3915 ILE Chi-restraints excluded: chain A residue 3926 LEU Chi-restraints excluded: chain A residue 3965 LEU Chi-restraints excluded: chain A residue 4150 LEU Chi-restraints excluded: chain A residue 4154 VAL Chi-restraints excluded: chain A residue 4571 PHE Chi-restraints excluded: chain A residue 4580 TYR Chi-restraints excluded: chain A residue 4648 LEU Chi-restraints excluded: chain A residue 4657 CYS Chi-restraints excluded: chain A residue 4720 VAL Chi-restraints excluded: chain A residue 4782 VAL Chi-restraints excluded: chain A residue 4814 LEU Chi-restraints excluded: chain A residue 4827 LEU Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4877 ASP Chi-restraints excluded: chain A residue 4880 MET Chi-restraints excluded: chain A residue 4881 THR Chi-restraints excluded: chain A residue 4911 LEU Chi-restraints excluded: chain A residue 5018 CYS Chi-restraints excluded: chain A residue 5020 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 748 LEU Chi-restraints excluded: chain B residue 778 PHE Chi-restraints excluded: chain B residue 1039 LEU Chi-restraints excluded: chain B residue 1123 VAL Chi-restraints excluded: chain B residue 1158 ASN Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1453 VAL Chi-restraints excluded: chain B residue 1514 LEU Chi-restraints excluded: chain B residue 1560 ASN Chi-restraints excluded: chain B residue 1575 LEU Chi-restraints excluded: chain B residue 1650 ILE Chi-restraints excluded: chain B residue 1653 LEU Chi-restraints excluded: chain B residue 1673 VAL Chi-restraints excluded: chain B residue 1681 VAL Chi-restraints excluded: chain B residue 1685 LEU Chi-restraints excluded: chain B residue 1713 ASP Chi-restraints excluded: chain B residue 1841 VAL Chi-restraints excluded: chain B residue 1858 ASP Chi-restraints excluded: chain B residue 2011 HIS Chi-restraints excluded: chain B residue 2128 TYR Chi-restraints excluded: chain B residue 2138 LEU Chi-restraints excluded: chain B residue 2182 ILE Chi-restraints excluded: chain B residue 2251 PHE Chi-restraints excluded: chain B residue 2294 ASP Chi-restraints excluded: chain B residue 2356 LEU Chi-restraints excluded: chain B residue 2461 VAL Chi-restraints excluded: chain B residue 2932 MET Chi-restraints excluded: chain B residue 3409 TYR Chi-restraints excluded: chain B residue 3415 TYR Chi-restraints excluded: chain B residue 3666 ASP Chi-restraints excluded: chain B residue 3698 LEU Chi-restraints excluded: chain B residue 3717 ASP Chi-restraints excluded: chain B residue 3721 LEU Chi-restraints excluded: chain B residue 3899 PHE Chi-restraints excluded: chain B residue 3915 ILE Chi-restraints excluded: chain B residue 3926 LEU Chi-restraints excluded: chain B residue 3965 LEU Chi-restraints excluded: chain B residue 4150 LEU Chi-restraints excluded: chain B residue 4154 VAL Chi-restraints excluded: chain B residue 4571 PHE Chi-restraints excluded: chain B residue 4580 TYR Chi-restraints excluded: chain B residue 4648 LEU Chi-restraints excluded: chain B residue 4657 CYS Chi-restraints excluded: chain B residue 4720 VAL Chi-restraints excluded: chain B residue 4782 VAL Chi-restraints excluded: chain B residue 4827 LEU Chi-restraints excluded: chain B residue 4853 VAL Chi-restraints excluded: chain B residue 4877 ASP Chi-restraints excluded: chain B residue 4880 MET Chi-restraints excluded: chain B residue 4881 THR Chi-restraints excluded: chain B residue 4911 LEU Chi-restraints excluded: chain B residue 4993 MET Chi-restraints excluded: chain B residue 5020 ASP Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 600 LEU Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 778 PHE Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1123 VAL Chi-restraints excluded: chain C residue 1158 ASN Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1453 VAL Chi-restraints excluded: chain C residue 1560 ASN Chi-restraints excluded: chain C residue 1575 LEU Chi-restraints excluded: chain C residue 1650 ILE Chi-restraints excluded: chain C residue 1653 LEU Chi-restraints excluded: chain C residue 1673 VAL Chi-restraints excluded: chain C residue 1681 VAL Chi-restraints excluded: chain C residue 1685 LEU Chi-restraints excluded: chain C residue 1713 ASP Chi-restraints excluded: chain C residue 1841 VAL Chi-restraints excluded: chain C residue 1858 ASP Chi-restraints excluded: chain C residue 1939 MET Chi-restraints excluded: chain C residue 2138 LEU Chi-restraints excluded: chain C residue 2251 PHE Chi-restraints excluded: chain C residue 2294 ASP Chi-restraints excluded: chain C residue 2461 VAL Chi-restraints excluded: chain C residue 2932 MET Chi-restraints excluded: chain C residue 3409 TYR Chi-restraints excluded: chain C residue 3666 ASP Chi-restraints excluded: chain C residue 3698 LEU Chi-restraints excluded: chain C residue 3717 ASP Chi-restraints excluded: chain C residue 3899 PHE Chi-restraints excluded: chain C residue 3915 ILE Chi-restraints excluded: chain C residue 3926 LEU Chi-restraints excluded: chain C residue 4150 LEU Chi-restraints excluded: chain C residue 4154 VAL Chi-restraints excluded: chain C residue 4571 PHE Chi-restraints excluded: chain C residue 4580 TYR Chi-restraints excluded: chain C residue 4648 LEU Chi-restraints excluded: chain C residue 4657 CYS Chi-restraints excluded: chain C residue 4720 VAL Chi-restraints excluded: chain C residue 4782 VAL Chi-restraints excluded: chain C residue 4814 LEU Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4827 LEU Chi-restraints excluded: chain C residue 4853 VAL Chi-restraints excluded: chain C residue 4877 ASP Chi-restraints excluded: chain C residue 4880 MET Chi-restraints excluded: chain C residue 4881 THR Chi-restraints excluded: chain C residue 4911 LEU Chi-restraints excluded: chain C residue 5018 CYS Chi-restraints excluded: chain C residue 5020 ASP Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 167 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 778 PHE Chi-restraints excluded: chain D residue 1039 LEU Chi-restraints excluded: chain D residue 1123 VAL Chi-restraints excluded: chain D residue 1158 ASN Chi-restraints excluded: chain D residue 1168 VAL Chi-restraints excluded: chain D residue 1453 VAL Chi-restraints excluded: chain D residue 1514 LEU Chi-restraints excluded: chain D residue 1560 ASN Chi-restraints excluded: chain D residue 1575 LEU Chi-restraints excluded: chain D residue 1599 MET Chi-restraints excluded: chain D residue 1650 ILE Chi-restraints excluded: chain D residue 1653 LEU Chi-restraints excluded: chain D residue 1673 VAL Chi-restraints excluded: chain D residue 1681 VAL Chi-restraints excluded: chain D residue 1685 LEU Chi-restraints excluded: chain D residue 1713 ASP Chi-restraints excluded: chain D residue 1841 VAL Chi-restraints excluded: chain D residue 1858 ASP Chi-restraints excluded: chain D residue 1939 MET Chi-restraints excluded: chain D residue 2128 TYR Chi-restraints excluded: chain D residue 2138 LEU Chi-restraints excluded: chain D residue 2182 ILE Chi-restraints excluded: chain D residue 2203 MET Chi-restraints excluded: chain D residue 2251 PHE Chi-restraints excluded: chain D residue 2294 ASP Chi-restraints excluded: chain D residue 2461 VAL Chi-restraints excluded: chain D residue 2932 MET Chi-restraints excluded: chain D residue 3409 TYR Chi-restraints excluded: chain D residue 3666 ASP Chi-restraints excluded: chain D residue 3698 LEU Chi-restraints excluded: chain D residue 3717 ASP Chi-restraints excluded: chain D residue 3721 LEU Chi-restraints excluded: chain D residue 3899 PHE Chi-restraints excluded: chain D residue 3915 ILE Chi-restraints excluded: chain D residue 3926 LEU Chi-restraints excluded: chain D residue 3965 LEU Chi-restraints excluded: chain D residue 4150 LEU Chi-restraints excluded: chain D residue 4154 VAL Chi-restraints excluded: chain D residue 4571 PHE Chi-restraints excluded: chain D residue 4580 TYR Chi-restraints excluded: chain D residue 4648 LEU Chi-restraints excluded: chain D residue 4657 CYS Chi-restraints excluded: chain D residue 4720 VAL Chi-restraints excluded: chain D residue 4782 VAL Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4827 LEU Chi-restraints excluded: chain D residue 4853 VAL Chi-restraints excluded: chain D residue 4877 ASP Chi-restraints excluded: chain D residue 4880 MET Chi-restraints excluded: chain D residue 4881 THR Chi-restraints excluded: chain D residue 4886 HIS Chi-restraints excluded: chain D residue 4911 LEU Chi-restraints excluded: chain D residue 4993 MET Chi-restraints excluded: chain D residue 5020 ASP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1736 random chunks: chunk 1093 optimal weight: 9.9990 chunk 1467 optimal weight: 0.0670 chunk 421 optimal weight: 9.9990 chunk 1269 optimal weight: 10.0000 chunk 203 optimal weight: 2.9990 chunk 382 optimal weight: 4.9990 chunk 1379 optimal weight: 3.9990 chunk 577 optimal weight: 0.9980 chunk 1416 optimal weight: 5.9990 chunk 174 optimal weight: 9.9990 chunk 254 optimal weight: 30.0000 overall best weight: 2.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3851 ASN ** A4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3851 ASN ** B4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3851 ASN C3998 HIS ** C4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1558 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2498 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3851 ASN ** D4162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4201 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 = 0.4108 r_free = 0.4108 target = 0.095987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.080516 restraints weight = 691893.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.078602 restraints weight = 906185.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.077181 restraints weight = 715501.577| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 137180 Z= 0.190 Angle : 0.579 13.916 186348 Z= 0.277 Chirality : 0.038 0.193 20956 Planarity : 0.003 0.044 24244 Dihedral : 3.621 22.027 18656 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.15 % Favored : 91.57 % Rotamer: Outliers : 1.79 % Allowed : 16.13 % Favored : 82.08 % 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: -0.09 (0.07), residues: 17208 helix: 2.09 (0.06), residues: 8356 sheet: -1.63 (0.14), residues: 1300 loop : -2.42 (0.07), residues: 7552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C2105 HIS 0.008 0.001 HIS A2621 PHE 0.032 0.001 PHE B3096 TYR 0.040 0.001 TYR B3968 ARG 0.012 0.000 ARG B3093 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27036.96 seconds wall clock time: 475 minutes 29.13 seconds (28529.13 seconds total)