Starting phenix.real_space_refine on Thu Feb 15 23:22:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvv_27746/02_2024/8dvv_27746.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvv_27746/02_2024/8dvv_27746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvv_27746/02_2024/8dvv_27746.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvv_27746/02_2024/8dvv_27746.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvv_27746/02_2024/8dvv_27746.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dvv_27746/02_2024/8dvv_27746.pdb" } resolution = 3.68 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= 0.001 sd= 0.033 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: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 S 684 5.16 5 C 75664 2.51 5 N 20292 2.21 5 O 22632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1608": "OD1" <-> "OD2" Residue "A TYR 2267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2310": "OE1" <-> "OE2" Residue "A TYR 3095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4198": "OE1" <-> "OE2" Residue "A PHE 4849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1608": "OD1" <-> "OD2" Residue "B TYR 2267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2310": "OE1" <-> "OE2" Residue "B TYR 3095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4198": "OE1" <-> "OE2" Residue "B PHE 4849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1608": "OD1" <-> "OD2" Residue "C TYR 2267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2310": "OE1" <-> "OE2" Residue "C TYR 3095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 3418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4198": "OE1" <-> "OE2" Residue "C PHE 4849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1608": "OD1" <-> "OD2" Residue "D TYR 2267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2310": "OE1" <-> "OE2" Residue "D TYR 3095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 3418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4198": "OE1" <-> "OE2" Residue "D PHE 4849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 80": "OD1" <-> "OD2" Residue "F ASP 80": "OD1" <-> "OD2" Residue "G ASP 80": "OD1" <-> "OD2" Residue "H ASP 80": "OD1" <-> "OD2" Time to flip residues: 0.33s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 119280 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 29055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3886, 29055 Classifications: {'peptide': 3886} Incomplete info: {'truncation_to_alanine': 495} Link IDs: {'PTRANS': 132, 'TRANS': 3753} Chain breaks: 33 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 2173 Unresolved non-hydrogen angles: 2659 Unresolved non-hydrogen dihedrals: 1904 Unresolved non-hydrogen chiralities: 70 Planarities with less than four sites: {'GLN:plan1': 29, 'ASP:plan': 27, 'TYR:plan': 21, 'ASN:plan1': 19, 'TRP:plan': 10, 'HIS:plan': 15, 'PHE:plan': 24, 'GLU:plan': 77, 'ARG:plan': 67} Unresolved non-hydrogen planarities: 1353 Chain: "B" Number of atoms: 29055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3886, 29055 Classifications: {'peptide': 3886} Incomplete info: {'truncation_to_alanine': 495} Link IDs: {'PTRANS': 132, 'TRANS': 3753} Chain breaks: 33 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 2173 Unresolved non-hydrogen angles: 2659 Unresolved non-hydrogen dihedrals: 1904 Unresolved non-hydrogen chiralities: 70 Planarities with less than four sites: {'GLN:plan1': 29, 'ASP:plan': 27, 'TYR:plan': 21, 'ASN:plan1': 19, 'TRP:plan': 10, 'HIS:plan': 15, 'PHE:plan': 24, 'GLU:plan': 77, 'ARG:plan': 67} Unresolved non-hydrogen planarities: 1353 Chain: "C" Number of atoms: 29055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3886, 29055 Classifications: {'peptide': 3886} Incomplete info: {'truncation_to_alanine': 495} Link IDs: {'PTRANS': 132, 'TRANS': 3753} Chain breaks: 33 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 2173 Unresolved non-hydrogen angles: 2659 Unresolved non-hydrogen dihedrals: 1904 Unresolved non-hydrogen chiralities: 70 Planarities with less than four sites: {'GLN:plan1': 29, 'ASP:plan': 27, 'TYR:plan': 21, 'ASN:plan1': 19, 'TRP:plan': 10, 'HIS:plan': 15, 'PHE:plan': 24, 'GLU:plan': 77, 'ARG:plan': 67} Unresolved non-hydrogen planarities: 1353 Chain: "D" Number of atoms: 29055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3886, 29055 Classifications: {'peptide': 3886} Incomplete info: {'truncation_to_alanine': 495} Link IDs: {'PTRANS': 132, 'TRANS': 3753} Chain breaks: 33 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 2173 Unresolved non-hydrogen angles: 2659 Unresolved non-hydrogen dihedrals: 1904 Unresolved non-hydrogen chiralities: 70 Planarities with less than four sites: {'GLN:plan1': 29, 'ASP:plan': 27, 'TYR:plan': 21, 'ASN:plan1': 19, 'TRP:plan': 10, 'HIS:plan': 15, 'PHE:plan': 24, 'GLU:plan': 77, 'ARG:plan': 67} Unresolved non-hydrogen planarities: 1353 Chain: "E" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 763 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 7, 'TRANS': 99} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "F" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 763 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 7, 'TRANS': 99} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "G" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 763 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 7, 'TRANS': 99} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "H" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 763 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 7, 'TRANS': 99} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 51 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 28386 SG CYS A4887 204.851 188.667 126.275 1.00 45.74 S ATOM 28411 SG CYS A4890 203.659 190.239 122.743 1.00 49.37 S ATOM 57441 SG CYS B4887 180.669 204.822 126.284 1.00 45.74 S ATOM 57466 SG CYS B4890 179.096 203.628 122.753 1.00 49.37 S ATOM 86496 SG CYS C4887 164.531 180.685 126.277 1.00 45.74 S ATOM 86521 SG CYS C4890 165.723 179.113 122.744 1.00 49.37 S ATOM A0BZZ SG CYS D4887 188.675 164.518 126.276 1.00 45.74 S ATOM A0C0O SG CYS D4890 190.247 165.710 122.744 1.00 49.37 S Residues with excluded nonbonded symmetry interactions: 20 residue: pdb=" N ILE A 659 " occ=0.73 ... (6 atoms not shown) pdb=" CD1 ILE A 659 " occ=0.73 residue: pdb=" N VAL A 663 " occ=0.33 ... (5 atoms not shown) pdb=" CG2 VAL A 663 " occ=0.33 residue: pdb=" N CYS A 736 " occ=0.00 ... (4 atoms not shown) pdb=" SG CYS A 736 " occ=0.00 residue: pdb=" N SER A 742 " occ=0.60 ... (4 atoms not shown) pdb=" OG SER A 742 " occ=0.60 residue: pdb=" N ASP A 752 " occ=0.66 ... (6 atoms not shown) pdb=" OD2 ASP A 752 " occ=0.66 residue: pdb=" N ILE B 659 " occ=0.73 ... (6 atoms not shown) pdb=" CD1 ILE B 659 " occ=0.73 residue: pdb=" N VAL B 663 " occ=0.33 ... (5 atoms not shown) pdb=" CG2 VAL B 663 " occ=0.33 residue: pdb=" N CYS B 736 " occ=0.00 ... (4 atoms not shown) pdb=" SG CYS B 736 " occ=0.00 residue: pdb=" N SER B 742 " occ=0.60 ... (4 atoms not shown) pdb=" OG SER B 742 " occ=0.60 residue: pdb=" N ASP B 752 " occ=0.66 ... (6 atoms not shown) pdb=" OD2 ASP B 752 " occ=0.66 residue: pdb=" N ILE C 659 " occ=0.73 ... (6 atoms not shown) pdb=" CD1 ILE C 659 " occ=0.73 residue: pdb=" N VAL C 663 " occ=0.33 ... (5 atoms not shown) pdb=" CG2 VAL C 663 " occ=0.33 ... (remaining 8 not shown) Time building chain proxies: 44.12, per 1000 atoms: 0.37 Number of scatterers: 119280 At special positions: 0 Unit cell: (370.44, 370.44, 211.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 684 16.00 O 22632 8.00 N 20292 7.00 C 75664 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: 33.39 Conformation dependent library (CDL) restraints added in 15.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5002 " pdb="ZN ZN A5002 " - pdb=" ND1 HIS A4912 " pdb="ZN ZN A5002 " - pdb=" NE2 HIS A4907 " pdb="ZN ZN A5002 " - pdb=" SG CYS A4887 " pdb="ZN ZN A5002 " - pdb=" SG CYS A4890 " pdb=" ZN B5002 " pdb="ZN ZN B5002 " - pdb=" ND1 HIS B4912 " pdb="ZN ZN B5002 " - pdb=" NE2 HIS B4907 " pdb="ZN ZN B5002 " - pdb=" SG CYS B4887 " pdb="ZN ZN B5002 " - pdb=" SG CYS B4890 " pdb=" ZN C5002 " pdb="ZN ZN C5002 " - pdb=" ND1 HIS C4912 " pdb="ZN ZN C5002 " - pdb=" NE2 HIS C4907 " pdb="ZN ZN C5002 " - pdb=" SG CYS C4887 " pdb="ZN ZN C5002 " - pdb=" SG CYS C4890 " pdb=" ZN D5002 " pdb="ZN ZN D5002 " - pdb=" ND1 HIS D4912 " pdb="ZN ZN D5002 " - pdb=" NE2 HIS D4907 " pdb="ZN ZN D5002 " - pdb=" SG CYS D4887 " pdb="ZN ZN D5002 " - pdb=" SG CYS D4890 " Number of angles added : 8 31384 Ramachandran restraints generated. 15692 Oldfield, 0 Emsley, 15692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 29896 Finding SS restraints... Secondary structure from input PDB file: 592 helices and 79 sheets defined 49.7% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 13.77 Creating SS restraints... Processing helix chain 'A' and resid 412 through 438 Processing helix chain 'A' and resid 449 through 463 Processing helix chain 'A' and resid 471 through 492 removed outlier: 3.753A pdb=" N GLU A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 512 through 519 removed outlier: 3.563A pdb=" N ASP A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 543 removed outlier: 4.035A pdb=" N GLY A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 553 Processing helix chain 'A' and resid 554 through 562 Processing helix chain 'A' and resid 569 through 579 removed outlier: 3.988A pdb=" N LEU A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 588 Processing helix chain 'A' and resid 590 through 604 Processing helix chain 'A' and resid 609 through 618 Processing helix chain 'A' and resid 629 through 641 removed outlier: 3.637A pdb=" N LEU A 637 " --> pdb=" O CYS A 633 " (cutoff:3.500A) Proline residue: A 638 - end of helix removed outlier: 3.660A pdb=" N ASP A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 899 removed outlier: 3.785A pdb=" N GLU A 899 " --> pdb=" O MET A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 919 removed outlier: 3.575A pdb=" N VAL A 919 " --> pdb=" O PRO A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 924 removed outlier: 3.511A pdb=" N LEU A 924 " --> pdb=" O PHE A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 947 Processing helix chain 'A' and resid 958 through 962 Processing helix chain 'A' and resid 964 through 969 removed outlier: 4.069A pdb=" N ASN A 969 " --> pdb=" O LYS A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1015 Processing helix chain 'A' and resid 1043 through 1061 removed outlier: 3.569A pdb=" N GLY A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1095 removed outlier: 3.816A pdb=" N TYR A1094 " --> pdb=" O GLU A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1224 Processing helix chain 'A' and resid 1225 through 1229 removed outlier: 4.212A pdb=" N THR A1228 " --> pdb=" O LYS A1225 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1235 Processing helix chain 'A' and resid 1642 through 1647 Processing helix chain 'A' and resid 1651 through 1665 Processing helix chain 'A' and resid 1671 through 1681 removed outlier: 3.957A pdb=" N SER A1679 " --> pdb=" O HIS A1675 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS A1680 " --> pdb=" O ALA A1676 " (cutoff:3.500A) Processing helix chain 'A' and resid 1682 through 1692 Processing helix chain 'A' and resid 1696 through 1711 Processing helix chain 'A' and resid 1713 through 1723 Processing helix chain 'A' and resid 1784 through 1806 removed outlier: 3.630A pdb=" N LEU A1788 " --> pdb=" O PRO A1784 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A1793 " --> pdb=" O LYS A1789 " (cutoff:3.500A) Processing helix chain 'A' and resid 1814 through 1833 removed outlier: 3.627A pdb=" N LEU A1818 " --> pdb=" O THR A1814 " (cutoff:3.500A) Proline residue: A1821 - end of helix Processing helix chain 'A' and resid 1836 through 1847 Processing helix chain 'A' and resid 1898 through 1941 removed outlier: 3.918A pdb=" N VAL A1932 " --> pdb=" O SER A1928 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A1933 " --> pdb=" O ASP A1929 " (cutoff:3.500A) Processing helix chain 'A' and resid 1997 through 2003 Processing helix chain 'A' and resid 2009 through 2016 Processing helix chain 'A' and resid 2024 through 2036 removed outlier: 3.885A pdb=" N LEU A2028 " --> pdb=" O ILE A2024 " (cutoff:3.500A) Processing helix chain 'A' and resid 2056 through 2072 removed outlier: 4.187A pdb=" N LEU A2060 " --> pdb=" O SER A2056 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER A2072 " --> pdb=" O TRP A2068 " (cutoff:3.500A) Processing helix chain 'A' and resid 2076 through 2092 removed outlier: 3.628A pdb=" N VAL A2080 " --> pdb=" O ASP A2076 " (cutoff:3.500A) Processing helix chain 'A' and resid 2092 through 2101 Processing helix chain 'A' and resid 2111 through 2129 Processing helix chain 'A' and resid 2136 through 2150 removed outlier: 4.289A pdb=" N LEU A2140 " --> pdb=" O GLU A2136 " (cutoff:3.500A) Processing helix chain 'A' and resid 2151 through 2157 removed outlier: 4.304A pdb=" N TYR A2155 " --> pdb=" O ASN A2151 " (cutoff:3.500A) Processing helix chain 'A' and resid 2157 through 2164 Processing helix chain 'A' and resid 2165 through 2179 removed outlier: 3.658A pdb=" N THR A2169 " --> pdb=" O GLY A2165 " (cutoff:3.500A) Processing helix chain 'A' and resid 2190 through 2196 Processing helix chain 'A' and resid 2197 through 2202 Processing helix chain 'A' and resid 2208 through 2214 Processing helix chain 'A' and resid 2216 through 2223 Processing helix chain 'A' and resid 2238 through 2246 removed outlier: 3.607A pdb=" N VAL A2246 " --> pdb=" O ALA A2242 " (cutoff:3.500A) Processing helix chain 'A' and resid 2249 through 2256 Processing helix chain 'A' and resid 2257 through 2270 removed outlier: 3.566A pdb=" N LEU A2261 " --> pdb=" O ARG A2257 " (cutoff:3.500A) Processing helix chain 'A' and resid 2294 through 2306 Processing helix chain 'A' and resid 2312 through 2325 removed outlier: 3.750A pdb=" N VAL A2318 " --> pdb=" O GLU A2314 " (cutoff:3.500A) Processing helix chain 'A' and resid 2341 through 2354 removed outlier: 4.282A pdb=" N MET A2346 " --> pdb=" O LEU A2342 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLU A2347 " --> pdb=" O LEU A2343 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU A2354 " --> pdb=" O ILE A2350 " (cutoff:3.500A) Processing helix chain 'A' and resid 2384 through 2402 removed outlier: 4.255A pdb=" N MET A2388 " --> pdb=" O GLY A2384 " (cutoff:3.500A) Processing helix chain 'A' and resid 2415 through 2425 removed outlier: 3.635A pdb=" N LEU A2425 " --> pdb=" O ILE A2421 " (cutoff:3.500A) Processing helix chain 'A' and resid 2434 through 2439 Processing helix chain 'A' and resid 2460 through 2463 Processing helix chain 'A' and resid 2464 through 2475 Processing helix chain 'A' and resid 2479 through 2487 removed outlier: 3.804A pdb=" N LEU A2483 " --> pdb=" O VAL A2479 " (cutoff:3.500A) Processing helix chain 'A' and resid 2490 through 2500 Processing helix chain 'A' and resid 2511 through 2521 removed outlier: 4.085A pdb=" N ARG A2517 " --> pdb=" O LEU A2513 " (cutoff:3.500A) Processing helix chain 'A' and resid 2582 through 2592 removed outlier: 3.944A pdb=" N LEU A2587 " --> pdb=" O MET A2583 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU A2588 " --> pdb=" O MET A2584 " (cutoff:3.500A) Processing helix chain 'A' and resid 2599 through 2602 removed outlier: 3.750A pdb=" N ALA A2602 " --> pdb=" O ASN A2599 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2599 through 2602' Processing helix chain 'A' and resid 2603 through 2614 Processing helix chain 'A' and resid 2621 through 2626 Processing helix chain 'A' and resid 2626 through 2633 Processing helix chain 'A' and resid 2640 through 2647 Processing helix chain 'A' and resid 2664 through 2669 Processing helix chain 'A' and resid 2690 through 2694 Processing helix chain 'A' and resid 2718 through 2739 Processing helix chain 'A' and resid 2758 through 2762 removed outlier: 3.510A pdb=" N LEU A2762 " --> pdb=" O TYR A2759 " (cutoff:3.500A) Processing helix chain 'A' and resid 2763 through 2785 Proline residue: A2773 - end of helix removed outlier: 3.764A pdb=" N TRP A2784 " --> pdb=" O THR A2780 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY A2785 " --> pdb=" O MET A2781 " (cutoff:3.500A) Processing helix chain 'A' and resid 2791 through 2795 removed outlier: 3.508A pdb=" N GLY A2794 " --> pdb=" O THR A2791 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP A2795 " --> pdb=" O ARG A2792 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2791 through 2795' Processing helix chain 'A' and resid 2816 through 2820 removed outlier: 3.693A pdb=" N GLY A2819 " --> pdb=" O ALA A2816 " (cutoff:3.500A) Processing helix chain 'A' and resid 2833 through 2863 Processing helix chain 'A' and resid 2877 through 2897 removed outlier: 3.849A pdb=" N LYS A2883 " --> pdb=" O LYS A2879 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE A2897 " --> pdb=" O LYS A2893 " (cutoff:3.500A) Processing helix chain 'A' and resid 2898 through 2900 No H-bonds generated for 'chain 'A' and resid 2898 through 2900' Processing helix chain 'A' and resid 2991 through 2998 Processing helix chain 'A' and resid 3000 through 3007 Processing helix chain 'A' and resid 3009 through 3014 Processing helix chain 'A' and resid 3036 through 3049 removed outlier: 4.780A pdb=" N ARG A3042 " --> pdb=" O THR A3038 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR A3043 " --> pdb=" O LEU A3039 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS A3046 " --> pdb=" O ARG A3042 " (cutoff:3.500A) Processing helix chain 'A' and resid 3054 through 3061 removed outlier: 3.811A pdb=" N ALA A3058 " --> pdb=" O SER A3054 " (cutoff:3.500A) Processing helix chain 'A' and resid 3066 through 3084 removed outlier: 4.159A pdb=" N ASN A3073 " --> pdb=" O LYS A3069 " (cutoff:3.500A) Processing helix chain 'A' and resid 3090 through 3096 removed outlier: 4.224A pdb=" N ASN A3094 " --> pdb=" O THR A3090 " (cutoff:3.500A) Processing helix chain 'A' and resid 3183 through 3193 Processing helix chain 'A' and resid 3214 through 3225 removed outlier: 4.169A pdb=" N ILE A3218 " --> pdb=" O MET A3214 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU A3222 " --> pdb=" O ILE A3218 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER A3223 " --> pdb=" O GLU A3219 " (cutoff:3.500A) Processing helix chain 'A' and resid 3237 through 3252 Processing helix chain 'A' and resid 3283 through 3292 Processing helix chain 'A' and resid 3308 through 3324 Proline residue: A3320 - end of helix Processing helix chain 'A' and resid 3331 through 3344 Processing helix chain 'A' and resid 3355 through 3375 Proline residue: A3370 - end of helix Processing helix chain 'A' and resid 3405 through 3431 removed outlier: 4.250A pdb=" N ILE A3431 " --> pdb=" O MET A3427 " (cutoff:3.500A) Processing helix chain 'A' and resid 3436 through 3472 removed outlier: 3.730A pdb=" N LYS A3440 " --> pdb=" O SER A3436 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG A3457 " --> pdb=" O ARG A3453 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER A3463 " --> pdb=" O SER A3459 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LEU A3464 " --> pdb=" O MET A3460 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG A3471 " --> pdb=" O ALA A3467 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU A3472 " --> pdb=" O ALA A3468 " (cutoff:3.500A) Processing helix chain 'A' and resid 3474 through 3491 Proline residue: A3482 - end of helix Processing helix chain 'A' and resid 3495 through 3508 removed outlier: 4.025A pdb=" N GLU A3502 " --> pdb=" O LYS A3498 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU A3503 " --> pdb=" O ASP A3499 " (cutoff:3.500A) Processing helix chain 'A' and resid 3557 through 3566 removed outlier: 3.809A pdb=" N TYR A3566 " --> pdb=" O GLN A3562 " (cutoff:3.500A) Processing helix chain 'A' and resid 3615 through 3626 removed outlier: 4.176A pdb=" N GLN A3621 " --> pdb=" O ASN A3617 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY A3622 " --> pdb=" O LEU A3618 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR A3623 " --> pdb=" O PHE A3619 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER A3626 " --> pdb=" O GLY A3622 " (cutoff:3.500A) Processing helix chain 'A' and resid 3628 through 3635 removed outlier: 4.224A pdb=" N GLU A3632 " --> pdb=" O ILE A3628 " (cutoff:3.500A) Processing helix chain 'A' and resid 3637 through 3644 Processing helix chain 'A' and resid 3661 through 3676 Processing helix chain 'A' and resid 3684 through 3698 removed outlier: 3.698A pdb=" N MET A3688 " --> pdb=" O ASP A3684 " (cutoff:3.500A) Processing helix chain 'A' and resid 3714 through 3732 Processing helix chain 'A' and resid 3734 through 3746 removed outlier: 3.543A pdb=" N SER A3746 " --> pdb=" O THR A3742 " (cutoff:3.500A) Processing helix chain 'A' and resid 3751 through 3765 removed outlier: 3.521A pdb=" N ALA A3755 " --> pdb=" O GLY A3751 " (cutoff:3.500A) Processing helix chain 'A' and resid 3769 through 3784 removed outlier: 3.552A pdb=" N GLN A3773 " --> pdb=" O ASN A3769 " (cutoff:3.500A) Processing helix chain 'A' and resid 3786 through 3798 Processing helix chain 'A' and resid 3803 through 3812 removed outlier: 3.578A pdb=" N PHE A3807 " --> pdb=" O ASP A3803 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS A3812 " --> pdb=" O GLU A3808 " (cutoff:3.500A) Processing helix chain 'A' and resid 3831 through 3846 removed outlier: 3.616A pdb=" N CYS A3846 " --> pdb=" O LEU A3842 " (cutoff:3.500A) Processing helix chain 'A' and resid 3851 through 3860 removed outlier: 3.540A pdb=" N ARG A3858 " --> pdb=" O GLN A3854 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR A3859 " --> pdb=" O ASN A3855 " (cutoff:3.500A) Processing helix chain 'A' and resid 3868 through 3892 Processing helix chain 'A' and resid 3898 through 3924 Processing helix chain 'A' and resid 3928 through 3936 Processing helix chain 'A' and resid 3938 through 3958 Processing helix chain 'A' and resid 3963 through 3985 Processing helix chain 'A' and resid 3992 through 4005 removed outlier: 3.548A pdb=" N SER A4005 " --> pdb=" O MET A4001 " (cutoff:3.500A) Processing helix chain 'A' and resid 4005 through 4019 Processing helix chain 'A' and resid 4044 through 4050 removed outlier: 3.935A pdb=" N HIS A4048 " --> pdb=" O LYS A4044 " (cutoff:3.500A) Processing helix chain 'A' and resid 4061 through 4069 removed outlier: 4.234A pdb=" N LEU A4065 " --> pdb=" O GLU A4061 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A4066 " --> pdb=" O THR A4062 " (cutoff:3.500A) Processing helix chain 'A' and resid 4078 through 4085 removed outlier: 4.244A pdb=" N PHE A4082 " --> pdb=" O ASP A4078 " (cutoff:3.500A) Processing helix chain 'A' and resid 4091 through 4108 removed outlier: 3.835A pdb=" N ASN A4096 " --> pdb=" O ASP A4092 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A4097 " --> pdb=" O ILE A4093 " (cutoff:3.500A) Processing helix chain 'A' and resid 4111 through 4128 removed outlier: 6.274A pdb=" N SER A4123 " --> pdb=" O GLU A4119 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL A4124 " --> pdb=" O LEU A4120 " (cutoff:3.500A) Processing helix chain 'A' and resid 4152 through 4160 removed outlier: 4.080A pdb=" N GLU A4160 " --> pdb=" O ARG A4156 " (cutoff:3.500A) Processing helix chain 'A' and resid 4161 through 4178 removed outlier: 4.124A pdb=" N GLU A4178 " --> pdb=" O ASP A4174 " (cutoff:3.500A) Processing helix chain 'A' and resid 4182 through 4203 Processing helix chain 'A' and resid 4484 through 4496 Processing helix chain 'A' and resid 4497 through 4517 Processing helix chain 'A' and resid 4566 through 4593 Processing helix chain 'A' and resid 4593 through 4612 Processing helix chain 'A' and resid 4624 through 4635 removed outlier: 4.392A pdb=" N LEU A4632 " --> pdb=" O GLN A4628 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL A4633 " --> pdb=" O TRP A4629 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE A4634 " --> pdb=" O ASP A4630 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ASN A4635 " --> pdb=" O ARG A4631 " (cutoff:3.500A) Processing helix chain 'A' and resid 4647 through 4661 removed outlier: 3.600A pdb=" N LYS A4651 " --> pdb=" O PHE A4647 " (cutoff:3.500A) Processing helix chain 'A' and resid 4661 through 4670 removed outlier: 3.905A pdb=" N ILE A4665 " --> pdb=" O GLY A4661 " (cutoff:3.500A) Processing helix chain 'A' and resid 4701 through 4713 Processing helix chain 'A' and resid 4715 through 4734 removed outlier: 3.989A pdb=" N HIS A4732 " --> pdb=" O SER A4728 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR A4733 " --> pdb=" O VAL A4729 " (cutoff:3.500A) Processing helix chain 'A' and resid 4736 through 4748 Processing helix chain 'A' and resid 4749 through 4762 removed outlier: 3.515A pdb=" N ARG A4753 " --> pdb=" O PHE A4749 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL A4759 " --> pdb=" O ILE A4755 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR A4760 " --> pdb=" O LEU A4756 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN A4762 " --> pdb=" O SER A4758 " (cutoff:3.500A) Processing helix chain 'A' and resid 4763 through 4787 Processing helix chain 'A' and resid 4807 through 4818 Processing helix chain 'A' and resid 4825 through 4829 removed outlier: 3.659A pdb=" N ASP A4828 " --> pdb=" O GLY A4825 " (cutoff:3.500A) Processing helix chain 'A' and resid 4839 through 4886 Processing helix chain 'A' and resid 4896 through 4900 removed outlier: 3.742A pdb=" N THR A4899 " --> pdb=" O TYR A4896 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL A4900 " --> pdb=" O PHE A4897 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4896 through 4900' Processing helix chain 'A' and resid 4902 through 4911 removed outlier: 3.759A pdb=" N THR A4906 " --> pdb=" O HIS A4902 " (cutoff:3.500A) Processing helix chain 'A' and resid 4914 through 4927 Processing helix chain 'A' and resid 4933 through 4945 Processing helix chain 'A' and resid 4956 through 4961 Processing helix chain 'B' and resid 412 through 438 Processing helix chain 'B' and resid 449 through 463 Processing helix chain 'B' and resid 471 through 492 removed outlier: 3.754A pdb=" N GLU B 492 " --> pdb=" O LEU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 512 through 519 removed outlier: 3.563A pdb=" N ASP B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 543 removed outlier: 4.036A pdb=" N GLY B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 553 Processing helix chain 'B' and resid 554 through 562 Processing helix chain 'B' and resid 569 through 579 removed outlier: 3.989A pdb=" N LEU B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 588 Processing helix chain 'B' and resid 590 through 604 Processing helix chain 'B' and resid 609 through 618 Processing helix chain 'B' and resid 629 through 641 removed outlier: 3.637A pdb=" N LEU B 637 " --> pdb=" O CYS B 633 " (cutoff:3.500A) Proline residue: B 638 - end of helix removed outlier: 3.659A pdb=" N ASP B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 899 removed outlier: 3.785A pdb=" N GLU B 899 " --> pdb=" O MET B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 919 removed outlier: 3.575A pdb=" N VAL B 919 " --> pdb=" O PRO B 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 924 removed outlier: 3.511A pdb=" N LEU B 924 " --> pdb=" O PHE B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 947 Processing helix chain 'B' and resid 958 through 962 Processing helix chain 'B' and resid 964 through 969 removed outlier: 4.069A pdb=" N ASN B 969 " --> pdb=" O LYS B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1015 Processing helix chain 'B' and resid 1043 through 1061 removed outlier: 3.569A pdb=" N GLY B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1095 removed outlier: 3.815A pdb=" N TYR B1094 " --> pdb=" O GLU B1091 " (cutoff:3.500A) Processing helix chain 'B' and resid 1220 through 1224 Processing helix chain 'B' and resid 1225 through 1229 removed outlier: 4.212A pdb=" N THR B1228 " --> pdb=" O LYS B1225 " (cutoff:3.500A) Processing helix chain 'B' and resid 1230 through 1235 Processing helix chain 'B' and resid 1642 through 1647 Processing helix chain 'B' and resid 1651 through 1665 Processing helix chain 'B' and resid 1671 through 1681 removed outlier: 3.956A pdb=" N SER B1679 " --> pdb=" O HIS B1675 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N HIS B1680 " --> pdb=" O ALA B1676 " (cutoff:3.500A) Processing helix chain 'B' and resid 1682 through 1692 Processing helix chain 'B' and resid 1696 through 1711 Processing helix chain 'B' and resid 1713 through 1723 Processing helix chain 'B' and resid 1784 through 1806 removed outlier: 3.631A pdb=" N LEU B1788 " --> pdb=" O PRO B1784 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B1793 " --> pdb=" O LYS B1789 " (cutoff:3.500A) Processing helix chain 'B' and resid 1814 through 1833 removed outlier: 3.627A pdb=" N LEU B1818 " --> pdb=" O THR B1814 " (cutoff:3.500A) Proline residue: B1821 - end of helix Processing helix chain 'B' and resid 1836 through 1847 Processing helix chain 'B' and resid 1898 through 1941 removed outlier: 3.919A pdb=" N VAL B1932 " --> pdb=" O SER B1928 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA B1933 " --> pdb=" O ASP B1929 " (cutoff:3.500A) Processing helix chain 'B' and resid 1997 through 2003 Processing helix chain 'B' and resid 2009 through 2016 Processing helix chain 'B' and resid 2024 through 2036 removed outlier: 3.884A pdb=" N LEU B2028 " --> pdb=" O ILE B2024 " (cutoff:3.500A) Processing helix chain 'B' and resid 2056 through 2072 removed outlier: 4.187A pdb=" N LEU B2060 " --> pdb=" O SER B2056 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER B2072 " --> pdb=" O TRP B2068 " (cutoff:3.500A) Processing helix chain 'B' and resid 2076 through 2092 removed outlier: 3.629A pdb=" N VAL B2080 " --> pdb=" O ASP B2076 " (cutoff:3.500A) Processing helix chain 'B' and resid 2092 through 2101 Processing helix chain 'B' and resid 2111 through 2129 Processing helix chain 'B' and resid 2136 through 2150 removed outlier: 4.289A pdb=" N LEU B2140 " --> pdb=" O GLU B2136 " (cutoff:3.500A) Processing helix chain 'B' and resid 2151 through 2157 removed outlier: 4.304A pdb=" N TYR B2155 " --> pdb=" O ASN B2151 " (cutoff:3.500A) Processing helix chain 'B' and resid 2157 through 2164 Processing helix chain 'B' and resid 2165 through 2179 removed outlier: 3.658A pdb=" N THR B2169 " --> pdb=" O GLY B2165 " (cutoff:3.500A) Processing helix chain 'B' and resid 2190 through 2196 Processing helix chain 'B' and resid 2197 through 2202 Processing helix chain 'B' and resid 2208 through 2214 Processing helix chain 'B' and resid 2216 through 2223 Processing helix chain 'B' and resid 2238 through 2246 removed outlier: 3.608A pdb=" N VAL B2246 " --> pdb=" O ALA B2242 " (cutoff:3.500A) Processing helix chain 'B' and resid 2249 through 2256 Processing helix chain 'B' and resid 2257 through 2270 removed outlier: 3.566A pdb=" N LEU B2261 " --> pdb=" O ARG B2257 " (cutoff:3.500A) Processing helix chain 'B' and resid 2294 through 2306 Processing helix chain 'B' and resid 2312 through 2325 removed outlier: 3.749A pdb=" N VAL B2318 " --> pdb=" O GLU B2314 " (cutoff:3.500A) Processing helix chain 'B' and resid 2341 through 2354 removed outlier: 4.283A pdb=" N MET B2346 " --> pdb=" O LEU B2342 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLU B2347 " --> pdb=" O LEU B2343 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU B2354 " --> pdb=" O ILE B2350 " (cutoff:3.500A) Processing helix chain 'B' and resid 2384 through 2402 removed outlier: 4.255A pdb=" N MET B2388 " --> pdb=" O GLY B2384 " (cutoff:3.500A) Processing helix chain 'B' and resid 2415 through 2425 removed outlier: 3.634A pdb=" N LEU B2425 " --> pdb=" O ILE B2421 " (cutoff:3.500A) Processing helix chain 'B' and resid 2434 through 2439 Processing helix chain 'B' and resid 2460 through 2463 Processing helix chain 'B' and resid 2464 through 2475 Processing helix chain 'B' and resid 2479 through 2487 removed outlier: 3.805A pdb=" N LEU B2483 " --> pdb=" O VAL B2479 " (cutoff:3.500A) Processing helix chain 'B' and resid 2490 through 2500 Processing helix chain 'B' and resid 2511 through 2521 removed outlier: 4.085A pdb=" N ARG B2517 " --> pdb=" O LEU B2513 " (cutoff:3.500A) Processing helix chain 'B' and resid 2582 through 2592 removed outlier: 3.944A pdb=" N LEU B2587 " --> pdb=" O MET B2583 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU B2588 " --> pdb=" O MET B2584 " (cutoff:3.500A) Processing helix chain 'B' and resid 2599 through 2602 removed outlier: 3.750A pdb=" N ALA B2602 " --> pdb=" O ASN B2599 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2599 through 2602' Processing helix chain 'B' and resid 2603 through 2614 Processing helix chain 'B' and resid 2621 through 2626 Processing helix chain 'B' and resid 2626 through 2633 Processing helix chain 'B' and resid 2640 through 2647 Processing helix chain 'B' and resid 2664 through 2669 Processing helix chain 'B' and resid 2690 through 2694 Processing helix chain 'B' and resid 2718 through 2739 Processing helix chain 'B' and resid 2758 through 2762 removed outlier: 3.511A pdb=" N LEU B2762 " --> pdb=" O TYR B2759 " (cutoff:3.500A) Processing helix chain 'B' and resid 2763 through 2785 Proline residue: B2773 - end of helix removed outlier: 3.764A pdb=" N TRP B2784 " --> pdb=" O THR B2780 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY B2785 " --> pdb=" O MET B2781 " (cutoff:3.500A) Processing helix chain 'B' and resid 2791 through 2795 removed outlier: 3.509A pdb=" N GLY B2794 " --> pdb=" O THR B2791 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP B2795 " --> pdb=" O ARG B2792 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2791 through 2795' Processing helix chain 'B' and resid 2816 through 2820 removed outlier: 3.694A pdb=" N GLY B2819 " --> pdb=" O ALA B2816 " (cutoff:3.500A) Processing helix chain 'B' and resid 2833 through 2863 Processing helix chain 'B' and resid 2877 through 2897 removed outlier: 3.848A pdb=" N LYS B2883 " --> pdb=" O LYS B2879 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE B2897 " --> pdb=" O LYS B2893 " (cutoff:3.500A) Processing helix chain 'B' and resid 2898 through 2900 No H-bonds generated for 'chain 'B' and resid 2898 through 2900' Processing helix chain 'B' and resid 2991 through 2998 Processing helix chain 'B' and resid 3000 through 3007 Processing helix chain 'B' and resid 3009 through 3014 Processing helix chain 'B' and resid 3036 through 3049 removed outlier: 4.780A pdb=" N ARG B3042 " --> pdb=" O THR B3038 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR B3043 " --> pdb=" O LEU B3039 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS B3046 " --> pdb=" O ARG B3042 " (cutoff:3.500A) Processing helix chain 'B' and resid 3054 through 3061 removed outlier: 3.811A pdb=" N ALA B3058 " --> pdb=" O SER B3054 " (cutoff:3.500A) Processing helix chain 'B' and resid 3066 through 3084 removed outlier: 4.159A pdb=" N ASN B3073 " --> pdb=" O LYS B3069 " (cutoff:3.500A) Processing helix chain 'B' and resid 3090 through 3096 removed outlier: 4.224A pdb=" N ASN B3094 " --> pdb=" O THR B3090 " (cutoff:3.500A) Processing helix chain 'B' and resid 3183 through 3193 Processing helix chain 'B' and resid 3214 through 3225 removed outlier: 4.170A pdb=" N ILE B3218 " --> pdb=" O MET B3214 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU B3222 " --> pdb=" O ILE B3218 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER B3223 " --> pdb=" O GLU B3219 " (cutoff:3.500A) Processing helix chain 'B' and resid 3237 through 3252 Processing helix chain 'B' and resid 3283 through 3292 Processing helix chain 'B' and resid 3308 through 3324 Proline residue: B3320 - end of helix Processing helix chain 'B' and resid 3331 through 3344 Processing helix chain 'B' and resid 3355 through 3375 Proline residue: B3370 - end of helix Processing helix chain 'B' and resid 3405 through 3431 removed outlier: 4.250A pdb=" N ILE B3431 " --> pdb=" O MET B3427 " (cutoff:3.500A) Processing helix chain 'B' and resid 3436 through 3472 removed outlier: 3.730A pdb=" N LYS B3440 " --> pdb=" O SER B3436 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG B3457 " --> pdb=" O ARG B3453 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER B3463 " --> pdb=" O SER B3459 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LEU B3464 " --> pdb=" O MET B3460 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG B3471 " --> pdb=" O ALA B3467 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU B3472 " --> pdb=" O ALA B3468 " (cutoff:3.500A) Processing helix chain 'B' and resid 3474 through 3491 Proline residue: B3482 - end of helix Processing helix chain 'B' and resid 3495 through 3508 removed outlier: 4.025A pdb=" N GLU B3502 " --> pdb=" O LYS B3498 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU B3503 " --> pdb=" O ASP B3499 " (cutoff:3.500A) Processing helix chain 'B' and resid 3557 through 3566 removed outlier: 3.809A pdb=" N TYR B3566 " --> pdb=" O GLN B3562 " (cutoff:3.500A) Processing helix chain 'B' and resid 3615 through 3626 removed outlier: 4.176A pdb=" N GLN B3621 " --> pdb=" O ASN B3617 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY B3622 " --> pdb=" O LEU B3618 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR B3623 " --> pdb=" O PHE B3619 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER B3626 " --> pdb=" O GLY B3622 " (cutoff:3.500A) Processing helix chain 'B' and resid 3628 through 3635 removed outlier: 4.224A pdb=" N GLU B3632 " --> pdb=" O ILE B3628 " (cutoff:3.500A) Processing helix chain 'B' and resid 3637 through 3644 Processing helix chain 'B' and resid 3661 through 3676 Processing helix chain 'B' and resid 3684 through 3698 removed outlier: 3.697A pdb=" N MET B3688 " --> pdb=" O ASP B3684 " (cutoff:3.500A) Processing helix chain 'B' and resid 3714 through 3732 Processing helix chain 'B' and resid 3734 through 3746 removed outlier: 3.543A pdb=" N SER B3746 " --> pdb=" O THR B3742 " (cutoff:3.500A) Processing helix chain 'B' and resid 3751 through 3765 removed outlier: 3.521A pdb=" N ALA B3755 " --> pdb=" O GLY B3751 " (cutoff:3.500A) Processing helix chain 'B' and resid 3769 through 3784 removed outlier: 3.553A pdb=" N GLN B3773 " --> pdb=" O ASN B3769 " (cutoff:3.500A) Processing helix chain 'B' and resid 3786 through 3798 Processing helix chain 'B' and resid 3803 through 3812 removed outlier: 3.579A pdb=" N PHE B3807 " --> pdb=" O ASP B3803 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS B3812 " --> pdb=" O GLU B3808 " (cutoff:3.500A) Processing helix chain 'B' and resid 3831 through 3846 removed outlier: 3.617A pdb=" N CYS B3846 " --> pdb=" O LEU B3842 " (cutoff:3.500A) Processing helix chain 'B' and resid 3851 through 3860 removed outlier: 3.540A pdb=" N ARG B3858 " --> pdb=" O GLN B3854 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR B3859 " --> pdb=" O ASN B3855 " (cutoff:3.500A) Processing helix chain 'B' and resid 3868 through 3892 Processing helix chain 'B' and resid 3898 through 3924 Processing helix chain 'B' and resid 3928 through 3936 Processing helix chain 'B' and resid 3938 through 3958 Processing helix chain 'B' and resid 3963 through 3985 Processing helix chain 'B' and resid 3992 through 4005 removed outlier: 3.548A pdb=" N SER B4005 " --> pdb=" O MET B4001 " (cutoff:3.500A) Processing helix chain 'B' and resid 4005 through 4019 Processing helix chain 'B' and resid 4044 through 4050 removed outlier: 3.933A pdb=" N HIS B4048 " --> pdb=" O LYS B4044 " (cutoff:3.500A) Processing helix chain 'B' and resid 4061 through 4069 removed outlier: 4.233A pdb=" N LEU B4065 " --> pdb=" O GLU B4061 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B4066 " --> pdb=" O THR B4062 " (cutoff:3.500A) Processing helix chain 'B' and resid 4078 through 4085 removed outlier: 4.244A pdb=" N PHE B4082 " --> pdb=" O ASP B4078 " (cutoff:3.500A) Processing helix chain 'B' and resid 4091 through 4108 removed outlier: 3.835A pdb=" N ASN B4096 " --> pdb=" O ASP B4092 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B4097 " --> pdb=" O ILE B4093 " (cutoff:3.500A) Processing helix chain 'B' and resid 4111 through 4128 removed outlier: 6.275A pdb=" N SER B4123 " --> pdb=" O GLU B4119 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL B4124 " --> pdb=" O LEU B4120 " (cutoff:3.500A) Processing helix chain 'B' and resid 4152 through 4160 removed outlier: 4.080A pdb=" N GLU B4160 " --> pdb=" O ARG B4156 " (cutoff:3.500A) Processing helix chain 'B' and resid 4161 through 4178 removed outlier: 4.125A pdb=" N GLU B4178 " --> pdb=" O ASP B4174 " (cutoff:3.500A) Processing helix chain 'B' and resid 4182 through 4203 Processing helix chain 'B' and resid 4484 through 4496 Processing helix chain 'B' and resid 4497 through 4517 Processing helix chain 'B' and resid 4566 through 4593 Processing helix chain 'B' and resid 4593 through 4612 Processing helix chain 'B' and resid 4624 through 4635 removed outlier: 4.393A pdb=" N LEU B4632 " --> pdb=" O GLN B4628 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL B4633 " --> pdb=" O TRP B4629 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE B4634 " --> pdb=" O ASP B4630 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ASN B4635 " --> pdb=" O ARG B4631 " (cutoff:3.500A) Processing helix chain 'B' and resid 4647 through 4661 removed outlier: 3.599A pdb=" N LYS B4651 " --> pdb=" O PHE B4647 " (cutoff:3.500A) Processing helix chain 'B' and resid 4661 through 4670 removed outlier: 3.905A pdb=" N ILE B4665 " --> pdb=" O GLY B4661 " (cutoff:3.500A) Processing helix chain 'B' and resid 4701 through 4713 Processing helix chain 'B' and resid 4715 through 4734 removed outlier: 3.988A pdb=" N HIS B4732 " --> pdb=" O SER B4728 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR B4733 " --> pdb=" O VAL B4729 " (cutoff:3.500A) Processing helix chain 'B' and resid 4736 through 4748 Processing helix chain 'B' and resid 4749 through 4762 removed outlier: 3.514A pdb=" N ARG B4753 " --> pdb=" O PHE B4749 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL B4759 " --> pdb=" O ILE B4755 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N THR B4760 " --> pdb=" O LEU B4756 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN B4762 " --> pdb=" O SER B4758 " (cutoff:3.500A) Processing helix chain 'B' and resid 4763 through 4787 Processing helix chain 'B' and resid 4807 through 4818 Processing helix chain 'B' and resid 4825 through 4829 removed outlier: 3.658A pdb=" N ASP B4828 " --> pdb=" O GLY B4825 " (cutoff:3.500A) Processing helix chain 'B' and resid 4839 through 4886 Processing helix chain 'B' and resid 4896 through 4900 removed outlier: 3.742A pdb=" N THR B4899 " --> pdb=" O TYR B4896 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL B4900 " --> pdb=" O PHE B4897 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4896 through 4900' Processing helix chain 'B' and resid 4902 through 4911 removed outlier: 3.759A pdb=" N THR B4906 " --> pdb=" O HIS B4902 " (cutoff:3.500A) Processing helix chain 'B' and resid 4914 through 4927 Processing helix chain 'B' and resid 4933 through 4945 Processing helix chain 'B' and resid 4956 through 4961 Processing helix chain 'C' and resid 412 through 438 Processing helix chain 'C' and resid 449 through 463 Processing helix chain 'C' and resid 471 through 492 removed outlier: 3.754A pdb=" N GLU C 492 " --> pdb=" O LEU C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 504 Processing helix chain 'C' and resid 512 through 519 removed outlier: 3.563A pdb=" N ASP C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 543 removed outlier: 4.036A pdb=" N GLY C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 553 Processing helix chain 'C' and resid 554 through 562 Processing helix chain 'C' and resid 569 through 579 removed outlier: 3.989A pdb=" N LEU C 579 " --> pdb=" O LEU C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 588 Processing helix chain 'C' and resid 590 through 604 Processing helix chain 'C' and resid 609 through 618 Processing helix chain 'C' and resid 629 through 641 removed outlier: 3.638A pdb=" N LEU C 637 " --> pdb=" O CYS C 633 " (cutoff:3.500A) Proline residue: C 638 - end of helix removed outlier: 3.659A pdb=" N ASP C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 899 removed outlier: 3.785A pdb=" N GLU C 899 " --> pdb=" O MET C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 919 removed outlier: 3.575A pdb=" N VAL C 919 " --> pdb=" O PRO C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 924 removed outlier: 3.511A pdb=" N LEU C 924 " --> pdb=" O PHE C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 947 Processing helix chain 'C' and resid 958 through 962 Processing helix chain 'C' and resid 964 through 969 removed outlier: 4.069A pdb=" N ASN C 969 " --> pdb=" O LYS C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1015 Processing helix chain 'C' and resid 1043 through 1061 removed outlier: 3.569A pdb=" N GLY C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1091 through 1095 removed outlier: 3.815A pdb=" N TYR C1094 " --> pdb=" O GLU C1091 " (cutoff:3.500A) Processing helix chain 'C' and resid 1220 through 1224 Processing helix chain 'C' and resid 1225 through 1229 removed outlier: 4.212A pdb=" N THR C1228 " --> pdb=" O LYS C1225 " (cutoff:3.500A) Processing helix chain 'C' and resid 1230 through 1235 Processing helix chain 'C' and resid 1642 through 1647 Processing helix chain 'C' and resid 1651 through 1665 Processing helix chain 'C' and resid 1671 through 1681 removed outlier: 3.956A pdb=" N SER C1679 " --> pdb=" O HIS C1675 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N HIS C1680 " --> pdb=" O ALA C1676 " (cutoff:3.500A) Processing helix chain 'C' and resid 1682 through 1692 Processing helix chain 'C' and resid 1696 through 1711 Processing helix chain 'C' and resid 1713 through 1723 Processing helix chain 'C' and resid 1784 through 1806 removed outlier: 3.631A pdb=" N LEU C1788 " --> pdb=" O PRO C1784 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE C1793 " --> pdb=" O LYS C1789 " (cutoff:3.500A) Processing helix chain 'C' and resid 1814 through 1833 removed outlier: 3.627A pdb=" N LEU C1818 " --> pdb=" O THR C1814 " (cutoff:3.500A) Proline residue: C1821 - end of helix Processing helix chain 'C' and resid 1836 through 1847 Processing helix chain 'C' and resid 1898 through 1941 removed outlier: 3.918A pdb=" N VAL C1932 " --> pdb=" O SER C1928 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA C1933 " --> pdb=" O ASP C1929 " (cutoff:3.500A) Processing helix chain 'C' and resid 1997 through 2003 Processing helix chain 'C' and resid 2009 through 2016 Processing helix chain 'C' and resid 2024 through 2036 removed outlier: 3.885A pdb=" N LEU C2028 " --> pdb=" O ILE C2024 " (cutoff:3.500A) Processing helix chain 'C' and resid 2056 through 2072 removed outlier: 4.188A pdb=" N LEU C2060 " --> pdb=" O SER C2056 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER C2072 " --> pdb=" O TRP C2068 " (cutoff:3.500A) Processing helix chain 'C' and resid 2076 through 2092 removed outlier: 3.628A pdb=" N VAL C2080 " --> pdb=" O ASP C2076 " (cutoff:3.500A) Processing helix chain 'C' and resid 2092 through 2101 Processing helix chain 'C' and resid 2111 through 2129 Processing helix chain 'C' and resid 2136 through 2150 removed outlier: 4.289A pdb=" N LEU C2140 " --> pdb=" O GLU C2136 " (cutoff:3.500A) Processing helix chain 'C' and resid 2151 through 2157 removed outlier: 4.303A pdb=" N TYR C2155 " --> pdb=" O ASN C2151 " (cutoff:3.500A) Processing helix chain 'C' and resid 2157 through 2164 Processing helix chain 'C' and resid 2165 through 2179 removed outlier: 3.658A pdb=" N THR C2169 " --> pdb=" O GLY C2165 " (cutoff:3.500A) Processing helix chain 'C' and resid 2190 through 2196 Processing helix chain 'C' and resid 2197 through 2202 Processing helix chain 'C' and resid 2208 through 2214 Processing helix chain 'C' and resid 2216 through 2223 Processing helix chain 'C' and resid 2238 through 2246 removed outlier: 3.608A pdb=" N VAL C2246 " --> pdb=" O ALA C2242 " (cutoff:3.500A) Processing helix chain 'C' and resid 2249 through 2256 Processing helix chain 'C' and resid 2257 through 2270 removed outlier: 3.566A pdb=" N LEU C2261 " --> pdb=" O ARG C2257 " (cutoff:3.500A) Processing helix chain 'C' and resid 2294 through 2306 Processing helix chain 'C' and resid 2312 through 2325 removed outlier: 3.750A pdb=" N VAL C2318 " --> pdb=" O GLU C2314 " (cutoff:3.500A) Processing helix chain 'C' and resid 2341 through 2354 removed outlier: 4.284A pdb=" N MET C2346 " --> pdb=" O LEU C2342 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLU C2347 " --> pdb=" O LEU C2343 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU C2354 " --> pdb=" O ILE C2350 " (cutoff:3.500A) Processing helix chain 'C' and resid 2384 through 2402 removed outlier: 4.256A pdb=" N MET C2388 " --> pdb=" O GLY C2384 " (cutoff:3.500A) Processing helix chain 'C' and resid 2415 through 2425 removed outlier: 3.634A pdb=" N LEU C2425 " --> pdb=" O ILE C2421 " (cutoff:3.500A) Processing helix chain 'C' and resid 2434 through 2439 Processing helix chain 'C' and resid 2460 through 2463 Processing helix chain 'C' and resid 2464 through 2475 Processing helix chain 'C' and resid 2479 through 2487 removed outlier: 3.804A pdb=" N LEU C2483 " --> pdb=" O VAL C2479 " (cutoff:3.500A) Processing helix chain 'C' and resid 2490 through 2500 Processing helix chain 'C' and resid 2511 through 2521 removed outlier: 4.085A pdb=" N ARG C2517 " --> pdb=" O LEU C2513 " (cutoff:3.500A) Processing helix chain 'C' and resid 2582 through 2592 removed outlier: 3.944A pdb=" N LEU C2587 " --> pdb=" O MET C2583 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU C2588 " --> pdb=" O MET C2584 " (cutoff:3.500A) Processing helix chain 'C' and resid 2599 through 2602 removed outlier: 3.749A pdb=" N ALA C2602 " --> pdb=" O ASN C2599 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2599 through 2602' Processing helix chain 'C' and resid 2603 through 2614 Processing helix chain 'C' and resid 2621 through 2626 Processing helix chain 'C' and resid 2626 through 2633 Processing helix chain 'C' and resid 2640 through 2647 Processing helix chain 'C' and resid 2664 through 2669 Processing helix chain 'C' and resid 2690 through 2694 Processing helix chain 'C' and resid 2718 through 2739 Processing helix chain 'C' and resid 2758 through 2762 removed outlier: 3.511A pdb=" N LEU C2762 " --> pdb=" O TYR C2759 " (cutoff:3.500A) Processing helix chain 'C' and resid 2763 through 2785 Proline residue: C2773 - end of helix removed outlier: 3.764A pdb=" N TRP C2784 " --> pdb=" O THR C2780 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY C2785 " --> pdb=" O MET C2781 " (cutoff:3.500A) Processing helix chain 'C' and resid 2791 through 2795 removed outlier: 3.509A pdb=" N GLY C2794 " --> pdb=" O THR C2791 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP C2795 " --> pdb=" O ARG C2792 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2791 through 2795' Processing helix chain 'C' and resid 2816 through 2820 removed outlier: 3.693A pdb=" N GLY C2819 " --> pdb=" O ALA C2816 " (cutoff:3.500A) Processing helix chain 'C' and resid 2833 through 2863 Processing helix chain 'C' and resid 2877 through 2897 removed outlier: 3.849A pdb=" N LYS C2883 " --> pdb=" O LYS C2879 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE C2897 " --> pdb=" O LYS C2893 " (cutoff:3.500A) Processing helix chain 'C' and resid 2898 through 2900 No H-bonds generated for 'chain 'C' and resid 2898 through 2900' Processing helix chain 'C' and resid 2991 through 2998 Processing helix chain 'C' and resid 3000 through 3007 Processing helix chain 'C' and resid 3009 through 3014 Processing helix chain 'C' and resid 3036 through 3049 removed outlier: 4.779A pdb=" N ARG C3042 " --> pdb=" O THR C3038 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR C3043 " --> pdb=" O LEU C3039 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS C3046 " --> pdb=" O ARG C3042 " (cutoff:3.500A) Processing helix chain 'C' and resid 3054 through 3061 removed outlier: 3.811A pdb=" N ALA C3058 " --> pdb=" O SER C3054 " (cutoff:3.500A) Processing helix chain 'C' and resid 3066 through 3084 removed outlier: 4.159A pdb=" N ASN C3073 " --> pdb=" O LYS C3069 " (cutoff:3.500A) Processing helix chain 'C' and resid 3090 through 3096 removed outlier: 4.223A pdb=" N ASN C3094 " --> pdb=" O THR C3090 " (cutoff:3.500A) Processing helix chain 'C' and resid 3183 through 3193 Processing helix chain 'C' and resid 3214 through 3225 removed outlier: 4.169A pdb=" N ILE C3218 " --> pdb=" O MET C3214 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU C3222 " --> pdb=" O ILE C3218 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER C3223 " --> pdb=" O GLU C3219 " (cutoff:3.500A) Processing helix chain 'C' and resid 3237 through 3252 Processing helix chain 'C' and resid 3283 through 3292 Processing helix chain 'C' and resid 3308 through 3324 Proline residue: C3320 - end of helix Processing helix chain 'C' and resid 3331 through 3344 Processing helix chain 'C' and resid 3355 through 3375 Proline residue: C3370 - end of helix Processing helix chain 'C' and resid 3405 through 3431 removed outlier: 4.250A pdb=" N ILE C3431 " --> pdb=" O MET C3427 " (cutoff:3.500A) Processing helix chain 'C' and resid 3436 through 3472 removed outlier: 3.730A pdb=" N LYS C3440 " --> pdb=" O SER C3436 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG C3457 " --> pdb=" O ARG C3453 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N SER C3463 " --> pdb=" O SER C3459 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LEU C3464 " --> pdb=" O MET C3460 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG C3471 " --> pdb=" O ALA C3467 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU C3472 " --> pdb=" O ALA C3468 " (cutoff:3.500A) Processing helix chain 'C' and resid 3474 through 3491 Proline residue: C3482 - end of helix Processing helix chain 'C' and resid 3495 through 3508 removed outlier: 4.025A pdb=" N GLU C3502 " --> pdb=" O LYS C3498 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU C3503 " --> pdb=" O ASP C3499 " (cutoff:3.500A) Processing helix chain 'C' and resid 3557 through 3566 removed outlier: 3.809A pdb=" N TYR C3566 " --> pdb=" O GLN C3562 " (cutoff:3.500A) Processing helix chain 'C' and resid 3615 through 3626 removed outlier: 4.176A pdb=" N GLN C3621 " --> pdb=" O ASN C3617 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY C3622 " --> pdb=" O LEU C3618 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR C3623 " --> pdb=" O PHE C3619 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER C3626 " --> pdb=" O GLY C3622 " (cutoff:3.500A) Processing helix chain 'C' and resid 3628 through 3635 removed outlier: 4.223A pdb=" N GLU C3632 " --> pdb=" O ILE C3628 " (cutoff:3.500A) Processing helix chain 'C' and resid 3637 through 3644 Processing helix chain 'C' and resid 3661 through 3676 Processing helix chain 'C' and resid 3684 through 3698 removed outlier: 3.698A pdb=" N MET C3688 " --> pdb=" O ASP C3684 " (cutoff:3.500A) Processing helix chain 'C' and resid 3714 through 3732 Processing helix chain 'C' and resid 3734 through 3746 removed outlier: 3.543A pdb=" N SER C3746 " --> pdb=" O THR C3742 " (cutoff:3.500A) Processing helix chain 'C' and resid 3751 through 3765 removed outlier: 3.521A pdb=" N ALA C3755 " --> pdb=" O GLY C3751 " (cutoff:3.500A) Processing helix chain 'C' and resid 3769 through 3784 removed outlier: 3.552A pdb=" N GLN C3773 " --> pdb=" O ASN C3769 " (cutoff:3.500A) Processing helix chain 'C' and resid 3786 through 3798 Processing helix chain 'C' and resid 3803 through 3812 removed outlier: 3.579A pdb=" N PHE C3807 " --> pdb=" O ASP C3803 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS C3812 " --> pdb=" O GLU C3808 " (cutoff:3.500A) Processing helix chain 'C' and resid 3831 through 3846 removed outlier: 3.616A pdb=" N CYS C3846 " --> pdb=" O LEU C3842 " (cutoff:3.500A) Processing helix chain 'C' and resid 3851 through 3860 removed outlier: 3.540A pdb=" N ARG C3858 " --> pdb=" O GLN C3854 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR C3859 " --> pdb=" O ASN C3855 " (cutoff:3.500A) Processing helix chain 'C' and resid 3868 through 3892 Processing helix chain 'C' and resid 3898 through 3924 Processing helix chain 'C' and resid 3928 through 3936 Processing helix chain 'C' and resid 3938 through 3958 Processing helix chain 'C' and resid 3963 through 3985 Processing helix chain 'C' and resid 3992 through 4005 removed outlier: 3.548A pdb=" N SER C4005 " --> pdb=" O MET C4001 " (cutoff:3.500A) Processing helix chain 'C' and resid 4005 through 4019 Processing helix chain 'C' and resid 4044 through 4050 removed outlier: 3.934A pdb=" N HIS C4048 " --> pdb=" O LYS C4044 " (cutoff:3.500A) Processing helix chain 'C' and resid 4061 through 4069 removed outlier: 4.234A pdb=" N LEU C4065 " --> pdb=" O GLU C4061 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU C4066 " --> pdb=" O THR C4062 " (cutoff:3.500A) Processing helix chain 'C' and resid 4078 through 4085 removed outlier: 4.244A pdb=" N PHE C4082 " --> pdb=" O ASP C4078 " (cutoff:3.500A) Processing helix chain 'C' and resid 4091 through 4108 removed outlier: 3.836A pdb=" N ASN C4096 " --> pdb=" O ASP C4092 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL C4097 " --> pdb=" O ILE C4093 " (cutoff:3.500A) Processing helix chain 'C' and resid 4111 through 4128 removed outlier: 6.274A pdb=" N SER C4123 " --> pdb=" O GLU C4119 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL C4124 " --> pdb=" O LEU C4120 " (cutoff:3.500A) Processing helix chain 'C' and resid 4152 through 4160 removed outlier: 4.080A pdb=" N GLU C4160 " --> pdb=" O ARG C4156 " (cutoff:3.500A) Processing helix chain 'C' and resid 4161 through 4178 removed outlier: 4.124A pdb=" N GLU C4178 " --> pdb=" O ASP C4174 " (cutoff:3.500A) Processing helix chain 'C' and resid 4182 through 4203 Processing helix chain 'C' and resid 4484 through 4496 Processing helix chain 'C' and resid 4497 through 4517 Processing helix chain 'C' and resid 4566 through 4593 Processing helix chain 'C' and resid 4593 through 4612 Processing helix chain 'C' and resid 4624 through 4635 removed outlier: 4.392A pdb=" N LEU C4632 " --> pdb=" O GLN C4628 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL C4633 " --> pdb=" O TRP C4629 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE C4634 " --> pdb=" O ASP C4630 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ASN C4635 " --> pdb=" O ARG C4631 " (cutoff:3.500A) Processing helix chain 'C' and resid 4647 through 4661 removed outlier: 3.600A pdb=" N LYS C4651 " --> pdb=" O PHE C4647 " (cutoff:3.500A) Processing helix chain 'C' and resid 4661 through 4670 removed outlier: 3.904A pdb=" N ILE C4665 " --> pdb=" O GLY C4661 " (cutoff:3.500A) Processing helix chain 'C' and resid 4701 through 4713 Processing helix chain 'C' and resid 4715 through 4734 removed outlier: 3.988A pdb=" N HIS C4732 " --> pdb=" O SER C4728 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR C4733 " --> pdb=" O VAL C4729 " (cutoff:3.500A) Processing helix chain 'C' and resid 4736 through 4748 Processing helix chain 'C' and resid 4749 through 4762 removed outlier: 3.514A pdb=" N ARG C4753 " --> pdb=" O PHE C4749 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL C4759 " --> pdb=" O ILE C4755 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR C4760 " --> pdb=" O LEU C4756 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN C4762 " --> pdb=" O SER C4758 " (cutoff:3.500A) Processing helix chain 'C' and resid 4763 through 4787 Processing helix chain 'C' and resid 4807 through 4818 Processing helix chain 'C' and resid 4825 through 4829 removed outlier: 3.659A pdb=" N ASP C4828 " --> pdb=" O GLY C4825 " (cutoff:3.500A) Processing helix chain 'C' and resid 4839 through 4886 Processing helix chain 'C' and resid 4896 through 4900 removed outlier: 3.742A pdb=" N THR C4899 " --> pdb=" O TYR C4896 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL C4900 " --> pdb=" O PHE C4897 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4896 through 4900' Processing helix chain 'C' and resid 4902 through 4911 removed outlier: 3.759A pdb=" N THR C4906 " --> pdb=" O HIS C4902 " (cutoff:3.500A) Processing helix chain 'C' and resid 4914 through 4927 Processing helix chain 'C' and resid 4933 through 4945 Processing helix chain 'C' and resid 4956 through 4961 Processing helix chain 'D' and resid 412 through 438 Processing helix chain 'D' and resid 449 through 463 Processing helix chain 'D' and resid 471 through 492 removed outlier: 3.753A pdb=" N GLU D 492 " --> pdb=" O LEU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 504 Processing helix chain 'D' and resid 512 through 519 removed outlier: 3.562A pdb=" N ASP D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 543 removed outlier: 4.035A pdb=" N GLY D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 553 Processing helix chain 'D' and resid 554 through 562 Processing helix chain 'D' and resid 569 through 579 removed outlier: 3.988A pdb=" N LEU D 579 " --> pdb=" O LEU D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 588 Processing helix chain 'D' and resid 590 through 604 Processing helix chain 'D' and resid 609 through 618 Processing helix chain 'D' and resid 629 through 641 removed outlier: 3.637A pdb=" N LEU D 637 " --> pdb=" O CYS D 633 " (cutoff:3.500A) Proline residue: D 638 - end of helix removed outlier: 3.659A pdb=" N ASP D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 879 through 899 removed outlier: 3.785A pdb=" N GLU D 899 " --> pdb=" O MET D 895 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 919 removed outlier: 3.575A pdb=" N VAL D 919 " --> pdb=" O PRO D 916 " (cutoff:3.500A) Processing helix chain 'D' and resid 920 through 924 removed outlier: 3.511A pdb=" N LEU D 924 " --> pdb=" O PHE D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 947 Processing helix chain 'D' and resid 958 through 962 Processing helix chain 'D' and resid 964 through 969 removed outlier: 4.069A pdb=" N ASN D 969 " --> pdb=" O LYS D 965 " (cutoff:3.500A) Processing helix chain 'D' and resid 989 through 1015 Processing helix chain 'D' and resid 1043 through 1061 removed outlier: 3.569A pdb=" N GLY D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) Processing helix chain 'D' and resid 1091 through 1095 removed outlier: 3.815A pdb=" N TYR D1094 " --> pdb=" O GLU D1091 " (cutoff:3.500A) Processing helix chain 'D' and resid 1220 through 1224 Processing helix chain 'D' and resid 1225 through 1229 removed outlier: 4.211A pdb=" N THR D1228 " --> pdb=" O LYS D1225 " (cutoff:3.500A) Processing helix chain 'D' and resid 1230 through 1235 Processing helix chain 'D' and resid 1642 through 1647 Processing helix chain 'D' and resid 1651 through 1665 Processing helix chain 'D' and resid 1671 through 1681 removed outlier: 3.956A pdb=" N SER D1679 " --> pdb=" O HIS D1675 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N HIS D1680 " --> pdb=" O ALA D1676 " (cutoff:3.500A) Processing helix chain 'D' and resid 1682 through 1692 Processing helix chain 'D' and resid 1696 through 1711 Processing helix chain 'D' and resid 1713 through 1723 Processing helix chain 'D' and resid 1784 through 1806 removed outlier: 3.631A pdb=" N LEU D1788 " --> pdb=" O PRO D1784 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE D1793 " --> pdb=" O LYS D1789 " (cutoff:3.500A) Processing helix chain 'D' and resid 1814 through 1833 removed outlier: 3.627A pdb=" N LEU D1818 " --> pdb=" O THR D1814 " (cutoff:3.500A) Proline residue: D1821 - end of helix Processing helix chain 'D' and resid 1836 through 1847 Processing helix chain 'D' and resid 1898 through 1941 removed outlier: 3.918A pdb=" N VAL D1932 " --> pdb=" O SER D1928 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA D1933 " --> pdb=" O ASP D1929 " (cutoff:3.500A) Processing helix chain 'D' and resid 1997 through 2003 Processing helix chain 'D' and resid 2009 through 2016 Processing helix chain 'D' and resid 2024 through 2036 removed outlier: 3.885A pdb=" N LEU D2028 " --> pdb=" O ILE D2024 " (cutoff:3.500A) Processing helix chain 'D' and resid 2056 through 2072 removed outlier: 4.187A pdb=" N LEU D2060 " --> pdb=" O SER D2056 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER D2072 " --> pdb=" O TRP D2068 " (cutoff:3.500A) Processing helix chain 'D' and resid 2076 through 2092 removed outlier: 3.628A pdb=" N VAL D2080 " --> pdb=" O ASP D2076 " (cutoff:3.500A) Processing helix chain 'D' and resid 2092 through 2101 Processing helix chain 'D' and resid 2111 through 2129 Processing helix chain 'D' and resid 2136 through 2150 removed outlier: 4.289A pdb=" N LEU D2140 " --> pdb=" O GLU D2136 " (cutoff:3.500A) Processing helix chain 'D' and resid 2151 through 2157 removed outlier: 4.304A pdb=" N TYR D2155 " --> pdb=" O ASN D2151 " (cutoff:3.500A) Processing helix chain 'D' and resid 2157 through 2164 Processing helix chain 'D' and resid 2165 through 2179 removed outlier: 3.657A pdb=" N THR D2169 " --> pdb=" O GLY D2165 " (cutoff:3.500A) Processing helix chain 'D' and resid 2190 through 2196 Processing helix chain 'D' and resid 2197 through 2202 Processing helix chain 'D' and resid 2208 through 2214 Processing helix chain 'D' and resid 2216 through 2223 Processing helix chain 'D' and resid 2238 through 2246 removed outlier: 3.607A pdb=" N VAL D2246 " --> pdb=" O ALA D2242 " (cutoff:3.500A) Processing helix chain 'D' and resid 2249 through 2256 Processing helix chain 'D' and resid 2257 through 2270 removed outlier: 3.566A pdb=" N LEU D2261 " --> pdb=" O ARG D2257 " (cutoff:3.500A) Processing helix chain 'D' and resid 2294 through 2306 Processing helix chain 'D' and resid 2312 through 2325 removed outlier: 3.750A pdb=" N VAL D2318 " --> pdb=" O GLU D2314 " (cutoff:3.500A) Processing helix chain 'D' and resid 2341 through 2354 removed outlier: 4.284A pdb=" N MET D2346 " --> pdb=" O LEU D2342 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLU D2347 " --> pdb=" O LEU D2343 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU D2354 " --> pdb=" O ILE D2350 " (cutoff:3.500A) Processing helix chain 'D' and resid 2384 through 2402 removed outlier: 4.255A pdb=" N MET D2388 " --> pdb=" O GLY D2384 " (cutoff:3.500A) Processing helix chain 'D' and resid 2415 through 2425 removed outlier: 3.634A pdb=" N LEU D2425 " --> pdb=" O ILE D2421 " (cutoff:3.500A) Processing helix chain 'D' and resid 2434 through 2439 Processing helix chain 'D' and resid 2460 through 2463 Processing helix chain 'D' and resid 2464 through 2475 Processing helix chain 'D' and resid 2479 through 2487 removed outlier: 3.804A pdb=" N LEU D2483 " --> pdb=" O VAL D2479 " (cutoff:3.500A) Processing helix chain 'D' and resid 2490 through 2500 Processing helix chain 'D' and resid 2511 through 2521 removed outlier: 4.086A pdb=" N ARG D2517 " --> pdb=" O LEU D2513 " (cutoff:3.500A) Processing helix chain 'D' and resid 2582 through 2592 removed outlier: 3.945A pdb=" N LEU D2587 " --> pdb=" O MET D2583 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU D2588 " --> pdb=" O MET D2584 " (cutoff:3.500A) Processing helix chain 'D' and resid 2599 through 2602 removed outlier: 3.749A pdb=" N ALA D2602 " --> pdb=" O ASN D2599 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2599 through 2602' Processing helix chain 'D' and resid 2603 through 2614 Processing helix chain 'D' and resid 2621 through 2626 Processing helix chain 'D' and resid 2626 through 2633 Processing helix chain 'D' and resid 2640 through 2647 Processing helix chain 'D' and resid 2664 through 2669 Processing helix chain 'D' and resid 2690 through 2694 Processing helix chain 'D' and resid 2718 through 2739 Processing helix chain 'D' and resid 2758 through 2762 removed outlier: 3.511A pdb=" N LEU D2762 " --> pdb=" O TYR D2759 " (cutoff:3.500A) Processing helix chain 'D' and resid 2763 through 2785 Proline residue: D2773 - end of helix removed outlier: 3.764A pdb=" N TRP D2784 " --> pdb=" O THR D2780 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY D2785 " --> pdb=" O MET D2781 " (cutoff:3.500A) Processing helix chain 'D' and resid 2791 through 2795 removed outlier: 3.509A pdb=" N GLY D2794 " --> pdb=" O THR D2791 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP D2795 " --> pdb=" O ARG D2792 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2791 through 2795' Processing helix chain 'D' and resid 2816 through 2820 removed outlier: 3.693A pdb=" N GLY D2819 " --> pdb=" O ALA D2816 " (cutoff:3.500A) Processing helix chain 'D' and resid 2833 through 2863 Processing helix chain 'D' and resid 2877 through 2897 removed outlier: 3.849A pdb=" N LYS D2883 " --> pdb=" O LYS D2879 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE D2897 " --> pdb=" O LYS D2893 " (cutoff:3.500A) Processing helix chain 'D' and resid 2898 through 2900 No H-bonds generated for 'chain 'D' and resid 2898 through 2900' Processing helix chain 'D' and resid 2991 through 2998 Processing helix chain 'D' and resid 3000 through 3007 Processing helix chain 'D' and resid 3009 through 3014 Processing helix chain 'D' and resid 3036 through 3049 removed outlier: 4.779A pdb=" N ARG D3042 " --> pdb=" O THR D3038 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR D3043 " --> pdb=" O LEU D3039 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS D3046 " --> pdb=" O ARG D3042 " (cutoff:3.500A) Processing helix chain 'D' and resid 3054 through 3061 removed outlier: 3.811A pdb=" N ALA D3058 " --> pdb=" O SER D3054 " (cutoff:3.500A) Processing helix chain 'D' and resid 3066 through 3084 removed outlier: 4.159A pdb=" N ASN D3073 " --> pdb=" O LYS D3069 " (cutoff:3.500A) Processing helix chain 'D' and resid 3090 through 3096 removed outlier: 4.223A pdb=" N ASN D3094 " --> pdb=" O THR D3090 " (cutoff:3.500A) Processing helix chain 'D' and resid 3183 through 3193 Processing helix chain 'D' and resid 3214 through 3225 removed outlier: 4.170A pdb=" N ILE D3218 " --> pdb=" O MET D3214 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU D3222 " --> pdb=" O ILE D3218 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER D3223 " --> pdb=" O GLU D3219 " (cutoff:3.500A) Processing helix chain 'D' and resid 3237 through 3252 Processing helix chain 'D' and resid 3283 through 3292 Processing helix chain 'D' and resid 3308 through 3324 Proline residue: D3320 - end of helix Processing helix chain 'D' and resid 3331 through 3344 Processing helix chain 'D' and resid 3355 through 3375 Proline residue: D3370 - end of helix Processing helix chain 'D' and resid 3405 through 3431 removed outlier: 4.252A pdb=" N ILE D3431 " --> pdb=" O MET D3427 " (cutoff:3.500A) Processing helix chain 'D' and resid 3436 through 3472 removed outlier: 3.729A pdb=" N LYS D3440 " --> pdb=" O SER D3436 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG D3457 " --> pdb=" O ARG D3453 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER D3463 " --> pdb=" O SER D3459 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LEU D3464 " --> pdb=" O MET D3460 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG D3471 " --> pdb=" O ALA D3467 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU D3472 " --> pdb=" O ALA D3468 " (cutoff:3.500A) Processing helix chain 'D' and resid 3474 through 3491 Proline residue: D3482 - end of helix Processing helix chain 'D' and resid 3495 through 3508 removed outlier: 4.025A pdb=" N GLU D3502 " --> pdb=" O LYS D3498 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU D3503 " --> pdb=" O ASP D3499 " (cutoff:3.500A) Processing helix chain 'D' and resid 3557 through 3566 removed outlier: 3.809A pdb=" N TYR D3566 " --> pdb=" O GLN D3562 " (cutoff:3.500A) Processing helix chain 'D' and resid 3615 through 3626 removed outlier: 4.176A pdb=" N GLN D3621 " --> pdb=" O ASN D3617 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY D3622 " --> pdb=" O LEU D3618 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR D3623 " --> pdb=" O PHE D3619 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER D3626 " --> pdb=" O GLY D3622 " (cutoff:3.500A) Processing helix chain 'D' and resid 3628 through 3635 removed outlier: 4.225A pdb=" N GLU D3632 " --> pdb=" O ILE D3628 " (cutoff:3.500A) Processing helix chain 'D' and resid 3637 through 3644 Processing helix chain 'D' and resid 3661 through 3676 Processing helix chain 'D' and resid 3684 through 3698 removed outlier: 3.696A pdb=" N MET D3688 " --> pdb=" O ASP D3684 " (cutoff:3.500A) Processing helix chain 'D' and resid 3714 through 3732 Processing helix chain 'D' and resid 3734 through 3746 removed outlier: 3.543A pdb=" N SER D3746 " --> pdb=" O THR D3742 " (cutoff:3.500A) Processing helix chain 'D' and resid 3751 through 3765 removed outlier: 3.521A pdb=" N ALA D3755 " --> pdb=" O GLY D3751 " (cutoff:3.500A) Processing helix chain 'D' and resid 3769 through 3784 removed outlier: 3.553A pdb=" N GLN D3773 " --> pdb=" O ASN D3769 " (cutoff:3.500A) Processing helix chain 'D' and resid 3786 through 3798 Processing helix chain 'D' and resid 3803 through 3812 removed outlier: 3.578A pdb=" N PHE D3807 " --> pdb=" O ASP D3803 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS D3812 " --> pdb=" O GLU D3808 " (cutoff:3.500A) Processing helix chain 'D' and resid 3831 through 3846 removed outlier: 3.617A pdb=" N CYS D3846 " --> pdb=" O LEU D3842 " (cutoff:3.500A) Processing helix chain 'D' and resid 3851 through 3860 removed outlier: 3.539A pdb=" N ARG D3858 " --> pdb=" O GLN D3854 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR D3859 " --> pdb=" O ASN D3855 " (cutoff:3.500A) Processing helix chain 'D' and resid 3868 through 3892 Processing helix chain 'D' and resid 3898 through 3924 Processing helix chain 'D' and resid 3928 through 3936 Processing helix chain 'D' and resid 3938 through 3958 Processing helix chain 'D' and resid 3963 through 3985 Processing helix chain 'D' and resid 3992 through 4005 removed outlier: 3.548A pdb=" N SER D4005 " --> pdb=" O MET D4001 " (cutoff:3.500A) Processing helix chain 'D' and resid 4005 through 4019 Processing helix chain 'D' and resid 4044 through 4050 removed outlier: 3.934A pdb=" N HIS D4048 " --> pdb=" O LYS D4044 " (cutoff:3.500A) Processing helix chain 'D' and resid 4061 through 4069 removed outlier: 4.234A pdb=" N LEU D4065 " --> pdb=" O GLU D4061 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU D4066 " --> pdb=" O THR D4062 " (cutoff:3.500A) Processing helix chain 'D' and resid 4078 through 4085 removed outlier: 4.244A pdb=" N PHE D4082 " --> pdb=" O ASP D4078 " (cutoff:3.500A) Processing helix chain 'D' and resid 4091 through 4108 removed outlier: 3.835A pdb=" N ASN D4096 " --> pdb=" O ASP D4092 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL D4097 " --> pdb=" O ILE D4093 " (cutoff:3.500A) Processing helix chain 'D' and resid 4111 through 4128 removed outlier: 6.274A pdb=" N SER D4123 " --> pdb=" O GLU D4119 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL D4124 " --> pdb=" O LEU D4120 " (cutoff:3.500A) Processing helix chain 'D' and resid 4152 through 4160 removed outlier: 4.081A pdb=" N GLU D4160 " --> pdb=" O ARG D4156 " (cutoff:3.500A) Processing helix chain 'D' and resid 4161 through 4178 removed outlier: 4.124A pdb=" N GLU D4178 " --> pdb=" O ASP D4174 " (cutoff:3.500A) Processing helix chain 'D' and resid 4182 through 4203 Processing helix chain 'D' and resid 4484 through 4496 Processing helix chain 'D' and resid 4497 through 4517 Processing helix chain 'D' and resid 4566 through 4593 Processing helix chain 'D' and resid 4593 through 4612 Processing helix chain 'D' and resid 4624 through 4635 removed outlier: 4.393A pdb=" N LEU D4632 " --> pdb=" O GLN D4628 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N VAL D4633 " --> pdb=" O TRP D4629 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE D4634 " --> pdb=" O ASP D4630 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASN D4635 " --> pdb=" O ARG D4631 " (cutoff:3.500A) Processing helix chain 'D' and resid 4647 through 4661 removed outlier: 3.599A pdb=" N LYS D4651 " --> pdb=" O PHE D4647 " (cutoff:3.500A) Processing helix chain 'D' and resid 4661 through 4670 removed outlier: 3.904A pdb=" N ILE D4665 " --> pdb=" O GLY D4661 " (cutoff:3.500A) Processing helix chain 'D' and resid 4701 through 4713 Processing helix chain 'D' and resid 4715 through 4734 removed outlier: 3.989A pdb=" N HIS D4732 " --> pdb=" O SER D4728 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR D4733 " --> pdb=" O VAL D4729 " (cutoff:3.500A) Processing helix chain 'D' and resid 4736 through 4748 Processing helix chain 'D' and resid 4749 through 4762 removed outlier: 3.515A pdb=" N ARG D4753 " --> pdb=" O PHE D4749 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL D4759 " --> pdb=" O ILE D4755 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR D4760 " --> pdb=" O LEU D4756 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASN D4762 " --> pdb=" O SER D4758 " (cutoff:3.500A) Processing helix chain 'D' and resid 4763 through 4787 Processing helix chain 'D' and resid 4807 through 4818 Processing helix chain 'D' and resid 4825 through 4829 removed outlier: 3.659A pdb=" N ASP D4828 " --> pdb=" O GLY D4825 " (cutoff:3.500A) Processing helix chain 'D' and resid 4839 through 4886 Processing helix chain 'D' and resid 4896 through 4900 removed outlier: 3.742A pdb=" N THR D4899 " --> pdb=" O TYR D4896 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL D4900 " --> pdb=" O PHE D4897 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4896 through 4900' Processing helix chain 'D' and resid 4902 through 4911 removed outlier: 3.758A pdb=" N THR D4906 " --> pdb=" O HIS D4902 " (cutoff:3.500A) Processing helix chain 'D' and resid 4914 through 4927 Processing helix chain 'D' and resid 4933 through 4945 Processing helix chain 'D' and resid 4956 through 4961 Processing helix chain 'E' and resid 57 through 65 Processing helix chain 'F' and resid 57 through 65 Processing helix chain 'G' and resid 57 through 65 Processing helix chain 'H' and resid 57 through 65 Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 50 removed outlier: 3.543A pdb=" N LEU A 37 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP A 212 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 69 Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 133 removed outlier: 4.320A pdb=" N ASP A 146 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 194 removed outlier: 3.620A pdb=" N ALA A 206 " --> pdb=" O TYR A 191 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS A 193 " --> pdb=" O ASP A 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 233 through 234 Processing sheet with id=AA6, first strand: chain 'A' and resid 360 through 361 Processing sheet with id=AA7, first strand: chain 'A' and resid 647 through 650 removed outlier: 3.691A pdb=" N ARG A 647 " --> pdb=" O HIS A1632 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 649 " --> pdb=" O SER A1630 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 678 through 682 removed outlier: 6.095A pdb=" N VAL A 679 " --> pdb=" O ARG A 801 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ARG A 801 " --> pdb=" O VAL A 679 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS A 681 " --> pdb=" O LYS A 799 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS A 799 " --> pdb=" O HIS A 681 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 768 through 769 removed outlier: 4.033A pdb=" N PHE A 768 " --> pdb=" O VAL A 775 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1101 through 1107 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1160 through 1161 current: chain 'A' and resid 1172 through 1177 Processing sheet with id=AB2, first strand: chain 'A' and resid 1143 through 1145 Processing sheet with id=AB3, first strand: chain 'A' and resid 1250 through 1252 Processing sheet with id=AB4, first strand: chain 'A' and resid 1270 through 1271 Processing sheet with id=AB5, first strand: chain 'A' and resid 1300 through 1301 removed outlier: 3.998A pdb=" N MET A1300 " --> pdb=" O ALA A1546 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA A1546 " --> pdb=" O MET A1300 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1466 through 1467 Processing sheet with id=AB7, first strand: chain 'A' and resid 1726 through 1729 removed outlier: 3.922A pdb=" N TYR A2105 " --> pdb=" O PHE A1726 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2787 through 2788 Processing sheet with id=AB9, first strand: chain 'A' and resid 4136 through 4137 removed outlier: 3.684A pdb=" N ILE A4137 " --> pdb=" O GLU A4145 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 50 removed outlier: 3.543A pdb=" N LEU B 37 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP B 212 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 67 through 69 Processing sheet with id=AC3, first strand: chain 'B' and resid 129 through 133 removed outlier: 4.320A pdb=" N ASP B 146 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 191 through 194 removed outlier: 3.620A pdb=" N ALA B 206 " --> pdb=" O TYR B 191 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS B 193 " --> pdb=" O ASP B 204 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 233 through 234 Processing sheet with id=AC6, first strand: chain 'B' and resid 360 through 361 Processing sheet with id=AC7, first strand: chain 'B' and resid 647 through 650 removed outlier: 3.691A pdb=" N ARG B 647 " --> pdb=" O HIS B1632 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 649 " --> pdb=" O SER B1630 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 678 through 682 removed outlier: 6.095A pdb=" N VAL B 679 " --> pdb=" O ARG B 801 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ARG B 801 " --> pdb=" O VAL B 679 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS B 681 " --> pdb=" O LYS B 799 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS B 799 " --> pdb=" O HIS B 681 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 768 through 769 removed outlier: 4.033A pdb=" N PHE B 768 " --> pdb=" O VAL B 775 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1101 through 1107 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1160 through 1161 current: chain 'B' and resid 1172 through 1177 Processing sheet with id=AD2, first strand: chain 'B' and resid 1143 through 1145 Processing sheet with id=AD3, first strand: chain 'B' and resid 1250 through 1252 Processing sheet with id=AD4, first strand: chain 'B' and resid 1270 through 1271 Processing sheet with id=AD5, first strand: chain 'B' and resid 1466 through 1467 Processing sheet with id=AD6, first strand: chain 'B' and resid 1726 through 1729 removed outlier: 3.922A pdb=" N TYR B2105 " --> pdb=" O PHE B1726 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 2787 through 2788 Processing sheet with id=AD8, first strand: chain 'B' and resid 4136 through 4137 removed outlier: 3.684A pdb=" N ILE B4137 " --> pdb=" O GLU B4145 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 50 removed outlier: 3.543A pdb=" N LEU C 37 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP C 212 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 67 through 69 Processing sheet with id=AE2, first strand: chain 'C' and resid 129 through 133 removed outlier: 4.319A pdb=" N ASP C 146 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 191 through 194 removed outlier: 3.619A pdb=" N ALA C 206 " --> pdb=" O TYR C 191 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS C 193 " --> pdb=" O ASP C 204 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 233 through 234 Processing sheet with id=AE5, first strand: chain 'C' and resid 360 through 361 Processing sheet with id=AE6, first strand: chain 'C' and resid 647 through 650 removed outlier: 3.690A pdb=" N ARG C 647 " --> pdb=" O HIS C1632 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL C 649 " --> pdb=" O SER C1630 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 678 through 682 removed outlier: 6.095A pdb=" N VAL C 679 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ARG C 801 " --> pdb=" O VAL C 679 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS C 681 " --> pdb=" O LYS C 799 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS C 799 " --> pdb=" O HIS C 681 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 768 through 769 removed outlier: 4.034A pdb=" N PHE C 768 " --> pdb=" O VAL C 775 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1101 through 1107 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 1160 through 1161 current: chain 'C' and resid 1172 through 1177 Processing sheet with id=AF1, first strand: chain 'C' and resid 1143 through 1145 Processing sheet with id=AF2, first strand: chain 'C' and resid 1250 through 1252 Processing sheet with id=AF3, first strand: chain 'C' and resid 1270 through 1271 Processing sheet with id=AF4, first strand: chain 'C' and resid 1300 through 1301 removed outlier: 3.997A pdb=" N MET C1300 " --> pdb=" O ALA C1546 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA C1546 " --> pdb=" O MET C1300 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'C' and resid 1466 through 1467 Processing sheet with id=AF6, first strand: chain 'C' and resid 1726 through 1729 removed outlier: 3.922A pdb=" N TYR C2105 " --> pdb=" O PHE C1726 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 2787 through 2788 Processing sheet with id=AF8, first strand: chain 'C' and resid 4136 through 4137 removed outlier: 3.683A pdb=" N ILE C4137 " --> pdb=" O GLU C4145 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 48 through 50 removed outlier: 3.543A pdb=" N LEU D 37 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP D 212 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 67 through 69 Processing sheet with id=AG2, first strand: chain 'D' and resid 129 through 133 removed outlier: 4.320A pdb=" N ASP D 146 " --> pdb=" O LEU D 133 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 191 through 194 removed outlier: 3.620A pdb=" N ALA D 206 " --> pdb=" O TYR D 191 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS D 193 " --> pdb=" O ASP D 204 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 233 through 234 Processing sheet with id=AG5, first strand: chain 'D' and resid 360 through 361 Processing sheet with id=AG6, first strand: chain 'D' and resid 647 through 650 removed outlier: 3.691A pdb=" N ARG D 647 " --> pdb=" O HIS D1632 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL D 649 " --> pdb=" O SER D1630 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'D' and resid 678 through 682 removed outlier: 6.094A pdb=" N VAL D 679 " --> pdb=" O ARG D 801 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ARG D 801 " --> pdb=" O VAL D 679 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS D 681 " --> pdb=" O LYS D 799 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS D 799 " --> pdb=" O HIS D 681 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'D' and resid 768 through 769 removed outlier: 4.033A pdb=" N PHE D 768 " --> pdb=" O VAL D 775 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 1101 through 1107 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 1160 through 1161 current: chain 'D' and resid 1172 through 1177 Processing sheet with id=AH1, first strand: chain 'D' and resid 1143 through 1145 Processing sheet with id=AH2, first strand: chain 'D' and resid 1250 through 1252 Processing sheet with id=AH3, first strand: chain 'D' and resid 1270 through 1271 Processing sheet with id=AH4, first strand: chain 'D' and resid 1300 through 1301 removed outlier: 3.998A pdb=" N MET D1300 " --> pdb=" O ALA D1546 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA D1546 " --> pdb=" O MET D1300 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'D' and resid 1466 through 1467 Processing sheet with id=AH6, first strand: chain 'D' and resid 1726 through 1729 removed outlier: 3.922A pdb=" N TYR D2105 " --> pdb=" O PHE D1726 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'D' and resid 2787 through 2788 Processing sheet with id=AH8, first strand: chain 'D' and resid 4136 through 4137 removed outlier: 3.683A pdb=" N ILE D4137 " --> pdb=" O GLU D4145 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'E' and resid 22 through 25 removed outlier: 3.598A pdb=" N ASN E 106 " --> pdb=" O VAL E 24 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'E' and resid 30 through 31 Processing sheet with id=AI2, first strand: chain 'F' and resid 22 through 25 removed outlier: 3.598A pdb=" N ASN F 106 " --> pdb=" O VAL F 24 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'F' and resid 30 through 31 Processing sheet with id=AI4, first strand: chain 'G' and resid 22 through 25 removed outlier: 3.598A pdb=" N ASN G 106 " --> pdb=" O VAL G 24 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'G' and resid 30 through 31 Processing sheet with id=AI6, first strand: chain 'H' and resid 22 through 25 removed outlier: 3.598A pdb=" N ASN H 106 " --> pdb=" O VAL H 24 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'H' and resid 30 through 31 5436 hydrogen bonds defined for protein. 15672 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: 67.43 Time building geometry restraints manager: 37.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 39730 1.34 - 1.46: 27362 1.46 - 1.58: 53396 1.58 - 1.70: 0 1.70 - 1.82: 1068 Bond restraints: 121556 Sorted by residual: bond pdb=" C LEU D2622 " pdb=" N PRO D2623 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.67e+00 bond pdb=" C LEU B2622 " pdb=" N PRO B2623 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.66e+00 bond pdb=" C LEU A2622 " pdb=" N PRO A2623 " ideal model delta sigma weight residual 1.334 1.371 -0.038 2.34e-02 1.83e+03 2.58e+00 bond pdb=" C LEU C2622 " pdb=" N PRO C2623 " ideal model delta sigma weight residual 1.334 1.371 -0.037 2.34e-02 1.83e+03 2.56e+00 bond pdb=" SD MET B1300 " pdb=" CE MET B1300 " ideal model delta sigma weight residual 1.791 1.760 0.031 2.50e-02 1.60e+03 1.57e+00 ... (remaining 121551 not shown) Histogram of bond angle deviations from ideal: 97.11 - 104.55: 1646 104.55 - 111.98: 59526 111.98 - 119.42: 41470 119.42 - 126.86: 61004 126.86 - 134.30: 1450 Bond angle restraints: 165096 Sorted by residual: angle pdb=" N PRO A1124 " pdb=" CA PRO A1124 " pdb=" CB PRO A1124 " ideal model delta sigma weight residual 103.20 110.24 -7.04 9.50e-01 1.11e+00 5.49e+01 angle pdb=" N PRO D1124 " pdb=" CA PRO D1124 " pdb=" CB PRO D1124 " ideal model delta sigma weight residual 103.20 110.24 -7.04 9.50e-01 1.11e+00 5.49e+01 angle pdb=" N PRO C1124 " pdb=" CA PRO C1124 " pdb=" CB PRO C1124 " ideal model delta sigma weight residual 103.20 110.23 -7.03 9.50e-01 1.11e+00 5.47e+01 angle pdb=" N PRO B1124 " pdb=" CA PRO B1124 " pdb=" CB PRO B1124 " ideal model delta sigma weight residual 103.20 110.19 -6.99 9.50e-01 1.11e+00 5.42e+01 angle pdb=" C SER A 413 " pdb=" CA SER A 413 " pdb=" CB SER A 413 " ideal model delta sigma weight residual 116.54 108.79 7.75 1.15e+00 7.56e-01 4.54e+01 ... (remaining 165091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 62429 17.96 - 35.93: 7181 35.93 - 53.89: 2106 53.89 - 71.86: 416 71.86 - 89.82: 184 Dihedral angle restraints: 72316 sinusoidal: 26088 harmonic: 46228 Sorted by residual: dihedral pdb=" CA GLU A4181 " pdb=" C GLU A4181 " pdb=" N LYS A4182 " pdb=" CA LYS A4182 " ideal model delta harmonic sigma weight residual 180.00 148.96 31.04 0 5.00e+00 4.00e-02 3.85e+01 dihedral pdb=" CA GLU B4181 " pdb=" C GLU B4181 " pdb=" N LYS B4182 " pdb=" CA LYS B4182 " ideal model delta harmonic sigma weight residual 180.00 148.96 31.04 0 5.00e+00 4.00e-02 3.85e+01 dihedral pdb=" CA GLU C4181 " pdb=" C GLU C4181 " pdb=" N LYS C4182 " pdb=" CA LYS C4182 " ideal model delta harmonic sigma weight residual 180.00 149.00 31.00 0 5.00e+00 4.00e-02 3.85e+01 ... (remaining 72313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 15801 0.053 - 0.105: 2837 0.105 - 0.158: 358 0.158 - 0.211: 20 0.211 - 0.263: 12 Chirality restraints: 19028 Sorted by residual: chirality pdb=" CG LEU B4002 " pdb=" CB LEU B4002 " pdb=" CD1 LEU B4002 " pdb=" CD2 LEU B4002 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CG LEU C4002 " pdb=" CB LEU C4002 " pdb=" CD1 LEU C4002 " pdb=" CD2 LEU C4002 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CG LEU A4002 " pdb=" CB LEU A4002 " pdb=" CD1 LEU A4002 " pdb=" CD2 LEU A4002 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 19025 not shown) Planarity restraints: 21400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 76 " -0.136 9.50e-02 1.11e+02 6.77e-02 1.32e+01 pdb=" NE ARG C 76 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG C 76 " 0.059 2.00e-02 2.50e+03 pdb=" NH1 ARG C 76 " -0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG C 76 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 76 " 0.137 9.50e-02 1.11e+02 6.79e-02 1.31e+01 pdb=" NE ARG A 76 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 76 " -0.058 2.00e-02 2.50e+03 pdb=" NH1 ARG A 76 " 0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG A 76 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 76 " 0.137 9.50e-02 1.11e+02 6.82e-02 1.31e+01 pdb=" NE ARG D 76 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG D 76 " -0.058 2.00e-02 2.50e+03 pdb=" NH1 ARG D 76 " 0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG D 76 " 0.024 2.00e-02 2.50e+03 ... (remaining 21397 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 7433 2.74 - 3.28: 123489 3.28 - 3.82: 197063 3.82 - 4.36: 208214 4.36 - 4.90: 365115 Nonbonded interactions: 901314 Sorted by model distance: nonbonded pdb=" O LYS B2184 " pdb=" OG1 THR B2187 " model vdw 2.197 2.440 nonbonded pdb=" O LYS D2184 " pdb=" OG1 THR D2187 " model vdw 2.197 2.440 nonbonded pdb=" O LYS A2184 " pdb=" OG1 THR A2187 " model vdw 2.197 2.440 nonbonded pdb=" O LYS C2184 " pdb=" OG1 THR C2187 " model vdw 2.197 2.440 nonbonded pdb=" O GLN D1794 " pdb=" OG1 THR D1797 " model vdw 2.215 2.440 ... (remaining 901309 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.040 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: 23.260 Check model and map are aligned: 1.270 Set scattering table: 0.800 Process input model: 269.660 Find NCS groups from input model: 6.310 Set up NCS constraints: 0.740 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 310.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 121556 Z= 0.167 Angle : 0.667 13.182 165096 Z= 0.341 Chirality : 0.040 0.263 19028 Planarity : 0.004 0.075 21400 Dihedral : 17.686 89.823 42420 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.52 % Allowed : 11.34 % Favored : 88.14 % Rotamer: Outliers : 0.26 % Allowed : 25.38 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.07), residues: 15692 helix: 0.71 (0.06), residues: 7228 sheet: -2.35 (0.19), residues: 736 loop : -2.98 (0.06), residues: 7728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 902 HIS 0.012 0.001 HIS B 29 PHE 0.023 0.001 PHE A 13 TYR 0.027 0.001 TYR C 508 ARG 0.057 0.001 ARG C 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31384 Ramachandran restraints generated. 15692 Oldfield, 0 Emsley, 15692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31384 Ramachandran restraints generated. 15692 Oldfield, 0 Emsley, 15692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 13992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 763 time to evaluate : 10.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 995 MET cc_start: 0.3221 (ttt) cc_final: 0.2959 (tmm) REVERT: B 995 MET cc_start: 0.3216 (ttt) cc_final: 0.2958 (tmm) REVERT: C 995 MET cc_start: 0.2877 (ttt) cc_final: 0.2635 (tmm) REVERT: D 995 MET cc_start: 0.3018 (ttt) cc_final: 0.2771 (tmm) outliers start: 31 outliers final: 14 residues processed: 784 average time/residue: 0.8785 time to fit residues: 1264.1934 Evaluate side-chains 756 residues out of total 13992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 742 time to evaluate : 9.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 2330 PHE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 2330 PHE Chi-restraints excluded: chain B residue 2997 ASN Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 2330 PHE Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 2330 PHE Chi-restraints excluded: chain G residue 30 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1592 random chunks: chunk 1344 optimal weight: 9.9990 chunk 1206 optimal weight: 6.9990 chunk 669 optimal weight: 8.9990 chunk 412 optimal weight: 20.0000 chunk 813 optimal weight: 5.9990 chunk 644 optimal weight: 9.9990 chunk 1247 optimal weight: 30.0000 chunk 482 optimal weight: 30.0000 chunk 758 optimal weight: 3.9990 chunk 928 optimal weight: 4.9990 chunk 1445 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS A 842 GLN A 888 ASN A 890 HIS A1147 GLN ** A1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1671 HIS A1711 HIS A1999 HIS ** A2249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3446 GLN ** A3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4158 GLN A4487 GLN A4786 ASN ** A4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4944 GLN B 193 HIS B 842 GLN B 888 ASN B 890 HIS B1147 GLN ** B1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1671 HIS B1711 HIS B1999 HIS B2249 ASN B3446 GLN ** B3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4158 GLN B4487 GLN B4786 ASN B4944 GLN C 193 HIS C 299 HIS C 842 GLN C 888 ASN C 890 HIS C1147 GLN ** C1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1671 HIS C1711 HIS C1999 HIS ** C2249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3446 GLN ** C3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4158 GLN C4487 GLN C4786 ASN ** C4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C4944 GLN D 193 HIS D 299 HIS D 842 GLN D 888 ASN D 890 HIS D1147 GLN D1169 ASN ** D1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1671 HIS D1711 HIS D1999 HIS ** D2249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3446 GLN ** D3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4158 GLN D4487 GLN D4786 ASN ** D4913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D4944 GLN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.119 121556 Z= 0.459 Angle : 0.726 9.366 165096 Z= 0.379 Chirality : 0.044 0.254 19028 Planarity : 0.005 0.078 21400 Dihedral : 4.773 37.870 16889 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.58 % Allowed : 11.79 % Favored : 87.63 % Rotamer: Outliers : 4.00 % Allowed : 24.08 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.07), residues: 15692 helix: 0.89 (0.06), residues: 7240 sheet: -2.57 (0.18), residues: 732 loop : -2.94 (0.07), residues: 7720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D4644 HIS 0.010 0.001 HIS A4912 PHE 0.045 0.003 PHE D4785 TYR 0.032 0.002 TYR D3690 ARG 0.008 0.001 ARG B4789 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31384 Ramachandran restraints generated. 15692 Oldfield, 0 Emsley, 15692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31384 Ramachandran restraints generated. 15692 Oldfield, 0 Emsley, 15692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1202 residues out of total 13992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 478 poor density : 724 time to evaluate : 9.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 995 MET cc_start: 0.2904 (ttt) cc_final: 0.2685 (tmm) REVERT: A 1300 MET cc_start: 0.7690 (ptt) cc_final: 0.7287 (ppp) REVERT: A 2286 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.6236 (t0) REVERT: A 2293 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6577 (pt0) REVERT: A 2694 MET cc_start: 0.6458 (mpp) cc_final: 0.5864 (mpp) REVERT: A 3202 ASP cc_start: -0.1026 (OUTLIER) cc_final: -0.2411 (t0) REVERT: A 3262 MET cc_start: -0.0868 (tmm) cc_final: -0.1747 (tpt) REVERT: A 3661 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7851 (m-30) REVERT: A 3905 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8409 (m-80) REVERT: A 3934 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.9030 (mp) REVERT: A 4001 MET cc_start: 0.8526 (tmm) cc_final: 0.8204 (tmm) REVERT: B 995 MET cc_start: 0.2901 (ttt) cc_final: 0.2689 (tmm) REVERT: B 1300 MET cc_start: 0.7737 (ptt) cc_final: 0.7298 (ppp) REVERT: B 2286 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.6239 (t0) REVERT: B 2293 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6494 (pt0) REVERT: B 2694 MET cc_start: 0.6071 (mpp) cc_final: 0.5358 (mpp) REVERT: B 3202 ASP cc_start: -0.1192 (OUTLIER) cc_final: -0.2447 (t0) REVERT: B 3661 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7901 (m-30) REVERT: B 3905 PHE cc_start: 0.8926 (OUTLIER) cc_final: 0.8366 (m-80) REVERT: B 4001 MET cc_start: 0.8586 (tmm) cc_final: 0.8232 (tmm) REVERT: C 995 MET cc_start: 0.3052 (ttt) cc_final: 0.2732 (tmm) REVERT: C 1300 MET cc_start: 0.7705 (ptt) cc_final: 0.7285 (ppp) REVERT: C 2286 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.6244 (t0) REVERT: C 2293 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6558 (pt0) REVERT: C 2694 MET cc_start: 0.6431 (mpp) cc_final: 0.5831 (mpp) REVERT: C 3202 ASP cc_start: -0.1197 (OUTLIER) cc_final: -0.2566 (t0) REVERT: C 3262 MET cc_start: -0.0856 (tmm) cc_final: -0.1691 (tpt) REVERT: C 3661 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7910 (m-30) REVERT: C 3905 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8410 (m-80) REVERT: C 3934 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9039 (mp) REVERT: C 4001 MET cc_start: 0.8557 (tmm) cc_final: 0.8202 (tmm) REVERT: D 995 MET cc_start: 0.2904 (ttt) cc_final: 0.2689 (tmm) REVERT: D 1300 MET cc_start: 0.7733 (ptt) cc_final: 0.7331 (ppp) REVERT: D 2286 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.6241 (t0) REVERT: D 2293 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6554 (pt0) REVERT: D 2694 MET cc_start: 0.6449 (mpp) cc_final: 0.5850 (mpp) REVERT: D 3262 MET cc_start: -0.0673 (tmm) cc_final: -0.1507 (tpt) REVERT: D 3661 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7845 (m-30) REVERT: D 3905 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8416 (m-80) REVERT: D 3934 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9044 (mp) REVERT: D 4001 MET cc_start: 0.8554 (tmm) cc_final: 0.8198 (tmm) outliers start: 478 outliers final: 229 residues processed: 1154 average time/residue: 0.8593 time to fit residues: 1833.2434 Evaluate side-chains 949 residues out of total 13992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 698 time to evaluate : 9.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 608 HIS Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain A residue 1146 HIS Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1467 VAL Chi-restraints excluded: chain A residue 1595 VAL Chi-restraints excluded: chain A residue 1663 SER Chi-restraints excluded: chain A residue 1777 TYR Chi-restraints excluded: chain A residue 1941 PHE Chi-restraints excluded: chain A residue 1998 PHE Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2286 ASP Chi-restraints excluded: chain A residue 2293 GLU Chi-restraints excluded: chain A residue 2305 VAL Chi-restraints excluded: chain A residue 2330 PHE Chi-restraints excluded: chain A residue 2454 ASP Chi-restraints excluded: chain A residue 2455 MET Chi-restraints excluded: chain A residue 2482 PHE Chi-restraints excluded: chain A residue 2516 ASN Chi-restraints excluded: chain A residue 2831 THR Chi-restraints excluded: chain A residue 3202 ASP Chi-restraints excluded: chain A residue 3215 THR Chi-restraints excluded: chain A residue 3616 VAL Chi-restraints excluded: chain A residue 3661 ASP Chi-restraints excluded: chain A residue 3693 ILE Chi-restraints excluded: chain A residue 3698 CYS Chi-restraints excluded: chain A residue 3713 PHE Chi-restraints excluded: chain A residue 3828 VAL Chi-restraints excluded: chain A residue 3865 THR Chi-restraints excluded: chain A residue 3905 PHE Chi-restraints excluded: chain A residue 3934 LEU Chi-restraints excluded: chain A residue 3958 SER Chi-restraints excluded: chain A residue 3997 GLN Chi-restraints excluded: chain A residue 4110 ASN Chi-restraints excluded: chain A residue 4175 VAL Chi-restraints excluded: chain A residue 4503 LEU Chi-restraints excluded: chain A residue 4516 LEU Chi-restraints excluded: chain A residue 4587 ILE Chi-restraints excluded: chain A residue 4654 ASP Chi-restraints excluded: chain A residue 4702 VAL Chi-restraints excluded: chain A residue 4788 PHE Chi-restraints excluded: chain A residue 4858 LEU Chi-restraints excluded: chain A residue 4860 ILE Chi-restraints excluded: chain A residue 4867 ASP Chi-restraints excluded: chain A residue 4879 VAL Chi-restraints excluded: chain A residue 4890 CYS Chi-restraints excluded: chain A residue 4921 LEU Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 608 HIS Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 650 ASN Chi-restraints excluded: chain B residue 751 THR Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 1087 ILE Chi-restraints excluded: chain B residue 1093 THR Chi-restraints excluded: chain B residue 1146 HIS Chi-restraints excluded: chain B residue 1441 VAL Chi-restraints excluded: chain B residue 1467 VAL Chi-restraints excluded: chain B residue 1595 VAL Chi-restraints excluded: chain B residue 1663 SER Chi-restraints excluded: chain B residue 1777 TYR Chi-restraints excluded: chain B residue 1915 CYS Chi-restraints excluded: chain B residue 1941 PHE Chi-restraints excluded: chain B residue 1995 LEU Chi-restraints excluded: chain B residue 1998 PHE Chi-restraints excluded: chain B residue 2237 THR Chi-restraints excluded: chain B residue 2286 ASP Chi-restraints excluded: chain B residue 2293 GLU Chi-restraints excluded: chain B residue 2305 VAL Chi-restraints excluded: chain B residue 2330 PHE Chi-restraints excluded: chain B residue 2454 ASP Chi-restraints excluded: chain B residue 2455 MET Chi-restraints excluded: chain B residue 2482 PHE Chi-restraints excluded: chain B residue 2516 ASN Chi-restraints excluded: chain B residue 2831 THR Chi-restraints excluded: chain B residue 3202 ASP Chi-restraints excluded: chain B residue 3215 THR Chi-restraints excluded: chain B residue 3616 VAL Chi-restraints excluded: chain B residue 3661 ASP Chi-restraints excluded: chain B residue 3693 ILE Chi-restraints excluded: chain B residue 3698 CYS Chi-restraints excluded: chain B residue 3713 PHE Chi-restraints excluded: chain B residue 3828 VAL Chi-restraints excluded: chain B residue 3865 THR Chi-restraints excluded: chain B residue 3905 PHE Chi-restraints excluded: chain B residue 3958 SER Chi-restraints excluded: chain B residue 3997 GLN Chi-restraints excluded: chain B residue 4110 ASN Chi-restraints excluded: chain B residue 4175 VAL Chi-restraints excluded: chain B residue 4503 LEU Chi-restraints excluded: chain B residue 4516 LEU Chi-restraints excluded: chain B residue 4587 ILE Chi-restraints excluded: chain B residue 4702 VAL Chi-restraints excluded: chain B residue 4788 PHE Chi-restraints excluded: chain B residue 4858 LEU Chi-restraints excluded: chain B residue 4860 ILE Chi-restraints excluded: chain B residue 4867 ASP Chi-restraints excluded: chain B residue 4879 VAL Chi-restraints excluded: chain B residue 4890 CYS Chi-restraints excluded: chain B residue 4921 LEU Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 608 HIS Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 650 ASN Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 1087 ILE Chi-restraints excluded: chain C residue 1093 THR Chi-restraints excluded: chain C residue 1146 HIS Chi-restraints excluded: chain C residue 1441 VAL Chi-restraints excluded: chain C residue 1467 VAL Chi-restraints excluded: chain C residue 1595 VAL Chi-restraints excluded: chain C residue 1663 SER Chi-restraints excluded: chain C residue 1777 TYR Chi-restraints excluded: chain C residue 1941 PHE Chi-restraints excluded: chain C residue 1995 LEU Chi-restraints excluded: chain C residue 1998 PHE Chi-restraints excluded: chain C residue 2237 THR Chi-restraints excluded: chain C residue 2286 ASP Chi-restraints excluded: chain C residue 2293 GLU Chi-restraints excluded: chain C residue 2305 VAL Chi-restraints excluded: chain C residue 2330 PHE Chi-restraints excluded: chain C residue 2454 ASP Chi-restraints excluded: chain C residue 2455 MET Chi-restraints excluded: chain C residue 2482 PHE Chi-restraints excluded: chain C residue 2516 ASN Chi-restraints excluded: chain C residue 2831 THR Chi-restraints excluded: chain C residue 3202 ASP Chi-restraints excluded: chain C residue 3215 THR Chi-restraints excluded: chain C residue 3616 VAL Chi-restraints excluded: chain C residue 3661 ASP Chi-restraints excluded: chain C residue 3693 ILE Chi-restraints excluded: chain C residue 3698 CYS Chi-restraints excluded: chain C residue 3713 PHE Chi-restraints excluded: chain C residue 3828 VAL Chi-restraints excluded: chain C residue 3865 THR Chi-restraints excluded: chain C residue 3905 PHE Chi-restraints excluded: chain C residue 3934 LEU Chi-restraints excluded: chain C residue 3958 SER Chi-restraints excluded: chain C residue 3997 GLN Chi-restraints excluded: chain C residue 4110 ASN Chi-restraints excluded: chain C residue 4175 VAL Chi-restraints excluded: chain C residue 4503 LEU Chi-restraints excluded: chain C residue 4516 LEU Chi-restraints excluded: chain C residue 4587 ILE Chi-restraints excluded: chain C residue 4702 VAL Chi-restraints excluded: chain C residue 4788 PHE Chi-restraints excluded: chain C residue 4858 LEU Chi-restraints excluded: chain C residue 4860 ILE Chi-restraints excluded: chain C residue 4867 ASP Chi-restraints excluded: chain C residue 4879 VAL Chi-restraints excluded: chain C residue 4890 CYS Chi-restraints excluded: chain C residue 4921 LEU Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 608 HIS Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 650 ASN Chi-restraints excluded: chain D residue 751 THR Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 1087 ILE Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1146 HIS Chi-restraints excluded: chain D residue 1441 VAL Chi-restraints excluded: chain D residue 1467 VAL Chi-restraints excluded: chain D residue 1595 VAL Chi-restraints excluded: chain D residue 1663 SER Chi-restraints excluded: chain D residue 1777 TYR Chi-restraints excluded: chain D residue 1941 PHE Chi-restraints excluded: chain D residue 1995 LEU Chi-restraints excluded: chain D residue 1998 PHE Chi-restraints excluded: chain D residue 2237 THR Chi-restraints excluded: chain D residue 2286 ASP Chi-restraints excluded: chain D residue 2293 GLU Chi-restraints excluded: chain D residue 2305 VAL Chi-restraints excluded: chain D residue 2330 PHE Chi-restraints excluded: chain D residue 2454 ASP Chi-restraints excluded: chain D residue 2455 MET Chi-restraints excluded: chain D residue 2482 PHE Chi-restraints excluded: chain D residue 2516 ASN Chi-restraints excluded: chain D residue 2831 THR Chi-restraints excluded: chain D residue 3215 THR Chi-restraints excluded: chain D residue 3616 VAL Chi-restraints excluded: chain D residue 3630 THR Chi-restraints excluded: chain D residue 3661 ASP Chi-restraints excluded: chain D residue 3693 ILE Chi-restraints excluded: chain D residue 3698 CYS Chi-restraints excluded: chain D residue 3713 PHE Chi-restraints excluded: chain D residue 3828 VAL Chi-restraints excluded: chain D residue 3865 THR Chi-restraints excluded: chain D residue 3905 PHE Chi-restraints excluded: chain D residue 3934 LEU Chi-restraints excluded: chain D residue 3958 SER Chi-restraints excluded: chain D residue 3997 GLN Chi-restraints excluded: chain D residue 4110 ASN Chi-restraints excluded: chain D residue 4175 VAL Chi-restraints excluded: chain D residue 4503 LEU Chi-restraints excluded: chain D residue 4516 LEU Chi-restraints excluded: chain D residue 4587 ILE Chi-restraints excluded: chain D residue 4702 VAL Chi-restraints excluded: chain D residue 4788 PHE Chi-restraints excluded: chain D residue 4858 LEU Chi-restraints excluded: chain D residue 4860 ILE Chi-restraints excluded: chain D residue 4867 ASP Chi-restraints excluded: chain D residue 4879 VAL Chi-restraints excluded: chain D residue 4890 CYS Chi-restraints excluded: chain D residue 4921 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 33 ASN Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 102 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1592 random chunks: chunk 803 optimal weight: 20.0000 chunk 448 optimal weight: 8.9990 chunk 1203 optimal weight: 7.9990 chunk 984 optimal weight: 9.9990 chunk 398 optimal weight: 0.0000 chunk 1448 optimal weight: 10.0000 chunk 1564 optimal weight: 20.0000 chunk 1289 optimal weight: 50.0000 chunk 1436 optimal weight: 10.0000 chunk 493 optimal weight: 30.0000 chunk 1161 optimal weight: 0.9990 overall best weight: 5.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS A 398 HIS A 731 HIS ** A1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1842 HIS A2249 ASN ** A3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3843 GLN B 288 HIS B 299 HIS B 398 HIS ** B1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1842 HIS B2249 ASN ** B3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3843 GLN C 288 HIS C 398 HIS C 731 HIS ** C1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1842 HIS C2249 ASN ** C3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3843 GLN D 288 HIS D 398 HIS ** D1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1842 HIS D2249 ASN ** D3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3843 GLN F 32 GLN G 26 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 121556 Z= 0.403 Angle : 0.674 9.276 165096 Z= 0.350 Chirality : 0.042 0.256 19028 Planarity : 0.004 0.071 21400 Dihedral : 4.895 37.310 16880 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.53 % Allowed : 12.52 % Favored : 86.96 % Rotamer: Outliers : 5.37 % Allowed : 23.60 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.07), residues: 15692 helix: 0.96 (0.06), residues: 7240 sheet: -2.68 (0.19), residues: 668 loop : -2.94 (0.07), residues: 7784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 733 HIS 0.011 0.001 HIS C3731 PHE 0.028 0.002 PHE B4845 TYR 0.022 0.002 TYR B 508 ARG 0.008 0.000 ARG B 504 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31384 Ramachandran restraints generated. 15692 Oldfield, 0 Emsley, 15692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31384 Ramachandran restraints generated. 15692 Oldfield, 0 Emsley, 15692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1346 residues out of total 13992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 643 poor density : 703 time to evaluate : 11.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 802 PHE cc_start: 0.6837 (OUTLIER) cc_final: 0.5898 (m-80) REVERT: A 989 THR cc_start: 0.3677 (OUTLIER) cc_final: 0.3367 (m) REVERT: A 1300 MET cc_start: 0.7754 (ptt) cc_final: 0.7259 (ppp) REVERT: A 1460 ASP cc_start: 0.6357 (OUTLIER) cc_final: 0.4107 (t0) REVERT: A 1629 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.7552 (ptp) REVERT: A 2286 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.6315 (t0) REVERT: A 2293 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6556 (pt0) REVERT: A 2480 GLN cc_start: 0.2059 (OUTLIER) cc_final: 0.0463 (mp10) REVERT: A 2694 MET cc_start: 0.6359 (mpp) cc_final: 0.5722 (mpp) REVERT: A 3262 MET cc_start: -0.0595 (tmm) cc_final: -0.1538 (tpt) REVERT: A 3661 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7746 (m-30) REVERT: A 3663 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.7927 (tt) REVERT: A 3905 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.8326 (m-80) REVERT: A 3923 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7985 (pt) REVERT: A 3997 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.7864 (mp10) REVERT: A 3998 MET cc_start: 0.8648 (mmt) cc_final: 0.8403 (mmt) REVERT: A 4001 MET cc_start: 0.8670 (tmm) cc_final: 0.8363 (tmm) REVERT: B 81 MET cc_start: 0.8312 (mpp) cc_final: 0.7515 (mpp) REVERT: B 802 PHE cc_start: 0.6846 (OUTLIER) cc_final: 0.5923 (m-80) REVERT: B 989 THR cc_start: 0.3666 (OUTLIER) cc_final: 0.3362 (m) REVERT: B 1300 MET cc_start: 0.7570 (ptt) cc_final: 0.7101 (ppp) REVERT: B 1460 ASP cc_start: 0.6398 (OUTLIER) cc_final: 0.4226 (t0) REVERT: B 1629 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.7480 (ptp) REVERT: B 2286 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.6260 (t0) REVERT: B 2293 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6565 (pt0) REVERT: B 2480 GLN cc_start: 0.2069 (OUTLIER) cc_final: 0.0633 (mp10) REVERT: B 2694 MET cc_start: 0.6265 (mpp) cc_final: 0.5568 (mpp) REVERT: B 3262 MET cc_start: 0.0187 (tmm) cc_final: -0.0452 (tpt) REVERT: B 3661 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7817 (m-30) REVERT: B 3663 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.7966 (tt) REVERT: B 3905 PHE cc_start: 0.8895 (OUTLIER) cc_final: 0.8332 (m-80) REVERT: B 3997 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.7970 (mp10) REVERT: B 4001 MET cc_start: 0.8660 (tmm) cc_final: 0.8258 (tmm) REVERT: C 802 PHE cc_start: 0.6869 (OUTLIER) cc_final: 0.5914 (m-80) REVERT: C 989 THR cc_start: 0.3697 (OUTLIER) cc_final: 0.3386 (m) REVERT: C 1300 MET cc_start: 0.7752 (ptt) cc_final: 0.7228 (ppp) REVERT: C 1460 ASP cc_start: 0.6380 (OUTLIER) cc_final: 0.4121 (t0) REVERT: C 1629 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.7528 (ptp) REVERT: C 2286 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.6385 (t0) REVERT: C 2293 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6493 (pt0) REVERT: C 2480 GLN cc_start: 0.2065 (OUTLIER) cc_final: 0.0403 (mp10) REVERT: C 2694 MET cc_start: 0.6290 (mpp) cc_final: 0.5653 (mpp) REVERT: C 3262 MET cc_start: -0.0685 (tmm) cc_final: -0.1566 (tpt) REVERT: C 3661 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7820 (m-30) REVERT: C 3663 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.7962 (tt) REVERT: C 3905 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8328 (m-80) REVERT: C 3923 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7989 (pt) REVERT: C 3997 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.7951 (mp10) REVERT: C 4001 MET cc_start: 0.8632 (tmm) cc_final: 0.8274 (tmm) REVERT: D 802 PHE cc_start: 0.6873 (OUTLIER) cc_final: 0.5913 (m-80) REVERT: D 989 THR cc_start: 0.3689 (OUTLIER) cc_final: 0.3379 (m) REVERT: D 1300 MET cc_start: 0.7662 (ptt) cc_final: 0.7203 (ppp) REVERT: D 1460 ASP cc_start: 0.6391 (OUTLIER) cc_final: 0.4144 (t0) REVERT: D 1629 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.7506 (ptp) REVERT: D 2168 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7544 (mm-30) REVERT: D 2286 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.6317 (t0) REVERT: D 2293 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6507 (pt0) REVERT: D 2480 GLN cc_start: 0.1835 (OUTLIER) cc_final: 0.0243 (mp10) REVERT: D 2694 MET cc_start: 0.6352 (mpp) cc_final: 0.5668 (mpp) REVERT: D 3262 MET cc_start: -0.0675 (tmm) cc_final: -0.1540 (tpt) REVERT: D 3661 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7774 (m-30) REVERT: D 3663 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.7939 (tt) REVERT: D 3905 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8333 (m-80) REVERT: D 3923 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7989 (pt) REVERT: D 3997 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.7908 (mp10) REVERT: D 3998 MET cc_start: 0.8646 (mmt) cc_final: 0.8402 (mmt) REVERT: D 4001 MET cc_start: 0.8621 (tmm) cc_final: 0.8312 (tmm) REVERT: E 5 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.8028 (tp) REVERT: F 5 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7954 (tp) REVERT: G 5 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8118 (tp) REVERT: H 5 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8113 (tp) outliers start: 643 outliers final: 333 residues processed: 1266 average time/residue: 0.8673 time to fit residues: 2031.5529 Evaluate side-chains 1076 residues out of total 13992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 385 poor density : 691 time to evaluate : 9.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 608 HIS Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 733 TRP Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 890 HIS Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain A residue 1146 HIS Chi-restraints excluded: chain A residue 1195 PHE Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1442 TRP Chi-restraints excluded: chain A residue 1460 ASP Chi-restraints excluded: chain A residue 1595 VAL Chi-restraints excluded: chain A residue 1629 MET Chi-restraints excluded: chain A residue 1632 HIS Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1663 SER Chi-restraints excluded: chain A residue 1777 TYR Chi-restraints excluded: chain A residue 1915 CYS Chi-restraints excluded: chain A residue 1917 VAL Chi-restraints excluded: chain A residue 1941 PHE Chi-restraints excluded: chain A residue 2011 ASP Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2127 SER Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2250 ASN Chi-restraints excluded: chain A residue 2280 VAL Chi-restraints excluded: chain A residue 2286 ASP Chi-restraints excluded: chain A residue 2293 GLU Chi-restraints excluded: chain A residue 2330 PHE Chi-restraints excluded: chain A residue 2422 LEU Chi-restraints excluded: chain A residue 2425 LEU Chi-restraints excluded: chain A residue 2455 MET Chi-restraints excluded: chain A residue 2480 GLN Chi-restraints excluded: chain A residue 2482 PHE Chi-restraints excluded: chain A residue 2523 VAL Chi-restraints excluded: chain A residue 2831 THR Chi-restraints excluded: chain A residue 3215 THR Chi-restraints excluded: chain A residue 3630 THR Chi-restraints excluded: chain A residue 3661 ASP Chi-restraints excluded: chain A residue 3663 LEU Chi-restraints excluded: chain A residue 3713 PHE Chi-restraints excluded: chain A residue 3828 VAL Chi-restraints excluded: chain A residue 3865 THR Chi-restraints excluded: chain A residue 3905 PHE Chi-restraints excluded: chain A residue 3923 ILE Chi-restraints excluded: chain A residue 3964 ILE Chi-restraints excluded: chain A residue 3997 GLN Chi-restraints excluded: chain A residue 4105 SER Chi-restraints excluded: chain A residue 4110 ASN Chi-restraints excluded: chain A residue 4175 VAL Chi-restraints excluded: chain A residue 4516 LEU Chi-restraints excluded: chain A residue 4570 THR Chi-restraints excluded: chain A residue 4587 ILE Chi-restraints excluded: chain A residue 4654 ASP Chi-restraints excluded: chain A residue 4665 ILE Chi-restraints excluded: chain A residue 4671 MET Chi-restraints excluded: chain A residue 4712 VAL Chi-restraints excluded: chain A residue 4752 LEU Chi-restraints excluded: chain A residue 4775 VAL Chi-restraints excluded: chain A residue 4846 ASP Chi-restraints excluded: chain A residue 4853 VAL Chi-restraints excluded: chain A residue 4860 ILE Chi-restraints excluded: chain A residue 4867 ASP Chi-restraints excluded: chain A residue 4879 VAL Chi-restraints excluded: chain A residue 4889 ILE Chi-restraints excluded: chain A residue 4890 CYS Chi-restraints excluded: chain A residue 4921 LEU Chi-restraints excluded: chain A residue 4933 THR Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 608 HIS Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 650 ASN Chi-restraints excluded: chain B residue 733 TRP Chi-restraints excluded: chain B residue 751 THR Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 890 HIS Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 1093 THR Chi-restraints excluded: chain B residue 1146 HIS Chi-restraints excluded: chain B residue 1195 PHE Chi-restraints excluded: chain B residue 1251 LEU Chi-restraints excluded: chain B residue 1441 VAL Chi-restraints excluded: chain B residue 1442 TRP Chi-restraints excluded: chain B residue 1460 ASP Chi-restraints excluded: chain B residue 1595 VAL Chi-restraints excluded: chain B residue 1629 MET Chi-restraints excluded: chain B residue 1651 LEU Chi-restraints excluded: chain B residue 1663 SER Chi-restraints excluded: chain B residue 1777 TYR Chi-restraints excluded: chain B residue 1829 LEU Chi-restraints excluded: chain B residue 1915 CYS Chi-restraints excluded: chain B residue 1917 VAL Chi-restraints excluded: chain B residue 1941 PHE Chi-restraints excluded: chain B residue 1995 LEU Chi-restraints excluded: chain B residue 1998 PHE Chi-restraints excluded: chain B residue 2097 LEU Chi-restraints excluded: chain B residue 2237 THR Chi-restraints excluded: chain B residue 2250 ASN Chi-restraints excluded: chain B residue 2280 VAL Chi-restraints excluded: chain B residue 2286 ASP Chi-restraints excluded: chain B residue 2293 GLU Chi-restraints excluded: chain B residue 2330 PHE Chi-restraints excluded: chain B residue 2422 LEU Chi-restraints excluded: chain B residue 2425 LEU Chi-restraints excluded: chain B residue 2480 GLN Chi-restraints excluded: chain B residue 2482 PHE Chi-restraints excluded: chain B residue 2831 THR Chi-restraints excluded: chain B residue 2997 ASN Chi-restraints excluded: chain B residue 3215 THR Chi-restraints excluded: chain B residue 3630 THR Chi-restraints excluded: chain B residue 3661 ASP Chi-restraints excluded: chain B residue 3663 LEU Chi-restraints excluded: chain B residue 3713 PHE Chi-restraints excluded: chain B residue 3828 VAL Chi-restraints excluded: chain B residue 3865 THR Chi-restraints excluded: chain B residue 3905 PHE Chi-restraints excluded: chain B residue 3997 GLN Chi-restraints excluded: chain B residue 4105 SER Chi-restraints excluded: chain B residue 4110 ASN Chi-restraints excluded: chain B residue 4175 VAL Chi-restraints excluded: chain B residue 4516 LEU Chi-restraints excluded: chain B residue 4570 THR Chi-restraints excluded: chain B residue 4587 ILE Chi-restraints excluded: chain B residue 4654 ASP Chi-restraints excluded: chain B residue 4665 ILE Chi-restraints excluded: chain B residue 4671 MET Chi-restraints excluded: chain B residue 4712 VAL Chi-restraints excluded: chain B residue 4752 LEU Chi-restraints excluded: chain B residue 4775 VAL Chi-restraints excluded: chain B residue 4846 ASP Chi-restraints excluded: chain B residue 4853 VAL Chi-restraints excluded: chain B residue 4860 ILE Chi-restraints excluded: chain B residue 4867 ASP Chi-restraints excluded: chain B residue 4879 VAL Chi-restraints excluded: chain B residue 4889 ILE Chi-restraints excluded: chain B residue 4890 CYS Chi-restraints excluded: chain B residue 4921 LEU Chi-restraints excluded: chain B residue 4933 THR Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 608 HIS Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 650 ASN Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 802 PHE Chi-restraints excluded: chain C residue 890 HIS Chi-restraints excluded: chain C residue 989 THR Chi-restraints excluded: chain C residue 1093 THR Chi-restraints excluded: chain C residue 1146 HIS Chi-restraints excluded: chain C residue 1195 PHE Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1441 VAL Chi-restraints excluded: chain C residue 1442 TRP Chi-restraints excluded: chain C residue 1460 ASP Chi-restraints excluded: chain C residue 1595 VAL Chi-restraints excluded: chain C residue 1629 MET Chi-restraints excluded: chain C residue 1632 HIS Chi-restraints excluded: chain C residue 1651 LEU Chi-restraints excluded: chain C residue 1663 SER Chi-restraints excluded: chain C residue 1777 TYR Chi-restraints excluded: chain C residue 1915 CYS Chi-restraints excluded: chain C residue 1917 VAL Chi-restraints excluded: chain C residue 1941 PHE Chi-restraints excluded: chain C residue 1995 LEU Chi-restraints excluded: chain C residue 2011 ASP Chi-restraints excluded: chain C residue 2097 LEU Chi-restraints excluded: chain C residue 2127 SER Chi-restraints excluded: chain C residue 2237 THR Chi-restraints excluded: chain C residue 2250 ASN Chi-restraints excluded: chain C residue 2280 VAL Chi-restraints excluded: chain C residue 2286 ASP Chi-restraints excluded: chain C residue 2293 GLU Chi-restraints excluded: chain C residue 2330 PHE Chi-restraints excluded: chain C residue 2422 LEU Chi-restraints excluded: chain C residue 2425 LEU Chi-restraints excluded: chain C residue 2455 MET Chi-restraints excluded: chain C residue 2480 GLN Chi-restraints excluded: chain C residue 2482 PHE Chi-restraints excluded: chain C residue 2663 LEU Chi-restraints excluded: chain C residue 2831 THR Chi-restraints excluded: chain C residue 3215 THR Chi-restraints excluded: chain C residue 3630 THR Chi-restraints excluded: chain C residue 3661 ASP Chi-restraints excluded: chain C residue 3663 LEU Chi-restraints excluded: chain C residue 3713 PHE Chi-restraints excluded: chain C residue 3828 VAL Chi-restraints excluded: chain C residue 3865 THR Chi-restraints excluded: chain C residue 3905 PHE Chi-restraints excluded: chain C residue 3923 ILE Chi-restraints excluded: chain C residue 3964 ILE Chi-restraints excluded: chain C residue 3997 GLN Chi-restraints excluded: chain C residue 4105 SER Chi-restraints excluded: chain C residue 4110 ASN Chi-restraints excluded: chain C residue 4175 VAL Chi-restraints excluded: chain C residue 4516 LEU Chi-restraints excluded: chain C residue 4570 THR Chi-restraints excluded: chain C residue 4587 ILE Chi-restraints excluded: chain C residue 4654 ASP Chi-restraints excluded: chain C residue 4665 ILE Chi-restraints excluded: chain C residue 4671 MET Chi-restraints excluded: chain C residue 4712 VAL Chi-restraints excluded: chain C residue 4752 LEU Chi-restraints excluded: chain C residue 4775 VAL Chi-restraints excluded: chain C residue 4846 ASP Chi-restraints excluded: chain C residue 4853 VAL Chi-restraints excluded: chain C residue 4860 ILE Chi-restraints excluded: chain C residue 4867 ASP Chi-restraints excluded: chain C residue 4879 VAL Chi-restraints excluded: chain C residue 4889 ILE Chi-restraints excluded: chain C residue 4890 CYS Chi-restraints excluded: chain C residue 4921 LEU Chi-restraints excluded: chain C residue 4933 THR Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 608 HIS Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 650 ASN Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 733 TRP Chi-restraints excluded: chain D residue 751 THR Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 802 PHE Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 989 THR Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1146 HIS Chi-restraints excluded: chain D residue 1195 PHE Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1441 VAL Chi-restraints excluded: chain D residue 1442 TRP Chi-restraints excluded: chain D residue 1460 ASP Chi-restraints excluded: chain D residue 1595 VAL Chi-restraints excluded: chain D residue 1629 MET Chi-restraints excluded: chain D residue 1632 HIS Chi-restraints excluded: chain D residue 1651 LEU Chi-restraints excluded: chain D residue 1663 SER Chi-restraints excluded: chain D residue 1777 TYR Chi-restraints excluded: chain D residue 1915 CYS Chi-restraints excluded: chain D residue 1917 VAL Chi-restraints excluded: chain D residue 1941 PHE Chi-restraints excluded: chain D residue 1995 LEU Chi-restraints excluded: chain D residue 2011 ASP Chi-restraints excluded: chain D residue 2097 LEU Chi-restraints excluded: chain D residue 2127 SER Chi-restraints excluded: chain D residue 2168 GLU Chi-restraints excluded: chain D residue 2237 THR Chi-restraints excluded: chain D residue 2250 ASN Chi-restraints excluded: chain D residue 2280 VAL Chi-restraints excluded: chain D residue 2286 ASP Chi-restraints excluded: chain D residue 2293 GLU Chi-restraints excluded: chain D residue 2330 PHE Chi-restraints excluded: chain D residue 2422 LEU Chi-restraints excluded: chain D residue 2425 LEU Chi-restraints excluded: chain D residue 2480 GLN Chi-restraints excluded: chain D residue 2482 PHE Chi-restraints excluded: chain D residue 2523 VAL Chi-restraints excluded: chain D residue 2663 LEU Chi-restraints excluded: chain D residue 2831 THR Chi-restraints excluded: chain D residue 3202 ASP Chi-restraints excluded: chain D residue 3215 THR Chi-restraints excluded: chain D residue 3661 ASP Chi-restraints excluded: chain D residue 3663 LEU Chi-restraints excluded: chain D residue 3713 PHE Chi-restraints excluded: chain D residue 3828 VAL Chi-restraints excluded: chain D residue 3865 THR Chi-restraints excluded: chain D residue 3905 PHE Chi-restraints excluded: chain D residue 3923 ILE Chi-restraints excluded: chain D residue 3964 ILE Chi-restraints excluded: chain D residue 3997 GLN Chi-restraints excluded: chain D residue 4105 SER Chi-restraints excluded: chain D residue 4110 ASN Chi-restraints excluded: chain D residue 4175 VAL Chi-restraints excluded: chain D residue 4516 LEU Chi-restraints excluded: chain D residue 4570 THR Chi-restraints excluded: chain D residue 4587 ILE Chi-restraints excluded: chain D residue 4654 ASP Chi-restraints excluded: chain D residue 4665 ILE Chi-restraints excluded: chain D residue 4671 MET Chi-restraints excluded: chain D residue 4712 VAL Chi-restraints excluded: chain D residue 4752 LEU Chi-restraints excluded: chain D residue 4775 VAL Chi-restraints excluded: chain D residue 4846 ASP Chi-restraints excluded: chain D residue 4853 VAL Chi-restraints excluded: chain D residue 4860 ILE Chi-restraints excluded: chain D residue 4867 ASP Chi-restraints excluded: chain D residue 4879 VAL Chi-restraints excluded: chain D residue 4889 ILE Chi-restraints excluded: chain D residue 4890 CYS Chi-restraints excluded: chain D residue 4921 LEU Chi-restraints excluded: chain D residue 4933 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 5 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 ASN Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 102 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1592 random chunks: chunk 1430 optimal weight: 30.0000 chunk 1088 optimal weight: 0.6980 chunk 751 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 691 optimal weight: 8.9990 chunk 972 optimal weight: 0.9990 chunk 1453 optimal weight: 5.9990 chunk 1538 optimal weight: 0.7980 chunk 759 optimal weight: 2.9990 chunk 1377 optimal weight: 20.0000 chunk 414 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 GLN A1169 ASN ** A1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2209 ASN ** A3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 629 GLN ** B1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2249 ASN ** B3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 629 GLN C1169 ASN ** C1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2209 ASN ** C3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2209 ASN ** D3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 121556 Z= 0.167 Angle : 0.556 9.644 165096 Z= 0.285 Chirality : 0.039 0.160 19028 Planarity : 0.004 0.066 21400 Dihedral : 4.642 37.695 16880 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.01 % Favored : 88.52 % Rotamer: Outliers : 3.98 % Allowed : 25.01 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.07), residues: 15692 helix: 1.39 (0.06), residues: 7228 sheet: -2.56 (0.20), residues: 632 loop : -2.88 (0.07), residues: 7832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 733 HIS 0.016 0.001 HIS G 26 PHE 0.016 0.001 PHE C4845 TYR 0.015 0.001 TYR B3888 ARG 0.004 0.000 ARG B 504 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31384 Ramachandran restraints generated. 15692 Oldfield, 0 Emsley, 15692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31384 Ramachandran restraints generated. 15692 Oldfield, 0 Emsley, 15692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1227 residues out of total 13992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 476 poor density : 751 time to evaluate : 9.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 489 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8483 (t80) REVERT: A 802 PHE cc_start: 0.6830 (OUTLIER) cc_final: 0.5859 (m-80) REVERT: A 989 THR cc_start: 0.3645 (OUTLIER) cc_final: 0.3365 (m) REVERT: A 1300 MET cc_start: 0.7603 (ptt) cc_final: 0.7121 (ppp) REVERT: A 1460 ASP cc_start: 0.6273 (OUTLIER) cc_final: 0.4101 (t0) REVERT: A 1629 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7211 (ptp) REVERT: A 2286 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.6396 (t0) REVERT: A 2694 MET cc_start: 0.6138 (mpp) cc_final: 0.5392 (mpp) REVERT: A 3262 MET cc_start: -0.0681 (tmm) cc_final: -0.1562 (tpt) REVERT: A 3663 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.7783 (tt) REVERT: A 3905 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.8290 (m-80) REVERT: A 3934 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8904 (mp) REVERT: A 3997 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.7744 (mp10) REVERT: A 4001 MET cc_start: 0.8604 (tmm) cc_final: 0.8263 (tmm) REVERT: A 4518 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.7954 (m-80) REVERT: A 4807 ASP cc_start: 0.8248 (OUTLIER) cc_final: 0.7946 (p0) REVERT: B 81 MET cc_start: 0.8104 (mpp) cc_final: 0.7372 (mpp) REVERT: B 489 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8526 (t80) REVERT: B 802 PHE cc_start: 0.6838 (OUTLIER) cc_final: 0.5885 (m-80) REVERT: B 989 THR cc_start: 0.3574 (OUTLIER) cc_final: 0.3290 (m) REVERT: B 1300 MET cc_start: 0.7530 (ptt) cc_final: 0.7061 (ppp) REVERT: B 1460 ASP cc_start: 0.6315 (OUTLIER) cc_final: 0.4176 (t0) REVERT: B 1629 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7171 (ptp) REVERT: B 2286 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.6409 (t0) REVERT: B 2293 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6452 (pt0) REVERT: B 2694 MET cc_start: 0.6227 (mpp) cc_final: 0.5531 (mpp) REVERT: B 3262 MET cc_start: 0.0208 (tmm) cc_final: -0.0466 (tpt) REVERT: B 3663 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.7815 (tt) REVERT: B 3905 PHE cc_start: 0.8855 (OUTLIER) cc_final: 0.8197 (m-80) REVERT: B 3997 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.7693 (mp10) REVERT: B 4001 MET cc_start: 0.8643 (tmm) cc_final: 0.8259 (tmm) REVERT: B 4518 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.7932 (m-80) REVERT: B 4592 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8168 (tp) REVERT: B 4807 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7896 (p0) REVERT: C 489 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.8546 (t80) REVERT: C 802 PHE cc_start: 0.6904 (OUTLIER) cc_final: 0.5904 (m-80) REVERT: C 989 THR cc_start: 0.3602 (OUTLIER) cc_final: 0.3313 (m) REVERT: C 1300 MET cc_start: 0.7639 (ptt) cc_final: 0.7146 (ppp) REVERT: C 1460 ASP cc_start: 0.6309 (OUTLIER) cc_final: 0.4115 (t0) REVERT: C 1629 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.7194 (ptp) REVERT: C 2286 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.6489 (t0) REVERT: C 2694 MET cc_start: 0.6130 (mpp) cc_final: 0.5375 (mpp) REVERT: C 3262 MET cc_start: -0.0515 (tmm) cc_final: -0.1430 (tpt) REVERT: C 3663 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.7785 (tt) REVERT: C 3905 PHE cc_start: 0.8859 (OUTLIER) cc_final: 0.8204 (m-80) REVERT: C 3934 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8906 (mp) REVERT: C 3997 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7683 (mp10) REVERT: C 4001 MET cc_start: 0.8607 (tmm) cc_final: 0.8230 (tmm) REVERT: C 4518 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.7938 (m-80) REVERT: C 4807 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7941 (p0) REVERT: D 489 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8559 (t80) REVERT: D 802 PHE cc_start: 0.6907 (OUTLIER) cc_final: 0.5898 (m-80) REVERT: D 989 THR cc_start: 0.3592 (OUTLIER) cc_final: 0.3304 (m) REVERT: D 1300 MET cc_start: 0.7618 (ptt) cc_final: 0.7133 (ppp) REVERT: D 1460 ASP cc_start: 0.6318 (OUTLIER) cc_final: 0.4134 (t0) REVERT: D 1629 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.7210 (ptp) REVERT: D 2286 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.6487 (t0) REVERT: D 2694 MET cc_start: 0.6299 (mpp) cc_final: 0.5577 (mpp) REVERT: D 3262 MET cc_start: -0.0490 (tmm) cc_final: -0.1355 (tpt) REVERT: D 3663 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.7786 (tt) REVERT: D 3905 PHE cc_start: 0.8861 (OUTLIER) cc_final: 0.8291 (m-80) REVERT: D 3934 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8902 (mp) REVERT: D 3997 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.7741 (mp10) REVERT: D 4001 MET cc_start: 0.8597 (tmm) cc_final: 0.8221 (tmm) REVERT: D 4518 TYR cc_start: 0.8503 (OUTLIER) cc_final: 0.7956 (m-80) REVERT: D 4807 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7962 (p0) REVERT: F 4 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7379 (tm-30) outliers start: 476 outliers final: 275 residues processed: 1167 average time/residue: 0.8676 time to fit residues: 1867.7411 Evaluate side-chains 1036 residues out of total 13992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 324 poor density : 712 time to evaluate : 9.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 608 HIS Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 731 HIS Chi-restraints excluded: chain A residue 733 TRP Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 890 HIS Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1460 ASP Chi-restraints excluded: chain A residue 1595 VAL Chi-restraints excluded: chain A residue 1629 MET Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1777 TYR Chi-restraints excluded: chain A residue 1844 LEU Chi-restraints excluded: chain A residue 1941 PHE Chi-restraints excluded: chain A residue 2083 MET Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2104 THR Chi-restraints excluded: chain A residue 2195 CYS Chi-restraints excluded: chain A residue 2280 VAL Chi-restraints excluded: chain A residue 2286 ASP Chi-restraints excluded: chain A residue 2305 VAL Chi-restraints excluded: chain A residue 2330 PHE Chi-restraints excluded: chain A residue 2454 ASP Chi-restraints excluded: chain A residue 2455 MET Chi-restraints excluded: chain A residue 2482 PHE Chi-restraints excluded: chain A residue 2516 ASN Chi-restraints excluded: chain A residue 2598 LEU Chi-restraints excluded: chain A residue 2831 THR Chi-restraints excluded: chain A residue 2997 ASN Chi-restraints excluded: chain A residue 3215 THR Chi-restraints excluded: chain A residue 3630 THR Chi-restraints excluded: chain A residue 3663 LEU Chi-restraints excluded: chain A residue 3697 SER Chi-restraints excluded: chain A residue 3713 PHE Chi-restraints excluded: chain A residue 3769 ASN Chi-restraints excluded: chain A residue 3801 VAL Chi-restraints excluded: chain A residue 3865 THR Chi-restraints excluded: chain A residue 3869 ILE Chi-restraints excluded: chain A residue 3905 PHE Chi-restraints excluded: chain A residue 3927 CYS Chi-restraints excluded: chain A residue 3934 LEU Chi-restraints excluded: chain A residue 3997 GLN Chi-restraints excluded: chain A residue 4110 ASN Chi-restraints excluded: chain A residue 4175 VAL Chi-restraints excluded: chain A residue 4518 TYR Chi-restraints excluded: chain A residue 4560 LEU Chi-restraints excluded: chain A residue 4587 ILE Chi-restraints excluded: chain A residue 4807 ASP Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4858 LEU Chi-restraints excluded: chain A residue 4860 ILE Chi-restraints excluded: chain A residue 4889 ILE Chi-restraints excluded: chain A residue 4890 CYS Chi-restraints excluded: chain A residue 4921 LEU Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 521 GLU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 608 HIS Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 650 ASN Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 731 HIS Chi-restraints excluded: chain B residue 733 TRP Chi-restraints excluded: chain B residue 751 THR Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 890 HIS Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 1087 ILE Chi-restraints excluded: chain B residue 1093 THR Chi-restraints excluded: chain B residue 1251 LEU Chi-restraints excluded: chain B residue 1441 VAL Chi-restraints excluded: chain B residue 1442 TRP Chi-restraints excluded: chain B residue 1460 ASP Chi-restraints excluded: chain B residue 1595 VAL Chi-restraints excluded: chain B residue 1629 MET Chi-restraints excluded: chain B residue 1651 LEU Chi-restraints excluded: chain B residue 1777 TYR Chi-restraints excluded: chain B residue 1844 LEU Chi-restraints excluded: chain B residue 1941 PHE Chi-restraints excluded: chain B residue 1995 LEU Chi-restraints excluded: chain B residue 2083 MET Chi-restraints excluded: chain B residue 2097 LEU Chi-restraints excluded: chain B residue 2104 THR Chi-restraints excluded: chain B residue 2195 CYS Chi-restraints excluded: chain B residue 2286 ASP Chi-restraints excluded: chain B residue 2293 GLU Chi-restraints excluded: chain B residue 2305 VAL Chi-restraints excluded: chain B residue 2330 PHE Chi-restraints excluded: chain B residue 2454 ASP Chi-restraints excluded: chain B residue 2455 MET Chi-restraints excluded: chain B residue 2482 PHE Chi-restraints excluded: chain B residue 2598 LEU Chi-restraints excluded: chain B residue 2831 THR Chi-restraints excluded: chain B residue 2997 ASN Chi-restraints excluded: chain B residue 3215 THR Chi-restraints excluded: chain B residue 3630 THR Chi-restraints excluded: chain B residue 3663 LEU Chi-restraints excluded: chain B residue 3692 ASP Chi-restraints excluded: chain B residue 3697 SER Chi-restraints excluded: chain B residue 3713 PHE Chi-restraints excluded: chain B residue 3769 ASN Chi-restraints excluded: chain B residue 3801 VAL Chi-restraints excluded: chain B residue 3865 THR Chi-restraints excluded: chain B residue 3905 PHE Chi-restraints excluded: chain B residue 3964 ILE Chi-restraints excluded: chain B residue 3997 GLN Chi-restraints excluded: chain B residue 4110 ASN Chi-restraints excluded: chain B residue 4175 VAL Chi-restraints excluded: chain B residue 4518 TYR Chi-restraints excluded: chain B residue 4560 LEU Chi-restraints excluded: chain B residue 4587 ILE Chi-restraints excluded: chain B residue 4592 LEU Chi-restraints excluded: chain B residue 4654 ASP Chi-restraints excluded: chain B residue 4669 LEU Chi-restraints excluded: chain B residue 4807 ASP Chi-restraints excluded: chain B residue 4820 VAL Chi-restraints excluded: chain B residue 4858 LEU Chi-restraints excluded: chain B residue 4860 ILE Chi-restraints excluded: chain B residue 4889 ILE Chi-restraints excluded: chain B residue 4890 CYS Chi-restraints excluded: chain B residue 4921 LEU Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 489 PHE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 608 HIS Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 650 ASN Chi-restraints excluded: chain C residue 721 ASP Chi-restraints excluded: chain C residue 731 HIS Chi-restraints excluded: chain C residue 733 TRP Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 802 PHE Chi-restraints excluded: chain C residue 890 HIS Chi-restraints excluded: chain C residue 989 THR Chi-restraints excluded: chain C residue 1087 ILE Chi-restraints excluded: chain C residue 1093 THR Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1441 VAL Chi-restraints excluded: chain C residue 1460 ASP Chi-restraints excluded: chain C residue 1595 VAL Chi-restraints excluded: chain C residue 1623 LEU Chi-restraints excluded: chain C residue 1629 MET Chi-restraints excluded: chain C residue 1651 LEU Chi-restraints excluded: chain C residue 1777 TYR Chi-restraints excluded: chain C residue 1844 LEU Chi-restraints excluded: chain C residue 1941 PHE Chi-restraints excluded: chain C residue 1995 LEU Chi-restraints excluded: chain C residue 2083 MET Chi-restraints excluded: chain C residue 2097 LEU Chi-restraints excluded: chain C residue 2104 THR Chi-restraints excluded: chain C residue 2195 CYS Chi-restraints excluded: chain C residue 2280 VAL Chi-restraints excluded: chain C residue 2286 ASP Chi-restraints excluded: chain C residue 2305 VAL Chi-restraints excluded: chain C residue 2330 PHE Chi-restraints excluded: chain C residue 2454 ASP Chi-restraints excluded: chain C residue 2455 MET Chi-restraints excluded: chain C residue 2482 PHE Chi-restraints excluded: chain C residue 2598 LEU Chi-restraints excluded: chain C residue 2831 THR Chi-restraints excluded: chain C residue 2997 ASN Chi-restraints excluded: chain C residue 3215 THR Chi-restraints excluded: chain C residue 3630 THR Chi-restraints excluded: chain C residue 3663 LEU Chi-restraints excluded: chain C residue 3697 SER Chi-restraints excluded: chain C residue 3713 PHE Chi-restraints excluded: chain C residue 3769 ASN Chi-restraints excluded: chain C residue 3801 VAL Chi-restraints excluded: chain C residue 3865 THR Chi-restraints excluded: chain C residue 3905 PHE Chi-restraints excluded: chain C residue 3934 LEU Chi-restraints excluded: chain C residue 3997 GLN Chi-restraints excluded: chain C residue 4110 ASN Chi-restraints excluded: chain C residue 4175 VAL Chi-restraints excluded: chain C residue 4518 TYR Chi-restraints excluded: chain C residue 4560 LEU Chi-restraints excluded: chain C residue 4587 ILE Chi-restraints excluded: chain C residue 4654 ASP Chi-restraints excluded: chain C residue 4669 LEU Chi-restraints excluded: chain C residue 4807 ASP Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4858 LEU Chi-restraints excluded: chain C residue 4860 ILE Chi-restraints excluded: chain C residue 4889 ILE Chi-restraints excluded: chain C residue 4890 CYS Chi-restraints excluded: chain C residue 4921 LEU Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 489 PHE Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 608 HIS Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 629 GLN Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 650 ASN Chi-restraints excluded: chain D residue 721 ASP Chi-restraints excluded: chain D residue 731 HIS Chi-restraints excluded: chain D residue 733 TRP Chi-restraints excluded: chain D residue 751 THR Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 802 PHE Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 989 THR Chi-restraints excluded: chain D residue 1087 ILE Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1441 VAL Chi-restraints excluded: chain D residue 1442 TRP Chi-restraints excluded: chain D residue 1460 ASP Chi-restraints excluded: chain D residue 1595 VAL Chi-restraints excluded: chain D residue 1623 LEU Chi-restraints excluded: chain D residue 1629 MET Chi-restraints excluded: chain D residue 1651 LEU Chi-restraints excluded: chain D residue 1777 TYR Chi-restraints excluded: chain D residue 1844 LEU Chi-restraints excluded: chain D residue 1941 PHE Chi-restraints excluded: chain D residue 1995 LEU Chi-restraints excluded: chain D residue 2083 MET Chi-restraints excluded: chain D residue 2097 LEU Chi-restraints excluded: chain D residue 2104 THR Chi-restraints excluded: chain D residue 2195 CYS Chi-restraints excluded: chain D residue 2280 VAL Chi-restraints excluded: chain D residue 2286 ASP Chi-restraints excluded: chain D residue 2305 VAL Chi-restraints excluded: chain D residue 2330 PHE Chi-restraints excluded: chain D residue 2454 ASP Chi-restraints excluded: chain D residue 2455 MET Chi-restraints excluded: chain D residue 2482 PHE Chi-restraints excluded: chain D residue 2598 LEU Chi-restraints excluded: chain D residue 2831 THR Chi-restraints excluded: chain D residue 2997 ASN Chi-restraints excluded: chain D residue 3202 ASP Chi-restraints excluded: chain D residue 3215 THR Chi-restraints excluded: chain D residue 3663 LEU Chi-restraints excluded: chain D residue 3697 SER Chi-restraints excluded: chain D residue 3713 PHE Chi-restraints excluded: chain D residue 3769 ASN Chi-restraints excluded: chain D residue 3801 VAL Chi-restraints excluded: chain D residue 3865 THR Chi-restraints excluded: chain D residue 3869 ILE Chi-restraints excluded: chain D residue 3905 PHE Chi-restraints excluded: chain D residue 3934 LEU Chi-restraints excluded: chain D residue 3997 GLN Chi-restraints excluded: chain D residue 4110 ASN Chi-restraints excluded: chain D residue 4175 VAL Chi-restraints excluded: chain D residue 4518 TYR Chi-restraints excluded: chain D residue 4560 LEU Chi-restraints excluded: chain D residue 4587 ILE Chi-restraints excluded: chain D residue 4654 ASP Chi-restraints excluded: chain D residue 4669 LEU Chi-restraints excluded: chain D residue 4807 ASP Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4858 LEU Chi-restraints excluded: chain D residue 4860 ILE Chi-restraints excluded: chain D residue 4889 ILE Chi-restraints excluded: chain D residue 4890 CYS Chi-restraints excluded: chain D residue 4921 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 102 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1592 random chunks: chunk 1281 optimal weight: 10.0000 chunk 873 optimal weight: 40.0000 chunk 22 optimal weight: 5.9990 chunk 1145 optimal weight: 1.9990 chunk 634 optimal weight: 9.9990 chunk 1313 optimal weight: 20.0000 chunk 1063 optimal weight: 20.0000 chunk 1 optimal weight: 3.9990 chunk 785 optimal weight: 20.0000 chunk 1381 optimal weight: 0.0470 chunk 388 optimal weight: 20.0000 overall best weight: 4.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2249 ASN ** A3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1692 ASN B2249 ASN ** B3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2249 ASN ** C3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1692 ASN D2249 ASN ** D3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 121556 Z= 0.338 Angle : 0.638 12.096 165096 Z= 0.328 Chirality : 0.041 0.202 19028 Planarity : 0.004 0.066 21400 Dihedral : 4.747 38.094 16880 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.50 % Allowed : 12.64 % Favored : 86.87 % Rotamer: Outliers : 5.11 % Allowed : 24.57 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.07), residues: 15692 helix: 1.26 (0.06), residues: 7200 sheet: -2.52 (0.19), residues: 724 loop : -2.92 (0.07), residues: 7768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B4644 HIS 0.022 0.001 HIS G 26 PHE 0.027 0.002 PHE D4785 TYR 0.020 0.002 TYR A3690 ARG 0.005 0.000 ARG B4789 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31384 Ramachandran restraints generated. 15692 Oldfield, 0 Emsley, 15692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31384 Ramachandran restraints generated. 15692 Oldfield, 0 Emsley, 15692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1318 residues out of total 13992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 611 poor density : 707 time to evaluate : 9.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6812 (tt0) REVERT: A 489 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8521 (t80) REVERT: A 513 HIS cc_start: 0.7915 (OUTLIER) cc_final: 0.7545 (p-80) REVERT: A 802 PHE cc_start: 0.6888 (OUTLIER) cc_final: 0.5953 (m-80) REVERT: A 944 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6523 (mm) REVERT: A 989 THR cc_start: 0.3617 (OUTLIER) cc_final: 0.3328 (m) REVERT: A 1300 MET cc_start: 0.7696 (ptt) cc_final: 0.7152 (ppp) REVERT: A 1460 ASP cc_start: 0.6314 (OUTLIER) cc_final: 0.4096 (t0) REVERT: A 1629 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.7399 (ptp) REVERT: A 2025 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.5650 (ppt90) REVERT: A 2286 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.6625 (t0) REVERT: A 2293 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6632 (pt0) REVERT: A 2480 GLN cc_start: 0.1650 (OUTLIER) cc_final: 0.0235 (mp10) REVERT: A 2694 MET cc_start: 0.6265 (mpp) cc_final: 0.5541 (mpp) REVERT: A 3262 MET cc_start: -0.0488 (tmm) cc_final: -0.1145 (tpt) REVERT: A 3663 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.7943 (tt) REVERT: A 3905 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8307 (m-80) REVERT: A 3934 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8976 (mp) REVERT: A 4001 MET cc_start: 0.8590 (tmm) cc_final: 0.8272 (tmm) REVERT: A 4104 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8515 (mm) REVERT: A 4518 TYR cc_start: 0.8688 (OUTLIER) cc_final: 0.8267 (m-80) REVERT: B 50 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6784 (tt0) REVERT: B 81 MET cc_start: 0.8293 (mpp) cc_final: 0.7919 (mpp) REVERT: B 489 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8523 (t80) REVERT: B 513 HIS cc_start: 0.7860 (OUTLIER) cc_final: 0.7444 (p-80) REVERT: B 802 PHE cc_start: 0.6874 (OUTLIER) cc_final: 0.5953 (m-80) REVERT: B 989 THR cc_start: 0.3546 (OUTLIER) cc_final: 0.3249 (m) REVERT: B 1300 MET cc_start: 0.7709 (ptt) cc_final: 0.7164 (ppp) REVERT: B 1460 ASP cc_start: 0.6346 (OUTLIER) cc_final: 0.4163 (t0) REVERT: B 1629 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.7305 (ptp) REVERT: B 2025 ARG cc_start: 0.6972 (OUTLIER) cc_final: 0.5547 (ppt90) REVERT: B 2286 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.6292 (t0) REVERT: B 2293 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6559 (pt0) REVERT: B 2480 GLN cc_start: 0.2251 (OUTLIER) cc_final: 0.0775 (mp10) REVERT: B 2694 MET cc_start: 0.6257 (mpp) cc_final: 0.5553 (mpp) REVERT: B 3262 MET cc_start: 0.0421 (tmm) cc_final: -0.0278 (tpt) REVERT: B 3663 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.7945 (tt) REVERT: B 3905 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8308 (m-80) REVERT: B 3923 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8102 (pt) REVERT: B 3934 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8949 (mp) REVERT: B 4001 MET cc_start: 0.8641 (tmm) cc_final: 0.8304 (tmm) REVERT: B 4518 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.8248 (m-80) REVERT: C 50 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6787 (tt0) REVERT: C 489 PHE cc_start: 0.8939 (OUTLIER) cc_final: 0.8534 (t80) REVERT: C 513 HIS cc_start: 0.7910 (OUTLIER) cc_final: 0.7538 (p-80) REVERT: C 802 PHE cc_start: 0.6911 (OUTLIER) cc_final: 0.5929 (m-80) REVERT: C 989 THR cc_start: 0.3638 (OUTLIER) cc_final: 0.3347 (m) REVERT: C 1300 MET cc_start: 0.7643 (ptt) cc_final: 0.7157 (ppp) REVERT: C 1460 ASP cc_start: 0.6348 (OUTLIER) cc_final: 0.4109 (t0) REVERT: C 1629 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.7345 (ptp) REVERT: C 1671 HIS cc_start: 0.6102 (OUTLIER) cc_final: 0.5815 (p90) REVERT: C 2025 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.5610 (ppt90) REVERT: C 2286 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.6472 (t0) REVERT: C 2293 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6542 (pt0) REVERT: C 2480 GLN cc_start: 0.1795 (OUTLIER) cc_final: 0.0336 (mp10) REVERT: C 2694 MET cc_start: 0.6191 (mpp) cc_final: 0.5448 (mpp) REVERT: C 3262 MET cc_start: -0.0445 (tmm) cc_final: -0.1327 (tpt) REVERT: C 3663 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.7917 (tt) REVERT: C 3905 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.8303 (m-80) REVERT: C 3934 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8974 (mp) REVERT: C 4001 MET cc_start: 0.8621 (tmm) cc_final: 0.8289 (tmm) REVERT: C 4104 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8452 (mm) REVERT: C 4518 TYR cc_start: 0.8692 (OUTLIER) cc_final: 0.8272 (m-80) REVERT: D 50 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6797 (tt0) REVERT: D 489 PHE cc_start: 0.8967 (OUTLIER) cc_final: 0.8567 (t80) REVERT: D 513 HIS cc_start: 0.7912 (OUTLIER) cc_final: 0.7545 (p-80) REVERT: D 802 PHE cc_start: 0.6898 (OUTLIER) cc_final: 0.5899 (m-80) REVERT: D 944 LEU cc_start: 0.6728 (OUTLIER) cc_final: 0.6527 (mm) REVERT: D 989 THR cc_start: 0.3748 (OUTLIER) cc_final: 0.3460 (m) REVERT: D 1300 MET cc_start: 0.7751 (ptt) cc_final: 0.7191 (ppp) REVERT: D 1460 ASP cc_start: 0.6360 (OUTLIER) cc_final: 0.4131 (t0) REVERT: D 1629 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.7362 (ptp) REVERT: D 1671 HIS cc_start: 0.6115 (OUTLIER) cc_final: 0.5829 (p90) REVERT: D 2025 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.5602 (ppt90) REVERT: D 2286 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.6620 (t0) REVERT: D 2293 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6626 (pt0) REVERT: D 2480 GLN cc_start: 0.1672 (OUTLIER) cc_final: 0.0241 (mp10) REVERT: D 2694 MET cc_start: 0.6172 (mpp) cc_final: 0.5427 (mpp) REVERT: D 3262 MET cc_start: -0.0483 (tmm) cc_final: -0.1139 (tpt) REVERT: D 3663 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.7971 (tt) REVERT: D 3905 PHE cc_start: 0.8914 (OUTLIER) cc_final: 0.8316 (m-80) REVERT: D 3934 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9007 (mp) REVERT: D 4001 MET cc_start: 0.8584 (tmm) cc_final: 0.8275 (tmm) REVERT: D 4104 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8515 (mm) REVERT: D 4518 TYR cc_start: 0.8696 (OUTLIER) cc_final: 0.8269 (m-80) REVERT: F 5 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7997 (tp) REVERT: G 5 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.8080 (tp) outliers start: 611 outliers final: 394 residues processed: 1254 average time/residue: 0.8940 time to fit residues: 2076.7750 Evaluate side-chains 1158 residues out of total 13992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 464 poor density : 694 time to evaluate : 9.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 513 HIS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 608 HIS Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 733 TRP Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 890 HIS Chi-restraints excluded: chain A residue 939 THR Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain A residue 1146 HIS Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1442 TRP Chi-restraints excluded: chain A residue 1460 ASP Chi-restraints excluded: chain A residue 1595 VAL Chi-restraints excluded: chain A residue 1629 MET Chi-restraints excluded: chain A residue 1632 HIS Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1663 SER Chi-restraints excluded: chain A residue 1777 TYR Chi-restraints excluded: chain A residue 1814 THR Chi-restraints excluded: chain A residue 1829 LEU Chi-restraints excluded: chain A residue 1915 CYS Chi-restraints excluded: chain A residue 1941 PHE Chi-restraints excluded: chain A residue 2025 ARG Chi-restraints excluded: chain A residue 2083 MET Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2104 THR Chi-restraints excluded: chain A residue 2127 SER Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2250 ASN Chi-restraints excluded: chain A residue 2280 VAL Chi-restraints excluded: chain A residue 2286 ASP Chi-restraints excluded: chain A residue 2293 GLU Chi-restraints excluded: chain A residue 2305 VAL Chi-restraints excluded: chain A residue 2330 PHE Chi-restraints excluded: chain A residue 2454 ASP Chi-restraints excluded: chain A residue 2455 MET Chi-restraints excluded: chain A residue 2480 GLN Chi-restraints excluded: chain A residue 2482 PHE Chi-restraints excluded: chain A residue 2516 ASN Chi-restraints excluded: chain A residue 2663 LEU Chi-restraints excluded: chain A residue 2831 THR Chi-restraints excluded: chain A residue 2997 ASN Chi-restraints excluded: chain A residue 3101 LEU Chi-restraints excluded: chain A residue 3215 THR Chi-restraints excluded: chain A residue 3616 VAL Chi-restraints excluded: chain A residue 3630 THR Chi-restraints excluded: chain A residue 3663 LEU Chi-restraints excluded: chain A residue 3692 ASP Chi-restraints excluded: chain A residue 3693 ILE Chi-restraints excluded: chain A residue 3697 SER Chi-restraints excluded: chain A residue 3713 PHE Chi-restraints excluded: chain A residue 3769 ASN Chi-restraints excluded: chain A residue 3828 VAL Chi-restraints excluded: chain A residue 3853 PHE Chi-restraints excluded: chain A residue 3865 THR Chi-restraints excluded: chain A residue 3869 ILE Chi-restraints excluded: chain A residue 3905 PHE Chi-restraints excluded: chain A residue 3927 CYS Chi-restraints excluded: chain A residue 3934 LEU Chi-restraints excluded: chain A residue 3958 SER Chi-restraints excluded: chain A residue 3964 ILE Chi-restraints excluded: chain A residue 4104 LEU Chi-restraints excluded: chain A residue 4110 ASN Chi-restraints excluded: chain A residue 4175 VAL Chi-restraints excluded: chain A residue 4503 LEU Chi-restraints excluded: chain A residue 4518 TYR Chi-restraints excluded: chain A residue 4560 LEU Chi-restraints excluded: chain A residue 4587 ILE Chi-restraints excluded: chain A residue 4654 ASP Chi-restraints excluded: chain A residue 4671 MET Chi-restraints excluded: chain A residue 4782 VAL Chi-restraints excluded: chain A residue 4795 SER Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4846 ASP Chi-restraints excluded: chain A residue 4847 ILE Chi-restraints excluded: chain A residue 4858 LEU Chi-restraints excluded: chain A residue 4860 ILE Chi-restraints excluded: chain A residue 4867 ASP Chi-restraints excluded: chain A residue 4879 VAL Chi-restraints excluded: chain A residue 4889 ILE Chi-restraints excluded: chain A residue 4890 CYS Chi-restraints excluded: chain A residue 4921 LEU Chi-restraints excluded: chain B residue 17 ASP Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 513 HIS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 608 HIS Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 650 ASN Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 733 TRP Chi-restraints excluded: chain B residue 751 THR Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 890 HIS Chi-restraints excluded: chain B residue 939 THR Chi-restraints excluded: chain B residue 989 THR Chi-restraints excluded: chain B residue 1087 ILE Chi-restraints excluded: chain B residue 1093 THR Chi-restraints excluded: chain B residue 1146 HIS Chi-restraints excluded: chain B residue 1251 LEU Chi-restraints excluded: chain B residue 1441 VAL Chi-restraints excluded: chain B residue 1442 TRP Chi-restraints excluded: chain B residue 1460 ASP Chi-restraints excluded: chain B residue 1508 ILE Chi-restraints excluded: chain B residue 1595 VAL Chi-restraints excluded: chain B residue 1600 MET Chi-restraints excluded: chain B residue 1629 MET Chi-restraints excluded: chain B residue 1651 LEU Chi-restraints excluded: chain B residue 1663 SER Chi-restraints excluded: chain B residue 1777 TYR Chi-restraints excluded: chain B residue 1814 THR Chi-restraints excluded: chain B residue 1829 LEU Chi-restraints excluded: chain B residue 1844 LEU Chi-restraints excluded: chain B residue 1941 PHE Chi-restraints excluded: chain B residue 1995 LEU Chi-restraints excluded: chain B residue 2011 ASP Chi-restraints excluded: chain B residue 2025 ARG Chi-restraints excluded: chain B residue 2083 MET Chi-restraints excluded: chain B residue 2097 LEU Chi-restraints excluded: chain B residue 2104 THR Chi-restraints excluded: chain B residue 2237 THR Chi-restraints excluded: chain B residue 2250 ASN Chi-restraints excluded: chain B residue 2280 VAL Chi-restraints excluded: chain B residue 2286 ASP Chi-restraints excluded: chain B residue 2293 GLU Chi-restraints excluded: chain B residue 2305 VAL Chi-restraints excluded: chain B residue 2330 PHE Chi-restraints excluded: chain B residue 2454 ASP Chi-restraints excluded: chain B residue 2455 MET Chi-restraints excluded: chain B residue 2480 GLN Chi-restraints excluded: chain B residue 2482 PHE Chi-restraints excluded: chain B residue 2516 ASN Chi-restraints excluded: chain B residue 2831 THR Chi-restraints excluded: chain B residue 2997 ASN Chi-restraints excluded: chain B residue 3101 LEU Chi-restraints excluded: chain B residue 3202 ASP Chi-restraints excluded: chain B residue 3215 THR Chi-restraints excluded: chain B residue 3630 THR Chi-restraints excluded: chain B residue 3663 LEU Chi-restraints excluded: chain B residue 3692 ASP Chi-restraints excluded: chain B residue 3693 ILE Chi-restraints excluded: chain B residue 3697 SER Chi-restraints excluded: chain B residue 3713 PHE Chi-restraints excluded: chain B residue 3769 ASN Chi-restraints excluded: chain B residue 3828 VAL Chi-restraints excluded: chain B residue 3853 PHE Chi-restraints excluded: chain B residue 3865 THR Chi-restraints excluded: chain B residue 3869 ILE Chi-restraints excluded: chain B residue 3905 PHE Chi-restraints excluded: chain B residue 3923 ILE Chi-restraints excluded: chain B residue 3927 CYS Chi-restraints excluded: chain B residue 3934 LEU Chi-restraints excluded: chain B residue 3958 SER Chi-restraints excluded: chain B residue 3964 ILE Chi-restraints excluded: chain B residue 4110 ASN Chi-restraints excluded: chain B residue 4175 VAL Chi-restraints excluded: chain B residue 4503 LEU Chi-restraints excluded: chain B residue 4518 TYR Chi-restraints excluded: chain B residue 4560 LEU Chi-restraints excluded: chain B residue 4587 ILE Chi-restraints excluded: chain B residue 4654 ASP Chi-restraints excluded: chain B residue 4671 MET Chi-restraints excluded: chain B residue 4782 VAL Chi-restraints excluded: chain B residue 4795 SER Chi-restraints excluded: chain B residue 4820 VAL Chi-restraints excluded: chain B residue 4846 ASP Chi-restraints excluded: chain B residue 4847 ILE Chi-restraints excluded: chain B residue 4858 LEU Chi-restraints excluded: chain B residue 4860 ILE Chi-restraints excluded: chain B residue 4867 ASP Chi-restraints excluded: chain B residue 4879 VAL Chi-restraints excluded: chain B residue 4889 ILE Chi-restraints excluded: chain B residue 4890 CYS Chi-restraints excluded: chain B residue 4921 LEU Chi-restraints excluded: chain C residue 17 ASP Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 489 PHE Chi-restraints excluded: chain C residue 513 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 608 HIS Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 650 ASN Chi-restraints excluded: chain C residue 687 THR Chi-restraints excluded: chain C residue 721 ASP Chi-restraints excluded: chain C residue 733 TRP Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 802 PHE Chi-restraints excluded: chain C residue 890 HIS Chi-restraints excluded: chain C residue 939 THR Chi-restraints excluded: chain C residue 989 THR Chi-restraints excluded: chain C residue 1042 THR Chi-restraints excluded: chain C residue 1087 ILE Chi-restraints excluded: chain C residue 1093 THR Chi-restraints excluded: chain C residue 1146 HIS Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1441 VAL Chi-restraints excluded: chain C residue 1442 TRP Chi-restraints excluded: chain C residue 1460 ASP Chi-restraints excluded: chain C residue 1595 VAL Chi-restraints excluded: chain C residue 1629 MET Chi-restraints excluded: chain C residue 1632 HIS Chi-restraints excluded: chain C residue 1651 LEU Chi-restraints excluded: chain C residue 1663 SER Chi-restraints excluded: chain C residue 1671 HIS Chi-restraints excluded: chain C residue 1777 TYR Chi-restraints excluded: chain C residue 1814 THR Chi-restraints excluded: chain C residue 1829 LEU Chi-restraints excluded: chain C residue 1915 CYS Chi-restraints excluded: chain C residue 1941 PHE Chi-restraints excluded: chain C residue 1995 LEU Chi-restraints excluded: chain C residue 2025 ARG Chi-restraints excluded: chain C residue 2083 MET Chi-restraints excluded: chain C residue 2097 LEU Chi-restraints excluded: chain C residue 2104 THR Chi-restraints excluded: chain C residue 2127 SER Chi-restraints excluded: chain C residue 2237 THR Chi-restraints excluded: chain C residue 2250 ASN Chi-restraints excluded: chain C residue 2280 VAL Chi-restraints excluded: chain C residue 2286 ASP Chi-restraints excluded: chain C residue 2293 GLU Chi-restraints excluded: chain C residue 2305 VAL Chi-restraints excluded: chain C residue 2330 PHE Chi-restraints excluded: chain C residue 2454 ASP Chi-restraints excluded: chain C residue 2455 MET Chi-restraints excluded: chain C residue 2480 GLN Chi-restraints excluded: chain C residue 2482 PHE Chi-restraints excluded: chain C residue 2516 ASN Chi-restraints excluded: chain C residue 2663 LEU Chi-restraints excluded: chain C residue 2831 THR Chi-restraints excluded: chain C residue 2997 ASN Chi-restraints excluded: chain C residue 3101 LEU Chi-restraints excluded: chain C residue 3215 THR Chi-restraints excluded: chain C residue 3630 THR Chi-restraints excluded: chain C residue 3663 LEU Chi-restraints excluded: chain C residue 3692 ASP Chi-restraints excluded: chain C residue 3693 ILE Chi-restraints excluded: chain C residue 3697 SER Chi-restraints excluded: chain C residue 3713 PHE Chi-restraints excluded: chain C residue 3769 ASN Chi-restraints excluded: chain C residue 3828 VAL Chi-restraints excluded: chain C residue 3853 PHE Chi-restraints excluded: chain C residue 3865 THR Chi-restraints excluded: chain C residue 3869 ILE Chi-restraints excluded: chain C residue 3905 PHE Chi-restraints excluded: chain C residue 3927 CYS Chi-restraints excluded: chain C residue 3934 LEU Chi-restraints excluded: chain C residue 3958 SER Chi-restraints excluded: chain C residue 3964 ILE Chi-restraints excluded: chain C residue 4104 LEU Chi-restraints excluded: chain C residue 4110 ASN Chi-restraints excluded: chain C residue 4175 VAL Chi-restraints excluded: chain C residue 4503 LEU Chi-restraints excluded: chain C residue 4518 TYR Chi-restraints excluded: chain C residue 4560 LEU Chi-restraints excluded: chain C residue 4587 ILE Chi-restraints excluded: chain C residue 4654 ASP Chi-restraints excluded: chain C residue 4671 MET Chi-restraints excluded: chain C residue 4782 VAL Chi-restraints excluded: chain C residue 4795 SER Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4846 ASP Chi-restraints excluded: chain C residue 4847 ILE Chi-restraints excluded: chain C residue 4858 LEU Chi-restraints excluded: chain C residue 4860 ILE Chi-restraints excluded: chain C residue 4867 ASP Chi-restraints excluded: chain C residue 4879 VAL Chi-restraints excluded: chain C residue 4889 ILE Chi-restraints excluded: chain C residue 4890 CYS Chi-restraints excluded: chain C residue 4921 LEU Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 489 PHE Chi-restraints excluded: chain D residue 513 HIS Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 608 HIS Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 629 GLN Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 650 ASN Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 721 ASP Chi-restraints excluded: chain D residue 731 HIS Chi-restraints excluded: chain D residue 733 TRP Chi-restraints excluded: chain D residue 751 THR Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 802 PHE Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 939 THR Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 989 THR Chi-restraints excluded: chain D residue 1087 ILE Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1146 HIS Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1441 VAL Chi-restraints excluded: chain D residue 1442 TRP Chi-restraints excluded: chain D residue 1460 ASP Chi-restraints excluded: chain D residue 1595 VAL Chi-restraints excluded: chain D residue 1629 MET Chi-restraints excluded: chain D residue 1632 HIS Chi-restraints excluded: chain D residue 1651 LEU Chi-restraints excluded: chain D residue 1663 SER Chi-restraints excluded: chain D residue 1671 HIS Chi-restraints excluded: chain D residue 1777 TYR Chi-restraints excluded: chain D residue 1814 THR Chi-restraints excluded: chain D residue 1829 LEU Chi-restraints excluded: chain D residue 1844 LEU Chi-restraints excluded: chain D residue 1915 CYS Chi-restraints excluded: chain D residue 1941 PHE Chi-restraints excluded: chain D residue 1995 LEU Chi-restraints excluded: chain D residue 2025 ARG Chi-restraints excluded: chain D residue 2083 MET Chi-restraints excluded: chain D residue 2097 LEU Chi-restraints excluded: chain D residue 2104 THR Chi-restraints excluded: chain D residue 2127 SER Chi-restraints excluded: chain D residue 2237 THR Chi-restraints excluded: chain D residue 2250 ASN Chi-restraints excluded: chain D residue 2280 VAL Chi-restraints excluded: chain D residue 2286 ASP Chi-restraints excluded: chain D residue 2293 GLU Chi-restraints excluded: chain D residue 2305 VAL Chi-restraints excluded: chain D residue 2330 PHE Chi-restraints excluded: chain D residue 2454 ASP Chi-restraints excluded: chain D residue 2455 MET Chi-restraints excluded: chain D residue 2480 GLN Chi-restraints excluded: chain D residue 2482 PHE Chi-restraints excluded: chain D residue 2516 ASN Chi-restraints excluded: chain D residue 2663 LEU Chi-restraints excluded: chain D residue 2831 THR Chi-restraints excluded: chain D residue 2997 ASN Chi-restraints excluded: chain D residue 3101 LEU Chi-restraints excluded: chain D residue 3202 ASP Chi-restraints excluded: chain D residue 3215 THR Chi-restraints excluded: chain D residue 3630 THR Chi-restraints excluded: chain D residue 3663 LEU Chi-restraints excluded: chain D residue 3692 ASP Chi-restraints excluded: chain D residue 3693 ILE Chi-restraints excluded: chain D residue 3697 SER Chi-restraints excluded: chain D residue 3713 PHE Chi-restraints excluded: chain D residue 3769 ASN Chi-restraints excluded: chain D residue 3828 VAL Chi-restraints excluded: chain D residue 3853 PHE Chi-restraints excluded: chain D residue 3865 THR Chi-restraints excluded: chain D residue 3869 ILE Chi-restraints excluded: chain D residue 3905 PHE Chi-restraints excluded: chain D residue 3927 CYS Chi-restraints excluded: chain D residue 3934 LEU Chi-restraints excluded: chain D residue 3958 SER Chi-restraints excluded: chain D residue 3964 ILE Chi-restraints excluded: chain D residue 3985 LEU Chi-restraints excluded: chain D residue 4104 LEU Chi-restraints excluded: chain D residue 4110 ASN Chi-restraints excluded: chain D residue 4175 VAL Chi-restraints excluded: chain D residue 4503 LEU Chi-restraints excluded: chain D residue 4518 TYR Chi-restraints excluded: chain D residue 4560 LEU Chi-restraints excluded: chain D residue 4587 ILE Chi-restraints excluded: chain D residue 4654 ASP Chi-restraints excluded: chain D residue 4671 MET Chi-restraints excluded: chain D residue 4782 VAL Chi-restraints excluded: chain D residue 4795 SER Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4846 ASP Chi-restraints excluded: chain D residue 4847 ILE Chi-restraints excluded: chain D residue 4858 LEU Chi-restraints excluded: chain D residue 4860 ILE Chi-restraints excluded: chain D residue 4867 ASP Chi-restraints excluded: chain D residue 4879 VAL Chi-restraints excluded: chain D residue 4889 ILE Chi-restraints excluded: chain D residue 4890 CYS Chi-restraints excluded: chain D residue 4921 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 ASN Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 102 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1592 random chunks: chunk 517 optimal weight: 40.0000 chunk 1385 optimal weight: 50.0000 chunk 304 optimal weight: 0.9980 chunk 903 optimal weight: 2.9990 chunk 379 optimal weight: 0.6980 chunk 1540 optimal weight: 0.7980 chunk 1278 optimal weight: 20.0000 chunk 713 optimal weight: 5.9990 chunk 128 optimal weight: 0.5980 chunk 509 optimal weight: 9.9990 chunk 808 optimal weight: 30.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2249 ASN ** A3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2249 ASN ** B3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2249 ASN ** C3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2249 ASN ** D3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN G 26 HIS G 32 GLN H 32 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 121556 Z= 0.159 Angle : 0.561 10.762 165096 Z= 0.284 Chirality : 0.039 0.178 19028 Planarity : 0.004 0.060 21400 Dihedral : 4.557 37.612 16880 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.46 % Allowed : 10.84 % Favored : 88.70 % Rotamer: Outliers : 4.11 % Allowed : 25.39 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.07), residues: 15692 helix: 1.53 (0.06), residues: 7220 sheet: -2.39 (0.20), residues: 672 loop : -2.87 (0.07), residues: 7800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 733 HIS 0.020 0.001 HIS G 26 PHE 0.016 0.001 PHE D4845 TYR 0.023 0.001 TYR A2619 ARG 0.002 0.000 ARG B 504 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31384 Ramachandran restraints generated. 15692 Oldfield, 0 Emsley, 15692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31384 Ramachandran restraints generated. 15692 Oldfield, 0 Emsley, 15692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1224 residues out of total 13992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 492 poor density : 732 time to evaluate : 9.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 489 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8448 (t80) REVERT: A 513 HIS cc_start: 0.7823 (OUTLIER) cc_final: 0.7427 (p-80) REVERT: A 802 PHE cc_start: 0.6914 (OUTLIER) cc_final: 0.5924 (m-80) REVERT: A 944 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.6574 (mm) REVERT: A 1300 MET cc_start: 0.7683 (ptt) cc_final: 0.7150 (ppp) REVERT: A 1460 ASP cc_start: 0.6318 (OUTLIER) cc_final: 0.4147 (t0) REVERT: A 1604 PHE cc_start: 0.6046 (OUTLIER) cc_final: 0.4816 (t80) REVERT: A 1629 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.7362 (ptp) REVERT: A 2025 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.5584 (ppt90) REVERT: A 2286 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.6250 (t0) REVERT: A 2293 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6684 (pt0) REVERT: A 2694 MET cc_start: 0.6308 (mpp) cc_final: 0.5598 (mpp) REVERT: A 3262 MET cc_start: -0.0452 (tmm) cc_final: -0.1318 (tpt) REVERT: A 3663 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.7668 (tt) REVERT: A 3905 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8286 (m-80) REVERT: A 3934 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8885 (mp) REVERT: A 3997 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8142 (mp10) REVERT: A 3998 MET cc_start: 0.8679 (mmt) cc_final: 0.8420 (mmt) REVERT: A 4001 MET cc_start: 0.8537 (tmm) cc_final: 0.8227 (tmm) REVERT: A 4104 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8422 (mm) REVERT: A 4518 TYR cc_start: 0.8446 (OUTLIER) cc_final: 0.7782 (m-80) REVERT: A 4807 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7947 (p0) REVERT: B 81 MET cc_start: 0.8179 (mpp) cc_final: 0.7857 (mpp) REVERT: B 262 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.8110 (t80) REVERT: B 396 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.6998 (mp0) REVERT: B 489 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8464 (t80) REVERT: B 513 HIS cc_start: 0.7823 (OUTLIER) cc_final: 0.7319 (p-80) REVERT: B 802 PHE cc_start: 0.6893 (OUTLIER) cc_final: 0.5929 (m-80) REVERT: B 1300 MET cc_start: 0.7785 (ptt) cc_final: 0.7244 (ppp) REVERT: B 1460 ASP cc_start: 0.6291 (OUTLIER) cc_final: 0.4158 (t0) REVERT: B 1604 PHE cc_start: 0.6099 (OUTLIER) cc_final: 0.4870 (t80) REVERT: B 1629 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.7251 (ptp) REVERT: B 2025 ARG cc_start: 0.7024 (OUTLIER) cc_final: 0.5666 (ppt90) REVERT: B 2286 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.6219 (t0) REVERT: B 2480 GLN cc_start: 0.2116 (OUTLIER) cc_final: 0.0746 (mp10) REVERT: B 2694 MET cc_start: 0.6454 (mpp) cc_final: 0.5727 (mpp) REVERT: B 3262 MET cc_start: 0.0401 (tmm) cc_final: -0.0268 (tpt) REVERT: B 3663 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.7686 (tt) REVERT: B 3905 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8201 (m-80) REVERT: B 3934 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8903 (mp) REVERT: B 4001 MET cc_start: 0.8576 (tmm) cc_final: 0.8291 (tmm) REVERT: B 4518 TYR cc_start: 0.8370 (OUTLIER) cc_final: 0.7762 (m-80) REVERT: B 4807 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7694 (p0) REVERT: C 489 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8441 (t80) REVERT: C 513 HIS cc_start: 0.7819 (OUTLIER) cc_final: 0.7426 (p-80) REVERT: C 802 PHE cc_start: 0.6977 (OUTLIER) cc_final: 0.5961 (m-80) REVERT: C 1300 MET cc_start: 0.7768 (ptt) cc_final: 0.7228 (ppp) REVERT: C 1460 ASP cc_start: 0.6292 (OUTLIER) cc_final: 0.4119 (t0) REVERT: C 1604 PHE cc_start: 0.6112 (OUTLIER) cc_final: 0.4883 (t80) REVERT: C 1629 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.7311 (ptp) REVERT: C 2025 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.5623 (ppt90) REVERT: C 2286 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.6215 (t0) REVERT: C 2293 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6611 (pt0) REVERT: C 2694 MET cc_start: 0.6306 (mpp) cc_final: 0.5586 (mpp) REVERT: C 3262 MET cc_start: -0.0483 (tmm) cc_final: -0.1344 (tpt) REVERT: C 3663 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.7672 (tt) REVERT: C 3905 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.8182 (m-80) REVERT: C 3934 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8897 (mp) REVERT: C 3997 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8110 (mp10) REVERT: C 4001 MET cc_start: 0.8553 (tmm) cc_final: 0.8246 (tmm) REVERT: C 4104 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8430 (mm) REVERT: C 4518 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.7876 (m-80) REVERT: C 4807 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7982 (p0) REVERT: D 489 PHE cc_start: 0.8917 (OUTLIER) cc_final: 0.8442 (t80) REVERT: D 513 HIS cc_start: 0.7819 (OUTLIER) cc_final: 0.7392 (p-80) REVERT: D 802 PHE cc_start: 0.6979 (OUTLIER) cc_final: 0.5954 (m-80) REVERT: D 1300 MET cc_start: 0.7766 (ptt) cc_final: 0.7230 (ppp) REVERT: D 1460 ASP cc_start: 0.6300 (OUTLIER) cc_final: 0.4139 (t0) REVERT: D 1604 PHE cc_start: 0.6101 (OUTLIER) cc_final: 0.4884 (t80) REVERT: D 1629 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7311 (ptp) REVERT: D 2025 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.5565 (ppt90) REVERT: D 2286 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.6251 (t0) REVERT: D 2293 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6618 (pt0) REVERT: D 2511 MET cc_start: 0.7659 (mmm) cc_final: 0.7293 (mmm) REVERT: D 2694 MET cc_start: 0.6486 (mpp) cc_final: 0.5802 (mpp) REVERT: D 3262 MET cc_start: -0.0475 (tmm) cc_final: -0.1332 (tpt) REVERT: D 3663 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.7666 (tt) REVERT: D 3905 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8272 (m-80) REVERT: D 3934 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8908 (mp) REVERT: D 3997 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8167 (mp10) REVERT: D 4001 MET cc_start: 0.8542 (tmm) cc_final: 0.8227 (tmm) REVERT: D 4104 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8393 (mm) REVERT: D 4518 TYR cc_start: 0.8457 (OUTLIER) cc_final: 0.7879 (m-80) REVERT: D 4807 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7990 (p0) REVERT: F 4 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7356 (tm-30) REVERT: F 5 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7908 (tp) REVERT: G 95 ASN cc_start: 0.7920 (t0) cc_final: 0.7710 (t0) REVERT: H 95 ASN cc_start: 0.7930 (t0) cc_final: 0.7714 (t0) outliers start: 492 outliers final: 314 residues processed: 1155 average time/residue: 0.8711 time to fit residues: 1862.2694 Evaluate side-chains 1098 residues out of total 13992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 380 poor density : 718 time to evaluate : 9.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 513 HIS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 608 HIS Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 731 HIS Chi-restraints excluded: chain A residue 733 TRP Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 890 HIS Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1442 TRP Chi-restraints excluded: chain A residue 1460 ASP Chi-restraints excluded: chain A residue 1595 VAL Chi-restraints excluded: chain A residue 1604 PHE Chi-restraints excluded: chain A residue 1629 MET Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1663 SER Chi-restraints excluded: chain A residue 1777 TYR Chi-restraints excluded: chain A residue 1941 PHE Chi-restraints excluded: chain A residue 2025 ARG Chi-restraints excluded: chain A residue 2083 MET Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2104 THR Chi-restraints excluded: chain A residue 2195 CYS Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2286 ASP Chi-restraints excluded: chain A residue 2293 GLU Chi-restraints excluded: chain A residue 2305 VAL Chi-restraints excluded: chain A residue 2330 PHE Chi-restraints excluded: chain A residue 2454 ASP Chi-restraints excluded: chain A residue 2455 MET Chi-restraints excluded: chain A residue 2482 PHE Chi-restraints excluded: chain A residue 2831 THR Chi-restraints excluded: chain A residue 2997 ASN Chi-restraints excluded: chain A residue 3215 THR Chi-restraints excluded: chain A residue 3630 THR Chi-restraints excluded: chain A residue 3663 LEU Chi-restraints excluded: chain A residue 3692 ASP Chi-restraints excluded: chain A residue 3697 SER Chi-restraints excluded: chain A residue 3713 PHE Chi-restraints excluded: chain A residue 3769 ASN Chi-restraints excluded: chain A residue 3801 VAL Chi-restraints excluded: chain A residue 3828 VAL Chi-restraints excluded: chain A residue 3853 PHE Chi-restraints excluded: chain A residue 3905 PHE Chi-restraints excluded: chain A residue 3927 CYS Chi-restraints excluded: chain A residue 3934 LEU Chi-restraints excluded: chain A residue 3964 ILE Chi-restraints excluded: chain A residue 3985 LEU Chi-restraints excluded: chain A residue 3997 GLN Chi-restraints excluded: chain A residue 4104 LEU Chi-restraints excluded: chain A residue 4110 ASN Chi-restraints excluded: chain A residue 4175 VAL Chi-restraints excluded: chain A residue 4518 TYR Chi-restraints excluded: chain A residue 4581 ILE Chi-restraints excluded: chain A residue 4654 ASP Chi-restraints excluded: chain A residue 4671 MET Chi-restraints excluded: chain A residue 4795 SER Chi-restraints excluded: chain A residue 4807 ASP Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4846 ASP Chi-restraints excluded: chain A residue 4858 LEU Chi-restraints excluded: chain A residue 4860 ILE Chi-restraints excluded: chain A residue 4879 VAL Chi-restraints excluded: chain A residue 4889 ILE Chi-restraints excluded: chain A residue 4890 CYS Chi-restraints excluded: chain A residue 4921 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 513 HIS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 608 HIS Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 650 ASN Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 731 HIS Chi-restraints excluded: chain B residue 733 TRP Chi-restraints excluded: chain B residue 751 THR Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 890 HIS Chi-restraints excluded: chain B residue 1087 ILE Chi-restraints excluded: chain B residue 1093 THR Chi-restraints excluded: chain B residue 1251 LEU Chi-restraints excluded: chain B residue 1441 VAL Chi-restraints excluded: chain B residue 1442 TRP Chi-restraints excluded: chain B residue 1460 ASP Chi-restraints excluded: chain B residue 1595 VAL Chi-restraints excluded: chain B residue 1604 PHE Chi-restraints excluded: chain B residue 1629 MET Chi-restraints excluded: chain B residue 1651 LEU Chi-restraints excluded: chain B residue 1663 SER Chi-restraints excluded: chain B residue 1777 TYR Chi-restraints excluded: chain B residue 1941 PHE Chi-restraints excluded: chain B residue 1995 LEU Chi-restraints excluded: chain B residue 2021 ASP Chi-restraints excluded: chain B residue 2025 ARG Chi-restraints excluded: chain B residue 2083 MET Chi-restraints excluded: chain B residue 2097 LEU Chi-restraints excluded: chain B residue 2104 THR Chi-restraints excluded: chain B residue 2195 CYS Chi-restraints excluded: chain B residue 2237 THR Chi-restraints excluded: chain B residue 2280 VAL Chi-restraints excluded: chain B residue 2286 ASP Chi-restraints excluded: chain B residue 2305 VAL Chi-restraints excluded: chain B residue 2330 PHE Chi-restraints excluded: chain B residue 2454 ASP Chi-restraints excluded: chain B residue 2455 MET Chi-restraints excluded: chain B residue 2480 GLN Chi-restraints excluded: chain B residue 2482 PHE Chi-restraints excluded: chain B residue 2598 LEU Chi-restraints excluded: chain B residue 2831 THR Chi-restraints excluded: chain B residue 2997 ASN Chi-restraints excluded: chain B residue 3101 LEU Chi-restraints excluded: chain B residue 3215 THR Chi-restraints excluded: chain B residue 3630 THR Chi-restraints excluded: chain B residue 3663 LEU Chi-restraints excluded: chain B residue 3697 SER Chi-restraints excluded: chain B residue 3713 PHE Chi-restraints excluded: chain B residue 3769 ASN Chi-restraints excluded: chain B residue 3801 VAL Chi-restraints excluded: chain B residue 3828 VAL Chi-restraints excluded: chain B residue 3831 ASP Chi-restraints excluded: chain B residue 3853 PHE Chi-restraints excluded: chain B residue 3905 PHE Chi-restraints excluded: chain B residue 3927 CYS Chi-restraints excluded: chain B residue 3934 LEU Chi-restraints excluded: chain B residue 3964 ILE Chi-restraints excluded: chain B residue 4092 ASP Chi-restraints excluded: chain B residue 4110 ASN Chi-restraints excluded: chain B residue 4175 VAL Chi-restraints excluded: chain B residue 4518 TYR Chi-restraints excluded: chain B residue 4581 ILE Chi-restraints excluded: chain B residue 4587 ILE Chi-restraints excluded: chain B residue 4654 ASP Chi-restraints excluded: chain B residue 4671 MET Chi-restraints excluded: chain B residue 4795 SER Chi-restraints excluded: chain B residue 4807 ASP Chi-restraints excluded: chain B residue 4820 VAL Chi-restraints excluded: chain B residue 4846 ASP Chi-restraints excluded: chain B residue 4858 LEU Chi-restraints excluded: chain B residue 4860 ILE Chi-restraints excluded: chain B residue 4879 VAL Chi-restraints excluded: chain B residue 4889 ILE Chi-restraints excluded: chain B residue 4890 CYS Chi-restraints excluded: chain B residue 4921 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 489 PHE Chi-restraints excluded: chain C residue 513 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 608 HIS Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 650 ASN Chi-restraints excluded: chain C residue 687 THR Chi-restraints excluded: chain C residue 721 ASP Chi-restraints excluded: chain C residue 731 HIS Chi-restraints excluded: chain C residue 733 TRP Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 802 PHE Chi-restraints excluded: chain C residue 890 HIS Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 1087 ILE Chi-restraints excluded: chain C residue 1093 THR Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1441 VAL Chi-restraints excluded: chain C residue 1442 TRP Chi-restraints excluded: chain C residue 1460 ASP Chi-restraints excluded: chain C residue 1508 ILE Chi-restraints excluded: chain C residue 1595 VAL Chi-restraints excluded: chain C residue 1604 PHE Chi-restraints excluded: chain C residue 1629 MET Chi-restraints excluded: chain C residue 1651 LEU Chi-restraints excluded: chain C residue 1663 SER Chi-restraints excluded: chain C residue 1777 TYR Chi-restraints excluded: chain C residue 1941 PHE Chi-restraints excluded: chain C residue 1995 LEU Chi-restraints excluded: chain C residue 2025 ARG Chi-restraints excluded: chain C residue 2083 MET Chi-restraints excluded: chain C residue 2097 LEU Chi-restraints excluded: chain C residue 2104 THR Chi-restraints excluded: chain C residue 2195 CYS Chi-restraints excluded: chain C residue 2237 THR Chi-restraints excluded: chain C residue 2286 ASP Chi-restraints excluded: chain C residue 2293 GLU Chi-restraints excluded: chain C residue 2305 VAL Chi-restraints excluded: chain C residue 2330 PHE Chi-restraints excluded: chain C residue 2454 ASP Chi-restraints excluded: chain C residue 2455 MET Chi-restraints excluded: chain C residue 2482 PHE Chi-restraints excluded: chain C residue 2516 ASN Chi-restraints excluded: chain C residue 2663 LEU Chi-restraints excluded: chain C residue 2831 THR Chi-restraints excluded: chain C residue 2997 ASN Chi-restraints excluded: chain C residue 3215 THR Chi-restraints excluded: chain C residue 3630 THR Chi-restraints excluded: chain C residue 3663 LEU Chi-restraints excluded: chain C residue 3692 ASP Chi-restraints excluded: chain C residue 3697 SER Chi-restraints excluded: chain C residue 3713 PHE Chi-restraints excluded: chain C residue 3769 ASN Chi-restraints excluded: chain C residue 3801 VAL Chi-restraints excluded: chain C residue 3828 VAL Chi-restraints excluded: chain C residue 3853 PHE Chi-restraints excluded: chain C residue 3905 PHE Chi-restraints excluded: chain C residue 3927 CYS Chi-restraints excluded: chain C residue 3934 LEU Chi-restraints excluded: chain C residue 3964 ILE Chi-restraints excluded: chain C residue 3997 GLN Chi-restraints excluded: chain C residue 4104 LEU Chi-restraints excluded: chain C residue 4110 ASN Chi-restraints excluded: chain C residue 4175 VAL Chi-restraints excluded: chain C residue 4518 TYR Chi-restraints excluded: chain C residue 4581 ILE Chi-restraints excluded: chain C residue 4587 ILE Chi-restraints excluded: chain C residue 4654 ASP Chi-restraints excluded: chain C residue 4671 MET Chi-restraints excluded: chain C residue 4795 SER Chi-restraints excluded: chain C residue 4807 ASP Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4846 ASP Chi-restraints excluded: chain C residue 4858 LEU Chi-restraints excluded: chain C residue 4860 ILE Chi-restraints excluded: chain C residue 4879 VAL Chi-restraints excluded: chain C residue 4889 ILE Chi-restraints excluded: chain C residue 4890 CYS Chi-restraints excluded: chain C residue 4921 LEU Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 489 PHE Chi-restraints excluded: chain D residue 513 HIS Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 608 HIS Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 629 GLN Chi-restraints excluded: chain D residue 650 ASN Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 721 ASP Chi-restraints excluded: chain D residue 731 HIS Chi-restraints excluded: chain D residue 733 TRP Chi-restraints excluded: chain D residue 751 THR Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 802 PHE Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 1042 THR Chi-restraints excluded: chain D residue 1087 ILE Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1441 VAL Chi-restraints excluded: chain D residue 1442 TRP Chi-restraints excluded: chain D residue 1460 ASP Chi-restraints excluded: chain D residue 1508 ILE Chi-restraints excluded: chain D residue 1595 VAL Chi-restraints excluded: chain D residue 1604 PHE Chi-restraints excluded: chain D residue 1629 MET Chi-restraints excluded: chain D residue 1651 LEU Chi-restraints excluded: chain D residue 1663 SER Chi-restraints excluded: chain D residue 1777 TYR Chi-restraints excluded: chain D residue 1844 LEU Chi-restraints excluded: chain D residue 1941 PHE Chi-restraints excluded: chain D residue 1995 LEU Chi-restraints excluded: chain D residue 2025 ARG Chi-restraints excluded: chain D residue 2083 MET Chi-restraints excluded: chain D residue 2097 LEU Chi-restraints excluded: chain D residue 2104 THR Chi-restraints excluded: chain D residue 2195 CYS Chi-restraints excluded: chain D residue 2237 THR Chi-restraints excluded: chain D residue 2286 ASP Chi-restraints excluded: chain D residue 2293 GLU Chi-restraints excluded: chain D residue 2305 VAL Chi-restraints excluded: chain D residue 2330 PHE Chi-restraints excluded: chain D residue 2454 ASP Chi-restraints excluded: chain D residue 2455 MET Chi-restraints excluded: chain D residue 2482 PHE Chi-restraints excluded: chain D residue 2516 ASN Chi-restraints excluded: chain D residue 2663 LEU Chi-restraints excluded: chain D residue 2831 THR Chi-restraints excluded: chain D residue 2997 ASN Chi-restraints excluded: chain D residue 3101 LEU Chi-restraints excluded: chain D residue 3202 ASP Chi-restraints excluded: chain D residue 3215 THR Chi-restraints excluded: chain D residue 3630 THR Chi-restraints excluded: chain D residue 3663 LEU Chi-restraints excluded: chain D residue 3692 ASP Chi-restraints excluded: chain D residue 3697 SER Chi-restraints excluded: chain D residue 3713 PHE Chi-restraints excluded: chain D residue 3769 ASN Chi-restraints excluded: chain D residue 3801 VAL Chi-restraints excluded: chain D residue 3828 VAL Chi-restraints excluded: chain D residue 3853 PHE Chi-restraints excluded: chain D residue 3905 PHE Chi-restraints excluded: chain D residue 3927 CYS Chi-restraints excluded: chain D residue 3934 LEU Chi-restraints excluded: chain D residue 3964 ILE Chi-restraints excluded: chain D residue 3985 LEU Chi-restraints excluded: chain D residue 3997 GLN Chi-restraints excluded: chain D residue 4104 LEU Chi-restraints excluded: chain D residue 4110 ASN Chi-restraints excluded: chain D residue 4175 VAL Chi-restraints excluded: chain D residue 4518 TYR Chi-restraints excluded: chain D residue 4581 ILE Chi-restraints excluded: chain D residue 4654 ASP Chi-restraints excluded: chain D residue 4671 MET Chi-restraints excluded: chain D residue 4795 SER Chi-restraints excluded: chain D residue 4807 ASP Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4846 ASP Chi-restraints excluded: chain D residue 4858 LEU Chi-restraints excluded: chain D residue 4860 ILE Chi-restraints excluded: chain D residue 4879 VAL Chi-restraints excluded: chain D residue 4889 ILE Chi-restraints excluded: chain D residue 4890 CYS Chi-restraints excluded: chain D residue 4921 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 102 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1592 random chunks: chunk 1485 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 877 optimal weight: 7.9990 chunk 1124 optimal weight: 0.8980 chunk 871 optimal weight: 8.9990 chunk 1296 optimal weight: 0.2980 chunk 860 optimal weight: 8.9990 chunk 1534 optimal weight: 3.9990 chunk 960 optimal weight: 0.6980 chunk 935 optimal weight: 9.9990 chunk 708 optimal weight: 6.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2249 ASN ** A3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2249 ASN ** C3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2249 ASN ** D3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 HIS F 26 HIS G 26 HIS H 26 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 121556 Z= 0.225 Angle : 0.584 11.141 165096 Z= 0.295 Chirality : 0.039 0.164 19028 Planarity : 0.004 0.060 21400 Dihedral : 4.509 37.597 16880 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.46 % Allowed : 11.60 % Favored : 87.94 % Rotamer: Outliers : 4.33 % Allowed : 25.48 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.07), residues: 15692 helix: 1.52 (0.06), residues: 7224 sheet: -2.31 (0.19), residues: 696 loop : -2.87 (0.07), residues: 7772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 733 HIS 0.013 0.001 HIS G 26 PHE 0.021 0.001 PHE C4785 TYR 0.016 0.001 TYR D3690 ARG 0.003 0.000 ARG D4789 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31384 Ramachandran restraints generated. 15692 Oldfield, 0 Emsley, 15692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31384 Ramachandran restraints generated. 15692 Oldfield, 0 Emsley, 15692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1239 residues out of total 13992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 518 poor density : 721 time to evaluate : 9.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 489 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8443 (t80) REVERT: A 513 HIS cc_start: 0.7795 (OUTLIER) cc_final: 0.7395 (p-80) REVERT: A 802 PHE cc_start: 0.6899 (OUTLIER) cc_final: 0.5907 (m-80) REVERT: A 944 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.6580 (mm) REVERT: A 1300 MET cc_start: 0.7695 (ptt) cc_final: 0.7180 (ppp) REVERT: A 1460 ASP cc_start: 0.6279 (OUTLIER) cc_final: 0.4105 (t0) REVERT: A 1604 PHE cc_start: 0.6184 (OUTLIER) cc_final: 0.4958 (t80) REVERT: A 1629 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7344 (ptp) REVERT: A 2025 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.5627 (ppt90) REVERT: A 2286 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.6370 (t0) REVERT: A 2293 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6704 (pt0) REVERT: A 2342 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.8043 (mm) REVERT: A 2480 GLN cc_start: 0.1576 (OUTLIER) cc_final: 0.0295 (mp10) REVERT: A 2694 MET cc_start: 0.6581 (mpp) cc_final: 0.5916 (mpp) REVERT: A 3262 MET cc_start: -0.0377 (tmm) cc_final: -0.1214 (tpt) REVERT: A 3663 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.7875 (tt) REVERT: A 3905 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.8256 (m-80) REVERT: A 3934 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8934 (mp) REVERT: A 3997 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8197 (mp10) REVERT: A 3998 MET cc_start: 0.8701 (mmt) cc_final: 0.8473 (mmt) REVERT: A 4001 MET cc_start: 0.8538 (tmm) cc_final: 0.8229 (tmm) REVERT: A 4104 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8438 (mm) REVERT: A 4518 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.7998 (m-80) REVERT: A 4807 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.8095 (p0) REVERT: B 81 MET cc_start: 0.8293 (mpp) cc_final: 0.7547 (mpp) REVERT: B 262 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.8123 (t80) REVERT: B 396 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6843 (mp0) REVERT: B 489 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.8460 (t80) REVERT: B 513 HIS cc_start: 0.7650 (OUTLIER) cc_final: 0.7241 (p-80) REVERT: B 802 PHE cc_start: 0.6893 (OUTLIER) cc_final: 0.5927 (m-80) REVERT: B 1300 MET cc_start: 0.7706 (ptt) cc_final: 0.7203 (ppp) REVERT: B 1460 ASP cc_start: 0.6245 (OUTLIER) cc_final: 0.4134 (t0) REVERT: B 1604 PHE cc_start: 0.6182 (OUTLIER) cc_final: 0.4952 (t80) REVERT: B 1629 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.7278 (ptp) REVERT: B 2025 ARG cc_start: 0.7032 (OUTLIER) cc_final: 0.5572 (ppt90) REVERT: B 2065 MET cc_start: 0.9169 (tpp) cc_final: 0.8573 (mpp) REVERT: B 2286 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.6189 (t0) REVERT: B 2293 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6496 (pt0) REVERT: B 2480 GLN cc_start: 0.2068 (OUTLIER) cc_final: 0.0684 (mp10) REVERT: B 2694 MET cc_start: 0.6491 (mpp) cc_final: 0.5761 (mpp) REVERT: B 3262 MET cc_start: 0.0480 (tmm) cc_final: -0.0174 (tpt) REVERT: B 3427 MET cc_start: 0.4938 (mmt) cc_final: 0.4564 (mtm) REVERT: B 3661 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7806 (m-30) REVERT: B 3663 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.7868 (tt) REVERT: B 3905 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.8256 (m-80) REVERT: B 3934 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8921 (mp) REVERT: B 3997 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8134 (mp10) REVERT: B 4001 MET cc_start: 0.8611 (tmm) cc_final: 0.8299 (tmm) REVERT: B 4518 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.7982 (m-80) REVERT: B 4807 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7854 (p0) REVERT: C 396 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: C 489 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8462 (t80) REVERT: C 513 HIS cc_start: 0.7792 (OUTLIER) cc_final: 0.7377 (p-80) REVERT: C 802 PHE cc_start: 0.6988 (OUTLIER) cc_final: 0.5965 (m-80) REVERT: C 1300 MET cc_start: 0.7703 (ptt) cc_final: 0.7185 (ppp) REVERT: C 1460 ASP cc_start: 0.6253 (OUTLIER) cc_final: 0.4100 (t0) REVERT: C 1604 PHE cc_start: 0.6193 (OUTLIER) cc_final: 0.4981 (t80) REVERT: C 1629 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.7343 (ptp) REVERT: C 2025 ARG cc_start: 0.7020 (OUTLIER) cc_final: 0.5572 (ppt90) REVERT: C 2164 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8567 (mp) REVERT: C 2286 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.6258 (t0) REVERT: C 2293 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6634 (pt0) REVERT: C 2480 GLN cc_start: 0.1590 (OUTLIER) cc_final: 0.0310 (mp10) REVERT: C 2694 MET cc_start: 0.6329 (mpp) cc_final: 0.5607 (mpp) REVERT: C 3262 MET cc_start: -0.0399 (tmm) cc_final: -0.1218 (tpt) REVERT: C 3663 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.7871 (tt) REVERT: C 3905 PHE cc_start: 0.8875 (OUTLIER) cc_final: 0.8295 (m-80) REVERT: C 3934 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8950 (mp) REVERT: C 4001 MET cc_start: 0.8559 (tmm) cc_final: 0.8238 (tmm) REVERT: C 4518 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.8004 (m-80) REVERT: C 4807 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8097 (p0) REVERT: D 396 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7147 (mp0) REVERT: D 489 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.8459 (t80) REVERT: D 513 HIS cc_start: 0.7794 (OUTLIER) cc_final: 0.7382 (p-80) REVERT: D 802 PHE cc_start: 0.6986 (OUTLIER) cc_final: 0.5957 (m-80) REVERT: D 1300 MET cc_start: 0.7756 (ptt) cc_final: 0.7215 (ppp) REVERT: D 1460 ASP cc_start: 0.6261 (OUTLIER) cc_final: 0.4119 (t0) REVERT: D 1604 PHE cc_start: 0.6181 (OUTLIER) cc_final: 0.4977 (t80) REVERT: D 1629 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.7348 (ptp) REVERT: D 2025 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.5565 (ppt90) REVERT: D 2164 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8567 (mp) REVERT: D 2286 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.6251 (t0) REVERT: D 2293 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6642 (pt0) REVERT: D 2480 GLN cc_start: 0.1597 (OUTLIER) cc_final: 0.0310 (mp10) REVERT: D 2511 MET cc_start: 0.7855 (mmm) cc_final: 0.7521 (mmm) REVERT: D 2694 MET cc_start: 0.6489 (mpp) cc_final: 0.5792 (mpp) REVERT: D 3262 MET cc_start: -0.0384 (tmm) cc_final: -0.1202 (tpt) REVERT: D 3663 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.7856 (tt) REVERT: D 3905 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8260 (m-80) REVERT: D 3934 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8934 (mp) REVERT: D 4001 MET cc_start: 0.8554 (tmm) cc_final: 0.8224 (tmm) REVERT: D 4104 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8450 (mm) REVERT: D 4518 TYR cc_start: 0.8570 (OUTLIER) cc_final: 0.8003 (m-80) REVERT: D 4807 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8094 (p0) REVERT: F 4 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7402 (tm-30) REVERT: F 5 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7876 (tp) REVERT: G 95 ASN cc_start: 0.7954 (t0) cc_final: 0.7745 (t0) REVERT: H 95 ASN cc_start: 0.7951 (t0) cc_final: 0.7737 (t0) outliers start: 518 outliers final: 361 residues processed: 1175 average time/residue: 0.8844 time to fit residues: 1918.6318 Evaluate side-chains 1150 residues out of total 13992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 435 poor density : 715 time to evaluate : 9.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 513 HIS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 608 HIS Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 733 TRP Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 890 HIS Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain A residue 1146 HIS Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1442 TRP Chi-restraints excluded: chain A residue 1460 ASP Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1595 VAL Chi-restraints excluded: chain A residue 1604 PHE Chi-restraints excluded: chain A residue 1629 MET Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1663 SER Chi-restraints excluded: chain A residue 1777 TYR Chi-restraints excluded: chain A residue 1814 THR Chi-restraints excluded: chain A residue 1941 PHE Chi-restraints excluded: chain A residue 2021 ASP Chi-restraints excluded: chain A residue 2025 ARG Chi-restraints excluded: chain A residue 2083 MET Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2104 THR Chi-restraints excluded: chain A residue 2195 CYS Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2286 ASP Chi-restraints excluded: chain A residue 2293 GLU Chi-restraints excluded: chain A residue 2305 VAL Chi-restraints excluded: chain A residue 2330 PHE Chi-restraints excluded: chain A residue 2342 LEU Chi-restraints excluded: chain A residue 2454 ASP Chi-restraints excluded: chain A residue 2480 GLN Chi-restraints excluded: chain A residue 2482 PHE Chi-restraints excluded: chain A residue 2516 ASN Chi-restraints excluded: chain A residue 2831 THR Chi-restraints excluded: chain A residue 2997 ASN Chi-restraints excluded: chain A residue 3101 LEU Chi-restraints excluded: chain A residue 3215 THR Chi-restraints excluded: chain A residue 3630 THR Chi-restraints excluded: chain A residue 3661 ASP Chi-restraints excluded: chain A residue 3663 LEU Chi-restraints excluded: chain A residue 3692 ASP Chi-restraints excluded: chain A residue 3697 SER Chi-restraints excluded: chain A residue 3713 PHE Chi-restraints excluded: chain A residue 3769 ASN Chi-restraints excluded: chain A residue 3828 VAL Chi-restraints excluded: chain A residue 3853 PHE Chi-restraints excluded: chain A residue 3865 THR Chi-restraints excluded: chain A residue 3905 PHE Chi-restraints excluded: chain A residue 3927 CYS Chi-restraints excluded: chain A residue 3934 LEU Chi-restraints excluded: chain A residue 3958 SER Chi-restraints excluded: chain A residue 3964 ILE Chi-restraints excluded: chain A residue 3985 LEU Chi-restraints excluded: chain A residue 3997 GLN Chi-restraints excluded: chain A residue 4104 LEU Chi-restraints excluded: chain A residue 4110 ASN Chi-restraints excluded: chain A residue 4175 VAL Chi-restraints excluded: chain A residue 4516 LEU Chi-restraints excluded: chain A residue 4518 TYR Chi-restraints excluded: chain A residue 4581 ILE Chi-restraints excluded: chain A residue 4587 ILE Chi-restraints excluded: chain A residue 4654 ASP Chi-restraints excluded: chain A residue 4671 MET Chi-restraints excluded: chain A residue 4782 VAL Chi-restraints excluded: chain A residue 4795 SER Chi-restraints excluded: chain A residue 4807 ASP Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4846 ASP Chi-restraints excluded: chain A residue 4858 LEU Chi-restraints excluded: chain A residue 4860 ILE Chi-restraints excluded: chain A residue 4879 VAL Chi-restraints excluded: chain A residue 4889 ILE Chi-restraints excluded: chain A residue 4890 CYS Chi-restraints excluded: chain A residue 4921 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 396 GLU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 513 HIS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 608 HIS Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 650 ASN Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 733 TRP Chi-restraints excluded: chain B residue 751 THR Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 890 HIS Chi-restraints excluded: chain B residue 1087 ILE Chi-restraints excluded: chain B residue 1093 THR Chi-restraints excluded: chain B residue 1146 HIS Chi-restraints excluded: chain B residue 1251 LEU Chi-restraints excluded: chain B residue 1441 VAL Chi-restraints excluded: chain B residue 1442 TRP Chi-restraints excluded: chain B residue 1460 ASP Chi-restraints excluded: chain B residue 1595 VAL Chi-restraints excluded: chain B residue 1604 PHE Chi-restraints excluded: chain B residue 1629 MET Chi-restraints excluded: chain B residue 1651 LEU Chi-restraints excluded: chain B residue 1663 SER Chi-restraints excluded: chain B residue 1671 HIS Chi-restraints excluded: chain B residue 1777 TYR Chi-restraints excluded: chain B residue 1814 THR Chi-restraints excluded: chain B residue 1915 CYS Chi-restraints excluded: chain B residue 1941 PHE Chi-restraints excluded: chain B residue 1995 LEU Chi-restraints excluded: chain B residue 2021 ASP Chi-restraints excluded: chain B residue 2025 ARG Chi-restraints excluded: chain B residue 2083 MET Chi-restraints excluded: chain B residue 2097 LEU Chi-restraints excluded: chain B residue 2104 THR Chi-restraints excluded: chain B residue 2127 SER Chi-restraints excluded: chain B residue 2195 CYS Chi-restraints excluded: chain B residue 2237 THR Chi-restraints excluded: chain B residue 2280 VAL Chi-restraints excluded: chain B residue 2286 ASP Chi-restraints excluded: chain B residue 2293 GLU Chi-restraints excluded: chain B residue 2305 VAL Chi-restraints excluded: chain B residue 2330 PHE Chi-restraints excluded: chain B residue 2454 ASP Chi-restraints excluded: chain B residue 2455 MET Chi-restraints excluded: chain B residue 2480 GLN Chi-restraints excluded: chain B residue 2482 PHE Chi-restraints excluded: chain B residue 2516 ASN Chi-restraints excluded: chain B residue 2831 THR Chi-restraints excluded: chain B residue 2997 ASN Chi-restraints excluded: chain B residue 3101 LEU Chi-restraints excluded: chain B residue 3215 THR Chi-restraints excluded: chain B residue 3616 VAL Chi-restraints excluded: chain B residue 3630 THR Chi-restraints excluded: chain B residue 3661 ASP Chi-restraints excluded: chain B residue 3663 LEU Chi-restraints excluded: chain B residue 3692 ASP Chi-restraints excluded: chain B residue 3697 SER Chi-restraints excluded: chain B residue 3713 PHE Chi-restraints excluded: chain B residue 3769 ASN Chi-restraints excluded: chain B residue 3828 VAL Chi-restraints excluded: chain B residue 3831 ASP Chi-restraints excluded: chain B residue 3853 PHE Chi-restraints excluded: chain B residue 3865 THR Chi-restraints excluded: chain B residue 3905 PHE Chi-restraints excluded: chain B residue 3927 CYS Chi-restraints excluded: chain B residue 3934 LEU Chi-restraints excluded: chain B residue 3958 SER Chi-restraints excluded: chain B residue 3964 ILE Chi-restraints excluded: chain B residue 3997 GLN Chi-restraints excluded: chain B residue 4110 ASN Chi-restraints excluded: chain B residue 4175 VAL Chi-restraints excluded: chain B residue 4516 LEU Chi-restraints excluded: chain B residue 4518 TYR Chi-restraints excluded: chain B residue 4581 ILE Chi-restraints excluded: chain B residue 4587 ILE Chi-restraints excluded: chain B residue 4654 ASP Chi-restraints excluded: chain B residue 4671 MET Chi-restraints excluded: chain B residue 4782 VAL Chi-restraints excluded: chain B residue 4795 SER Chi-restraints excluded: chain B residue 4807 ASP Chi-restraints excluded: chain B residue 4820 VAL Chi-restraints excluded: chain B residue 4846 ASP Chi-restraints excluded: chain B residue 4858 LEU Chi-restraints excluded: chain B residue 4860 ILE Chi-restraints excluded: chain B residue 4879 VAL Chi-restraints excluded: chain B residue 4889 ILE Chi-restraints excluded: chain B residue 4890 CYS Chi-restraints excluded: chain B residue 4921 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 489 PHE Chi-restraints excluded: chain C residue 513 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 608 HIS Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 650 ASN Chi-restraints excluded: chain C residue 687 THR Chi-restraints excluded: chain C residue 721 ASP Chi-restraints excluded: chain C residue 733 TRP Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 802 PHE Chi-restraints excluded: chain C residue 890 HIS Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 1087 ILE Chi-restraints excluded: chain C residue 1093 THR Chi-restraints excluded: chain C residue 1146 HIS Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1441 VAL Chi-restraints excluded: chain C residue 1442 TRP Chi-restraints excluded: chain C residue 1460 ASP Chi-restraints excluded: chain C residue 1508 ILE Chi-restraints excluded: chain C residue 1595 VAL Chi-restraints excluded: chain C residue 1604 PHE Chi-restraints excluded: chain C residue 1629 MET Chi-restraints excluded: chain C residue 1651 LEU Chi-restraints excluded: chain C residue 1663 SER Chi-restraints excluded: chain C residue 1777 TYR Chi-restraints excluded: chain C residue 1814 THR Chi-restraints excluded: chain C residue 1941 PHE Chi-restraints excluded: chain C residue 1995 LEU Chi-restraints excluded: chain C residue 2021 ASP Chi-restraints excluded: chain C residue 2025 ARG Chi-restraints excluded: chain C residue 2083 MET Chi-restraints excluded: chain C residue 2097 LEU Chi-restraints excluded: chain C residue 2104 THR Chi-restraints excluded: chain C residue 2164 LEU Chi-restraints excluded: chain C residue 2195 CYS Chi-restraints excluded: chain C residue 2237 THR Chi-restraints excluded: chain C residue 2286 ASP Chi-restraints excluded: chain C residue 2293 GLU Chi-restraints excluded: chain C residue 2305 VAL Chi-restraints excluded: chain C residue 2330 PHE Chi-restraints excluded: chain C residue 2454 ASP Chi-restraints excluded: chain C residue 2455 MET Chi-restraints excluded: chain C residue 2480 GLN Chi-restraints excluded: chain C residue 2482 PHE Chi-restraints excluded: chain C residue 2516 ASN Chi-restraints excluded: chain C residue 2663 LEU Chi-restraints excluded: chain C residue 2831 THR Chi-restraints excluded: chain C residue 2997 ASN Chi-restraints excluded: chain C residue 3101 LEU Chi-restraints excluded: chain C residue 3215 THR Chi-restraints excluded: chain C residue 3630 THR Chi-restraints excluded: chain C residue 3661 ASP Chi-restraints excluded: chain C residue 3663 LEU Chi-restraints excluded: chain C residue 3692 ASP Chi-restraints excluded: chain C residue 3697 SER Chi-restraints excluded: chain C residue 3713 PHE Chi-restraints excluded: chain C residue 3769 ASN Chi-restraints excluded: chain C residue 3828 VAL Chi-restraints excluded: chain C residue 3853 PHE Chi-restraints excluded: chain C residue 3865 THR Chi-restraints excluded: chain C residue 3905 PHE Chi-restraints excluded: chain C residue 3927 CYS Chi-restraints excluded: chain C residue 3934 LEU Chi-restraints excluded: chain C residue 3958 SER Chi-restraints excluded: chain C residue 3964 ILE Chi-restraints excluded: chain C residue 3985 LEU Chi-restraints excluded: chain C residue 4110 ASN Chi-restraints excluded: chain C residue 4175 VAL Chi-restraints excluded: chain C residue 4516 LEU Chi-restraints excluded: chain C residue 4518 TYR Chi-restraints excluded: chain C residue 4581 ILE Chi-restraints excluded: chain C residue 4587 ILE Chi-restraints excluded: chain C residue 4654 ASP Chi-restraints excluded: chain C residue 4671 MET Chi-restraints excluded: chain C residue 4782 VAL Chi-restraints excluded: chain C residue 4795 SER Chi-restraints excluded: chain C residue 4807 ASP Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4846 ASP Chi-restraints excluded: chain C residue 4847 ILE Chi-restraints excluded: chain C residue 4858 LEU Chi-restraints excluded: chain C residue 4860 ILE Chi-restraints excluded: chain C residue 4879 VAL Chi-restraints excluded: chain C residue 4889 ILE Chi-restraints excluded: chain C residue 4890 CYS Chi-restraints excluded: chain C residue 4921 LEU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 396 GLU Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 489 PHE Chi-restraints excluded: chain D residue 513 HIS Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 608 HIS Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 629 GLN Chi-restraints excluded: chain D residue 650 ASN Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 721 ASP Chi-restraints excluded: chain D residue 731 HIS Chi-restraints excluded: chain D residue 733 TRP Chi-restraints excluded: chain D residue 751 THR Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 802 PHE Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 1042 THR Chi-restraints excluded: chain D residue 1087 ILE Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1146 HIS Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1441 VAL Chi-restraints excluded: chain D residue 1442 TRP Chi-restraints excluded: chain D residue 1460 ASP Chi-restraints excluded: chain D residue 1508 ILE Chi-restraints excluded: chain D residue 1595 VAL Chi-restraints excluded: chain D residue 1604 PHE Chi-restraints excluded: chain D residue 1629 MET Chi-restraints excluded: chain D residue 1651 LEU Chi-restraints excluded: chain D residue 1663 SER Chi-restraints excluded: chain D residue 1777 TYR Chi-restraints excluded: chain D residue 1814 THR Chi-restraints excluded: chain D residue 1941 PHE Chi-restraints excluded: chain D residue 1995 LEU Chi-restraints excluded: chain D residue 2021 ASP Chi-restraints excluded: chain D residue 2025 ARG Chi-restraints excluded: chain D residue 2083 MET Chi-restraints excluded: chain D residue 2097 LEU Chi-restraints excluded: chain D residue 2104 THR Chi-restraints excluded: chain D residue 2164 LEU Chi-restraints excluded: chain D residue 2195 CYS Chi-restraints excluded: chain D residue 2237 THR Chi-restraints excluded: chain D residue 2286 ASP Chi-restraints excluded: chain D residue 2293 GLU Chi-restraints excluded: chain D residue 2305 VAL Chi-restraints excluded: chain D residue 2330 PHE Chi-restraints excluded: chain D residue 2454 ASP Chi-restraints excluded: chain D residue 2455 MET Chi-restraints excluded: chain D residue 2480 GLN Chi-restraints excluded: chain D residue 2482 PHE Chi-restraints excluded: chain D residue 2516 ASN Chi-restraints excluded: chain D residue 2663 LEU Chi-restraints excluded: chain D residue 2831 THR Chi-restraints excluded: chain D residue 2997 ASN Chi-restraints excluded: chain D residue 3101 LEU Chi-restraints excluded: chain D residue 3202 ASP Chi-restraints excluded: chain D residue 3215 THR Chi-restraints excluded: chain D residue 3630 THR Chi-restraints excluded: chain D residue 3661 ASP Chi-restraints excluded: chain D residue 3663 LEU Chi-restraints excluded: chain D residue 3692 ASP Chi-restraints excluded: chain D residue 3697 SER Chi-restraints excluded: chain D residue 3713 PHE Chi-restraints excluded: chain D residue 3769 ASN Chi-restraints excluded: chain D residue 3828 VAL Chi-restraints excluded: chain D residue 3853 PHE Chi-restraints excluded: chain D residue 3865 THR Chi-restraints excluded: chain D residue 3905 PHE Chi-restraints excluded: chain D residue 3927 CYS Chi-restraints excluded: chain D residue 3934 LEU Chi-restraints excluded: chain D residue 3958 SER Chi-restraints excluded: chain D residue 3964 ILE Chi-restraints excluded: chain D residue 3985 LEU Chi-restraints excluded: chain D residue 4104 LEU Chi-restraints excluded: chain D residue 4110 ASN Chi-restraints excluded: chain D residue 4175 VAL Chi-restraints excluded: chain D residue 4516 LEU Chi-restraints excluded: chain D residue 4518 TYR Chi-restraints excluded: chain D residue 4581 ILE Chi-restraints excluded: chain D residue 4587 ILE Chi-restraints excluded: chain D residue 4654 ASP Chi-restraints excluded: chain D residue 4671 MET Chi-restraints excluded: chain D residue 4782 VAL Chi-restraints excluded: chain D residue 4795 SER Chi-restraints excluded: chain D residue 4807 ASP Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4846 ASP Chi-restraints excluded: chain D residue 4858 LEU Chi-restraints excluded: chain D residue 4860 ILE Chi-restraints excluded: chain D residue 4879 VAL Chi-restraints excluded: chain D residue 4889 ILE Chi-restraints excluded: chain D residue 4890 CYS Chi-restraints excluded: chain D residue 4921 LEU Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 ASN Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 102 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1592 random chunks: chunk 949 optimal weight: 5.9990 chunk 612 optimal weight: 40.0000 chunk 916 optimal weight: 2.9990 chunk 462 optimal weight: 20.0000 chunk 301 optimal weight: 1.9990 chunk 297 optimal weight: 5.9990 chunk 975 optimal weight: 4.9990 chunk 1045 optimal weight: 10.0000 chunk 758 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 1206 optimal weight: 0.1980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2249 ASN A2485 HIS ** A3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2249 ASN ** B3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2249 ASN ** C3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2249 ASN ** D3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 HIS F 26 HIS H 26 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 121556 Z= 0.174 Angle : 0.572 12.090 165096 Z= 0.287 Chirality : 0.039 0.170 19028 Planarity : 0.004 0.059 21400 Dihedral : 4.464 37.381 16880 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.46 % Allowed : 11.32 % Favored : 88.22 % Rotamer: Outliers : 3.88 % Allowed : 25.89 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.07), residues: 15692 helix: 1.58 (0.06), residues: 7224 sheet: -2.18 (0.19), residues: 744 loop : -2.86 (0.07), residues: 7724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 733 HIS 0.016 0.001 HIS F 26 PHE 0.017 0.001 PHE B4845 TYR 0.015 0.001 TYR B2619 ARG 0.003 0.000 ARG A4789 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31384 Ramachandran restraints generated. 15692 Oldfield, 0 Emsley, 15692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31384 Ramachandran restraints generated. 15692 Oldfield, 0 Emsley, 15692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1191 residues out of total 13992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 464 poor density : 727 time to evaluate : 9.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 489 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8444 (t80) REVERT: A 513 HIS cc_start: 0.7728 (OUTLIER) cc_final: 0.7330 (p-80) REVERT: A 802 PHE cc_start: 0.6913 (OUTLIER) cc_final: 0.5918 (m-80) REVERT: A 1300 MET cc_start: 0.7684 (ptt) cc_final: 0.7186 (ppp) REVERT: A 1460 ASP cc_start: 0.6220 (OUTLIER) cc_final: 0.4072 (t0) REVERT: A 1604 PHE cc_start: 0.6132 (OUTLIER) cc_final: 0.4910 (t80) REVERT: A 2025 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.5613 (ppt90) REVERT: A 2164 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8556 (mp) REVERT: A 2286 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.6291 (t0) REVERT: A 2293 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6669 (pt0) REVERT: A 2342 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.8039 (mm) REVERT: A 2480 GLN cc_start: 0.1900 (OUTLIER) cc_final: 0.0547 (mp10) REVERT: A 2694 MET cc_start: 0.6554 (mpp) cc_final: 0.5881 (mpp) REVERT: A 3262 MET cc_start: -0.0381 (tmm) cc_final: -0.1207 (tpt) REVERT: A 3663 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.7760 (tt) REVERT: A 3905 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8293 (m-80) REVERT: A 3934 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8889 (mp) REVERT: A 3997 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8186 (mp10) REVERT: A 3998 MET cc_start: 0.8709 (mmt) cc_final: 0.8497 (mmt) REVERT: A 4001 MET cc_start: 0.8521 (tmm) cc_final: 0.8198 (tmm) REVERT: A 4104 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8404 (mm) REVERT: A 4518 TYR cc_start: 0.8490 (OUTLIER) cc_final: 0.7813 (m-80) REVERT: A 4807 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.8053 (p0) REVERT: B 81 MET cc_start: 0.8256 (mpp) cc_final: 0.7530 (mpp) REVERT: B 262 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.8112 (t80) REVERT: B 489 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.8452 (t80) REVERT: B 513 HIS cc_start: 0.7658 (OUTLIER) cc_final: 0.7195 (p-80) REVERT: B 802 PHE cc_start: 0.6903 (OUTLIER) cc_final: 0.5940 (m-80) REVERT: B 1300 MET cc_start: 0.7691 (ptt) cc_final: 0.7189 (ppp) REVERT: B 1460 ASP cc_start: 0.6264 (OUTLIER) cc_final: 0.4086 (t0) REVERT: B 1604 PHE cc_start: 0.6129 (OUTLIER) cc_final: 0.4911 (t80) REVERT: B 2025 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.5599 (ppt90) REVERT: B 2065 MET cc_start: 0.9135 (tpp) cc_final: 0.8529 (mpp) REVERT: B 2164 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8543 (mp) REVERT: B 2286 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.6248 (t0) REVERT: B 2293 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6585 (pt0) REVERT: B 2480 GLN cc_start: 0.2093 (OUTLIER) cc_final: 0.0722 (mp10) REVERT: B 2694 MET cc_start: 0.6477 (mpp) cc_final: 0.5763 (mpp) REVERT: B 3262 MET cc_start: 0.0334 (tmm) cc_final: -0.0237 (tpt) REVERT: B 3427 MET cc_start: 0.4974 (mmt) cc_final: 0.4601 (mtm) REVERT: B 3663 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.7769 (tt) REVERT: B 3905 PHE cc_start: 0.8867 (OUTLIER) cc_final: 0.8273 (m-80) REVERT: B 3934 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8898 (mp) REVERT: B 3997 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8101 (mp10) REVERT: B 4001 MET cc_start: 0.8572 (tmm) cc_final: 0.8270 (tmm) REVERT: B 4518 TYR cc_start: 0.8434 (OUTLIER) cc_final: 0.7905 (m-80) REVERT: B 4807 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7752 (p0) REVERT: C 489 PHE cc_start: 0.8922 (OUTLIER) cc_final: 0.8449 (t80) REVERT: C 513 HIS cc_start: 0.7650 (OUTLIER) cc_final: 0.7274 (p-80) REVERT: C 802 PHE cc_start: 0.6971 (OUTLIER) cc_final: 0.5952 (m-80) REVERT: C 1300 MET cc_start: 0.7693 (ptt) cc_final: 0.7167 (ppp) REVERT: C 1460 ASP cc_start: 0.6251 (OUTLIER) cc_final: 0.4106 (t0) REVERT: C 1604 PHE cc_start: 0.6163 (OUTLIER) cc_final: 0.4949 (t80) REVERT: C 2025 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.5540 (ppt90) REVERT: C 2164 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8616 (mp) REVERT: C 2286 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.6234 (t0) REVERT: C 2293 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.6655 (pt0) REVERT: C 2480 GLN cc_start: 0.1819 (OUTLIER) cc_final: 0.0463 (mp10) REVERT: C 2694 MET cc_start: 0.6433 (mpp) cc_final: 0.5746 (mpp) REVERT: C 3262 MET cc_start: -0.0397 (tmm) cc_final: -0.1208 (tpt) REVERT: C 3663 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.7788 (tt) REVERT: C 3905 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8268 (m-80) REVERT: C 3934 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8919 (mp) REVERT: C 4001 MET cc_start: 0.8559 (tmm) cc_final: 0.8222 (tmm) REVERT: C 4518 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.7901 (m-80) REVERT: C 4807 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.8044 (p0) REVERT: D 489 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8459 (t80) REVERT: D 513 HIS cc_start: 0.7654 (OUTLIER) cc_final: 0.7281 (p-80) REVERT: D 802 PHE cc_start: 0.6969 (OUTLIER) cc_final: 0.5945 (m-80) REVERT: D 1300 MET cc_start: 0.7693 (ptt) cc_final: 0.7168 (ppp) REVERT: D 1460 ASP cc_start: 0.6263 (OUTLIER) cc_final: 0.4130 (t0) REVERT: D 1604 PHE cc_start: 0.6148 (OUTLIER) cc_final: 0.4946 (t80) REVERT: D 2025 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.5548 (ppt90) REVERT: D 2164 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8648 (mp) REVERT: D 2286 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.6229 (t0) REVERT: D 2293 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6664 (pt0) REVERT: D 2480 GLN cc_start: 0.1568 (OUTLIER) cc_final: 0.0277 (mp10) REVERT: D 2511 MET cc_start: 0.7854 (mmm) cc_final: 0.7520 (mmm) REVERT: D 2694 MET cc_start: 0.6402 (mpp) cc_final: 0.5703 (mpp) REVERT: D 3262 MET cc_start: -0.0384 (tmm) cc_final: -0.1191 (tpt) REVERT: D 3663 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.7816 (tt) REVERT: D 3905 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.8282 (m-80) REVERT: D 3934 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8924 (mp) REVERT: D 4001 MET cc_start: 0.8548 (tmm) cc_final: 0.8227 (tmm) REVERT: D 4104 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8410 (mm) REVERT: D 4518 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.7910 (m-80) REVERT: D 4807 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.8058 (p0) REVERT: F 4 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7407 (tm-30) REVERT: F 5 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7917 (tp) outliers start: 464 outliers final: 365 residues processed: 1137 average time/residue: 0.8893 time to fit residues: 1873.6392 Evaluate side-chains 1145 residues out of total 13992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 432 poor density : 713 time to evaluate : 9.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 513 HIS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 608 HIS Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 733 TRP Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 890 HIS Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain A residue 1146 HIS Chi-restraints excluded: chain A residue 1165 MET Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1442 TRP Chi-restraints excluded: chain A residue 1460 ASP Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1595 VAL Chi-restraints excluded: chain A residue 1604 PHE Chi-restraints excluded: chain A residue 1629 MET Chi-restraints excluded: chain A residue 1632 HIS Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1663 SER Chi-restraints excluded: chain A residue 1671 HIS Chi-restraints excluded: chain A residue 1777 TYR Chi-restraints excluded: chain A residue 1814 THR Chi-restraints excluded: chain A residue 1941 PHE Chi-restraints excluded: chain A residue 2021 ASP Chi-restraints excluded: chain A residue 2025 ARG Chi-restraints excluded: chain A residue 2083 MET Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2104 THR Chi-restraints excluded: chain A residue 2164 LEU Chi-restraints excluded: chain A residue 2195 CYS Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2286 ASP Chi-restraints excluded: chain A residue 2293 GLU Chi-restraints excluded: chain A residue 2305 VAL Chi-restraints excluded: chain A residue 2330 PHE Chi-restraints excluded: chain A residue 2342 LEU Chi-restraints excluded: chain A residue 2454 ASP Chi-restraints excluded: chain A residue 2455 MET Chi-restraints excluded: chain A residue 2480 GLN Chi-restraints excluded: chain A residue 2482 PHE Chi-restraints excluded: chain A residue 2485 HIS Chi-restraints excluded: chain A residue 2831 THR Chi-restraints excluded: chain A residue 2997 ASN Chi-restraints excluded: chain A residue 3101 LEU Chi-restraints excluded: chain A residue 3215 THR Chi-restraints excluded: chain A residue 3630 THR Chi-restraints excluded: chain A residue 3661 ASP Chi-restraints excluded: chain A residue 3663 LEU Chi-restraints excluded: chain A residue 3697 SER Chi-restraints excluded: chain A residue 3713 PHE Chi-restraints excluded: chain A residue 3769 ASN Chi-restraints excluded: chain A residue 3801 VAL Chi-restraints excluded: chain A residue 3828 VAL Chi-restraints excluded: chain A residue 3853 PHE Chi-restraints excluded: chain A residue 3865 THR Chi-restraints excluded: chain A residue 3905 PHE Chi-restraints excluded: chain A residue 3934 LEU Chi-restraints excluded: chain A residue 3958 SER Chi-restraints excluded: chain A residue 3964 ILE Chi-restraints excluded: chain A residue 3985 LEU Chi-restraints excluded: chain A residue 3997 GLN Chi-restraints excluded: chain A residue 4104 LEU Chi-restraints excluded: chain A residue 4110 ASN Chi-restraints excluded: chain A residue 4175 VAL Chi-restraints excluded: chain A residue 4518 TYR Chi-restraints excluded: chain A residue 4581 ILE Chi-restraints excluded: chain A residue 4587 ILE Chi-restraints excluded: chain A residue 4654 ASP Chi-restraints excluded: chain A residue 4671 MET Chi-restraints excluded: chain A residue 4782 VAL Chi-restraints excluded: chain A residue 4795 SER Chi-restraints excluded: chain A residue 4807 ASP Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4846 ASP Chi-restraints excluded: chain A residue 4858 LEU Chi-restraints excluded: chain A residue 4860 ILE Chi-restraints excluded: chain A residue 4879 VAL Chi-restraints excluded: chain A residue 4889 ILE Chi-restraints excluded: chain A residue 4890 CYS Chi-restraints excluded: chain A residue 4921 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 513 HIS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 608 HIS Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 650 ASN Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 733 TRP Chi-restraints excluded: chain B residue 751 THR Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 890 HIS Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 1087 ILE Chi-restraints excluded: chain B residue 1093 THR Chi-restraints excluded: chain B residue 1146 HIS Chi-restraints excluded: chain B residue 1165 MET Chi-restraints excluded: chain B residue 1251 LEU Chi-restraints excluded: chain B residue 1441 VAL Chi-restraints excluded: chain B residue 1442 TRP Chi-restraints excluded: chain B residue 1460 ASP Chi-restraints excluded: chain B residue 1467 VAL Chi-restraints excluded: chain B residue 1508 ILE Chi-restraints excluded: chain B residue 1595 VAL Chi-restraints excluded: chain B residue 1604 PHE Chi-restraints excluded: chain B residue 1629 MET Chi-restraints excluded: chain B residue 1651 LEU Chi-restraints excluded: chain B residue 1663 SER Chi-restraints excluded: chain B residue 1671 HIS Chi-restraints excluded: chain B residue 1777 TYR Chi-restraints excluded: chain B residue 1814 THR Chi-restraints excluded: chain B residue 1915 CYS Chi-restraints excluded: chain B residue 1941 PHE Chi-restraints excluded: chain B residue 1995 LEU Chi-restraints excluded: chain B residue 2021 ASP Chi-restraints excluded: chain B residue 2025 ARG Chi-restraints excluded: chain B residue 2083 MET Chi-restraints excluded: chain B residue 2097 LEU Chi-restraints excluded: chain B residue 2104 THR Chi-restraints excluded: chain B residue 2164 LEU Chi-restraints excluded: chain B residue 2195 CYS Chi-restraints excluded: chain B residue 2237 THR Chi-restraints excluded: chain B residue 2280 VAL Chi-restraints excluded: chain B residue 2286 ASP Chi-restraints excluded: chain B residue 2293 GLU Chi-restraints excluded: chain B residue 2305 VAL Chi-restraints excluded: chain B residue 2330 PHE Chi-restraints excluded: chain B residue 2454 ASP Chi-restraints excluded: chain B residue 2455 MET Chi-restraints excluded: chain B residue 2480 GLN Chi-restraints excluded: chain B residue 2482 PHE Chi-restraints excluded: chain B residue 2598 LEU Chi-restraints excluded: chain B residue 2831 THR Chi-restraints excluded: chain B residue 2997 ASN Chi-restraints excluded: chain B residue 3101 LEU Chi-restraints excluded: chain B residue 3215 THR Chi-restraints excluded: chain B residue 3630 THR Chi-restraints excluded: chain B residue 3663 LEU Chi-restraints excluded: chain B residue 3697 SER Chi-restraints excluded: chain B residue 3713 PHE Chi-restraints excluded: chain B residue 3769 ASN Chi-restraints excluded: chain B residue 3801 VAL Chi-restraints excluded: chain B residue 3828 VAL Chi-restraints excluded: chain B residue 3831 ASP Chi-restraints excluded: chain B residue 3853 PHE Chi-restraints excluded: chain B residue 3905 PHE Chi-restraints excluded: chain B residue 3927 CYS Chi-restraints excluded: chain B residue 3934 LEU Chi-restraints excluded: chain B residue 3958 SER Chi-restraints excluded: chain B residue 3964 ILE Chi-restraints excluded: chain B residue 3985 LEU Chi-restraints excluded: chain B residue 3997 GLN Chi-restraints excluded: chain B residue 4110 ASN Chi-restraints excluded: chain B residue 4175 VAL Chi-restraints excluded: chain B residue 4516 LEU Chi-restraints excluded: chain B residue 4518 TYR Chi-restraints excluded: chain B residue 4581 ILE Chi-restraints excluded: chain B residue 4587 ILE Chi-restraints excluded: chain B residue 4654 ASP Chi-restraints excluded: chain B residue 4795 SER Chi-restraints excluded: chain B residue 4807 ASP Chi-restraints excluded: chain B residue 4820 VAL Chi-restraints excluded: chain B residue 4846 ASP Chi-restraints excluded: chain B residue 4858 LEU Chi-restraints excluded: chain B residue 4860 ILE Chi-restraints excluded: chain B residue 4879 VAL Chi-restraints excluded: chain B residue 4889 ILE Chi-restraints excluded: chain B residue 4890 CYS Chi-restraints excluded: chain B residue 4921 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 489 PHE Chi-restraints excluded: chain C residue 513 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 608 HIS Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 650 ASN Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 687 THR Chi-restraints excluded: chain C residue 721 ASP Chi-restraints excluded: chain C residue 733 TRP Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 802 PHE Chi-restraints excluded: chain C residue 890 HIS Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 1087 ILE Chi-restraints excluded: chain C residue 1093 THR Chi-restraints excluded: chain C residue 1146 HIS Chi-restraints excluded: chain C residue 1165 MET Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1441 VAL Chi-restraints excluded: chain C residue 1442 TRP Chi-restraints excluded: chain C residue 1460 ASP Chi-restraints excluded: chain C residue 1508 ILE Chi-restraints excluded: chain C residue 1595 VAL Chi-restraints excluded: chain C residue 1604 PHE Chi-restraints excluded: chain C residue 1629 MET Chi-restraints excluded: chain C residue 1632 HIS Chi-restraints excluded: chain C residue 1651 LEU Chi-restraints excluded: chain C residue 1663 SER Chi-restraints excluded: chain C residue 1777 TYR Chi-restraints excluded: chain C residue 1814 THR Chi-restraints excluded: chain C residue 1941 PHE Chi-restraints excluded: chain C residue 1995 LEU Chi-restraints excluded: chain C residue 2021 ASP Chi-restraints excluded: chain C residue 2025 ARG Chi-restraints excluded: chain C residue 2083 MET Chi-restraints excluded: chain C residue 2097 LEU Chi-restraints excluded: chain C residue 2104 THR Chi-restraints excluded: chain C residue 2164 LEU Chi-restraints excluded: chain C residue 2195 CYS Chi-restraints excluded: chain C residue 2237 THR Chi-restraints excluded: chain C residue 2286 ASP Chi-restraints excluded: chain C residue 2293 GLU Chi-restraints excluded: chain C residue 2305 VAL Chi-restraints excluded: chain C residue 2330 PHE Chi-restraints excluded: chain C residue 2454 ASP Chi-restraints excluded: chain C residue 2455 MET Chi-restraints excluded: chain C residue 2480 GLN Chi-restraints excluded: chain C residue 2482 PHE Chi-restraints excluded: chain C residue 2516 ASN Chi-restraints excluded: chain C residue 2663 LEU Chi-restraints excluded: chain C residue 2831 THR Chi-restraints excluded: chain C residue 2997 ASN Chi-restraints excluded: chain C residue 3101 LEU Chi-restraints excluded: chain C residue 3215 THR Chi-restraints excluded: chain C residue 3630 THR Chi-restraints excluded: chain C residue 3661 ASP Chi-restraints excluded: chain C residue 3663 LEU Chi-restraints excluded: chain C residue 3692 ASP Chi-restraints excluded: chain C residue 3697 SER Chi-restraints excluded: chain C residue 3713 PHE Chi-restraints excluded: chain C residue 3769 ASN Chi-restraints excluded: chain C residue 3801 VAL Chi-restraints excluded: chain C residue 3828 VAL Chi-restraints excluded: chain C residue 3853 PHE Chi-restraints excluded: chain C residue 3865 THR Chi-restraints excluded: chain C residue 3905 PHE Chi-restraints excluded: chain C residue 3927 CYS Chi-restraints excluded: chain C residue 3934 LEU Chi-restraints excluded: chain C residue 3958 SER Chi-restraints excluded: chain C residue 3964 ILE Chi-restraints excluded: chain C residue 3985 LEU Chi-restraints excluded: chain C residue 4110 ASN Chi-restraints excluded: chain C residue 4175 VAL Chi-restraints excluded: chain C residue 4516 LEU Chi-restraints excluded: chain C residue 4518 TYR Chi-restraints excluded: chain C residue 4581 ILE Chi-restraints excluded: chain C residue 4587 ILE Chi-restraints excluded: chain C residue 4654 ASP Chi-restraints excluded: chain C residue 4782 VAL Chi-restraints excluded: chain C residue 4795 SER Chi-restraints excluded: chain C residue 4807 ASP Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4846 ASP Chi-restraints excluded: chain C residue 4858 LEU Chi-restraints excluded: chain C residue 4860 ILE Chi-restraints excluded: chain C residue 4879 VAL Chi-restraints excluded: chain C residue 4889 ILE Chi-restraints excluded: chain C residue 4890 CYS Chi-restraints excluded: chain C residue 4921 LEU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 489 PHE Chi-restraints excluded: chain D residue 513 HIS Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 608 HIS Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 650 ASN Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 721 ASP Chi-restraints excluded: chain D residue 731 HIS Chi-restraints excluded: chain D residue 733 TRP Chi-restraints excluded: chain D residue 751 THR Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 802 PHE Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 1042 THR Chi-restraints excluded: chain D residue 1087 ILE Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1146 HIS Chi-restraints excluded: chain D residue 1165 MET Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1441 VAL Chi-restraints excluded: chain D residue 1442 TRP Chi-restraints excluded: chain D residue 1460 ASP Chi-restraints excluded: chain D residue 1508 ILE Chi-restraints excluded: chain D residue 1595 VAL Chi-restraints excluded: chain D residue 1604 PHE Chi-restraints excluded: chain D residue 1629 MET Chi-restraints excluded: chain D residue 1651 LEU Chi-restraints excluded: chain D residue 1663 SER Chi-restraints excluded: chain D residue 1671 HIS Chi-restraints excluded: chain D residue 1777 TYR Chi-restraints excluded: chain D residue 1814 THR Chi-restraints excluded: chain D residue 1941 PHE Chi-restraints excluded: chain D residue 1995 LEU Chi-restraints excluded: chain D residue 2021 ASP Chi-restraints excluded: chain D residue 2025 ARG Chi-restraints excluded: chain D residue 2083 MET Chi-restraints excluded: chain D residue 2097 LEU Chi-restraints excluded: chain D residue 2104 THR Chi-restraints excluded: chain D residue 2164 LEU Chi-restraints excluded: chain D residue 2195 CYS Chi-restraints excluded: chain D residue 2237 THR Chi-restraints excluded: chain D residue 2286 ASP Chi-restraints excluded: chain D residue 2293 GLU Chi-restraints excluded: chain D residue 2305 VAL Chi-restraints excluded: chain D residue 2330 PHE Chi-restraints excluded: chain D residue 2454 ASP Chi-restraints excluded: chain D residue 2455 MET Chi-restraints excluded: chain D residue 2463 HIS Chi-restraints excluded: chain D residue 2480 GLN Chi-restraints excluded: chain D residue 2482 PHE Chi-restraints excluded: chain D residue 2516 ASN Chi-restraints excluded: chain D residue 2663 LEU Chi-restraints excluded: chain D residue 2831 THR Chi-restraints excluded: chain D residue 2997 ASN Chi-restraints excluded: chain D residue 3101 LEU Chi-restraints excluded: chain D residue 3215 THR Chi-restraints excluded: chain D residue 3630 THR Chi-restraints excluded: chain D residue 3661 ASP Chi-restraints excluded: chain D residue 3663 LEU Chi-restraints excluded: chain D residue 3692 ASP Chi-restraints excluded: chain D residue 3697 SER Chi-restraints excluded: chain D residue 3713 PHE Chi-restraints excluded: chain D residue 3769 ASN Chi-restraints excluded: chain D residue 3801 VAL Chi-restraints excluded: chain D residue 3828 VAL Chi-restraints excluded: chain D residue 3853 PHE Chi-restraints excluded: chain D residue 3865 THR Chi-restraints excluded: chain D residue 3905 PHE Chi-restraints excluded: chain D residue 3927 CYS Chi-restraints excluded: chain D residue 3934 LEU Chi-restraints excluded: chain D residue 3958 SER Chi-restraints excluded: chain D residue 3964 ILE Chi-restraints excluded: chain D residue 3985 LEU Chi-restraints excluded: chain D residue 4104 LEU Chi-restraints excluded: chain D residue 4110 ASN Chi-restraints excluded: chain D residue 4175 VAL Chi-restraints excluded: chain D residue 4518 TYR Chi-restraints excluded: chain D residue 4581 ILE Chi-restraints excluded: chain D residue 4587 ILE Chi-restraints excluded: chain D residue 4654 ASP Chi-restraints excluded: chain D residue 4752 LEU Chi-restraints excluded: chain D residue 4782 VAL Chi-restraints excluded: chain D residue 4795 SER Chi-restraints excluded: chain D residue 4807 ASP Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4846 ASP Chi-restraints excluded: chain D residue 4858 LEU Chi-restraints excluded: chain D residue 4860 ILE Chi-restraints excluded: chain D residue 4879 VAL Chi-restraints excluded: chain D residue 4889 ILE Chi-restraints excluded: chain D residue 4890 CYS Chi-restraints excluded: chain D residue 4921 LEU Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 102 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1592 random chunks: chunk 1395 optimal weight: 3.9990 chunk 1470 optimal weight: 3.9990 chunk 1341 optimal weight: 6.9990 chunk 1429 optimal weight: 50.0000 chunk 1469 optimal weight: 9.9990 chunk 860 optimal weight: 0.8980 chunk 622 optimal weight: 40.0000 chunk 1122 optimal weight: 0.9980 chunk 438 optimal weight: 3.9990 chunk 1292 optimal weight: 30.0000 chunk 1352 optimal weight: 8.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2249 ASN A2485 HIS ** A3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2249 ASN C2485 HIS ** C3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 629 GLN ** D1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 HIS F 26 HIS G 26 HIS H 26 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 121556 Z= 0.233 Angle : 0.592 11.796 165096 Z= 0.297 Chirality : 0.039 0.225 19028 Planarity : 0.004 0.060 21400 Dihedral : 4.472 37.419 16880 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.46 % Allowed : 11.69 % Favored : 87.85 % Rotamer: Outliers : 4.11 % Allowed : 25.89 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.07), residues: 15692 helix: 1.53 (0.06), residues: 7228 sheet: -2.21 (0.19), residues: 744 loop : -2.86 (0.07), residues: 7720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 733 HIS 0.019 0.001 HIS H 26 PHE 0.022 0.001 PHE D4785 TYR 0.035 0.001 TYR B1715 ARG 0.006 0.000 ARG B1763 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31384 Ramachandran restraints generated. 15692 Oldfield, 0 Emsley, 15692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31384 Ramachandran restraints generated. 15692 Oldfield, 0 Emsley, 15692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1209 residues out of total 13992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 492 poor density : 717 time to evaluate : 9.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 489 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.8465 (t80) REVERT: A 513 HIS cc_start: 0.7693 (OUTLIER) cc_final: 0.7311 (p-80) REVERT: A 802 PHE cc_start: 0.6895 (OUTLIER) cc_final: 0.5905 (m-80) REVERT: A 1300 MET cc_start: 0.7676 (ptt) cc_final: 0.7163 (ppp) REVERT: A 1460 ASP cc_start: 0.6176 (OUTLIER) cc_final: 0.3998 (t0) REVERT: A 1604 PHE cc_start: 0.6216 (OUTLIER) cc_final: 0.4979 (t80) REVERT: A 2025 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.5386 (ppt90) REVERT: A 2164 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8550 (mp) REVERT: A 2286 ASP cc_start: 0.7819 (OUTLIER) cc_final: 0.6274 (t0) REVERT: A 2293 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6608 (pt0) REVERT: A 2342 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8050 (mm) REVERT: A 2480 GLN cc_start: 0.1755 (OUTLIER) cc_final: 0.0435 (mp10) REVERT: A 2694 MET cc_start: 0.6410 (mpp) cc_final: 0.5714 (mpp) REVERT: A 3262 MET cc_start: -0.0342 (tmm) cc_final: -0.1173 (tpt) REVERT: A 3663 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.7875 (tt) REVERT: A 3905 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.8258 (m-80) REVERT: A 3934 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8930 (mp) REVERT: A 3997 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8260 (mp10) REVERT: A 4001 MET cc_start: 0.8529 (tmm) cc_final: 0.8201 (tmm) REVERT: A 4104 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8426 (mm) REVERT: A 4518 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.7982 (m-80) REVERT: B 81 MET cc_start: 0.8226 (mpp) cc_final: 0.7858 (mpp) REVERT: B 262 TYR cc_start: 0.8341 (OUTLIER) cc_final: 0.8066 (t80) REVERT: B 489 PHE cc_start: 0.8933 (OUTLIER) cc_final: 0.8459 (t80) REVERT: B 513 HIS cc_start: 0.7795 (OUTLIER) cc_final: 0.7353 (p-80) REVERT: B 802 PHE cc_start: 0.6891 (OUTLIER) cc_final: 0.5923 (m-80) REVERT: B 1300 MET cc_start: 0.7677 (ptt) cc_final: 0.7179 (ppp) REVERT: B 1460 ASP cc_start: 0.6223 (OUTLIER) cc_final: 0.4011 (t0) REVERT: B 1604 PHE cc_start: 0.6169 (OUTLIER) cc_final: 0.4959 (t80) REVERT: B 1629 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.7318 (ptp) REVERT: B 2025 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.5348 (ppt90) REVERT: B 2164 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8558 (mp) REVERT: B 2286 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.6293 (t0) REVERT: B 2293 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6542 (pt0) REVERT: B 2480 GLN cc_start: 0.2050 (OUTLIER) cc_final: 0.0677 (mp10) REVERT: B 2694 MET cc_start: 0.6478 (mpp) cc_final: 0.5731 (mpp) REVERT: B 3262 MET cc_start: 0.0364 (tmm) cc_final: -0.0215 (tpt) REVERT: B 3427 MET cc_start: 0.5071 (mmt) cc_final: 0.4753 (mtm) REVERT: B 3661 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7695 (m-30) REVERT: B 3663 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.7847 (tt) REVERT: B 3905 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.8277 (m-80) REVERT: B 3934 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8928 (mp) REVERT: B 3997 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8157 (mp10) REVERT: B 4001 MET cc_start: 0.8610 (tmm) cc_final: 0.8310 (tmm) REVERT: B 4518 TYR cc_start: 0.8499 (OUTLIER) cc_final: 0.7972 (m-80) REVERT: B 4807 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7853 (p0) REVERT: C 489 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8456 (t80) REVERT: C 513 HIS cc_start: 0.7715 (OUTLIER) cc_final: 0.7327 (p-80) REVERT: C 802 PHE cc_start: 0.6993 (OUTLIER) cc_final: 0.5969 (m-80) REVERT: C 1300 MET cc_start: 0.7676 (ptt) cc_final: 0.7165 (ppp) REVERT: C 1460 ASP cc_start: 0.6232 (OUTLIER) cc_final: 0.4065 (t0) REVERT: C 1604 PHE cc_start: 0.6160 (OUTLIER) cc_final: 0.4959 (t80) REVERT: C 1629 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.7370 (ptp) REVERT: C 2025 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.5555 (ppt90) REVERT: C 2164 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8534 (mp) REVERT: C 2286 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.6262 (t0) REVERT: C 2293 GLU cc_start: 0.6982 (OUTLIER) cc_final: 0.6598 (pt0) REVERT: C 2480 GLN cc_start: 0.1833 (OUTLIER) cc_final: 0.0476 (mp10) REVERT: C 2694 MET cc_start: 0.6442 (mpp) cc_final: 0.5743 (mpp) REVERT: C 3262 MET cc_start: -0.0241 (tmm) cc_final: -0.0886 (tpt) REVERT: C 3663 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.7875 (tt) REVERT: C 3905 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8253 (m-80) REVERT: C 3934 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8943 (mp) REVERT: C 4001 MET cc_start: 0.8558 (tmm) cc_final: 0.8229 (tmm) REVERT: C 4518 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.7990 (m-80) REVERT: D 489 PHE cc_start: 0.8927 (OUTLIER) cc_final: 0.8457 (t80) REVERT: D 513 HIS cc_start: 0.7714 (OUTLIER) cc_final: 0.7329 (p-80) REVERT: D 802 PHE cc_start: 0.6989 (OUTLIER) cc_final: 0.5965 (m-80) REVERT: D 1300 MET cc_start: 0.7678 (ptt) cc_final: 0.7166 (ppp) REVERT: D 1460 ASP cc_start: 0.6245 (OUTLIER) cc_final: 0.4093 (t0) REVERT: D 1604 PHE cc_start: 0.6188 (OUTLIER) cc_final: 0.4981 (t80) REVERT: D 2025 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.5585 (ppt90) REVERT: D 2164 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8567 (mp) REVERT: D 2286 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.6266 (t0) REVERT: D 2293 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6605 (pt0) REVERT: D 2480 GLN cc_start: 0.1585 (OUTLIER) cc_final: 0.0290 (mp10) REVERT: D 2511 MET cc_start: 0.7887 (mmm) cc_final: 0.7573 (mmm) REVERT: D 2694 MET cc_start: 0.6410 (mpp) cc_final: 0.5708 (mpp) REVERT: D 3262 MET cc_start: -0.0227 (tmm) cc_final: -0.0871 (tpt) REVERT: D 3663 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.7870 (tt) REVERT: D 3905 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8262 (m-80) REVERT: D 3934 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8949 (mp) REVERT: D 4001 MET cc_start: 0.8561 (tmm) cc_final: 0.8223 (tmm) REVERT: D 4104 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8438 (mm) REVERT: D 4518 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.7982 (m-80) REVERT: F 4 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7413 (tm-30) REVERT: F 5 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7937 (tp) outliers start: 492 outliers final: 385 residues processed: 1156 average time/residue: 0.8697 time to fit residues: 1861.5873 Evaluate side-chains 1169 residues out of total 13992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 452 poor density : 717 time to evaluate : 9.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 513 HIS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 608 HIS Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 733 TRP Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 890 HIS Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain A residue 1146 HIS Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1442 TRP Chi-restraints excluded: chain A residue 1460 ASP Chi-restraints excluded: chain A residue 1467 VAL Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1595 VAL Chi-restraints excluded: chain A residue 1604 PHE Chi-restraints excluded: chain A residue 1629 MET Chi-restraints excluded: chain A residue 1632 HIS Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1663 SER Chi-restraints excluded: chain A residue 1671 HIS Chi-restraints excluded: chain A residue 1777 TYR Chi-restraints excluded: chain A residue 1814 THR Chi-restraints excluded: chain A residue 1941 PHE Chi-restraints excluded: chain A residue 2021 ASP Chi-restraints excluded: chain A residue 2025 ARG Chi-restraints excluded: chain A residue 2083 MET Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2104 THR Chi-restraints excluded: chain A residue 2164 LEU Chi-restraints excluded: chain A residue 2195 CYS Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2280 VAL Chi-restraints excluded: chain A residue 2286 ASP Chi-restraints excluded: chain A residue 2293 GLU Chi-restraints excluded: chain A residue 2305 VAL Chi-restraints excluded: chain A residue 2330 PHE Chi-restraints excluded: chain A residue 2342 LEU Chi-restraints excluded: chain A residue 2454 ASP Chi-restraints excluded: chain A residue 2455 MET Chi-restraints excluded: chain A residue 2463 HIS Chi-restraints excluded: chain A residue 2480 GLN Chi-restraints excluded: chain A residue 2482 PHE Chi-restraints excluded: chain A residue 2516 ASN Chi-restraints excluded: chain A residue 2831 THR Chi-restraints excluded: chain A residue 2997 ASN Chi-restraints excluded: chain A residue 3101 LEU Chi-restraints excluded: chain A residue 3215 THR Chi-restraints excluded: chain A residue 3630 THR Chi-restraints excluded: chain A residue 3661 ASP Chi-restraints excluded: chain A residue 3663 LEU Chi-restraints excluded: chain A residue 3697 SER Chi-restraints excluded: chain A residue 3713 PHE Chi-restraints excluded: chain A residue 3769 ASN Chi-restraints excluded: chain A residue 3828 VAL Chi-restraints excluded: chain A residue 3853 PHE Chi-restraints excluded: chain A residue 3865 THR Chi-restraints excluded: chain A residue 3905 PHE Chi-restraints excluded: chain A residue 3927 CYS Chi-restraints excluded: chain A residue 3934 LEU Chi-restraints excluded: chain A residue 3958 SER Chi-restraints excluded: chain A residue 3964 ILE Chi-restraints excluded: chain A residue 3985 LEU Chi-restraints excluded: chain A residue 3997 GLN Chi-restraints excluded: chain A residue 4104 LEU Chi-restraints excluded: chain A residue 4110 ASN Chi-restraints excluded: chain A residue 4175 VAL Chi-restraints excluded: chain A residue 4516 LEU Chi-restraints excluded: chain A residue 4518 TYR Chi-restraints excluded: chain A residue 4581 ILE Chi-restraints excluded: chain A residue 4587 ILE Chi-restraints excluded: chain A residue 4654 ASP Chi-restraints excluded: chain A residue 4671 MET Chi-restraints excluded: chain A residue 4752 LEU Chi-restraints excluded: chain A residue 4782 VAL Chi-restraints excluded: chain A residue 4795 SER Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4846 ASP Chi-restraints excluded: chain A residue 4847 ILE Chi-restraints excluded: chain A residue 4858 LEU Chi-restraints excluded: chain A residue 4860 ILE Chi-restraints excluded: chain A residue 4879 VAL Chi-restraints excluded: chain A residue 4889 ILE Chi-restraints excluded: chain A residue 4890 CYS Chi-restraints excluded: chain A residue 4921 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 262 TYR Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 513 HIS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 608 HIS Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 650 ASN Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 733 TRP Chi-restraints excluded: chain B residue 751 THR Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 890 HIS Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 1087 ILE Chi-restraints excluded: chain B residue 1093 THR Chi-restraints excluded: chain B residue 1146 HIS Chi-restraints excluded: chain B residue 1165 MET Chi-restraints excluded: chain B residue 1251 LEU Chi-restraints excluded: chain B residue 1441 VAL Chi-restraints excluded: chain B residue 1442 TRP Chi-restraints excluded: chain B residue 1460 ASP Chi-restraints excluded: chain B residue 1467 VAL Chi-restraints excluded: chain B residue 1508 ILE Chi-restraints excluded: chain B residue 1595 VAL Chi-restraints excluded: chain B residue 1604 PHE Chi-restraints excluded: chain B residue 1629 MET Chi-restraints excluded: chain B residue 1651 LEU Chi-restraints excluded: chain B residue 1663 SER Chi-restraints excluded: chain B residue 1671 HIS Chi-restraints excluded: chain B residue 1777 TYR Chi-restraints excluded: chain B residue 1814 THR Chi-restraints excluded: chain B residue 1915 CYS Chi-restraints excluded: chain B residue 1941 PHE Chi-restraints excluded: chain B residue 1995 LEU Chi-restraints excluded: chain B residue 2021 ASP Chi-restraints excluded: chain B residue 2025 ARG Chi-restraints excluded: chain B residue 2083 MET Chi-restraints excluded: chain B residue 2097 LEU Chi-restraints excluded: chain B residue 2104 THR Chi-restraints excluded: chain B residue 2164 LEU Chi-restraints excluded: chain B residue 2195 CYS Chi-restraints excluded: chain B residue 2237 THR Chi-restraints excluded: chain B residue 2280 VAL Chi-restraints excluded: chain B residue 2286 ASP Chi-restraints excluded: chain B residue 2293 GLU Chi-restraints excluded: chain B residue 2305 VAL Chi-restraints excluded: chain B residue 2330 PHE Chi-restraints excluded: chain B residue 2454 ASP Chi-restraints excluded: chain B residue 2455 MET Chi-restraints excluded: chain B residue 2463 HIS Chi-restraints excluded: chain B residue 2480 GLN Chi-restraints excluded: chain B residue 2482 PHE Chi-restraints excluded: chain B residue 2516 ASN Chi-restraints excluded: chain B residue 2598 LEU Chi-restraints excluded: chain B residue 2831 THR Chi-restraints excluded: chain B residue 2997 ASN Chi-restraints excluded: chain B residue 3101 LEU Chi-restraints excluded: chain B residue 3215 THR Chi-restraints excluded: chain B residue 3630 THR Chi-restraints excluded: chain B residue 3661 ASP Chi-restraints excluded: chain B residue 3663 LEU Chi-restraints excluded: chain B residue 3697 SER Chi-restraints excluded: chain B residue 3713 PHE Chi-restraints excluded: chain B residue 3769 ASN Chi-restraints excluded: chain B residue 3828 VAL Chi-restraints excluded: chain B residue 3831 ASP Chi-restraints excluded: chain B residue 3853 PHE Chi-restraints excluded: chain B residue 3865 THR Chi-restraints excluded: chain B residue 3905 PHE Chi-restraints excluded: chain B residue 3927 CYS Chi-restraints excluded: chain B residue 3934 LEU Chi-restraints excluded: chain B residue 3958 SER Chi-restraints excluded: chain B residue 3964 ILE Chi-restraints excluded: chain B residue 3985 LEU Chi-restraints excluded: chain B residue 3997 GLN Chi-restraints excluded: chain B residue 4110 ASN Chi-restraints excluded: chain B residue 4175 VAL Chi-restraints excluded: chain B residue 4516 LEU Chi-restraints excluded: chain B residue 4518 TYR Chi-restraints excluded: chain B residue 4581 ILE Chi-restraints excluded: chain B residue 4587 ILE Chi-restraints excluded: chain B residue 4654 ASP Chi-restraints excluded: chain B residue 4752 LEU Chi-restraints excluded: chain B residue 4782 VAL Chi-restraints excluded: chain B residue 4795 SER Chi-restraints excluded: chain B residue 4807 ASP Chi-restraints excluded: chain B residue 4810 THR Chi-restraints excluded: chain B residue 4820 VAL Chi-restraints excluded: chain B residue 4846 ASP Chi-restraints excluded: chain B residue 4847 ILE Chi-restraints excluded: chain B residue 4858 LEU Chi-restraints excluded: chain B residue 4860 ILE Chi-restraints excluded: chain B residue 4879 VAL Chi-restraints excluded: chain B residue 4889 ILE Chi-restraints excluded: chain B residue 4890 CYS Chi-restraints excluded: chain B residue 4921 LEU Chi-restraints excluded: chain B residue 4933 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 489 PHE Chi-restraints excluded: chain C residue 513 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 608 HIS Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 650 ASN Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 687 THR Chi-restraints excluded: chain C residue 721 ASP Chi-restraints excluded: chain C residue 733 TRP Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 802 PHE Chi-restraints excluded: chain C residue 890 HIS Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 1087 ILE Chi-restraints excluded: chain C residue 1093 THR Chi-restraints excluded: chain C residue 1146 HIS Chi-restraints excluded: chain C residue 1165 MET Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1441 VAL Chi-restraints excluded: chain C residue 1442 TRP Chi-restraints excluded: chain C residue 1460 ASP Chi-restraints excluded: chain C residue 1467 VAL Chi-restraints excluded: chain C residue 1508 ILE Chi-restraints excluded: chain C residue 1595 VAL Chi-restraints excluded: chain C residue 1604 PHE Chi-restraints excluded: chain C residue 1629 MET Chi-restraints excluded: chain C residue 1632 HIS Chi-restraints excluded: chain C residue 1651 LEU Chi-restraints excluded: chain C residue 1663 SER Chi-restraints excluded: chain C residue 1671 HIS Chi-restraints excluded: chain C residue 1777 TYR Chi-restraints excluded: chain C residue 1814 THR Chi-restraints excluded: chain C residue 1941 PHE Chi-restraints excluded: chain C residue 1995 LEU Chi-restraints excluded: chain C residue 2021 ASP Chi-restraints excluded: chain C residue 2025 ARG Chi-restraints excluded: chain C residue 2083 MET Chi-restraints excluded: chain C residue 2097 LEU Chi-restraints excluded: chain C residue 2104 THR Chi-restraints excluded: chain C residue 2164 LEU Chi-restraints excluded: chain C residue 2195 CYS Chi-restraints excluded: chain C residue 2237 THR Chi-restraints excluded: chain C residue 2280 VAL Chi-restraints excluded: chain C residue 2286 ASP Chi-restraints excluded: chain C residue 2293 GLU Chi-restraints excluded: chain C residue 2305 VAL Chi-restraints excluded: chain C residue 2330 PHE Chi-restraints excluded: chain C residue 2454 ASP Chi-restraints excluded: chain C residue 2455 MET Chi-restraints excluded: chain C residue 2480 GLN Chi-restraints excluded: chain C residue 2482 PHE Chi-restraints excluded: chain C residue 2485 HIS Chi-restraints excluded: chain C residue 2516 ASN Chi-restraints excluded: chain C residue 2663 LEU Chi-restraints excluded: chain C residue 2831 THR Chi-restraints excluded: chain C residue 2997 ASN Chi-restraints excluded: chain C residue 3101 LEU Chi-restraints excluded: chain C residue 3215 THR Chi-restraints excluded: chain C residue 3630 THR Chi-restraints excluded: chain C residue 3661 ASP Chi-restraints excluded: chain C residue 3663 LEU Chi-restraints excluded: chain C residue 3697 SER Chi-restraints excluded: chain C residue 3713 PHE Chi-restraints excluded: chain C residue 3769 ASN Chi-restraints excluded: chain C residue 3828 VAL Chi-restraints excluded: chain C residue 3853 PHE Chi-restraints excluded: chain C residue 3865 THR Chi-restraints excluded: chain C residue 3905 PHE Chi-restraints excluded: chain C residue 3927 CYS Chi-restraints excluded: chain C residue 3934 LEU Chi-restraints excluded: chain C residue 3958 SER Chi-restraints excluded: chain C residue 3964 ILE Chi-restraints excluded: chain C residue 3985 LEU Chi-restraints excluded: chain C residue 4110 ASN Chi-restraints excluded: chain C residue 4175 VAL Chi-restraints excluded: chain C residue 4516 LEU Chi-restraints excluded: chain C residue 4518 TYR Chi-restraints excluded: chain C residue 4581 ILE Chi-restraints excluded: chain C residue 4587 ILE Chi-restraints excluded: chain C residue 4654 ASP Chi-restraints excluded: chain C residue 4752 LEU Chi-restraints excluded: chain C residue 4782 VAL Chi-restraints excluded: chain C residue 4795 SER Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4846 ASP Chi-restraints excluded: chain C residue 4858 LEU Chi-restraints excluded: chain C residue 4860 ILE Chi-restraints excluded: chain C residue 4879 VAL Chi-restraints excluded: chain C residue 4889 ILE Chi-restraints excluded: chain C residue 4890 CYS Chi-restraints excluded: chain C residue 4921 LEU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 489 PHE Chi-restraints excluded: chain D residue 513 HIS Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 608 HIS Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 650 ASN Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 721 ASP Chi-restraints excluded: chain D residue 731 HIS Chi-restraints excluded: chain D residue 733 TRP Chi-restraints excluded: chain D residue 751 THR Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 802 PHE Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 1042 THR Chi-restraints excluded: chain D residue 1087 ILE Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1146 HIS Chi-restraints excluded: chain D residue 1165 MET Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1441 VAL Chi-restraints excluded: chain D residue 1442 TRP Chi-restraints excluded: chain D residue 1460 ASP Chi-restraints excluded: chain D residue 1467 VAL Chi-restraints excluded: chain D residue 1508 ILE Chi-restraints excluded: chain D residue 1595 VAL Chi-restraints excluded: chain D residue 1604 PHE Chi-restraints excluded: chain D residue 1629 MET Chi-restraints excluded: chain D residue 1632 HIS Chi-restraints excluded: chain D residue 1651 LEU Chi-restraints excluded: chain D residue 1663 SER Chi-restraints excluded: chain D residue 1671 HIS Chi-restraints excluded: chain D residue 1777 TYR Chi-restraints excluded: chain D residue 1814 THR Chi-restraints excluded: chain D residue 1941 PHE Chi-restraints excluded: chain D residue 1995 LEU Chi-restraints excluded: chain D residue 2021 ASP Chi-restraints excluded: chain D residue 2025 ARG Chi-restraints excluded: chain D residue 2083 MET Chi-restraints excluded: chain D residue 2097 LEU Chi-restraints excluded: chain D residue 2104 THR Chi-restraints excluded: chain D residue 2164 LEU Chi-restraints excluded: chain D residue 2195 CYS Chi-restraints excluded: chain D residue 2237 THR Chi-restraints excluded: chain D residue 2280 VAL Chi-restraints excluded: chain D residue 2286 ASP Chi-restraints excluded: chain D residue 2293 GLU Chi-restraints excluded: chain D residue 2305 VAL Chi-restraints excluded: chain D residue 2330 PHE Chi-restraints excluded: chain D residue 2454 ASP Chi-restraints excluded: chain D residue 2455 MET Chi-restraints excluded: chain D residue 2480 GLN Chi-restraints excluded: chain D residue 2482 PHE Chi-restraints excluded: chain D residue 2516 ASN Chi-restraints excluded: chain D residue 2663 LEU Chi-restraints excluded: chain D residue 2831 THR Chi-restraints excluded: chain D residue 2997 ASN Chi-restraints excluded: chain D residue 3101 LEU Chi-restraints excluded: chain D residue 3215 THR Chi-restraints excluded: chain D residue 3630 THR Chi-restraints excluded: chain D residue 3661 ASP Chi-restraints excluded: chain D residue 3663 LEU Chi-restraints excluded: chain D residue 3692 ASP Chi-restraints excluded: chain D residue 3697 SER Chi-restraints excluded: chain D residue 3713 PHE Chi-restraints excluded: chain D residue 3769 ASN Chi-restraints excluded: chain D residue 3828 VAL Chi-restraints excluded: chain D residue 3853 PHE Chi-restraints excluded: chain D residue 3865 THR Chi-restraints excluded: chain D residue 3905 PHE Chi-restraints excluded: chain D residue 3927 CYS Chi-restraints excluded: chain D residue 3934 LEU Chi-restraints excluded: chain D residue 3958 SER Chi-restraints excluded: chain D residue 3964 ILE Chi-restraints excluded: chain D residue 3985 LEU Chi-restraints excluded: chain D residue 4104 LEU Chi-restraints excluded: chain D residue 4110 ASN Chi-restraints excluded: chain D residue 4175 VAL Chi-restraints excluded: chain D residue 4516 LEU Chi-restraints excluded: chain D residue 4518 TYR Chi-restraints excluded: chain D residue 4581 ILE Chi-restraints excluded: chain D residue 4587 ILE Chi-restraints excluded: chain D residue 4654 ASP Chi-restraints excluded: chain D residue 4752 LEU Chi-restraints excluded: chain D residue 4782 VAL Chi-restraints excluded: chain D residue 4795 SER Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4846 ASP Chi-restraints excluded: chain D residue 4847 ILE Chi-restraints excluded: chain D residue 4858 LEU Chi-restraints excluded: chain D residue 4860 ILE Chi-restraints excluded: chain D residue 4879 VAL Chi-restraints excluded: chain D residue 4889 ILE Chi-restraints excluded: chain D residue 4890 CYS Chi-restraints excluded: chain D residue 4921 LEU Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 102 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1592 random chunks: chunk 1424 optimal weight: 40.0000 chunk 938 optimal weight: 9.9990 chunk 1512 optimal weight: 0.8980 chunk 922 optimal weight: 7.9990 chunk 717 optimal weight: 3.9990 chunk 1051 optimal weight: 40.0000 chunk 1586 optimal weight: 10.0000 chunk 1459 optimal weight: 1.9990 chunk 1262 optimal weight: 20.0000 chunk 131 optimal weight: 10.0000 chunk 975 optimal weight: 6.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1692 ASN ** A3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1692 ASN C2485 HIS ** C3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2485 HIS ** D3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 HIS G 26 HIS H 26 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 121556 Z= 0.331 Angle : 0.650 11.415 165096 Z= 0.329 Chirality : 0.041 0.209 19028 Planarity : 0.004 0.061 21400 Dihedral : 4.621 37.867 16880 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.48 % Allowed : 12.63 % Favored : 86.89 % Rotamer: Outliers : 4.01 % Allowed : 25.82 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.07), residues: 15692 helix: 1.34 (0.06), residues: 7240 sheet: -2.28 (0.19), residues: 732 loop : -2.89 (0.07), residues: 7720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C4644 HIS 0.034 0.001 HIS F 26 PHE 0.026 0.002 PHE B4785 TYR 0.020 0.002 TYR B1715 ARG 0.006 0.000 ARG D 626 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 31384 Ramachandran restraints generated. 15692 Oldfield, 0 Emsley, 15692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 31384 Ramachandran restraints generated. 15692 Oldfield, 0 Emsley, 15692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1202 residues out of total 13992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 480 poor density : 722 time to evaluate : 9.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 489 PHE cc_start: 0.8953 (OUTLIER) cc_final: 0.8511 (t80) REVERT: A 513 HIS cc_start: 0.7758 (OUTLIER) cc_final: 0.7404 (p-80) REVERT: A 802 PHE cc_start: 0.6868 (OUTLIER) cc_final: 0.5888 (m-80) REVERT: A 1300 MET cc_start: 0.7627 (ptt) cc_final: 0.7181 (ppp) REVERT: A 1460 ASP cc_start: 0.6171 (OUTLIER) cc_final: 0.3981 (t0) REVERT: A 1604 PHE cc_start: 0.6421 (OUTLIER) cc_final: 0.5180 (t80) REVERT: A 2025 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.5549 (ppt90) REVERT: A 2164 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8668 (mp) REVERT: A 2286 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.6381 (t0) REVERT: A 2293 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6705 (pt0) REVERT: A 2342 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8052 (mm) REVERT: A 2480 GLN cc_start: 0.1584 (OUTLIER) cc_final: 0.0299 (mp10) REVERT: A 2694 MET cc_start: 0.6433 (mpp) cc_final: 0.5721 (mpp) REVERT: A 3262 MET cc_start: -0.0122 (tmm) cc_final: -0.0976 (tpt) REVERT: A 3663 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.7982 (tt) REVERT: A 3905 PHE cc_start: 0.8913 (OUTLIER) cc_final: 0.8319 (m-80) REVERT: A 3934 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8959 (mp) REVERT: A 4001 MET cc_start: 0.8547 (tmm) cc_final: 0.8225 (tmm) REVERT: A 4104 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8459 (mm) REVERT: A 4518 TYR cc_start: 0.8660 (OUTLIER) cc_final: 0.8222 (m-80) REVERT: B 50 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7036 (tt0) REVERT: B 81 MET cc_start: 0.8289 (mpp) cc_final: 0.7924 (mpp) REVERT: B 489 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8499 (t80) REVERT: B 513 HIS cc_start: 0.7795 (OUTLIER) cc_final: 0.7371 (p-80) REVERT: B 802 PHE cc_start: 0.6882 (OUTLIER) cc_final: 0.5926 (m-80) REVERT: B 1300 MET cc_start: 0.7542 (ptt) cc_final: 0.7114 (ppp) REVERT: B 1460 ASP cc_start: 0.6214 (OUTLIER) cc_final: 0.3998 (t0) REVERT: B 1604 PHE cc_start: 0.6413 (OUTLIER) cc_final: 0.5181 (t80) REVERT: B 1629 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.7379 (ptp) REVERT: B 2025 ARG cc_start: 0.7044 (OUTLIER) cc_final: 0.5569 (ppt90) REVERT: B 2286 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.6060 (t0) REVERT: B 2293 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6605 (pt0) REVERT: B 2480 GLN cc_start: 0.1842 (OUTLIER) cc_final: 0.0527 (mp10) REVERT: B 2694 MET cc_start: 0.6483 (mpp) cc_final: 0.5746 (mpp) REVERT: B 3262 MET cc_start: 0.0712 (tmm) cc_final: 0.0137 (tpt) REVERT: B 3427 MET cc_start: 0.4956 (mmt) cc_final: 0.4641 (mtm) REVERT: B 3663 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.7989 (tt) REVERT: B 3905 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.8313 (m-80) REVERT: B 3934 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8984 (mp) REVERT: B 3997 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8158 (mp10) REVERT: B 4001 MET cc_start: 0.8649 (tmm) cc_final: 0.8310 (tmm) REVERT: B 4518 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.8198 (m-80) REVERT: B 4807 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.7916 (p0) REVERT: C 50 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7031 (tt0) REVERT: C 489 PHE cc_start: 0.8947 (OUTLIER) cc_final: 0.8491 (t80) REVERT: C 513 HIS cc_start: 0.7818 (OUTLIER) cc_final: 0.7420 (p-80) REVERT: C 802 PHE cc_start: 0.6906 (OUTLIER) cc_final: 0.5905 (m-80) REVERT: C 1300 MET cc_start: 0.7627 (ptt) cc_final: 0.7179 (ppp) REVERT: C 1460 ASP cc_start: 0.6197 (OUTLIER) cc_final: 0.4011 (t0) REVERT: C 1604 PHE cc_start: 0.6437 (OUTLIER) cc_final: 0.5195 (t80) REVERT: C 1629 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.7450 (ptp) REVERT: C 2025 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.5568 (ppt90) REVERT: C 2286 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.6380 (t0) REVERT: C 2293 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6694 (pt0) REVERT: C 2480 GLN cc_start: 0.1565 (OUTLIER) cc_final: 0.0292 (mp10) REVERT: C 2694 MET cc_start: 0.6465 (mpp) cc_final: 0.5756 (mpp) REVERT: C 3262 MET cc_start: -0.0145 (tmm) cc_final: -0.0792 (tpt) REVERT: C 3663 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.7988 (tt) REVERT: C 3905 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.8300 (m-80) REVERT: C 3934 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8972 (mp) REVERT: C 4001 MET cc_start: 0.8552 (tmm) cc_final: 0.8218 (tmm) REVERT: C 4518 TYR cc_start: 0.8676 (OUTLIER) cc_final: 0.8233 (m-80) REVERT: D 489 PHE cc_start: 0.8957 (OUTLIER) cc_final: 0.8516 (t80) REVERT: D 513 HIS cc_start: 0.7816 (OUTLIER) cc_final: 0.7419 (p-80) REVERT: D 802 PHE cc_start: 0.6904 (OUTLIER) cc_final: 0.5903 (m-80) REVERT: D 1300 MET cc_start: 0.7635 (ptt) cc_final: 0.7184 (ppp) REVERT: D 1460 ASP cc_start: 0.6209 (OUTLIER) cc_final: 0.4013 (t0) REVERT: D 1604 PHE cc_start: 0.6426 (OUTLIER) cc_final: 0.5193 (t80) REVERT: D 1629 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.7452 (ptp) REVERT: D 2025 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.5578 (ppt90) REVERT: D 2164 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8635 (mp) REVERT: D 2286 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.6283 (t0) REVERT: D 2293 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6651 (pt0) REVERT: D 2480 GLN cc_start: 0.1617 (OUTLIER) cc_final: 0.0311 (mp10) REVERT: D 2511 MET cc_start: 0.7844 (mmm) cc_final: 0.7533 (mmm) REVERT: D 2694 MET cc_start: 0.6430 (mpp) cc_final: 0.5715 (mpp) REVERT: D 3262 MET cc_start: -0.0047 (tmm) cc_final: -0.0717 (tpt) REVERT: D 3663 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.7984 (tt) REVERT: D 3905 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.8321 (m-80) REVERT: D 3934 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8979 (mp) REVERT: D 4001 MET cc_start: 0.8571 (tmm) cc_final: 0.8230 (tmm) REVERT: D 4104 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8458 (mm) REVERT: D 4518 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.8226 (m-80) REVERT: F 4 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7400 (tm-30) REVERT: F 5 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7955 (tp) REVERT: G 95 ASN cc_start: 0.7983 (t0) cc_final: 0.7780 (t0) REVERT: H 95 ASN cc_start: 0.7991 (t0) cc_final: 0.7778 (t0) outliers start: 480 outliers final: 387 residues processed: 1151 average time/residue: 0.8872 time to fit residues: 1889.7848 Evaluate side-chains 1165 residues out of total 13992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 452 poor density : 713 time to evaluate : 9.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 513 HIS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 608 HIS Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 733 TRP Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 802 PHE Chi-restraints excluded: chain A residue 890 HIS Chi-restraints excluded: chain A residue 1087 ILE Chi-restraints excluded: chain A residue 1093 THR Chi-restraints excluded: chain A residue 1146 HIS Chi-restraints excluded: chain A residue 1165 MET Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1441 VAL Chi-restraints excluded: chain A residue 1442 TRP Chi-restraints excluded: chain A residue 1460 ASP Chi-restraints excluded: chain A residue 1467 VAL Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1595 VAL Chi-restraints excluded: chain A residue 1604 PHE Chi-restraints excluded: chain A residue 1629 MET Chi-restraints excluded: chain A residue 1632 HIS Chi-restraints excluded: chain A residue 1651 LEU Chi-restraints excluded: chain A residue 1663 SER Chi-restraints excluded: chain A residue 1777 TYR Chi-restraints excluded: chain A residue 1814 THR Chi-restraints excluded: chain A residue 1941 PHE Chi-restraints excluded: chain A residue 2021 ASP Chi-restraints excluded: chain A residue 2025 ARG Chi-restraints excluded: chain A residue 2097 LEU Chi-restraints excluded: chain A residue 2104 THR Chi-restraints excluded: chain A residue 2164 LEU Chi-restraints excluded: chain A residue 2195 CYS Chi-restraints excluded: chain A residue 2237 THR Chi-restraints excluded: chain A residue 2280 VAL Chi-restraints excluded: chain A residue 2286 ASP Chi-restraints excluded: chain A residue 2293 GLU Chi-restraints excluded: chain A residue 2305 VAL Chi-restraints excluded: chain A residue 2330 PHE Chi-restraints excluded: chain A residue 2342 LEU Chi-restraints excluded: chain A residue 2454 ASP Chi-restraints excluded: chain A residue 2455 MET Chi-restraints excluded: chain A residue 2463 HIS Chi-restraints excluded: chain A residue 2480 GLN Chi-restraints excluded: chain A residue 2482 PHE Chi-restraints excluded: chain A residue 2516 ASN Chi-restraints excluded: chain A residue 2831 THR Chi-restraints excluded: chain A residue 2997 ASN Chi-restraints excluded: chain A residue 3101 LEU Chi-restraints excluded: chain A residue 3215 THR Chi-restraints excluded: chain A residue 3630 THR Chi-restraints excluded: chain A residue 3661 ASP Chi-restraints excluded: chain A residue 3663 LEU Chi-restraints excluded: chain A residue 3697 SER Chi-restraints excluded: chain A residue 3713 PHE Chi-restraints excluded: chain A residue 3769 ASN Chi-restraints excluded: chain A residue 3828 VAL Chi-restraints excluded: chain A residue 3853 PHE Chi-restraints excluded: chain A residue 3865 THR Chi-restraints excluded: chain A residue 3905 PHE Chi-restraints excluded: chain A residue 3927 CYS Chi-restraints excluded: chain A residue 3934 LEU Chi-restraints excluded: chain A residue 3958 SER Chi-restraints excluded: chain A residue 3964 ILE Chi-restraints excluded: chain A residue 3985 LEU Chi-restraints excluded: chain A residue 4104 LEU Chi-restraints excluded: chain A residue 4110 ASN Chi-restraints excluded: chain A residue 4175 VAL Chi-restraints excluded: chain A residue 4516 LEU Chi-restraints excluded: chain A residue 4518 TYR Chi-restraints excluded: chain A residue 4560 LEU Chi-restraints excluded: chain A residue 4581 ILE Chi-restraints excluded: chain A residue 4587 ILE Chi-restraints excluded: chain A residue 4654 ASP Chi-restraints excluded: chain A residue 4671 MET Chi-restraints excluded: chain A residue 4782 VAL Chi-restraints excluded: chain A residue 4795 SER Chi-restraints excluded: chain A residue 4820 VAL Chi-restraints excluded: chain A residue 4846 ASP Chi-restraints excluded: chain A residue 4847 ILE Chi-restraints excluded: chain A residue 4858 LEU Chi-restraints excluded: chain A residue 4860 ILE Chi-restraints excluded: chain A residue 4879 VAL Chi-restraints excluded: chain A residue 4889 ILE Chi-restraints excluded: chain A residue 4890 CYS Chi-restraints excluded: chain A residue 4921 LEU Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 513 HIS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 608 HIS Chi-restraints excluded: chain B residue 619 VAL Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 650 ASN Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 731 HIS Chi-restraints excluded: chain B residue 733 TRP Chi-restraints excluded: chain B residue 751 THR Chi-restraints excluded: chain B residue 778 MET Chi-restraints excluded: chain B residue 802 PHE Chi-restraints excluded: chain B residue 890 HIS Chi-restraints excluded: chain B residue 944 LEU Chi-restraints excluded: chain B residue 1087 ILE Chi-restraints excluded: chain B residue 1093 THR Chi-restraints excluded: chain B residue 1146 HIS Chi-restraints excluded: chain B residue 1165 MET Chi-restraints excluded: chain B residue 1251 LEU Chi-restraints excluded: chain B residue 1441 VAL Chi-restraints excluded: chain B residue 1442 TRP Chi-restraints excluded: chain B residue 1460 ASP Chi-restraints excluded: chain B residue 1467 VAL Chi-restraints excluded: chain B residue 1508 ILE Chi-restraints excluded: chain B residue 1595 VAL Chi-restraints excluded: chain B residue 1604 PHE Chi-restraints excluded: chain B residue 1629 MET Chi-restraints excluded: chain B residue 1651 LEU Chi-restraints excluded: chain B residue 1663 SER Chi-restraints excluded: chain B residue 1777 TYR Chi-restraints excluded: chain B residue 1814 THR Chi-restraints excluded: chain B residue 1915 CYS Chi-restraints excluded: chain B residue 1941 PHE Chi-restraints excluded: chain B residue 1995 LEU Chi-restraints excluded: chain B residue 2021 ASP Chi-restraints excluded: chain B residue 2025 ARG Chi-restraints excluded: chain B residue 2097 LEU Chi-restraints excluded: chain B residue 2104 THR Chi-restraints excluded: chain B residue 2127 SER Chi-restraints excluded: chain B residue 2195 CYS Chi-restraints excluded: chain B residue 2237 THR Chi-restraints excluded: chain B residue 2280 VAL Chi-restraints excluded: chain B residue 2286 ASP Chi-restraints excluded: chain B residue 2293 GLU Chi-restraints excluded: chain B residue 2305 VAL Chi-restraints excluded: chain B residue 2330 PHE Chi-restraints excluded: chain B residue 2454 ASP Chi-restraints excluded: chain B residue 2455 MET Chi-restraints excluded: chain B residue 2480 GLN Chi-restraints excluded: chain B residue 2482 PHE Chi-restraints excluded: chain B residue 2516 ASN Chi-restraints excluded: chain B residue 2831 THR Chi-restraints excluded: chain B residue 2997 ASN Chi-restraints excluded: chain B residue 3101 LEU Chi-restraints excluded: chain B residue 3215 THR Chi-restraints excluded: chain B residue 3616 VAL Chi-restraints excluded: chain B residue 3630 THR Chi-restraints excluded: chain B residue 3663 LEU Chi-restraints excluded: chain B residue 3697 SER Chi-restraints excluded: chain B residue 3713 PHE Chi-restraints excluded: chain B residue 3769 ASN Chi-restraints excluded: chain B residue 3828 VAL Chi-restraints excluded: chain B residue 3853 PHE Chi-restraints excluded: chain B residue 3865 THR Chi-restraints excluded: chain B residue 3905 PHE Chi-restraints excluded: chain B residue 3927 CYS Chi-restraints excluded: chain B residue 3934 LEU Chi-restraints excluded: chain B residue 3958 SER Chi-restraints excluded: chain B residue 3964 ILE Chi-restraints excluded: chain B residue 3985 LEU Chi-restraints excluded: chain B residue 3997 GLN Chi-restraints excluded: chain B residue 4110 ASN Chi-restraints excluded: chain B residue 4175 VAL Chi-restraints excluded: chain B residue 4516 LEU Chi-restraints excluded: chain B residue 4518 TYR Chi-restraints excluded: chain B residue 4581 ILE Chi-restraints excluded: chain B residue 4587 ILE Chi-restraints excluded: chain B residue 4654 ASP Chi-restraints excluded: chain B residue 4782 VAL Chi-restraints excluded: chain B residue 4795 SER Chi-restraints excluded: chain B residue 4807 ASP Chi-restraints excluded: chain B residue 4810 THR Chi-restraints excluded: chain B residue 4811 CYS Chi-restraints excluded: chain B residue 4820 VAL Chi-restraints excluded: chain B residue 4846 ASP Chi-restraints excluded: chain B residue 4847 ILE Chi-restraints excluded: chain B residue 4858 LEU Chi-restraints excluded: chain B residue 4860 ILE Chi-restraints excluded: chain B residue 4879 VAL Chi-restraints excluded: chain B residue 4889 ILE Chi-restraints excluded: chain B residue 4890 CYS Chi-restraints excluded: chain B residue 4921 LEU Chi-restraints excluded: chain B residue 4933 THR Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 158 CYS Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain C residue 422 THR Chi-restraints excluded: chain C residue 489 PHE Chi-restraints excluded: chain C residue 513 HIS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 608 HIS Chi-restraints excluded: chain C residue 619 VAL Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 650 ASN Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 687 THR Chi-restraints excluded: chain C residue 721 ASP Chi-restraints excluded: chain C residue 733 TRP Chi-restraints excluded: chain C residue 751 THR Chi-restraints excluded: chain C residue 778 MET Chi-restraints excluded: chain C residue 802 PHE Chi-restraints excluded: chain C residue 890 HIS Chi-restraints excluded: chain C residue 944 LEU Chi-restraints excluded: chain C residue 1087 ILE Chi-restraints excluded: chain C residue 1093 THR Chi-restraints excluded: chain C residue 1146 HIS Chi-restraints excluded: chain C residue 1165 MET Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1441 VAL Chi-restraints excluded: chain C residue 1442 TRP Chi-restraints excluded: chain C residue 1460 ASP Chi-restraints excluded: chain C residue 1467 VAL Chi-restraints excluded: chain C residue 1508 ILE Chi-restraints excluded: chain C residue 1595 VAL Chi-restraints excluded: chain C residue 1604 PHE Chi-restraints excluded: chain C residue 1629 MET Chi-restraints excluded: chain C residue 1632 HIS Chi-restraints excluded: chain C residue 1651 LEU Chi-restraints excluded: chain C residue 1663 SER Chi-restraints excluded: chain C residue 1777 TYR Chi-restraints excluded: chain C residue 1814 THR Chi-restraints excluded: chain C residue 1941 PHE Chi-restraints excluded: chain C residue 1995 LEU Chi-restraints excluded: chain C residue 2021 ASP Chi-restraints excluded: chain C residue 2025 ARG Chi-restraints excluded: chain C residue 2097 LEU Chi-restraints excluded: chain C residue 2104 THR Chi-restraints excluded: chain C residue 2195 CYS Chi-restraints excluded: chain C residue 2237 THR Chi-restraints excluded: chain C residue 2250 ASN Chi-restraints excluded: chain C residue 2280 VAL Chi-restraints excluded: chain C residue 2286 ASP Chi-restraints excluded: chain C residue 2293 GLU Chi-restraints excluded: chain C residue 2305 VAL Chi-restraints excluded: chain C residue 2330 PHE Chi-restraints excluded: chain C residue 2454 ASP Chi-restraints excluded: chain C residue 2455 MET Chi-restraints excluded: chain C residue 2480 GLN Chi-restraints excluded: chain C residue 2482 PHE Chi-restraints excluded: chain C residue 2485 HIS Chi-restraints excluded: chain C residue 2516 ASN Chi-restraints excluded: chain C residue 2663 LEU Chi-restraints excluded: chain C residue 2831 THR Chi-restraints excluded: chain C residue 2997 ASN Chi-restraints excluded: chain C residue 3101 LEU Chi-restraints excluded: chain C residue 3215 THR Chi-restraints excluded: chain C residue 3616 VAL Chi-restraints excluded: chain C residue 3630 THR Chi-restraints excluded: chain C residue 3661 ASP Chi-restraints excluded: chain C residue 3663 LEU Chi-restraints excluded: chain C residue 3697 SER Chi-restraints excluded: chain C residue 3713 PHE Chi-restraints excluded: chain C residue 3769 ASN Chi-restraints excluded: chain C residue 3801 VAL Chi-restraints excluded: chain C residue 3828 VAL Chi-restraints excluded: chain C residue 3853 PHE Chi-restraints excluded: chain C residue 3865 THR Chi-restraints excluded: chain C residue 3905 PHE Chi-restraints excluded: chain C residue 3927 CYS Chi-restraints excluded: chain C residue 3934 LEU Chi-restraints excluded: chain C residue 3958 SER Chi-restraints excluded: chain C residue 3964 ILE Chi-restraints excluded: chain C residue 3985 LEU Chi-restraints excluded: chain C residue 4110 ASN Chi-restraints excluded: chain C residue 4175 VAL Chi-restraints excluded: chain C residue 4516 LEU Chi-restraints excluded: chain C residue 4518 TYR Chi-restraints excluded: chain C residue 4560 LEU Chi-restraints excluded: chain C residue 4581 ILE Chi-restraints excluded: chain C residue 4587 ILE Chi-restraints excluded: chain C residue 4654 ASP Chi-restraints excluded: chain C residue 4782 VAL Chi-restraints excluded: chain C residue 4795 SER Chi-restraints excluded: chain C residue 4820 VAL Chi-restraints excluded: chain C residue 4846 ASP Chi-restraints excluded: chain C residue 4858 LEU Chi-restraints excluded: chain C residue 4860 ILE Chi-restraints excluded: chain C residue 4879 VAL Chi-restraints excluded: chain C residue 4889 ILE Chi-restraints excluded: chain C residue 4890 CYS Chi-restraints excluded: chain C residue 4921 LEU Chi-restraints excluded: chain C residue 4933 THR Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 363 ILE Chi-restraints excluded: chain D residue 422 THR Chi-restraints excluded: chain D residue 489 PHE Chi-restraints excluded: chain D residue 513 HIS Chi-restraints excluded: chain D residue 533 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 608 HIS Chi-restraints excluded: chain D residue 619 VAL Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 650 ASN Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 687 THR Chi-restraints excluded: chain D residue 721 ASP Chi-restraints excluded: chain D residue 731 HIS Chi-restraints excluded: chain D residue 733 TRP Chi-restraints excluded: chain D residue 751 THR Chi-restraints excluded: chain D residue 778 MET Chi-restraints excluded: chain D residue 802 PHE Chi-restraints excluded: chain D residue 890 HIS Chi-restraints excluded: chain D residue 944 LEU Chi-restraints excluded: chain D residue 1042 THR Chi-restraints excluded: chain D residue 1087 ILE Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1146 HIS Chi-restraints excluded: chain D residue 1165 MET Chi-restraints excluded: chain D residue 1251 LEU Chi-restraints excluded: chain D residue 1441 VAL Chi-restraints excluded: chain D residue 1442 TRP Chi-restraints excluded: chain D residue 1460 ASP Chi-restraints excluded: chain D residue 1467 VAL Chi-restraints excluded: chain D residue 1508 ILE Chi-restraints excluded: chain D residue 1595 VAL Chi-restraints excluded: chain D residue 1604 PHE Chi-restraints excluded: chain D residue 1629 MET Chi-restraints excluded: chain D residue 1632 HIS Chi-restraints excluded: chain D residue 1651 LEU Chi-restraints excluded: chain D residue 1663 SER Chi-restraints excluded: chain D residue 1777 TYR Chi-restraints excluded: chain D residue 1814 THR Chi-restraints excluded: chain D residue 1941 PHE Chi-restraints excluded: chain D residue 1995 LEU Chi-restraints excluded: chain D residue 2021 ASP Chi-restraints excluded: chain D residue 2025 ARG Chi-restraints excluded: chain D residue 2097 LEU Chi-restraints excluded: chain D residue 2104 THR Chi-restraints excluded: chain D residue 2164 LEU Chi-restraints excluded: chain D residue 2195 CYS Chi-restraints excluded: chain D residue 2237 THR Chi-restraints excluded: chain D residue 2250 ASN Chi-restraints excluded: chain D residue 2280 VAL Chi-restraints excluded: chain D residue 2286 ASP Chi-restraints excluded: chain D residue 2293 GLU Chi-restraints excluded: chain D residue 2305 VAL Chi-restraints excluded: chain D residue 2330 PHE Chi-restraints excluded: chain D residue 2454 ASP Chi-restraints excluded: chain D residue 2455 MET Chi-restraints excluded: chain D residue 2463 HIS Chi-restraints excluded: chain D residue 2480 GLN Chi-restraints excluded: chain D residue 2482 PHE Chi-restraints excluded: chain D residue 2485 HIS Chi-restraints excluded: chain D residue 2516 ASN Chi-restraints excluded: chain D residue 2663 LEU Chi-restraints excluded: chain D residue 2831 THR Chi-restraints excluded: chain D residue 2997 ASN Chi-restraints excluded: chain D residue 3101 LEU Chi-restraints excluded: chain D residue 3215 THR Chi-restraints excluded: chain D residue 3616 VAL Chi-restraints excluded: chain D residue 3630 THR Chi-restraints excluded: chain D residue 3661 ASP Chi-restraints excluded: chain D residue 3663 LEU Chi-restraints excluded: chain D residue 3697 SER Chi-restraints excluded: chain D residue 3713 PHE Chi-restraints excluded: chain D residue 3769 ASN Chi-restraints excluded: chain D residue 3828 VAL Chi-restraints excluded: chain D residue 3853 PHE Chi-restraints excluded: chain D residue 3865 THR Chi-restraints excluded: chain D residue 3905 PHE Chi-restraints excluded: chain D residue 3927 CYS Chi-restraints excluded: chain D residue 3934 LEU Chi-restraints excluded: chain D residue 3958 SER Chi-restraints excluded: chain D residue 3964 ILE Chi-restraints excluded: chain D residue 3985 LEU Chi-restraints excluded: chain D residue 4104 LEU Chi-restraints excluded: chain D residue 4110 ASN Chi-restraints excluded: chain D residue 4175 VAL Chi-restraints excluded: chain D residue 4516 LEU Chi-restraints excluded: chain D residue 4518 TYR Chi-restraints excluded: chain D residue 4581 ILE Chi-restraints excluded: chain D residue 4587 ILE Chi-restraints excluded: chain D residue 4654 ASP Chi-restraints excluded: chain D residue 4752 LEU Chi-restraints excluded: chain D residue 4782 VAL Chi-restraints excluded: chain D residue 4795 SER Chi-restraints excluded: chain D residue 4820 VAL Chi-restraints excluded: chain D residue 4846 ASP Chi-restraints excluded: chain D residue 4847 ILE Chi-restraints excluded: chain D residue 4858 LEU Chi-restraints excluded: chain D residue 4860 ILE Chi-restraints excluded: chain D residue 4879 VAL Chi-restraints excluded: chain D residue 4889 ILE Chi-restraints excluded: chain D residue 4890 CYS Chi-restraints excluded: chain D residue 4921 LEU Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 101 ASP Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 28 THR Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 102 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1592 random chunks: chunk 774 optimal weight: 0.9990 chunk 1003 optimal weight: 50.0000 chunk 1345 optimal weight: 9.9990 chunk 386 optimal weight: 0.9990 chunk 1164 optimal weight: 20.0000 chunk 186 optimal weight: 10.0000 chunk 350 optimal weight: 9.9990 chunk 1264 optimal weight: 9.9990 chunk 529 optimal weight: 2.9990 chunk 1298 optimal weight: 20.0000 chunk 160 optimal weight: 0.5980 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2249 ASN ** A3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2485 HIS ** B3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2485 HIS ** C3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2485 HIS ** D3811 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 HIS F 26 HIS G 26 HIS H 26 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.123425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.107077 restraints weight = 498987.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.104837 restraints weight = 448390.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.096789 restraints weight = 419120.888| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3760 r_free = 0.3760 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3759 r_free = 0.3759 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 121556 Z= 0.255 Angle : 0.616 11.053 165096 Z= 0.310 Chirality : 0.040 0.195 19028 Planarity : 0.004 0.060 21400 Dihedral : 4.610 37.865 16880 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.46 % Allowed : 12.06 % Favored : 87.48 % Rotamer: Outliers : 3.94 % Allowed : 25.91 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.07), residues: 15692 helix: 1.40 (0.06), residues: 7208 sheet: -2.43 (0.19), residues: 768 loop : -2.88 (0.07), residues: 7716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C4644 HIS 0.015 0.001 HIS F 26 PHE 0.022 0.001 PHE C4785 TYR 0.017 0.001 TYR B1715 ARG 0.004 0.000 ARG D4789 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27708.43 seconds wall clock time: 485 minutes 3.25 seconds (29103.25 seconds total)