Starting phenix.real_space_refine on Mon Feb 26 23:47:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uq7_8596/02_2024/5uq7_8596_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uq7_8596/02_2024/5uq7_8596.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uq7_8596/02_2024/5uq7_8596_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uq7_8596/02_2024/5uq7_8596_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uq7_8596/02_2024/5uq7_8596_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uq7_8596/02_2024/5uq7_8596.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uq7_8596/02_2024/5uq7_8596.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uq7_8596/02_2024/5uq7_8596_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uq7_8596/02_2024/5uq7_8596_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 6 6.06 5 P 4702 5.49 5 S 130 5.16 5 C 74971 2.51 5 N 27973 2.21 5 O 40800 1.98 5 H 4 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 239": "NH1" <-> "NH2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "I ARG 50": "NH1" <-> "NH2" Residue "O ARG 107": "NH1" <-> "NH2" Residue "P ARG 7": "NH1" <-> "NH2" Residue "P ARG 15": "NH1" <-> "NH2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "R ARG 64": "NH1" <-> "NH2" Residue "R ARG 88": "NH1" <-> "NH2" Residue "T ARG 3": "NH1" <-> "NH2" Residue "U ARG 50": "NH1" <-> "NH2" Residue "U ARG 64": "NH1" <-> "NH2" Residue "V TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 65": "NH1" <-> "NH2" Residue "Z TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 79": "NH1" <-> "NH2" Residue "Z ARG 81": "NH1" <-> "NH2" Residue "Z ARG 82": "NH1" <-> "NH2" Residue "0 ARG 32": "NH1" <-> "NH2" Residue "1 ARG 61": "NH1" <-> "NH2" Residue "1 ARG 76": "NH1" <-> "NH2" Residue "2 ARG 55": "NH1" <-> "NH2" Residue "3 ARG 55": "NH1" <-> "NH2" Residue "4 ARG 68": "NH1" <-> "NH2" Residue "8 ARG 46": "NH1" <-> "NH2" Residue "c TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 49": "NH1" <-> "NH2" Residue "d ARG 115": "NH1" <-> "NH2" Residue "d ARG 168": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "h ARG 69": "NH1" <-> "NH2" Residue "i ARG 42": "NH1" <-> "NH2" Residue "i ARG 66": "NH1" <-> "NH2" Residue "i TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 3": "NH1" <-> "NH2" Residue "o PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 88": "NH1" <-> "NH2" Residue "p TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 38": "NH1" <-> "NH2" Residue "r ARG 42": "NH1" <-> "NH2" Residue "s ARG 3": "NH1" <-> "NH2" Residue "t ARG 89": "NH1" <-> "NH2" Residue "C PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.26s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 148590 Number of models: 1 Model: "" Number of chains: 63 Chain: "A" Number of atoms: 61758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2867, 61758 Classifications: {'RNA': 2867} Modifications used: {'5*END': 1, 'rna2p': 3, 'rna2p_pur': 290, 'rna2p_pyr': 142, 'rna3p': 7, 'rna3p_pur': 1388, 'rna3p_pyr': 1036} Link IDs: {'rna2p': 435, 'rna3p': 2431} Unresolved chain links: 1 Chain breaks: 9 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 2573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2573 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 59, 'rna3p_pyr': 49} Link IDs: {'rna2p': 11, 'rna3p': 108} Chain: "D" Number of atoms: 2136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2136 Classifications: {'peptide': 275} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 252} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1559 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 14, 'TRANS': 186} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1580 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 190} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1424 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 172} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "H" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1324 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 155} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1076 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 9, 'TRANS': 136} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 27 Chain: "N" Number of atoms: 1117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1117 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 127} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "O" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 933 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "P" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1135 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 138} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Q" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1122 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "R" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 968 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "S" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 870 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 108} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "T" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1083 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 126} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 959 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain: "V" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 771 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "W" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 886 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 108} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 750 Classifications: {'peptide': 95} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 89} Chain: "Y" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 99} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "Z" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1459 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 15, 'TRANS': 171} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "0" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 608 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "1" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 759 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 91} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "2" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 592 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "3" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 464 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 55} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "4" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 536 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 62} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "5" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 455 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 49} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "6" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 449 Classifications: {'peptide': 53} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 50} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "7" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 418 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "8" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 517 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "9" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 307 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "a" Number of atoms: 32532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1513, 32532 Classifications: {'RNA': 1513} Modifications used: {'rna2p': 2, 'rna2p_pur': 118, 'rna2p_pyr': 90, 'rna3p': 10, 'rna3p_pur': 733, 'rna3p_pyr': 560} Link IDs: {'rna2p': 210, 'rna3p': 1302} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 9 Chain: "b" Number of atoms: 1825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1825 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 11, 'TRANS': 219} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "c" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1542 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 200} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "d" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1668 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 11, 'TRANS': 196} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "e" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1133 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 8, 'TRANS': 139} Chain: "f" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 816 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 94} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "g" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1229 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 148} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "h" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1088 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 127} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "i" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 966 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "j" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 710 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 88} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 25 Chain: "k" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 833 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 106} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "l" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 932 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 113} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'0TD:plan-1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "m" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 895 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 109} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "n" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 492 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "o" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 728 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "p" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 677 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 77} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "q" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 823 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "r" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 555 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "s" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 645 Classifications: {'peptide': 83} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 79} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "t" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 733 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 95} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "u" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 199 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "y" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 37, 'rna3p_pyr': 36} Link IDs: {'rna2p': 4, 'rna3p': 72} Chain: "C" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1718 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 13, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "z" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1619 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 33, 'rna3p_pyr': 33} Link IDs: {'rna2p': 10, 'rna3p': 65} Chain: "x" Number of atoms: 1180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1180 Classifications: {'RNA': 55} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 3, 'rna3p_pur': 27, 'rna3p_pyr': 20} Link IDs: {'rna2p': 8, 'rna3p': 46} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 84603 SG CYS Y 76 259.909 61.234 142.360 1.00187.42 S ATOM 84621 SG CYS Y 79 260.771 59.130 139.110 1.00190.84 S ATOM 84785 SG CYS Y 99 257.754 58.200 140.518 1.00218.81 S ATOM 84805 SG CYS Y 102 260.703 57.047 142.263 1.00199.53 S ATOM 88840 SG CYS 4 16 67.791 53.000 100.777 1.00223.38 S ATOM 88850 SG CYS 4 18 63.962 54.143 99.068 1.00236.42 S ATOM 88984 SG CYS 4 36 68.272 52.010 97.505 1.00220.97 S ATOM 89005 SG CYS 4 39 68.006 55.386 98.347 1.00225.63 S ATOM 89503 SG CYS 5 33 242.754 133.338 93.632 1.00144.52 S ATOM 89525 SG CYS 5 36 244.538 131.157 95.705 1.00145.12 S ATOM 89596 SG CYS 5 46 241.109 131.448 96.191 1.00148.87 S ATOM 89618 SG CYS 5 49 242.527 135.267 96.423 1.00148.48 S ATOM 89797 SG CYS 6 13 133.292 37.306 133.889 1.00116.82 S ATOM 89819 SG CYS 6 16 136.771 38.403 135.579 1.00121.60 S ATOM 90030 SG CYS 6 40 136.961 36.200 133.009 1.00113.12 S ATOM 90057 SG CYS 6 43 134.854 34.160 134.791 1.00116.27 S ATOM 91178 SG CYS 9 11 142.560 111.766 48.076 1.00141.81 S ATOM 91201 SG CYS 9 14 144.896 110.038 50.024 1.00141.66 S ATOM 91312 SG CYS 9 27 145.424 113.518 47.302 1.00145.78 S ATOM A0L3W SG CYS d 9 75.837 188.896 94.495 1.00119.42 S ATOM A0L4L SG CYS d 12 77.643 190.071 101.492 1.00119.26 S ATOM A0T4U SG CYS n 24 54.559 130.031 103.132 1.00115.53 S ATOM A0T5I SG CYS n 27 57.965 130.454 103.456 1.00109.32 S ATOM A0T8H SG CYS n 40 57.463 129.459 106.716 1.00103.75 S ATOM A0T96 SG CYS n 43 55.893 132.264 105.491 1.00102.50 S Time building chain proxies: 58.10, per 1000 atoms: 0.39 Number of scatterers: 148590 At special positions: 0 Unit cell: (272, 254, 228, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 6 29.99 Fe 4 26.01 S 130 16.00 P 4702 15.00 O 40800 8.00 N 27973 7.00 C 74971 6.00 H 4 1.00 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: 81.15 Conformation dependent library (CDL) restraints added in 7.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 d 301 " pdb="FE1 SF4 d 301 " - pdb=" SG CYS d 9 " pdb="FE3 SF4 d 301 " - pdb=" SG CYS d 12 " pdb="FE4 SF4 d 301 " - pdb=" SG CYS d 31 " pdb="FE2 SF4 d 301 " - pdb=" SG CYS d 26 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 36 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 16 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 39 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 18 " pdb=" ZN 5 101 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 49 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 46 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 36 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 33 " pdb=" ZN 6 101 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 40 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 13 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 16 " pdb="ZN ZN 6 101 " - pdb=" SG CYS 6 43 " pdb=" ZN 9 101 " pdb="ZN ZN 9 101 " - pdb=" ND1 HIS 9 32 " pdb="ZN ZN 9 101 " - pdb=" SG CYS 9 14 " pdb="ZN ZN 9 101 " - pdb=" SG CYS 9 27 " pdb="ZN ZN 9 101 " - pdb=" SG CYS 9 11 " pdb=" ZN Y 201 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 102 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 76 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 79 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 99 " pdb=" ZN n 101 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 24 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 40 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 27 " pdb="ZN ZN n 101 " - pdb=" SG CYS n 43 " Number of angles added : 33 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11024 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 185 helices and 79 sheets defined 38.3% alpha, 19.7% beta 1636 base pairs and 2429 stacking pairs defined. Time for finding SS restraints: 76.76 Creating SS restraints... Processing helix chain 'D' and resid 10 through 16 removed outlier: 4.060A pdb=" N PHE D 15 " --> pdb=" O PRO D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 137 Proline residue: D 137 - end of helix Processing helix chain 'D' and resid 208 through 216 removed outlier: 3.880A pdb=" N SER D 212 " --> pdb=" O LYS D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 227 removed outlier: 3.983A pdb=" N MET D 226 " --> pdb=" O ARG D 222 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ASN D 227 " --> pdb=" O GLY D 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 222 through 227' Processing helix chain 'D' and resid 264 through 271 removed outlier: 4.282A pdb=" N ARG D 268 " --> pdb=" O LYS D 264 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N PHE D 269 " --> pdb=" O PRO D 265 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ILE D 271 " --> pdb=" O SER D 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 71 Processing helix chain 'E' and resid 115 through 120 Processing helix chain 'E' and resid 38 through 43 Processing helix chain 'F' and resid 29 through 45 removed outlier: 3.512A pdb=" N ARG F 44 " --> pdb=" O GLN F 40 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG F 45 " --> pdb=" O LEU F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 120 Processing helix chain 'F' and resid 135 through 147 Processing helix chain 'F' and resid 160 through 168 Processing helix chain 'F' and resid 182 through 190 removed outlier: 3.691A pdb=" N THR F 189 " --> pdb=" O ASP F 185 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N GLU F 190 " --> pdb=" O ILE F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 207 Processing helix chain 'G' and resid 5 through 23 removed outlier: 3.930A pdb=" N ARG G 16 " --> pdb=" O TYR G 12 " (cutoff:3.500A) Proline residue: G 17 - end of helix Processing helix chain 'G' and resid 44 through 49 removed outlier: 6.318A pdb=" N GLU G 48 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP G 49 " --> pdb=" O GLU G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 44 through 49' Processing helix chain 'G' and resid 53 through 65 removed outlier: 3.579A pdb=" N ALA G 57 " --> pdb=" O LEU G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 114 removed outlier: 4.589A pdb=" N LEU G 111 " --> pdb=" O LEU G 107 " (cutoff:3.500A) Proline residue: G 112 - end of helix Processing helix chain 'G' and resid 145 through 150 removed outlier: 5.248A pdb=" N ASP G 150 " --> pdb=" O TYR G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 177 Processing helix chain 'H' and resid 58 through 81 Processing helix chain 'H' and resid 137 through 153 removed outlier: 4.021A pdb=" N VAL H 141 " --> pdb=" O ASP H 137 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY H 142 " --> pdb=" O LYS H 138 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG H 152 " --> pdb=" O ILE H 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 27 removed outlier: 3.672A pdb=" N ALA I 26 " --> pdb=" O LYS I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 33 Proline residue: I 32 - end of helix No H-bonds generated for 'chain 'I' and resid 28 through 33' Processing helix chain 'I' and resid 40 through 47 Processing helix chain 'I' and resid 48 through 74 removed outlier: 6.780A pdb=" N ARG I 52 " --> pdb=" O GLU I 48 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA I 53 " --> pdb=" O ALA I 49 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE I 71 " --> pdb=" O ARG I 67 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASN I 74 " --> pdb=" O GLU I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 103 Processing helix chain 'I' and resid 110 through 115 removed outlier: 3.586A pdb=" N LEU I 114 " --> pdb=" O ASP I 110 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ALA I 115 " --> pdb=" O PRO I 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 110 through 115' Processing helix chain 'N' and resid 22 through 36 Processing helix chain 'N' and resid 86 through 94 Processing helix chain 'N' and resid 95 through 108 removed outlier: 3.504A pdb=" N MET N 106 " --> pdb=" O ALA N 102 " (cutoff:3.500A) Proline residue: N 108 - end of helix Processing helix chain 'N' and resid 110 through 121 removed outlier: 5.310A pdb=" N LYS N 121 " --> pdb=" O PHE N 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 103 through 110 removed outlier: 4.764A pdb=" N ARG O 107 " --> pdb=" O ALA O 103 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 118 Processing helix chain 'P' and resid 2 through 7 removed outlier: 3.593A pdb=" N LEU P 6 " --> pdb=" O LYS P 2 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ARG P 7 " --> pdb=" O LEU P 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 2 through 7' Processing helix chain 'P' and resid 37 through 42 removed outlier: 5.591A pdb=" N SER P 42 " --> pdb=" O GLN P 38 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 63 Proline residue: P 63 - end of helix Processing helix chain 'P' and resid 84 through 90 removed outlier: 4.583A pdb=" N ARG P 90 " --> pdb=" O LYS P 86 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 104 Processing helix chain 'P' and resid 131 through 142 removed outlier: 3.644A pdb=" N GLY P 142 " --> pdb=" O LEU P 138 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 59 Processing helix chain 'Q' and resid 110 through 126 Proline residue: Q 126 - end of helix Processing helix chain 'Q' and resid 135 through 141 Processing helix chain 'R' and resid 13 through 32 Processing helix chain 'R' and resid 38 through 58 removed outlier: 4.551A pdb=" N GLY R 46 " --> pdb=" O LYS R 42 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE R 47 " --> pdb=" O GLU R 43 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU R 51 " --> pdb=" O PHE R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 71 removed outlier: 3.755A pdb=" N ASP R 69 " --> pdb=" O LEU R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 88 removed outlier: 5.032A pdb=" N ALA R 84 " --> pdb=" O PHE R 80 " (cutoff:3.500A) Proline residue: R 85 - end of helix Processing helix chain 'S' and resid 5 through 22 removed outlier: 4.136A pdb=" N THR S 21 " --> pdb=" O ARG S 17 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY S 22 " --> pdb=" O ILE S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 57 Processing helix chain 'S' and resid 61 through 81 Processing helix chain 'S' and resid 96 through 109 Processing helix chain 'T' and resid 2 through 15 removed outlier: 3.952A pdb=" N ARG T 13 " --> pdb=" O LEU T 9 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR T 14 " --> pdb=" O VAL T 10 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 106 removed outlier: 4.750A pdb=" N ARG T 103 " --> pdb=" O LEU T 99 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASN T 104 " --> pdb=" O TYR T 100 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU T 105 " --> pdb=" O PHE T 101 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N SER T 106 " --> pdb=" O ILE T 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 99 through 106' Processing helix chain 'T' and resid 107 through 115 removed outlier: 4.228A pdb=" N ARG T 115 " --> pdb=" O ARG T 111 " (cutoff:3.500A) Processing helix chain 'T' and resid 117 through 129 removed outlier: 3.671A pdb=" N GLU T 128 " --> pdb=" O ASP T 124 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ARG T 129 " --> pdb=" O ARG T 125 " (cutoff:3.500A) Processing helix chain 'U' and resid 8 through 22 Processing helix chain 'U' and resid 26 through 31 removed outlier: 3.580A pdb=" N LYS U 30 " --> pdb=" O GLY U 26 " (cutoff:3.500A) Processing helix chain 'U' and resid 32 through 73 removed outlier: 4.043A pdb=" N LYS U 54 " --> pdb=" O ARG U 50 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG U 55 " --> pdb=" O LYS U 51 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS U 72 " --> pdb=" O ALA U 68 " (cutoff:3.500A) Processing helix chain 'U' and resid 75 through 87 Processing helix chain 'U' and resid 91 through 101 Processing helix chain 'U' and resid 102 through 117 Processing helix chain 'W' and resid 13 through 25 removed outlier: 3.554A pdb=" N LEU W 19 " --> pdb=" O ARG W 15 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL W 20 " --> pdb=" O LYS W 16 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU W 23 " --> pdb=" O LEU W 19 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE W 24 " --> pdb=" O VAL W 20 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 39 Processing helix chain 'W' and resid 41 through 60 removed outlier: 4.406A pdb=" N TYR W 45 " --> pdb=" O LYS W 41 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE W 46 " --> pdb=" O ARG W 42 " (cutoff:3.500A) Processing helix chain 'X' and resid 3 through 9 removed outlier: 3.953A pdb=" N VAL X 7 " --> pdb=" O THR X 3 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LEU X 9 " --> pdb=" O TYR X 5 " (cutoff:3.500A) Processing helix chain 'X' and resid 14 through 24 removed outlier: 4.055A pdb=" N GLY X 20 " --> pdb=" O LYS X 16 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE X 21 " --> pdb=" O ALA X 17 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA X 22 " --> pdb=" O TYR X 18 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU X 23 " --> pdb=" O ALA X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 35 through 47 Processing helix chain 'X' and resid 89 through 95 removed outlier: 3.982A pdb=" N GLY X 94 " --> pdb=" O GLU X 90 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU X 95 " --> pdb=" O ALA X 91 " (cutoff:3.500A) Processing helix chain 'Y' and resid 68 through 73 removed outlier: 4.096A pdb=" N VAL Y 72 " --> pdb=" O HIS Y 68 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ARG Y 73 " --> pdb=" O ALA Y 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 68 through 73' Processing helix chain 'Z' and resid 14 through 22 Processing helix chain 'Z' and resid 40 through 52 removed outlier: 3.563A pdb=" N GLN Z 50 " --> pdb=" O LYS Z 46 " (cutoff:3.500A) Processing helix chain 'Z' and resid 108 through 114 Processing helix chain 'Z' and resid 151 through 156 removed outlier: 3.919A pdb=" N LEU Z 155 " --> pdb=" O HIS Z 151 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LYS Z 156 " --> pdb=" O ALA Z 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 151 through 156' Processing helix chain 'Z' and resid 179 through 187 removed outlier: 3.941A pdb=" N LEU Z 183 " --> pdb=" O ASP Z 179 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA Z 184 " --> pdb=" O VAL Z 180 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N GLU Z 185 " --> pdb=" O GLU Z 181 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU Z 186 " --> pdb=" O LYS Z 182 " (cutoff:3.500A) Processing helix chain '1' and resid 63 through 81 Proline residue: 1 68 - end of helix removed outlier: 3.578A pdb=" N TYR 1 71 " --> pdb=" O ILE 1 67 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS 1 78 " --> pdb=" O VAL 1 74 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLY 1 79 " --> pdb=" O GLU 1 75 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU 1 80 " --> pdb=" O ARG 1 76 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LYS 1 81 " --> pdb=" O ALA 1 77 " (cutoff:3.500A) Processing helix chain '1' and resid 86 through 98 Processing helix chain '2' and resid 2 through 17 removed outlier: 5.196A pdb=" N SER 2 17 " --> pdb=" O ALA 2 13 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 42 Processing helix chain '2' and resid 46 through 70 removed outlier: 4.364A pdb=" N ILE 2 50 " --> pdb=" O GLN 2 46 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG 2 51 " --> pdb=" O ASN 2 47 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN 2 70 " --> pdb=" O GLU 2 66 " (cutoff:3.500A) Processing helix chain '3' and resid 16 through 27 Processing helix chain '3' and resid 40 through 51 Processing helix chain '4' and resid 40 through 45 removed outlier: 3.986A pdb=" N GLY 4 45 " --> pdb=" O PRO 4 41 " (cutoff:3.500A) Processing helix chain '5' and resid 12 through 22 removed outlier: 4.639A pdb=" N HIS 5 22 " --> pdb=" O ALA 5 18 " (cutoff:3.500A) Processing helix chain '6' and resid 26 through 31 Proline residue: 6 31 - end of helix Processing helix chain '7' and resid 8 through 16 Processing helix chain '7' and resid 17 through 25 removed outlier: 4.220A pdb=" N THR 7 24 " --> pdb=" O ALA 7 20 " (cutoff:3.500A) Proline residue: 7 25 - end of helix Processing helix chain '7' and resid 26 through 38 Processing helix chain '8' and resid 7 through 14 Processing helix chain '8' and resid 37 through 47 removed outlier: 3.939A pdb=" N ARG 8 46 " --> pdb=" O ARG 8 42 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LYS 8 47 " --> pdb=" O GLN 8 43 " (cutoff:3.500A) Processing helix chain '8' and resid 51 through 63 Proline residue: 8 63 - end of helix Processing helix chain '9' and resid 29 through 34 removed outlier: 5.839A pdb=" N GLN 9 34 " --> pdb=" O PRO 9 30 " (cutoff:3.500A) Processing helix chain 'b' and resid 10 through 16 removed outlier: 3.675A pdb=" N GLY b 14 " --> pdb=" O LEU b 10 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N HIS b 16 " --> pdb=" O GLU b 12 " (cutoff:3.500A) Processing helix chain 'b' and resid 25 through 33 removed outlier: 3.576A pdb=" N ALA b 29 " --> pdb=" O ASN b 25 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ARG b 30 " --> pdb=" O PRO b 26 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N TYR b 31 " --> pdb=" O LYS b 27 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE b 32 " --> pdb=" O PHE b 28 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N TYR b 33 " --> pdb=" O ALA b 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 25 through 33' Processing helix chain 'b' and resid 44 through 63 removed outlier: 3.801A pdb=" N GLU b 49 " --> pdb=" O GLN b 45 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU b 50 " --> pdb=" O LYS b 46 " (cutoff:3.500A) Processing helix chain 'b' and resid 77 through 89 removed outlier: 3.680A pdb=" N VAL b 81 " --> pdb=" O ALA b 77 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG b 82 " --> pdb=" O GLN b 78 " (cutoff:3.500A) Processing helix chain 'b' and resid 104 through 123 removed outlier: 3.575A pdb=" N VAL b 112 " --> pdb=" O ILE b 108 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS b 113 " --> pdb=" O SER b 109 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA b 123 " --> pdb=" O GLU b 119 " (cutoff:3.500A) Processing helix chain 'b' and resid 131 through 149 removed outlier: 3.846A pdb=" N TYR b 148 " --> pdb=" O ARG b 144 " (cutoff:3.500A) Processing helix chain 'b' and resid 150 through 156 removed outlier: 4.245A pdb=" N LEU b 154 " --> pdb=" O SER b 150 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU b 155 " --> pdb=" O GLY b 151 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N LYS b 156 " --> pdb=" O PHE b 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 150 through 156' Processing helix chain 'b' and resid 166 through 171 Processing helix chain 'b' and resid 172 through 181 removed outlier: 3.666A pdb=" N GLU b 176 " --> pdb=" O ILE b 172 " (cutoff:3.500A) Processing helix chain 'b' and resid 193 through 198 removed outlier: 3.798A pdb=" N VAL b 197 " --> pdb=" O ASP b 193 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ASP b 198 " --> pdb=" O PRO b 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 193 through 198' Processing helix chain 'b' and resid 207 through 227 removed outlier: 3.927A pdb=" N LEU b 215 " --> pdb=" O ILE b 211 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG b 217 " --> pdb=" O LEU b 213 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 Processing helix chain 'c' and resid 28 through 48 Processing helix chain 'c' and resid 72 through 78 Processing helix chain 'c' and resid 81 through 96 removed outlier: 3.782A pdb=" N ARG c 85 " --> pdb=" O GLY c 81 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA c 92 " --> pdb=" O ARG c 88 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 113 removed outlier: 4.083A pdb=" N SER c 112 " --> pdb=" O ASN c 108 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ALA c 113 " --> pdb=" O PRO c 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 108 through 113' Processing helix chain 'c' and resid 114 through 127 Processing helix chain 'c' and resid 129 through 145 removed outlier: 3.643A pdb=" N LYS c 135 " --> pdb=" O ARG c 131 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG c 140 " --> pdb=" O GLN c 136 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY c 145 " --> pdb=" O VAL c 141 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 16 removed outlier: 5.012A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N CYS d 12 " --> pdb=" O VAL d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 23 through 28 Processing helix chain 'd' and resid 31 through 36 Processing helix chain 'd' and resid 52 through 69 removed outlier: 3.683A pdb=" N TYR d 68 " --> pdb=" O LEU d 64 " (cutoff:3.500A) Processing helix chain 'd' and resid 71 through 86 removed outlier: 4.941A pdb=" N LYS d 86 " --> pdb=" O ALA d 82 " (cutoff:3.500A) Processing helix chain 'd' and resid 88 through 100 Processing helix chain 'd' and resid 101 through 109 Processing helix chain 'd' and resid 113 through 124 removed outlier: 3.508A pdb=" N GLN d 119 " --> pdb=" O ARG d 115 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU d 120 " --> pdb=" O GLN d 116 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL d 121 " --> pdb=" O ALA d 117 " (cutoff:3.500A) Processing helix chain 'd' and resid 149 through 156 removed outlier: 3.591A pdb=" N ASN d 154 " --> pdb=" O GLU d 150 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU d 155 " --> pdb=" O LYS d 151 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLU d 156 " --> pdb=" O SER d 152 " (cutoff:3.500A) Processing helix chain 'd' and resid 157 through 168 removed outlier: 4.843A pdb=" N GLY d 167 " --> pdb=" O GLU d 163 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG d 168 " --> pdb=" O ALA d 164 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 195 removed outlier: 4.801A pdb=" N ALA d 195 " --> pdb=" O ARG d 191 " (cutoff:3.500A) Processing helix chain 'd' and resid 199 through 209 removed outlier: 3.858A pdb=" N VAL d 203 " --> pdb=" O ASN d 199 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR d 207 " --> pdb=" O VAL d 203 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG d 209 " --> pdb=" O GLU d 205 " (cutoff:3.500A) Processing helix chain 'e' and resid 50 through 66 Processing helix chain 'e' and resid 103 through 114 Processing helix chain 'e' and resid 127 through 143 removed outlier: 3.552A pdb=" N LEU e 142 " --> pdb=" O ALA e 138 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ARG e 143 " --> pdb=" O LEU e 139 " (cutoff:3.500A) Processing helix chain 'e' and resid 144 through 152 removed outlier: 3.560A pdb=" N VAL e 148 " --> pdb=" O THR e 144 " (cutoff:3.500A) Processing helix chain 'f' and resid 15 through 34 Processing helix chain 'f' and resid 69 through 82 removed outlier: 4.504A pdb=" N ASN f 73 " --> pdb=" O GLU f 69 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ASP f 74 " --> pdb=" O ASP f 70 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE f 81 " --> pdb=" O ARG f 77 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ARG f 82 " --> pdb=" O GLU f 78 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 removed outlier: 3.581A pdb=" N THR g 24 " --> pdb=" O ASP g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 54 Processing helix chain 'g' and resid 57 through 70 Processing helix chain 'g' and resid 92 through 111 removed outlier: 3.633A pdb=" N SER g 98 " --> pdb=" O ARG g 94 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 Processing helix chain 'g' and resid 132 through 153 removed outlier: 3.556A pdb=" N ASN g 148 " --> pdb=" O MET g 144 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG g 149 " --> pdb=" O ALA g 145 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ALA g 150 " --> pdb=" O GLU g 146 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N TYR g 151 " --> pdb=" O ALA g 147 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA g 152 " --> pdb=" O ASN g 148 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N HIS g 153 " --> pdb=" O ARG g 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 20 removed outlier: 3.594A pdb=" N VAL h 19 " --> pdb=" O ASN h 15 " (cutoff:3.500A) Processing helix chain 'h' and resid 29 through 43 Processing helix chain 'h' and resid 102 through 107 removed outlier: 4.928A pdb=" N GLY h 106 " --> pdb=" O ARG h 102 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU h 107 " --> pdb=" O VAL h 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 102 through 107' Processing helix chain 'h' and resid 120 through 128 Processing helix chain 'i' and resid 32 through 38 Processing helix chain 'i' and resid 47 through 54 removed outlier: 3.721A pdb=" N ASP i 54 " --> pdb=" O LEU i 50 " (cutoff:3.500A) Processing helix chain 'i' and resid 69 through 90 removed outlier: 3.650A pdb=" N LEU i 85 " --> pdb=" O ILE i 81 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL i 86 " --> pdb=" O ALA i 82 " (cutoff:3.500A) Proline residue: i 90 - end of helix Processing helix chain 'i' and resid 91 through 100 removed outlier: 5.081A pdb=" N LYS i 95 " --> pdb=" O ASP i 91 " (cutoff:3.500A) Proline residue: i 98 - end of helix Processing helix chain 'i' and resid 41 through 46 removed outlier: 3.900A pdb=" N VAL i 44 " --> pdb=" O VAL i 41 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ALA i 46 " --> pdb=" O ALA i 43 " (cutoff:3.500A) Processing helix chain 'j' and resid 12 through 31 removed outlier: 3.850A pdb=" N LEU j 16 " --> pdb=" O ASP j 12 " (cutoff:3.500A) Processing helix chain 'j' and resid 78 through 88 removed outlier: 3.625A pdb=" N GLN j 84 " --> pdb=" O LYS j 80 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU j 88 " --> pdb=" O GLN j 84 " (cutoff:3.500A) Processing helix chain 'k' and resid 44 through 49 Processing helix chain 'k' and resid 52 through 58 removed outlier: 4.384A pdb=" N GLY k 56 " --> pdb=" O GLY k 52 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR k 57 " --> pdb=" O SER k 53 " (cutoff:3.500A) Proline residue: k 58 - end of helix No H-bonds generated for 'chain 'k' and resid 52 through 58' Processing helix chain 'k' and resid 59 through 76 removed outlier: 3.608A pdb=" N TYR k 75 " --> pdb=" O LYS k 71 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY k 76 " --> pdb=" O ALA k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 90 through 102 removed outlier: 3.628A pdb=" N ILE k 95 " --> pdb=" O ARG k 91 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG k 96 " --> pdb=" O GLU k 92 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLY k 102 " --> pdb=" O LEU k 98 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 14 Processing helix chain 'l' and resid 116 through 121 removed outlier: 4.481A pdb=" N TYR l 120 " --> pdb=" O SER l 116 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY l 121 " --> pdb=" O ARG l 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 116 through 121' Processing helix chain 'm' and resid 14 through 23 removed outlier: 3.704A pdb=" N ILE m 22 " --> pdb=" O ALA m 18 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N TYR m 23 " --> pdb=" O LEU m 19 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 removed outlier: 3.962A pdb=" N LEU m 34 " --> pdb=" O ALA m 30 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU m 35 " --> pdb=" O LYS m 31 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 64 Processing helix chain 'm' and resid 67 through 85 removed outlier: 3.721A pdb=" N ARG m 71 " --> pdb=" O GLU m 67 " (cutoff:3.500A) Processing helix chain 'm' and resid 86 through 95 Processing helix chain 'm' and resid 107 through 112 Processing helix chain 'n' and resid 2 through 13 removed outlier: 5.022A pdb=" N LEU n 6 " --> pdb=" O ALA n 2 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS n 11 " --> pdb=" O ILE n 7 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N THR n 13 " --> pdb=" O LYS n 9 " (cutoff:3.500A) Processing helix chain 'n' and resid 16 through 21 removed outlier: 4.194A pdb=" N ALA n 20 " --> pdb=" O PHE n 16 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N TYR n 21 " --> pdb=" O LYS n 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 16 through 21' Processing helix chain 'n' and resid 40 through 51 Processing helix chain 'o' and resid 4 through 16 Processing helix chain 'o' and resid 24 through 47 removed outlier: 3.773A pdb=" N LEU o 31 " --> pdb=" O VAL o 27 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU o 32 " --> pdb=" O GLN o 28 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG o 38 " --> pdb=" O LEU o 34 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 4.065A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 Processing helix chain 'p' and resid 52 through 63 removed outlier: 3.833A pdb=" N ALA p 56 " --> pdb=" O ASP p 52 " (cutoff:3.500A) Processing helix chain 'p' and resid 67 through 78 removed outlier: 3.746A pdb=" N LEU p 73 " --> pdb=" O THR p 69 " (cutoff:3.500A) Processing helix chain 'q' and resid 81 through 99 removed outlier: 3.559A pdb=" N VAL q 85 " --> pdb=" O ARG q 81 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU q 96 " --> pdb=" O ARG q 92 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER q 97 " --> pdb=" O GLN q 93 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU q 98 " --> pdb=" O ASN q 94 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER q 99 " --> pdb=" O TYR q 95 " (cutoff:3.500A) Processing helix chain 'r' and resid 21 through 27 removed outlier: 4.591A pdb=" N GLY r 27 " --> pdb=" O LYS r 23 " (cutoff:3.500A) Processing helix chain 'r' and resid 36 through 45 removed outlier: 3.587A pdb=" N LEU r 40 " --> pdb=" O ASN r 36 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE r 43 " --> pdb=" O VAL r 39 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU r 44 " --> pdb=" O LEU r 40 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N SER r 45 " --> pdb=" O LYS r 41 " (cutoff:3.500A) Processing helix chain 'r' and resid 52 through 57 Processing helix chain 'r' and resid 59 through 77 Processing helix chain 's' and resid 12 through 26 Processing helix chain 's' and resid 63 through 68 removed outlier: 3.785A pdb=" N VAL s 67 " --> pdb=" O THR s 63 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLY s 68 " --> pdb=" O GLU s 64 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 63 through 68' Processing helix chain 's' and resid 70 through 76 removed outlier: 4.466A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Proline residue: s 76 - end of helix No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 't' and resid 9 through 47 removed outlier: 3.624A pdb=" N LEU t 13 " --> pdb=" O ASN t 9 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ARG t 17 " --> pdb=" O LEU t 13 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLN t 18 " --> pdb=" O LYS t 14 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER t 19 " --> pdb=" O ARG t 15 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU t 20 " --> pdb=" O HIS t 16 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG t 25 " --> pdb=" O LYS t 21 " (cutoff:3.500A) Processing helix chain 't' and resid 48 through 70 removed outlier: 4.544A pdb=" N GLY t 69 " --> pdb=" O LYS t 65 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N SER t 70 " --> pdb=" O ALA t 66 " (cutoff:3.500A) Processing helix chain 't' and resid 73 through 96 removed outlier: 3.577A pdb=" N ARG t 89 " --> pdb=" O MET t 85 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA t 95 " --> pdb=" O LEU t 91 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY t 96 " --> pdb=" O LEU t 92 " (cutoff:3.500A) Processing helix chain 'u' and resid 8 through 16 Processing helix chain 'C' and resid 4 through 14 removed outlier: 3.788A pdb=" N LEU C 10 " --> pdb=" O ARG C 6 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL C 14 " --> pdb=" O LEU C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 33 removed outlier: 3.868A pdb=" N ALA C 25 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ALA C 26 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA C 33 " --> pdb=" O VAL C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 90 removed outlier: 4.003A pdb=" N GLU C 85 " --> pdb=" O GLU C 81 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLY C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 104 removed outlier: 5.385A pdb=" N LEU C 104 " --> pdb=" O ILE C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 removed outlier: 4.854A pdb=" N SER C 125 " --> pdb=" O GLY C 121 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LYS C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 121 through 126' Processing helix chain 'C' and resid 129 through 135 Proline residue: C 133 - end of helix No H-bonds generated for 'chain 'C' and resid 129 through 135' Processing helix chain 'C' and resid 148 through 159 removed outlier: 3.733A pdb=" N ALA C 158 " --> pdb=" O ARG C 154 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 200 removed outlier: 3.766A pdb=" N ASP C 187 " --> pdb=" O GLU C 183 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS C 200 " --> pdb=" O LEU C 196 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'D' and resid 33 through 36 No H-bonds generated for sheet with id= 1 Processing sheet with id= 2, first strand: chain 'D' and resid 81 through 84 removed outlier: 4.314A pdb=" N ALA D 81 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU D 94 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA D 80 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ILE D 75 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA D 119 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLN D 115 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'D' and resid 140 through 143 removed outlier: 4.306A pdb=" N THR D 140 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN D 164 " --> pdb=" O ARG D 176 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE D 174 " --> pdb=" O GLN D 166 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU D 181 " --> pdb=" O LEU D 177 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'D' and resid 91 through 97 removed outlier: 4.832A pdb=" N ARG D 91 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU D 101 " --> pdb=" O TYR D 97 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'E' and resid 2 through 6 removed outlier: 6.534A pdb=" N LYS E 2 " --> pdb=" O GLU E 200 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'E' and resid 10 through 15 removed outlier: 7.912A pdb=" N ASN E 180 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'E' and resid 77 through 82 removed outlier: 6.421A pdb=" N GLN E 48 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASP E 89 " --> pdb=" O VAL E 33 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 100 through 103 removed outlier: 4.113A pdb=" N GLU E 100 " --> pdb=" O VAL E 172 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'F' and resid 16 through 20 removed outlier: 3.720A pdb=" N ILE F 9 " --> pdb=" O LEU F 20 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'G' and resid 68 through 72 removed outlier: 3.985A pdb=" N LYS G 36 " --> pdb=" O VAL G 160 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N GLY G 42 " --> pdb=" O GLY G 154 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N GLY G 154 " --> pdb=" O GLY G 42 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'H' and resid 16 through 19 Processing sheet with id= 12, first strand: chain 'H' and resid 41 through 46 removed outlier: 3.573A pdb=" N GLU H 46 " --> pdb=" O VAL H 49 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'H' and resid 83 through 89 removed outlier: 5.664A pdb=" N THR H 129 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ARG H 130 " --> pdb=" O PRO H 126 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'H' and resid 94 through 98 Processing sheet with id= 15, first strand: chain 'I' and resid 7 through 10 removed outlier: 6.153A pdb=" N GLU I 7 " --> pdb=" O VAL I 15 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL I 15 " --> pdb=" O GLU I 7 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'I' and resid 17 through 21 removed outlier: 4.099A pdb=" N GLN I 17 " --> pdb=" O LEU I 5 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL I 21 " --> pdb=" O MET I 1 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET I 1 " --> pdb=" O VAL I 21 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LYS I 2 " --> pdb=" O ALA I 39 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU I 35 " --> pdb=" O LEU I 6 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'I' and resid 76 through 81 removed outlier: 6.255A pdb=" N ILE I 138 " --> pdb=" O TYR I 130 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY I 124 " --> pdb=" O VAL I 144 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'N' and resid 50 through 55 removed outlier: 3.889A pdb=" N PHE N 51 " --> pdb=" O ARG N 12 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASP N 17 " --> pdb=" O LEU N 138 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'N' and resid 72 through 76 removed outlier: 7.476A pdb=" N GLY N 81 " --> pdb=" O SER N 76 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'O' and resid 63 through 66 removed outlier: 5.981A pdb=" N ASP O 81 " --> pdb=" O LYS O 66 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ASN O 82 " --> pdb=" O TYR O 7 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR O 6 " --> pdb=" O CYS O 21 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL O 40 " --> pdb=" O ILE O 22 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASP O 37 " --> pdb=" O VAL O 62 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'O' and resid 68 through 71 removed outlier: 4.079A pdb=" N SER O 75 " --> pdb=" O ARG O 71 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'O' and resid 59 through 62 removed outlier: 4.475A pdb=" N LYS O 59 " --> pdb=" O ILE O 87 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'P' and resid 79 through 83 removed outlier: 3.930A pdb=" N LYS P 113 " --> pdb=" O GLN P 81 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'P' and resid 123 through 128 removed outlier: 3.621A pdb=" N ALA P 127 " --> pdb=" O VAL P 146 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'Q' and resid 39 through 42 Processing sheet with id= 26, first strand: chain 'Q' and resid 63 through 67 removed outlier: 5.732A pdb=" N MET Q 103 " --> pdb=" O ARG Q 67 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE Q 104 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ASP Q 31 " --> pdb=" O ARG Q 134 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'R' and resid 33 through 37 removed outlier: 5.118A pdb=" N LEU R 111 " --> pdb=" O LEU R 100 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'S' and resid 34 through 41 removed outlier: 3.649A pdb=" N HIS S 34 " --> pdb=" O SER S 31 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL S 28 " --> pdb=" O ASP S 88 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'T' and resid 40 through 47 removed outlier: 6.342A pdb=" N THR T 27 " --> pdb=" O VAL T 89 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'T' and resid 60 through 66 Processing sheet with id= 31, first strand: chain 'V' and resid 2 through 6 Processing sheet with id= 32, first strand: chain 'V' and resid 18 through 23 removed outlier: 3.519A pdb=" N LEU V 18 " --> pdb=" O ILE V 96 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N GLU V 93 " --> pdb=" O LEU V 62 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL V 58 " --> pdb=" O LYS V 97 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ALA V 31 " --> pdb=" O VAL V 61 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'V' and resid 55 through 58 Processing sheet with id= 34, first strand: chain 'V' and resid 64 through 67 removed outlier: 4.574A pdb=" N GLN V 89 " --> pdb=" O GLY V 67 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'V' and resid 69 through 76 removed outlier: 4.191A pdb=" N TYR V 81 " --> pdb=" O LYS V 76 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'W' and resid 2 through 7 Processing sheet with id= 37, first strand: chain 'W' and resid 72 through 79 removed outlier: 4.431A pdb=" N THR W 100 " --> pdb=" O GLY W 79 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'W' and resid 80 through 88 removed outlier: 4.185A pdb=" N THR W 100 " --> pdb=" O PRO W 80 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG W 92 " --> pdb=" O ARG W 88 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'X' and resid 25 through 29 removed outlier: 4.149A pdb=" N GLY X 61 " --> pdb=" O PRO X 74 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS X 62 " --> pdb=" O ARG X 73 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'Y' and resid 29 through 32 removed outlier: 3.521A pdb=" N GLU Y 29 " --> pdb=" O ILE Y 38 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'Y' and resid 43 through 50 removed outlier: 5.520A pdb=" N ASN Y 43 " --> pdb=" O ALA Y 65 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'Y' and resid 84 through 87 removed outlier: 6.822A pdb=" N ARG Y 84 " --> pdb=" O ALA Y 100 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'Z' and resid 65 through 69 removed outlier: 3.954A pdb=" N GLN Z 65 " --> pdb=" O LEU Z 61 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR Z 3 " --> pdb=" O VAL Z 56 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS Z 85 " --> pdb=" O ASN Z 75 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ASN Z 75 " --> pdb=" O GLU Z 84 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'Z' and resid 115 through 119 removed outlier: 3.858A pdb=" N ALA Z 172 " --> pdb=" O LEU Z 150 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'Z' and resid 122 through 127 removed outlier: 7.285A pdb=" N ARG Z 122 " --> pdb=" O LEU Z 102 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU Z 102 " --> pdb=" O ARG Z 122 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE Z 137 " --> pdb=" O PRO Z 101 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain '0' and resid 51 through 54 removed outlier: 4.208A pdb=" N THR 0 58 " --> pdb=" O GLY 0 54 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain '0' and resid 66 through 72 removed outlier: 4.685A pdb=" N GLY 0 76 " --> pdb=" O ARG 0 72 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain '1' and resid 32 through 35 removed outlier: 6.971A pdb=" N GLN 1 19 " --> pdb=" O THR 1 35 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain '1' and resid 48 through 52 Processing sheet with id= 50, first strand: chain '3' and resid 32 through 38 removed outlier: 3.811A pdb=" N GLN 3 33 " --> pdb=" O LEU 3 8 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain '4' and resid 19 through 24 Processing sheet with id= 52, first strand: chain '6' and resid 7 through 11 Processing sheet with id= 53, first strand: chain '6' and resid 35 through 38 Processing sheet with id= 54, first strand: chain '9' and resid 14 through 18 Processing sheet with id= 55, first strand: chain 'b' and resid 91 through 94 Processing sheet with id= 56, first strand: chain 'c' and resid 54 through 59 Processing sheet with id= 57, first strand: chain 'c' and resid 164 through 171 removed outlier: 3.556A pdb=" N GLY c 194 " --> pdb=" O THR c 191 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ASN c 181 " --> pdb=" O LEU c 204 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'd' and resid 144 through 148 removed outlier: 3.781A pdb=" N ASP d 144 " --> pdb=" O PHE d 185 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N MET d 181 " --> pdb=" O VAL d 148 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS d 182 " --> pdb=" O ASP d 177 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'e' and resid 6 through 10 Processing sheet with id= 60, first strand: chain 'e' and resid 78 through 83 removed outlier: 7.794A pdb=" N HIS e 78 " --> pdb=" O PRO e 93 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA e 94 " --> pdb=" O ASP e 117 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ASP e 117 " --> pdb=" O ALA e 94 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'e' and resid 28 through 36 removed outlier: 6.492A pdb=" N ARG e 40 " --> pdb=" O ASP e 36 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'f' and resid 38 through 43 removed outlier: 3.738A pdb=" N LEU f 43 " --> pdb=" O PHE f 60 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N PHE f 60 " --> pdb=" O LEU f 43 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'g' and resid 72 through 79 removed outlier: 6.199A pdb=" N ARG g 72 " --> pdb=" O VAL g 91 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'h' and resid 22 through 26 removed outlier: 6.198A pdb=" N GLU h 22 " --> pdb=" O LEU h 63 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL h 26 " --> pdb=" O LEU h 59 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'h' and resid 93 through 96 removed outlier: 4.985A pdb=" N VAL h 93 " --> pdb=" O LEU h 133 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'i' and resid 3 through 9 removed outlier: 4.057A pdb=" N LYS i 25 " --> pdb=" O PHE i 59 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'j' and resid 5 through 11 removed outlier: 3.868A pdb=" N ASP j 73 " --> pdb=" O SER j 35 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N GLN j 33 " --> pdb=" O ILE j 75 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'j' and resid 37 through 40 removed outlier: 4.344A pdb=" N ASN j 69 " --> pdb=" O LEU j 40 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'j' and resid 42 through 50 removed outlier: 3.813A pdb=" N ARG j 43 " --> pdb=" O THR j 67 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG j 45 " --> pdb=" O LEU j 65 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'k' and resid 40 through 43 removed outlier: 3.826A pdb=" N ASN k 27 " --> pdb=" O SER k 24 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY k 17 " --> pdb=" O SER k 79 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL k 82 " --> pdb=" O LYS k 106 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'l' and resid 32 through 35 removed outlier: 6.589A pdb=" N ILE l 85 " --> pdb=" O VAL l 101 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N VAL l 101 " --> pdb=" O ILE l 85 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLY l 87 " --> pdb=" O HIS l 99 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N HIS l 99 " --> pdb=" O GLY l 87 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ARG l 97 " --> pdb=" O ARG l 89 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'l' and resid 39 through 44 removed outlier: 5.175A pdb=" N LYS l 54 " --> pdb=" O ILE l 70 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TYR l 64 " --> pdb=" O LEU l 60 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'p' and resid 2 through 9 removed outlier: 3.542A pdb=" N LYS p 50 " --> pdb=" O TYR p 38 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N TRP p 48 " --> pdb=" O ASP p 40 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'q' and resid 19 through 28 removed outlier: 3.507A pdb=" N VAL q 19 " --> pdb=" O ALA q 44 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG q 25 " --> pdb=" O ARG q 38 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'q' and resid 58 through 62 removed outlier: 6.559A pdb=" N GLU q 58 " --> pdb=" O LEU q 74 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ARG q 70 " --> pdb=" O SER q 62 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 's' and resid 30 through 34 removed outlier: 4.016A pdb=" N HIS s 47 " --> pdb=" O ILE s 62 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'C' and resid 42 through 47 removed outlier: 4.466A pdb=" N VAL C 212 " --> pdb=" O ILE C 224 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.441A pdb=" N VAL C 58 " --> pdb=" O ASN C 165 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'C' and resid 73 through 78 1957 hydrogen bonds defined for protein. 5778 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4303 hydrogen bonds 6934 hydrogen bond angles 0 basepair planarities 1636 basepair parallelities 2429 stacking parallelities Total time for adding SS restraints: 248.21 Time building geometry restraints manager: 86.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.93 - 1.19: 5 1.19 - 1.45: 91235 1.45 - 1.71: 70022 1.71 - 1.97: 215 1.97 - 2.24: 19 Bond restraints: 161496 Sorted by residual: bond pdb=" N1 C a 71 " pdb=" C2 C a 71 " ideal model delta sigma weight residual 1.397 2.236 -0.839 2.00e-02 2.50e+03 1.76e+03 bond pdb=" N1 C a 71 " pdb=" C6 C a 71 " ideal model delta sigma weight residual 1.367 2.188 -0.821 2.00e-02 2.50e+03 1.68e+03 bond pdb=" C2 C a 71 " pdb=" N3 C a 71 " ideal model delta sigma weight residual 1.353 2.161 -0.808 2.00e-02 2.50e+03 1.63e+03 bond pdb=" N3 C a 71 " pdb=" C4 C a 71 " ideal model delta sigma weight residual 1.334 2.140 -0.806 2.00e-02 2.50e+03 1.62e+03 bond pdb=" O3' G a 64 " pdb=" P U a 65 " ideal model delta sigma weight residual 1.607 2.186 -0.579 1.50e-02 4.44e+03 1.49e+03 ... (remaining 161491 not shown) Histogram of bond angle deviations from ideal: 76.64 - 93.93: 28 93.93 - 111.21: 102091 111.21 - 128.49: 132430 128.49 - 145.77: 7113 145.77 - 163.05: 1 Bond angle restraints: 241663 Sorted by residual: angle pdb=" C3' G a 64 " pdb=" O3' G a 64 " pdb=" P U a 65 " ideal model delta sigma weight residual 120.20 163.05 -42.85 1.50e+00 4.44e-01 8.16e+02 angle pdb="FE1 SF4 d 301 " pdb=" S4 SF4 d 301 " pdb="FE2 SF4 d 301 " ideal model delta sigma weight residual 73.70 90.43 -16.73 1.50e+00 4.44e-01 1.24e+02 angle pdb="FE2 SF4 d 301 " pdb=" S1 SF4 d 301 " pdb="FE3 SF4 d 301 " ideal model delta sigma weight residual 73.70 90.20 -16.50 1.50e+00 4.44e-01 1.21e+02 angle pdb="FE1 SF4 d 301 " pdb=" S4 SF4 d 301 " pdb="FE3 SF4 d 301 " ideal model delta sigma weight residual 73.70 90.15 -16.45 1.50e+00 4.44e-01 1.20e+02 angle pdb="FE1 SF4 d 301 " pdb=" S3 SF4 d 301 " pdb="FE2 SF4 d 301 " ideal model delta sigma weight residual 73.70 90.11 -16.41 1.50e+00 4.44e-01 1.20e+02 ... (remaining 241658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 90398 35.97 - 71.94: 12229 71.94 - 107.91: 1609 107.91 - 143.88: 55 143.88 - 179.84: 48 Dihedral angle restraints: 104339 sinusoidal: 87160 harmonic: 17179 Sorted by residual: dihedral pdb=" C4' G a 70 " pdb=" C3' G a 70 " pdb=" C2' G a 70 " pdb=" C1' G a 70 " ideal model delta sinusoidal sigma weight residual -35.00 32.09 -67.09 1 8.00e+00 1.56e-02 9.16e+01 dihedral pdb=" O4' U y 36 " pdb=" C1' U y 36 " pdb=" N1 U y 36 " pdb=" C2 U y 36 " ideal model delta sinusoidal sigma weight residual -160.00 19.05 -179.05 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" C5' G a 70 " pdb=" C4' G a 70 " pdb=" C3' G a 70 " pdb=" O3' G a 70 " ideal model delta sinusoidal sigma weight residual 147.00 82.67 64.33 1 8.00e+00 1.56e-02 8.50e+01 ... (remaining 104336 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.389: 30605 0.389 - 0.777: 2 0.777 - 1.166: 0 1.166 - 1.555: 0 1.555 - 1.943: 2 Chirality restraints: 30609 Sorted by residual: chirality pdb=" P U A2884 " pdb=" OP1 U A2884 " pdb=" OP2 U A2884 " pdb=" O5' U A2884 " both_signs ideal model delta sigma weight residual True 2.41 0.47 1.94 2.00e-01 2.50e+01 9.44e+01 chirality pdb=" P A A2225 " pdb=" OP1 A A2225 " pdb=" OP2 A A2225 " pdb=" O5' A A2225 " both_signs ideal model delta sigma weight residual True 2.41 0.55 1.86 2.00e-01 2.50e+01 8.61e+01 chirality pdb=" P U a 65 " pdb=" OP1 U a 65 " pdb=" OP2 U a 65 " pdb=" O5' U a 65 " both_signs ideal model delta sigma weight residual True 2.41 -3.11 -0.70 2.00e-01 2.50e+01 1.22e+01 ... (remaining 30606 not shown) Planarity restraints: 13093 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2251 " 0.040 2.00e-02 2.50e+03 5.80e-01 7.56e+03 pdb=" C4' OMG A2251 " 0.446 2.00e-02 2.50e+03 pdb=" O4' OMG A2251 " 0.635 2.00e-02 2.50e+03 pdb=" C3' OMG A2251 " -0.591 2.00e-02 2.50e+03 pdb=" O3' OMG A2251 " -0.591 2.00e-02 2.50e+03 pdb=" C2' OMG A2251 " -0.209 2.00e-02 2.50e+03 pdb=" O2' OMG A2251 " 0.928 2.00e-02 2.50e+03 pdb=" C1' OMG A2251 " 0.219 2.00e-02 2.50e+03 pdb=" N9 OMG A2251 " -0.878 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 7MG a 527 " 0.009 2.00e-02 2.50e+03 5.68e-01 7.26e+03 pdb=" C4' 7MG a 527 " 0.447 2.00e-02 2.50e+03 pdb=" O4' 7MG a 527 " 0.684 2.00e-02 2.50e+03 pdb=" C3' 7MG a 527 " -0.578 2.00e-02 2.50e+03 pdb=" O3' 7MG a 527 " -0.534 2.00e-02 2.50e+03 pdb=" C2' 7MG a 527 " -0.234 2.00e-02 2.50e+03 pdb=" O2' 7MG a 527 " 0.862 2.00e-02 2.50e+03 pdb=" C1' 7MG a 527 " 0.222 2.00e-02 2.50e+03 pdb=" N9 7MG a 527 " -0.878 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC a1407 " -0.038 2.00e-02 2.50e+03 5.66e-01 7.20e+03 pdb=" C4' 5MC a1407 " -0.433 2.00e-02 2.50e+03 pdb=" O4' 5MC a1407 " -0.601 2.00e-02 2.50e+03 pdb=" C3' 5MC a1407 " 0.587 2.00e-02 2.50e+03 pdb=" O3' 5MC a1407 " 0.567 2.00e-02 2.50e+03 pdb=" C2' 5MC a1407 " 0.206 2.00e-02 2.50e+03 pdb=" O2' 5MC a1407 " -0.909 2.00e-02 2.50e+03 pdb=" C1' 5MC a1407 " -0.238 2.00e-02 2.50e+03 pdb=" N1 5MC a1407 " 0.859 2.00e-02 2.50e+03 ... (remaining 13090 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.45: 1861 2.45 - 2.99: 82393 2.99 - 3.53: 231172 3.53 - 4.06: 397859 4.06 - 4.60: 475033 Nonbonded interactions: 1188318 Sorted by model distance: nonbonded pdb=" O2' A a 101 " pdb=" OP1 A a 152 " model vdw 1.914 2.200 nonbonded pdb=" OP2 G a 66 " pdb=" O2' G a 199 " model vdw 1.986 2.200 nonbonded pdb=" O2' C x 26 " pdb=" O4' C x 27 " model vdw 1.986 2.200 nonbonded pdb=" O2' C a 103 " pdb=" O2' C a 174 " model vdw 1.993 2.200 nonbonded pdb=" O4' G a 102 " pdb=" O2' A a 151 " model vdw 1.998 2.200 ... (remaining 1188313 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.830 Extract box with map and model: 17.920 Check model and map are aligned: 1.660 Set scattering table: 1.020 Process input model: 617.200 Find NCS groups from input model: 2.890 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 650.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 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 : 0.009 0.839 161492 Z= 0.547 Angle : 0.760 42.854 241653 Z= 0.397 Chirality : 0.040 1.943 30609 Planarity : 0.017 0.580 13093 Dihedral : 24.481 179.844 93314 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 50.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.69 % Favored : 92.24 % Rotamer: Outliers : 0.04 % Allowed : 2.98 % Favored : 96.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.10), residues: 5916 helix: -2.31 (0.10), residues: 1785 sheet: -3.07 (0.13), residues: 1088 loop : -2.08 (0.11), residues: 3043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP U 61 HIS 0.017 0.002 HIS t 16 PHE 0.026 0.003 PHE G 178 TYR 0.044 0.002 TYR 1 71 ARG 0.013 0.001 ARG g 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2552 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 2550 time to evaluate : 6.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: D 20 ASP cc_start: 0.9137 (p0) cc_final: 0.8717 (p0) REVERT: D 54 ARG cc_start: 0.7810 (mtp85) cc_final: 0.6226 (mtp180) REVERT: D 62 TYR cc_start: 0.9077 (t80) cc_final: 0.8750 (t80) REVERT: D 112 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7683 (mm-40) REVERT: D 126 GLN cc_start: 0.8995 (mm110) cc_final: 0.8639 (mm-40) REVERT: D 135 PHE cc_start: 0.8742 (m-80) cc_final: 0.8399 (m-10) REVERT: D 146 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7547 (mt-10) REVERT: D 148 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7499 (mt-10) REVERT: D 172 TYR cc_start: 0.8508 (m-10) cc_final: 0.7982 (m-80) REVERT: D 181 GLU cc_start: 0.8063 (tt0) cc_final: 0.7801 (tt0) REVERT: D 186 HIS cc_start: 0.8442 (t-90) cc_final: 0.7968 (t-170) REVERT: D 188 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8095 (mp0) REVERT: D 189 CYS cc_start: 0.7531 (m) cc_final: 0.7325 (m) REVERT: D 198 ASN cc_start: 0.7396 (t0) cc_final: 0.6822 (t0) REVERT: D 201 HIS cc_start: 0.9078 (t70) cc_final: 0.8632 (t-90) REVERT: D 263 ARG cc_start: 0.8075 (mtm180) cc_final: 0.7578 (mtm110) REVERT: E 38 THR cc_start: 0.7972 (p) cc_final: 0.7628 (t) REVERT: E 45 THR cc_start: 0.8134 (m) cc_final: 0.7800 (p) REVERT: E 55 ASN cc_start: 0.8398 (t0) cc_final: 0.7925 (t0) REVERT: E 85 ASN cc_start: 0.9012 (t160) cc_final: 0.8771 (p0) REVERT: E 118 LYS cc_start: 0.9164 (ttmm) cc_final: 0.8952 (tttt) REVERT: E 154 LYS cc_start: 0.7942 (tppt) cc_final: 0.7624 (tptp) REVERT: E 178 GLU cc_start: 0.7955 (pm20) cc_final: 0.7188 (pm20) REVERT: F 116 ASP cc_start: 0.8127 (t70) cc_final: 0.7846 (t0) REVERT: F 133 ASN cc_start: 0.8439 (m110) cc_final: 0.8210 (m110) REVERT: F 195 ASP cc_start: 0.8536 (t0) cc_final: 0.8320 (t0) REVERT: F 204 ASN cc_start: 0.9220 (m-40) cc_final: 0.8956 (m-40) REVERT: G 18 GLU cc_start: 0.8890 (tp30) cc_final: 0.8545 (tp30) REVERT: G 104 GLU cc_start: 0.8473 (tt0) cc_final: 0.8175 (tt0) REVERT: G 114 ILE cc_start: 0.7771 (mt) cc_final: 0.7052 (mt) REVERT: G 143 GLU cc_start: 0.7778 (mp0) cc_final: 0.7126 (mp0) REVERT: G 144 ILE cc_start: 0.8566 (mm) cc_final: 0.8228 (tp) REVERT: G 146 TYR cc_start: 0.8878 (t80) cc_final: 0.8607 (t80) REVERT: H 70 THR cc_start: 0.9295 (m) cc_final: 0.9064 (t) REVERT: H 74 ASN cc_start: 0.8468 (m-40) cc_final: 0.8227 (t0) REVERT: H 121 ILE cc_start: 0.9024 (mm) cc_final: 0.8771 (mm) REVERT: H 147 ASN cc_start: 0.8843 (m-40) cc_final: 0.8614 (m-40) REVERT: I 4 ILE cc_start: 0.8363 (mt) cc_final: 0.7589 (mt) REVERT: I 14 ASP cc_start: 0.7751 (t0) cc_final: 0.7497 (t0) REVERT: I 19 VAL cc_start: 0.8664 (m) cc_final: 0.8311 (p) REVERT: N 17 ASP cc_start: 0.8402 (t0) cc_final: 0.8132 (t0) REVERT: N 39 ARG cc_start: 0.8461 (mtp85) cc_final: 0.7900 (mtp180) REVERT: N 41 ASP cc_start: 0.8022 (p0) cc_final: 0.7623 (p0) REVERT: N 45 ASN cc_start: 0.9202 (p0) cc_final: 0.8646 (p0) REVERT: N 51 PHE cc_start: 0.8138 (m-10) cc_final: 0.7777 (m-80) REVERT: N 56 ASN cc_start: 0.8720 (m-40) cc_final: 0.8513 (m-40) REVERT: N 85 ILE cc_start: 0.8437 (mm) cc_final: 0.7997 (mp) REVERT: N 104 LYS cc_start: 0.9382 (ttmt) cc_final: 0.9170 (ttmm) REVERT: O 12 ASP cc_start: 0.8794 (p0) cc_final: 0.8438 (p0) REVERT: O 20 MET cc_start: 0.8409 (ttm) cc_final: 0.7820 (ttm) REVERT: O 91 LEU cc_start: 0.8854 (mt) cc_final: 0.8649 (mt) REVERT: O 107 ARG cc_start: 0.8162 (mtp85) cc_final: 0.7847 (mtp180) REVERT: P 3 LEU cc_start: 0.8686 (mp) cc_final: 0.8361 (mp) REVERT: P 9 ASN cc_start: 0.7592 (m-40) cc_final: 0.7295 (m-40) REVERT: P 49 ARG cc_start: 0.8099 (mtm180) cc_final: 0.7740 (mtm180) REVERT: P 117 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6795 (mm-30) REVERT: Q 5 ARG cc_start: 0.8769 (mtm180) cc_final: 0.8466 (mpp80) REVERT: Q 8 LYS cc_start: 0.9102 (mtpt) cc_final: 0.8647 (mtpt) REVERT: Q 9 TYR cc_start: 0.8567 (m-80) cc_final: 0.7920 (m-80) REVERT: Q 32 TYR cc_start: 0.8047 (m-10) cc_final: 0.6142 (m-10) REVERT: Q 37 LEU cc_start: 0.8354 (mt) cc_final: 0.7404 (mt) REVERT: Q 38 GLU cc_start: 0.8253 (pt0) cc_final: 0.7843 (pt0) REVERT: Q 63 LYS cc_start: 0.8518 (tptm) cc_final: 0.8227 (mmmt) REVERT: Q 77 LYS cc_start: 0.8778 (mtpp) cc_final: 0.8468 (mttp) REVERT: Q 115 MET cc_start: 0.8348 (mmm) cc_final: 0.8020 (mmp) REVERT: R 45 ARG cc_start: 0.8512 (mtt180) cc_final: 0.8091 (mtm-85) REVERT: S 88 ASP cc_start: 0.7835 (t0) cc_final: 0.7445 (t0) REVERT: S 93 LYS cc_start: 0.8642 (tmtm) cc_final: 0.8369 (ttmt) REVERT: T 30 VAL cc_start: 0.9134 (t) cc_final: 0.8863 (p) REVERT: T 31 SER cc_start: 0.8680 (m) cc_final: 0.8331 (m) REVERT: T 45 PHE cc_start: 0.7490 (t80) cc_final: 0.5989 (t80) REVERT: T 46 GLU cc_start: 0.7416 (tt0) cc_final: 0.7132 (tt0) REVERT: T 73 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7404 (mt-10) REVERT: T 100 TYR cc_start: 0.9210 (m-10) cc_final: 0.8663 (m-80) REVERT: T 121 ILE cc_start: 0.8838 (mt) cc_final: 0.8549 (mt) REVERT: T 123 GLN cc_start: 0.8726 (mt0) cc_final: 0.8462 (mt0) REVERT: U 65 ILE cc_start: 0.8728 (mt) cc_final: 0.8216 (mt) REVERT: U 76 TYR cc_start: 0.8662 (t80) cc_final: 0.7680 (t80) REVERT: V 10 LYS cc_start: 0.7574 (mttp) cc_final: 0.6372 (mttp) REVERT: V 56 SER cc_start: 0.8121 (p) cc_final: 0.7903 (m) REVERT: V 66 ARG cc_start: 0.8041 (mtp180) cc_final: 0.7144 (mtp180) REVERT: V 88 ARG cc_start: 0.8524 (mtp180) cc_final: 0.7442 (mtm180) REVERT: V 94 LEU cc_start: 0.8743 (mt) cc_final: 0.8338 (mt) REVERT: W 33 ARG cc_start: 0.8666 (mtt180) cc_final: 0.8260 (mtt-85) REVERT: W 64 MET cc_start: 0.6054 (mtp) cc_final: 0.5722 (mtm) REVERT: W 65 LEU cc_start: 0.7825 (mt) cc_final: 0.7615 (tp) REVERT: W 109 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7532 (mm-30) REVERT: X 7 VAL cc_start: 0.9131 (t) cc_final: 0.8905 (t) REVERT: X 9 LEU cc_start: 0.8711 (mt) cc_final: 0.8400 (mt) REVERT: X 37 THR cc_start: 0.8597 (m) cc_final: 0.8172 (p) REVERT: Y 29 GLU cc_start: 0.8646 (tt0) cc_final: 0.8381 (tm-30) REVERT: Y 43 ASN cc_start: 0.7443 (t160) cc_final: 0.6705 (t0) REVERT: Y 68 HIS cc_start: 0.7580 (t-90) cc_final: 0.7378 (t-170) REVERT: Z 54 HIS cc_start: 0.7837 (m90) cc_final: 0.7481 (m-70) REVERT: Z 75 ASN cc_start: 0.8015 (m-40) cc_final: 0.7490 (m-40) REVERT: Z 125 LEU cc_start: 0.7924 (tp) cc_final: 0.7361 (tp) REVERT: Z 138 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6994 (tm-30) REVERT: 0 19 LYS cc_start: 0.8698 (mmpt) cc_final: 0.8489 (mmtm) REVERT: 0 25 ARG cc_start: 0.8781 (mmt-90) cc_final: 0.8348 (mmt90) REVERT: 0 68 GLU cc_start: 0.7936 (tp30) cc_final: 0.7605 (tt0) REVERT: 1 53 VAL cc_start: 0.8119 (t) cc_final: 0.7870 (p) REVERT: 1 56 GLN cc_start: 0.8730 (mm110) cc_final: 0.8425 (mm-40) REVERT: 1 96 LYS cc_start: 0.8562 (ttmp) cc_final: 0.8339 (mttt) REVERT: 2 24 LEU cc_start: 0.9036 (tp) cc_final: 0.8741 (tp) REVERT: 2 27 GLU cc_start: 0.9445 (mt-10) cc_final: 0.9186 (tp30) REVERT: 2 46 GLN cc_start: 0.8909 (mt0) cc_final: 0.8665 (mp10) REVERT: 3 5 LYS cc_start: 0.8624 (ttpt) cc_final: 0.8407 (ttpp) REVERT: 3 6 VAL cc_start: 0.8702 (t) cc_final: 0.8435 (m) REVERT: 3 31 LEU cc_start: 0.8640 (mm) cc_final: 0.7943 (mm) REVERT: 3 36 VAL cc_start: 0.6689 (t) cc_final: 0.6439 (t) REVERT: 4 25 TYR cc_start: 0.8199 (m-10) cc_final: 0.7880 (m-80) REVERT: 4 59 PHE cc_start: 0.7933 (p90) cc_final: 0.7687 (p90) REVERT: 5 20 ARG cc_start: 0.8973 (mtt180) cc_final: 0.8769 (mtt-85) REVERT: 5 22 HIS cc_start: 0.7839 (m-70) cc_final: 0.7413 (m-70) REVERT: 6 15 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6886 (mt-10) REVERT: 6 33 LYS cc_start: 0.8606 (mmtt) cc_final: 0.8308 (mmmt) REVERT: 6 35 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8283 (mt-10) REVERT: 7 10 ARG cc_start: 0.8293 (ttt90) cc_final: 0.7864 (ttt-90) REVERT: 7 18 PHE cc_start: 0.9154 (t80) cc_final: 0.8409 (t80) REVERT: 8 25 MET cc_start: 0.7790 (mmm) cc_final: 0.7451 (mmm) REVERT: 9 22 ARG cc_start: 0.7868 (mtt90) cc_final: 0.7503 (mtm-85) REVERT: 9 24 TYR cc_start: 0.8933 (m-10) cc_final: 0.8689 (m-10) REVERT: 9 29 ASN cc_start: 0.8705 (t0) cc_final: 0.8443 (t0) REVERT: b 8 LYS cc_start: 0.7623 (pmmt) cc_final: 0.6990 (pttt) REVERT: b 25 ASN cc_start: 0.8520 (t0) cc_final: 0.8281 (t0) REVERT: b 110 GLN cc_start: 0.9270 (tt0) cc_final: 0.9023 (mt0) REVERT: b 113 HIS cc_start: 0.8356 (m-70) cc_final: 0.8069 (t-170) REVERT: b 133 LYS cc_start: 0.7699 (mmtt) cc_final: 0.7272 (mptt) REVERT: b 142 LEU cc_start: 0.8985 (tt) cc_final: 0.8560 (tp) REVERT: b 147 LYS cc_start: 0.9064 (tppp) cc_final: 0.8720 (tptm) REVERT: b 192 SER cc_start: 0.7724 (m) cc_final: 0.7191 (p) REVERT: b 199 TYR cc_start: 0.8410 (m-80) cc_final: 0.8119 (m-80) REVERT: b 214 ILE cc_start: 0.9405 (mm) cc_final: 0.9191 (mm) REVERT: c 28 GLN cc_start: 0.8792 (mt0) cc_final: 0.8471 (mm-40) REVERT: c 31 HIS cc_start: 0.8287 (m90) cc_final: 0.7924 (m90) REVERT: c 35 GLU cc_start: 0.7853 (pt0) cc_final: 0.7621 (pt0) REVERT: c 104 GLN cc_start: 0.8652 (tp40) cc_final: 0.8345 (tp40) REVERT: c 106 VAL cc_start: 0.8355 (t) cc_final: 0.8136 (m) REVERT: c 118 GLN cc_start: 0.9122 (mt0) cc_final: 0.8774 (mt0) REVERT: c 126 ARG cc_start: 0.8502 (mtt90) cc_final: 0.8286 (mpp80) REVERT: c 162 GLN cc_start: 0.7928 (tp40) cc_final: 0.7610 (tp40) REVERT: c 181 ASN cc_start: 0.8724 (t0) cc_final: 0.8516 (t0) REVERT: c 183 ASP cc_start: 0.8704 (t0) cc_final: 0.7982 (t0) REVERT: d 34 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8107 (mm-30) REVERT: d 60 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8787 (tp30) REVERT: d 80 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8165 (mm-30) REVERT: d 91 SER cc_start: 0.9294 (m) cc_final: 0.9013 (p) REVERT: d 103 ASN cc_start: 0.8961 (t0) cc_final: 0.8658 (t0) REVERT: d 148 VAL cc_start: 0.7895 (t) cc_final: 0.7612 (p) REVERT: d 160 GLN cc_start: 0.9257 (mt0) cc_final: 0.8759 (mt0) REVERT: d 177 ASP cc_start: 0.7445 (t0) cc_final: 0.7096 (t0) REVERT: d 181 MET cc_start: 0.7855 (mtt) cc_final: 0.7611 (mtm) REVERT: d 189 PRO cc_start: 0.8140 (Cg_exo) cc_final: 0.6744 (Cg_endo) REVERT: e 57 LYS cc_start: 0.9275 (ttmp) cc_final: 0.8928 (tttm) REVERT: e 61 TYR cc_start: 0.9286 (m-80) cc_final: 0.8904 (m-80) REVERT: e 64 ARG cc_start: 0.8289 (ttp-110) cc_final: 0.7954 (mtm-85) REVERT: e 82 VAL cc_start: 0.8609 (t) cc_final: 0.8336 (m) REVERT: e 111 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8155 (mt-10) REVERT: e 125 SER cc_start: 0.8468 (t) cc_final: 0.7928 (p) REVERT: e 147 ASP cc_start: 0.8282 (m-30) cc_final: 0.7826 (m-30) REVERT: e 151 LEU cc_start: 0.9037 (mt) cc_final: 0.8763 (tp) REVERT: f 18 GLN cc_start: 0.8811 (mt0) cc_final: 0.8382 (mt0) REVERT: f 21 LEU cc_start: 0.9006 (tp) cc_final: 0.8724 (tp) REVERT: f 28 ARG cc_start: 0.9258 (mtt180) cc_final: 0.8829 (ttt180) REVERT: f 57 GLN cc_start: 0.8594 (mt0) cc_final: 0.8391 (mt0) REVERT: f 60 PHE cc_start: 0.7878 (m-10) cc_final: 0.7513 (m-10) REVERT: f 70 ASP cc_start: 0.8977 (p0) cc_final: 0.8772 (p0) REVERT: g 43 PHE cc_start: 0.8771 (t80) cc_final: 0.8464 (t80) REVERT: g 53 LYS cc_start: 0.8718 (mtpp) cc_final: 0.8263 (mmtm) REVERT: g 63 LYS cc_start: 0.8897 (mttm) cc_final: 0.8461 (pttm) REVERT: g 102 ARG cc_start: 0.8821 (ttm110) cc_final: 0.8532 (ttp-110) REVERT: g 103 TRP cc_start: 0.8878 (m-10) cc_final: 0.8669 (m-10) REVERT: g 106 GLN cc_start: 0.8885 (mt0) cc_final: 0.8477 (mt0) REVERT: g 136 LYS cc_start: 0.9181 (mmtm) cc_final: 0.8920 (tttt) REVERT: g 138 LYS cc_start: 0.8166 (tmtt) cc_final: 0.7948 (tptp) REVERT: g 142 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7858 (mt-10) REVERT: g 144 MET cc_start: 0.7871 (tpt) cc_final: 0.7627 (tpt) REVERT: g 153 HIS cc_start: 0.8094 (p-80) cc_final: 0.7866 (p90) REVERT: g 155 ARG cc_start: 0.5824 (pmt-80) cc_final: 0.5573 (ptp-170) REVERT: h 79 VAL cc_start: 0.8513 (t) cc_final: 0.8137 (t) REVERT: h 87 SER cc_start: 0.8879 (t) cc_final: 0.8236 (m) REVERT: h 94 TYR cc_start: 0.8757 (m-80) cc_final: 0.8479 (m-80) REVERT: h 119 LEU cc_start: 0.8931 (mt) cc_final: 0.8698 (mp) REVERT: h 132 GLU cc_start: 0.7824 (tt0) cc_final: 0.7246 (tt0) REVERT: i 37 PHE cc_start: 0.8607 (m-10) cc_final: 0.8289 (m-80) REVERT: i 73 GLN cc_start: 0.7969 (mt0) cc_final: 0.7038 (mt0) REVERT: i 103 THR cc_start: 0.8225 (t) cc_final: 0.7854 (m) REVERT: j 13 HIS cc_start: 0.7517 (p-80) cc_final: 0.6856 (p90) REVERT: j 43 ARG cc_start: 0.7606 (mmm-85) cc_final: 0.7189 (ttp80) REVERT: k 54 ARG cc_start: 0.8223 (mtp85) cc_final: 0.8018 (mtt180) REVERT: k 66 LEU cc_start: 0.8679 (mt) cc_final: 0.8451 (mt) REVERT: k 93 GLN cc_start: 0.8707 (tp-100) cc_final: 0.7749 (tm-30) REVERT: k 111 ASP cc_start: 0.7596 (t0) cc_final: 0.7024 (m-30) REVERT: l 7 ILE cc_start: 0.8933 (mm) cc_final: 0.8715 (mm) REVERT: l 37 CYS cc_start: 0.8550 (m) cc_final: 0.8091 (m) REVERT: l 50 SER cc_start: 0.8548 (t) cc_final: 0.8324 (t) REVERT: l 57 LYS cc_start: 0.8534 (ttmt) cc_final: 0.8322 (ttmm) REVERT: l 91 LYS cc_start: 0.8469 (tttm) cc_final: 0.8258 (ttmm) REVERT: m 22 ILE cc_start: 0.9527 (mm) cc_final: 0.9243 (mp) REVERT: m 23 TYR cc_start: 0.8159 (t80) cc_final: 0.7889 (t80) REVERT: m 77 ASN cc_start: 0.8958 (m-40) cc_final: 0.8704 (m-40) REVERT: m 82 MET cc_start: 0.8354 (mtt) cc_final: 0.8039 (mtt) REVERT: m 93 ARG cc_start: 0.8086 (mtm180) cc_final: 0.7864 (mtm-85) REVERT: n 8 GLU cc_start: 0.8650 (tp30) cc_final: 0.8410 (tp30) REVERT: o 18 PHE cc_start: 0.7419 (p90) cc_final: 0.7217 (p90) REVERT: o 34 LEU cc_start: 0.9462 (tp) cc_final: 0.9075 (tt) REVERT: p 14 ASN cc_start: 0.9054 (t0) cc_final: 0.8759 (t0) REVERT: p 21 VAL cc_start: 0.8887 (p) cc_final: 0.8482 (t) REVERT: p 23 ASP cc_start: 0.8353 (t0) cc_final: 0.8117 (t0) REVERT: p 27 LYS cc_start: 0.8205 (ptpt) cc_final: 0.7740 (pttt) REVERT: p 38 TYR cc_start: 0.7899 (p90) cc_final: 0.7669 (p90) REVERT: p 39 TYR cc_start: 0.9171 (t80) cc_final: 0.8156 (t80) REVERT: q 13 ASP cc_start: 0.8874 (p0) cc_final: 0.8600 (p0) REVERT: q 46 ASP cc_start: 0.8056 (t0) cc_final: 0.7785 (t70) REVERT: q 49 GLU cc_start: 0.7758 (tp30) cc_final: 0.7390 (tp30) REVERT: q 55 ASP cc_start: 0.8716 (m-30) cc_final: 0.8345 (m-30) REVERT: q 66 SER cc_start: 0.8764 (p) cc_final: 0.8500 (t) REVERT: q 74 LEU cc_start: 0.8551 (tm) cc_final: 0.7455 (tm) REVERT: q 90 ILE cc_start: 0.9174 (mm) cc_final: 0.8916 (mm) REVERT: q 94 ASN cc_start: 0.8608 (m-40) cc_final: 0.8213 (m-40) REVERT: r 26 LEU cc_start: 0.5520 (mm) cc_final: 0.4879 (mm) REVERT: r 33 ASP cc_start: 0.8627 (t0) cc_final: 0.8410 (t0) REVERT: r 36 ASN cc_start: 0.8170 (t0) cc_final: 0.7129 (t0) REVERT: r 42 ARG cc_start: 0.8941 (mtt-85) cc_final: 0.8473 (mmm160) REVERT: r 51 LEU cc_start: 0.8593 (mt) cc_final: 0.8135 (mt) REVERT: r 62 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8366 (mt-10) REVERT: s 4 SER cc_start: 0.8886 (t) cc_final: 0.8656 (t) REVERT: s 5 LEU cc_start: 0.8706 (pp) cc_final: 0.8439 (mt) REVERT: s 6 LYS cc_start: 0.8494 (ttpt) cc_final: 0.8254 (ttpt) REVERT: s 30 LEU cc_start: 0.8762 (tp) cc_final: 0.8353 (mt) REVERT: s 35 SER cc_start: 0.9330 (m) cc_final: 0.8550 (t) REVERT: s 40 ILE cc_start: 0.8146 (mp) cc_final: 0.7543 (mp) REVERT: t 9 ASN cc_start: 0.7839 (t160) cc_final: 0.7570 (t0) REVERT: t 22 ARG cc_start: 0.8590 (mtp85) cc_final: 0.7939 (mtt90) REVERT: t 25 ARG cc_start: 0.6682 (mtm-85) cc_final: 0.6085 (mtt180) REVERT: t 64 ASP cc_start: 0.8531 (m-30) cc_final: 0.8090 (m-30) REVERT: t 75 ASN cc_start: 0.8792 (m-40) cc_final: 0.8342 (t0) REVERT: u 5 ASP cc_start: 0.8090 (t0) cc_final: 0.7835 (t0) REVERT: u 21 TYR cc_start: 0.7291 (m-80) cc_final: 0.6241 (m-80) REVERT: C 225 ASN cc_start: 0.8548 (t0) cc_final: 0.8293 (t0) outliers start: 2 outliers final: 1 residues processed: 2552 average time/residue: 1.4992 time to fit residues: 6356.5024 Evaluate side-chains 1815 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1814 time to evaluate : 6.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1047 random chunks: chunk 884 optimal weight: 20.0000 chunk 793 optimal weight: 9.9990 chunk 440 optimal weight: 3.9990 chunk 271 optimal weight: 10.0000 chunk 535 optimal weight: 9.9990 chunk 423 optimal weight: 9.9990 chunk 820 optimal weight: 5.9990 chunk 317 optimal weight: 20.0000 chunk 498 optimal weight: 9.9990 chunk 610 optimal weight: 3.9990 chunk 950 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 ASN E 137 HIS ** E 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 GLN G 26 GLN ** G 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 ASN G 123 ASN H 74 ASN H 143 GLN I 11 ASN I 104 GLN ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN O 89 ASN P 27 HIS ** Q 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 13 HIS R 71 GLN ** T 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 GLN ** U 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 82 GLN ** Z 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 65 GLN Z 75 ASN ** Z 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 56 GLN ** 2 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 23 HIS ** 6 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 43 GLN 9 20 HIS ** b 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 162 GLN c 170 GLN ** d 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 161 ASN ** e 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 86 GLN ** g 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 ASN g 153 HIS ** h 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 73 GLN i 124 GLN j 69 ASN k 22 HIS ** k 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 9 GLN ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 53 HIS o 62 GLN ** p 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 26 GLN s 14 HIS ** s 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 83 HIS t 9 ASN t 26 ASN ** t 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.360 161492 Z= 0.304 Angle : 0.654 29.215 241653 Z= 0.349 Chirality : 0.036 1.891 30609 Planarity : 0.006 0.126 13093 Dihedral : 25.462 179.596 81410 Min Nonbonded Distance : 1.628 Molprobity Statistics. All-atom Clashscore : 61.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.09 % Favored : 93.85 % Rotamer: Outliers : 5.82 % Allowed : 16.85 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.11), residues: 5916 helix: -0.23 (0.11), residues: 1940 sheet: -2.58 (0.14), residues: 1123 loop : -1.65 (0.12), residues: 2853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP f 62 HIS 0.009 0.001 HIS 1 66 PHE 0.029 0.002 PHE b 28 TYR 0.021 0.002 TYR Q 32 ARG 0.009 0.001 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2228 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 1947 time to evaluate : 6.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 4 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7907 (ptmm) REVERT: D 46 GLN cc_start: 0.8466 (mm110) cc_final: 0.8200 (mm110) REVERT: D 49 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8850 (mp) REVERT: D 54 ARG cc_start: 0.7638 (mtp85) cc_final: 0.7416 (mtm180) REVERT: D 84 TYR cc_start: 0.8876 (t80) cc_final: 0.7830 (t80) REVERT: D 95 LEU cc_start: 0.8424 (mp) cc_final: 0.8016 (mp) REVERT: D 126 GLN cc_start: 0.9018 (mm110) cc_final: 0.8662 (mm-40) REVERT: D 146 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7621 (mt-10) REVERT: D 147 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9075 (mt) REVERT: D 169 GLU cc_start: 0.7938 (tp30) cc_final: 0.7738 (tt0) REVERT: D 172 TYR cc_start: 0.8493 (m-10) cc_final: 0.7939 (m-80) REVERT: D 186 HIS cc_start: 0.8602 (t-90) cc_final: 0.7801 (t-90) REVERT: D 188 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8176 (mp0) REVERT: D 198 ASN cc_start: 0.7948 (t0) cc_final: 0.7614 (t0) REVERT: D 201 HIS cc_start: 0.9038 (t70) cc_final: 0.8646 (t-90) REVERT: D 226 MET cc_start: 0.8478 (mtm) cc_final: 0.7931 (mtm) REVERT: D 261 LYS cc_start: 0.7553 (tptt) cc_final: 0.7003 (tptt) REVERT: D 263 ARG cc_start: 0.8163 (mtm180) cc_final: 0.7550 (mtp180) REVERT: E 45 THR cc_start: 0.8119 (m) cc_final: 0.7771 (p) REVERT: E 100 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6991 (mp0) REVERT: E 118 LYS cc_start: 0.9147 (ttmm) cc_final: 0.8947 (tttt) REVERT: E 154 LYS cc_start: 0.7993 (tppt) cc_final: 0.7713 (tptp) REVERT: F 67 GLN cc_start: 0.8059 (tp40) cc_final: 0.7735 (tp40) REVERT: F 195 ASP cc_start: 0.8408 (t0) cc_final: 0.8173 (t0) REVERT: F 204 ASN cc_start: 0.9179 (m-40) cc_final: 0.8857 (m-40) REVERT: G 12 TYR cc_start: 0.8961 (m-10) cc_final: 0.8760 (m-10) REVERT: G 13 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8204 (pp20) REVERT: G 104 GLU cc_start: 0.8685 (tt0) cc_final: 0.8362 (tt0) REVERT: G 114 ILE cc_start: 0.7475 (mt) cc_final: 0.7253 (mt) REVERT: G 140 ILE cc_start: 0.8955 (mm) cc_final: 0.8651 (mp) REVERT: H 121 ILE cc_start: 0.9213 (mm) cc_final: 0.8893 (mm) REVERT: H 143 GLN cc_start: 0.8770 (tp40) cc_final: 0.7888 (tp-100) REVERT: H 147 ASN cc_start: 0.8667 (m-40) cc_final: 0.8247 (m-40) REVERT: I 52 ARG cc_start: 0.7452 (mtm-85) cc_final: 0.7118 (mtm180) REVERT: I 121 LYS cc_start: 0.4635 (mmmt) cc_final: 0.3786 (mmtm) REVERT: N 39 ARG cc_start: 0.8366 (mtp85) cc_final: 0.7761 (mtp180) REVERT: N 41 ASP cc_start: 0.8206 (p0) cc_final: 0.7666 (p0) REVERT: N 45 ASN cc_start: 0.9195 (p0) cc_final: 0.8644 (p0) REVERT: N 48 MET cc_start: 0.7727 (ppp) cc_final: 0.5851 (ptm) REVERT: N 71 ILE cc_start: 0.8856 (mp) cc_final: 0.8622 (mm) REVERT: N 74 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7466 (ttm-80) REVERT: N 85 ILE cc_start: 0.8932 (mm) cc_final: 0.8610 (mp) REVERT: N 117 PHE cc_start: 0.8760 (t80) cc_final: 0.8470 (t80) REVERT: O 1 MET cc_start: 0.8226 (mmt) cc_final: 0.7946 (mmm) REVERT: O 20 MET cc_start: 0.8673 (ttm) cc_final: 0.8153 (ttm) REVERT: O 91 LEU cc_start: 0.8930 (mt) cc_final: 0.8582 (mt) REVERT: O 107 ARG cc_start: 0.8378 (mtp85) cc_final: 0.8075 (mtp180) REVERT: O 108 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8401 (mt-10) REVERT: P 47 ASP cc_start: 0.8389 (t0) cc_final: 0.7546 (t0) REVERT: P 49 ARG cc_start: 0.8168 (mtm180) cc_final: 0.7647 (mtm-85) REVERT: Q 1 MET cc_start: 0.8286 (ptp) cc_final: 0.7944 (ptp) REVERT: Q 5 ARG cc_start: 0.8641 (mtm180) cc_final: 0.8355 (mtm110) REVERT: Q 9 TYR cc_start: 0.8662 (m-80) cc_final: 0.7958 (m-80) REVERT: Q 17 LEU cc_start: 0.9077 (mm) cc_final: 0.8612 (mm) REVERT: Q 25 ASP cc_start: 0.8674 (p0) cc_final: 0.8464 (p0) REVERT: Q 37 LEU cc_start: 0.8075 (mt) cc_final: 0.7646 (mt) REVERT: Q 77 LYS cc_start: 0.8826 (mtpp) cc_final: 0.8576 (mttp) REVERT: Q 85 LYS cc_start: 0.8428 (mttp) cc_final: 0.8096 (mmtm) REVERT: Q 111 GLU cc_start: 0.7731 (tp30) cc_final: 0.7390 (tp30) REVERT: Q 128 LYS cc_start: 0.8631 (mtmt) cc_final: 0.8070 (mttm) REVERT: R 30 THR cc_start: 0.9237 (OUTLIER) cc_final: 0.8775 (p) REVERT: R 31 HIS cc_start: 0.8502 (m90) cc_final: 0.7961 (m-70) REVERT: R 83 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8108 (mp) REVERT: R 99 LYS cc_start: 0.8532 (mtmm) cc_final: 0.8212 (mtmm) REVERT: S 83 LYS cc_start: 0.8726 (mtpp) cc_final: 0.8280 (mtpp) REVERT: S 92 TYR cc_start: 0.8721 (m-80) cc_final: 0.8452 (m-80) REVERT: S 93 LYS cc_start: 0.8724 (tmtm) cc_final: 0.8501 (ttmt) REVERT: T 31 SER cc_start: 0.8941 (m) cc_final: 0.8646 (p) REVERT: T 46 GLU cc_start: 0.7535 (tt0) cc_final: 0.7219 (tt0) REVERT: T 73 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7700 (mt-10) REVERT: T 90 GLN cc_start: 0.7990 (tp-100) cc_final: 0.7777 (tp40) REVERT: V 11 GLN cc_start: 0.8457 (mt0) cc_final: 0.7949 (mt0) REVERT: V 12 TYR cc_start: 0.8585 (m-80) cc_final: 0.8218 (m-80) REVERT: V 93 GLU cc_start: 0.7550 (tm-30) cc_final: 0.7312 (tm-30) REVERT: W 39 THR cc_start: 0.7623 (m) cc_final: 0.7368 (m) REVERT: W 52 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8223 (tp30) REVERT: X 15 GLU cc_start: 0.9063 (mp0) cc_final: 0.8860 (mp0) REVERT: X 37 THR cc_start: 0.8359 (m) cc_final: 0.8117 (p) REVERT: X 60 ARG cc_start: 0.8343 (mtp180) cc_final: 0.7134 (mtp85) REVERT: Y 23 ARG cc_start: 0.7413 (mmp80) cc_final: 0.7063 (mmm-85) REVERT: Y 43 ASN cc_start: 0.8046 (t160) cc_final: 0.7308 (t0) REVERT: Z 54 HIS cc_start: 0.8385 (m90) cc_final: 0.7613 (m170) REVERT: Z 75 ASN cc_start: 0.8733 (m110) cc_final: 0.8385 (m-40) REVERT: Z 78 LYS cc_start: 0.8212 (mtmt) cc_final: 0.7615 (mmtp) REVERT: Z 138 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6745 (tm-30) REVERT: 0 19 LYS cc_start: 0.8776 (mmpt) cc_final: 0.8461 (mmtm) REVERT: 0 38 VAL cc_start: 0.9252 (t) cc_final: 0.9041 (t) REVERT: 0 68 GLU cc_start: 0.8136 (tp30) cc_final: 0.7708 (tp30) REVERT: 1 50 ARG cc_start: 0.8630 (ttm-80) cc_final: 0.8305 (ttm-80) REVERT: 1 56 GLN cc_start: 0.9051 (mm-40) cc_final: 0.8731 (mm-40) REVERT: 2 9 GLN cc_start: 0.8775 (tp-100) cc_final: 0.8307 (tp-100) REVERT: 2 20 GLU cc_start: 0.9460 (mm-30) cc_final: 0.9138 (mp0) REVERT: 2 26 ARG cc_start: 0.8438 (ttm110) cc_final: 0.8053 (mtm110) REVERT: 2 27 GLU cc_start: 0.9442 (mt-10) cc_final: 0.9209 (tp30) REVERT: 2 46 GLN cc_start: 0.8802 (mt0) cc_final: 0.8587 (mp10) REVERT: 2 51 ARG cc_start: 0.8822 (ttm110) cc_final: 0.8489 (ttm110) REVERT: 3 4 LEU cc_start: 0.8786 (mp) cc_final: 0.8521 (mp) REVERT: 5 39 MET cc_start: 0.8663 (mmm) cc_final: 0.8264 (mmm) REVERT: 5 51 TYR cc_start: 0.8345 (m-10) cc_final: 0.8128 (m-10) REVERT: 6 18 ARG cc_start: 0.7456 (mpp80) cc_final: 0.6781 (mtt-85) REVERT: 6 20 ASN cc_start: 0.7937 (m-40) cc_final: 0.7548 (m110) REVERT: 6 33 LYS cc_start: 0.8531 (mmtt) cc_final: 0.7440 (mmtt) REVERT: 7 6 GLN cc_start: 0.8799 (mm110) cc_final: 0.8530 (mm110) REVERT: 7 14 LYS cc_start: 0.9169 (mtpp) cc_final: 0.8946 (ttmt) REVERT: 7 18 PHE cc_start: 0.8977 (t80) cc_final: 0.8261 (t80) REVERT: 8 46 ARG cc_start: 0.7693 (mtp-110) cc_final: 0.7265 (mtp85) REVERT: 9 22 ARG cc_start: 0.8004 (mtt90) cc_final: 0.7587 (mtm-85) REVERT: b 8 LYS cc_start: 0.7806 (pmmt) cc_final: 0.6945 (pttt) REVERT: b 25 ASN cc_start: 0.8381 (t0) cc_final: 0.8035 (t0) REVERT: b 140 HIS cc_start: 0.8760 (OUTLIER) cc_final: 0.8237 (t70) REVERT: b 170 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7950 (mm-30) REVERT: b 179 LYS cc_start: 0.9191 (mtpp) cc_final: 0.8830 (mtmt) REVERT: b 192 SER cc_start: 0.7504 (m) cc_final: 0.6984 (p) REVERT: b 211 ILE cc_start: 0.9428 (mt) cc_final: 0.9142 (pt) REVERT: b 220 ASP cc_start: 0.9310 (t70) cc_final: 0.9037 (m-30) REVERT: c 19 GLU cc_start: 0.8046 (mp0) cc_final: 0.7787 (mp0) REVERT: c 28 GLN cc_start: 0.8725 (mt0) cc_final: 0.8438 (mm-40) REVERT: c 89 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7863 (mm-30) REVERT: c 118 GLN cc_start: 0.8989 (mt0) cc_final: 0.8689 (mt0) REVERT: c 139 GLN cc_start: 0.9219 (tp40) cc_final: 0.8766 (tp40) REVERT: c 181 ASN cc_start: 0.8508 (t0) cc_final: 0.8286 (t0) REVERT: c 183 ASP cc_start: 0.8595 (t0) cc_final: 0.7962 (t0) REVERT: c 190 ARG cc_start: 0.7920 (ptp-170) cc_final: 0.7675 (ptp90) REVERT: d 50 ARG cc_start: 0.8555 (ttt180) cc_final: 0.7993 (tpp80) REVERT: d 80 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8366 (mt-10) REVERT: d 177 ASP cc_start: 0.7979 (t0) cc_final: 0.7552 (t0) REVERT: e 61 TYR cc_start: 0.9271 (m-80) cc_final: 0.8960 (m-80) REVERT: e 65 ASN cc_start: 0.8174 (t0) cc_final: 0.7859 (t0) REVERT: e 82 VAL cc_start: 0.9031 (t) cc_final: 0.8749 (m) REVERT: e 111 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8140 (mt-10) REVERT: f 62 TRP cc_start: 0.7482 (t60) cc_final: 0.6984 (t60) REVERT: g 22 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9175 (tt) REVERT: g 43 PHE cc_start: 0.8681 (t80) cc_final: 0.8479 (t80) REVERT: g 53 LYS cc_start: 0.8634 (mtpp) cc_final: 0.8371 (mmtm) REVERT: g 64 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8249 (tm-30) REVERT: g 74 GLU cc_start: 0.9482 (pt0) cc_final: 0.8960 (pm20) REVERT: g 90 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7660 (tm-30) REVERT: g 97 GLN cc_start: 0.8590 (mt0) cc_final: 0.8329 (tt0) REVERT: g 102 ARG cc_start: 0.8460 (ttm110) cc_final: 0.7876 (ttp-110) REVERT: g 106 GLN cc_start: 0.8974 (mt0) cc_final: 0.8419 (mt0) REVERT: g 136 LYS cc_start: 0.9282 (mmtm) cc_final: 0.8932 (tttt) REVERT: g 138 LYS cc_start: 0.8480 (tmtt) cc_final: 0.8185 (tttm) REVERT: g 155 ARG cc_start: 0.6312 (pmt-80) cc_final: 0.5534 (ptp90) REVERT: h 33 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7421 (mt-10) REVERT: h 87 SER cc_start: 0.8843 (t) cc_final: 0.8413 (m) REVERT: h 93 VAL cc_start: 0.8264 (t) cc_final: 0.7494 (t) REVERT: h 94 TYR cc_start: 0.8750 (m-80) cc_final: 0.8270 (m-80) REVERT: h 132 GLU cc_start: 0.8030 (tt0) cc_final: 0.7464 (tt0) REVERT: i 73 GLN cc_start: 0.8243 (mt0) cc_final: 0.7937 (mt0) REVERT: j 13 HIS cc_start: 0.7922 (p-80) cc_final: 0.7593 (p-80) REVERT: j 43 ARG cc_start: 0.7747 (mmm-85) cc_final: 0.7091 (ttp80) REVERT: j 95 GLU cc_start: 0.6147 (tm-30) cc_final: 0.5702 (tm-30) REVERT: k 31 THR cc_start: 0.9009 (m) cc_final: 0.8797 (t) REVERT: k 50 TYR cc_start: 0.7818 (m-10) cc_final: 0.7381 (m-80) REVERT: k 93 GLN cc_start: 0.8009 (tp-100) cc_final: 0.7667 (tp-100) REVERT: k 104 GLN cc_start: 0.8106 (tt0) cc_final: 0.7540 (tt0) REVERT: k 126 ARG cc_start: 0.7631 (mtm180) cc_final: 0.7333 (mtm180) REVERT: l 37 CYS cc_start: 0.8842 (m) cc_final: 0.8430 (m) REVERT: l 50 SER cc_start: 0.8581 (t) cc_final: 0.8362 (t) REVERT: m 12 ASN cc_start: 0.7673 (m-40) cc_final: 0.6762 (t0) REVERT: m 22 ILE cc_start: 0.9433 (mm) cc_final: 0.9094 (mp) REVERT: m 23 TYR cc_start: 0.8042 (t80) cc_final: 0.7624 (t80) REVERT: m 35 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8589 (pt0) REVERT: m 67 GLU cc_start: 0.6871 (mm-30) cc_final: 0.6516 (mm-30) REVERT: m 70 LEU cc_start: 0.8858 (tp) cc_final: 0.8207 (tp) REVERT: m 82 MET cc_start: 0.8172 (mtt) cc_final: 0.7621 (mtp) REVERT: m 93 ARG cc_start: 0.7986 (mtm180) cc_final: 0.7745 (ptp90) REVERT: n 8 GLU cc_start: 0.8439 (tp30) cc_final: 0.8179 (tp30) REVERT: o 13 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8475 (pp30) REVERT: o 34 LEU cc_start: 0.9086 (tp) cc_final: 0.8858 (tt) REVERT: o 35 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8212 (mtm-85) REVERT: o 88 ARG cc_start: 0.8553 (ttp80) cc_final: 0.8160 (tpt90) REVERT: p 6 LEU cc_start: 0.8270 (mp) cc_final: 0.8049 (mt) REVERT: p 14 ASN cc_start: 0.9330 (t0) cc_final: 0.8849 (t0) REVERT: p 39 TYR cc_start: 0.8828 (t80) cc_final: 0.8196 (t80) REVERT: q 66 SER cc_start: 0.8769 (p) cc_final: 0.8548 (p) REVERT: r 33 ASP cc_start: 0.8725 (t0) cc_final: 0.8199 (p0) REVERT: r 51 LEU cc_start: 0.8589 (mt) cc_final: 0.8203 (mt) REVERT: r 68 LYS cc_start: 0.8827 (ttmm) cc_final: 0.8581 (tppt) REVERT: s 5 LEU cc_start: 0.8669 (pp) cc_final: 0.8105 (mt) REVERT: s 12 ASP cc_start: 0.8064 (m-30) cc_final: 0.7689 (m-30) REVERT: s 30 LEU cc_start: 0.8788 (tp) cc_final: 0.8561 (mt) REVERT: s 35 SER cc_start: 0.9333 (m) cc_final: 0.8369 (t) REVERT: u 20 LYS cc_start: 0.8167 (tttm) cc_final: 0.7952 (ttpp) REVERT: C 225 ASN cc_start: 0.8516 (t0) cc_final: 0.8302 (t0) outliers start: 281 outliers final: 186 residues processed: 2055 average time/residue: 1.3458 time to fit residues: 4697.9753 Evaluate side-chains 1931 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1735 time to evaluate : 6.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 4 LYS Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 43 ASN Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 74 ARG Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 28 SER Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 77 ILE Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 54 MET Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain R residue 10 LEU Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 59 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 69 ASP Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain S residue 47 THR Chi-restraints excluded: chain S residue 112 PHE Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 38 ASN Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 62 THR Chi-restraints excluded: chain T residue 80 SER Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain T residue 102 ILE Chi-restraints excluded: chain T residue 104 ASN Chi-restraints excluded: chain T residue 114 LEU Chi-restraints excluded: chain U residue 29 SER Chi-restraints excluded: chain U residue 38 THR Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 53 SER Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 14 SER Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 56 THR Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 165 VAL Chi-restraints excluded: chain 0 residue 10 THR Chi-restraints excluded: chain 0 residue 63 VAL Chi-restraints excluded: chain 0 residue 66 VAL Chi-restraints excluded: chain 0 residue 75 LEU Chi-restraints excluded: chain 1 residue 74 VAL Chi-restraints excluded: chain 1 residue 97 LEU Chi-restraints excluded: chain 2 residue 34 GLU Chi-restraints excluded: chain 2 residue 63 VAL Chi-restraints excluded: chain 4 residue 14 ILE Chi-restraints excluded: chain 5 residue 6 VAL Chi-restraints excluded: chain 5 residue 26 THR Chi-restraints excluded: chain 5 residue 44 THR Chi-restraints excluded: chain 6 residue 7 ILE Chi-restraints excluded: chain 6 residue 14 THR Chi-restraints excluded: chain 6 residue 23 THR Chi-restraints excluded: chain 6 residue 36 LEU Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 37 SER Chi-restraints excluded: chain 9 residue 7 VAL Chi-restraints excluded: chain 9 residue 17 ILE Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain b residue 107 THR Chi-restraints excluded: chain b residue 119 GLU Chi-restraints excluded: chain b residue 140 HIS Chi-restraints excluded: chain b residue 150 SER Chi-restraints excluded: chain b residue 189 ASP Chi-restraints excluded: chain b residue 198 ASP Chi-restraints excluded: chain b residue 210 SER Chi-restraints excluded: chain b residue 222 ILE Chi-restraints excluded: chain c residue 3 ASN Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 99 SER Chi-restraints excluded: chain d residue 127 THR Chi-restraints excluded: chain d residue 137 SER Chi-restraints excluded: chain d residue 155 LEU Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain e residue 144 THR Chi-restraints excluded: chain f residue 8 ILE Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 LEU Chi-restraints excluded: chain f residue 19 LEU Chi-restraints excluded: chain f residue 61 LEU Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 85 VAL Chi-restraints excluded: chain f residue 90 VAL Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain h residue 6 ILE Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 45 ILE Chi-restraints excluded: chain h residue 46 LYS Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 83 ILE Chi-restraints excluded: chain h residue 120 THR Chi-restraints excluded: chain i residue 7 THR Chi-restraints excluded: chain i residue 14 VAL Chi-restraints excluded: chain i residue 26 VAL Chi-restraints excluded: chain i residue 41 VAL Chi-restraints excluded: chain i residue 86 VAL Chi-restraints excluded: chain i residue 102 LEU Chi-restraints excluded: chain i residue 127 LYS Chi-restraints excluded: chain j residue 38 ILE Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain j residue 96 ILE Chi-restraints excluded: chain k residue 28 THR Chi-restraints excluded: chain k residue 41 THR Chi-restraints excluded: chain k residue 57 THR Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain l residue 44 THR Chi-restraints excluded: chain l residue 89 ARG Chi-restraints excluded: chain l residue 90 VAL Chi-restraints excluded: chain m residue 8 GLU Chi-restraints excluded: chain m residue 74 VAL Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain o residue 35 ARG Chi-restraints excluded: chain o residue 48 LYS Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain p residue 11 SER Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain p residue 79 VAL Chi-restraints excluded: chain q residue 36 ILE Chi-restraints excluded: chain q residue 62 SER Chi-restraints excluded: chain r residue 78 LEU Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain t residue 13 LEU Chi-restraints excluded: chain t residue 20 LEU Chi-restraints excluded: chain u residue 13 ILE Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 123 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1047 random chunks: chunk 528 optimal weight: 1.9990 chunk 295 optimal weight: 10.0000 chunk 791 optimal weight: 2.9990 chunk 647 optimal weight: 20.0000 chunk 262 optimal weight: 10.0000 chunk 952 optimal weight: 20.0000 chunk 1028 optimal weight: 8.9990 chunk 848 optimal weight: 10.0000 chunk 944 optimal weight: 2.9990 chunk 324 optimal weight: 0.0870 chunk 764 optimal weight: 20.0000 overall best weight: 3.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 ASN F 133 ASN ** G 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 ASN I 11 ASN ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 89 ASN P 38 GLN ** Q 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 ASN R 23 ASN ** R 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 65 GLN ** 0 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 56 GLN ** 2 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 43 GLN 9 20 HIS b 40 HIS ** b 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 113 HIS ** b 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 110 ASN c 170 GLN ** d 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 141 GLN ** f 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 ASN ** g 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 15 ASN h 78 GLN i 58 HIS k 26 ASN ** k 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 77 ASN ** n 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 ASN ** p 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 26 GLN ** s 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 16 HIS ** t 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.371 161492 Z= 0.234 Angle : 0.562 29.271 241653 Z= 0.306 Chirality : 0.034 1.912 30609 Planarity : 0.005 0.126 13093 Dihedral : 25.179 177.790 81410 Min Nonbonded Distance : 1.651 Molprobity Statistics. All-atom Clashscore : 57.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.94 % Favored : 95.01 % Rotamer: Outliers : 5.09 % Allowed : 21.51 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.11), residues: 5916 helix: 0.63 (0.12), residues: 1948 sheet: -2.17 (0.14), residues: 1102 loop : -1.26 (0.12), residues: 2866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP g 103 HIS 0.007 0.001 HIS b 113 PHE 0.025 0.002 PHE d 75 TYR 0.017 0.001 TYR X 26 ARG 0.008 0.000 ARG 7 47 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2095 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 1849 time to evaluate : 6.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 23 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8349 (mm-30) REVERT: D 28 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7237 (pm20) REVERT: D 46 GLN cc_start: 0.8453 (mm110) cc_final: 0.8173 (mm110) REVERT: D 53 PHE cc_start: 0.9094 (m-10) cc_final: 0.8891 (m-10) REVERT: D 54 ARG cc_start: 0.7776 (mtp85) cc_final: 0.7544 (mtm180) REVERT: D 66 ASP cc_start: 0.8438 (t0) cc_final: 0.7924 (m-30) REVERT: D 84 TYR cc_start: 0.8763 (t80) cc_final: 0.7640 (t80) REVERT: D 146 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7595 (mt-10) REVERT: D 172 TYR cc_start: 0.8295 (m-10) cc_final: 0.7656 (m-80) REVERT: D 175 LEU cc_start: 0.8404 (mt) cc_final: 0.8196 (mp) REVERT: D 186 HIS cc_start: 0.8665 (t-90) cc_final: 0.8163 (t70) REVERT: D 188 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8155 (mp0) REVERT: D 198 ASN cc_start: 0.8091 (t0) cc_final: 0.7726 (t0) REVERT: D 201 HIS cc_start: 0.8949 (t70) cc_final: 0.8556 (t-90) REVERT: D 226 MET cc_start: 0.8573 (mtm) cc_final: 0.7971 (mtm) REVERT: E 45 THR cc_start: 0.8182 (m) cc_final: 0.7765 (p) REVERT: E 83 ASP cc_start: 0.7871 (m-30) cc_final: 0.7521 (m-30) REVERT: E 154 LYS cc_start: 0.8052 (tppt) cc_final: 0.7705 (tptp) REVERT: F 67 GLN cc_start: 0.8033 (tp40) cc_final: 0.7800 (tp40) REVERT: F 195 ASP cc_start: 0.8420 (t0) cc_final: 0.8129 (t0) REVERT: F 203 GLN cc_start: 0.9115 (mm-40) cc_final: 0.8882 (mm-40) REVERT: F 204 ASN cc_start: 0.9175 (m-40) cc_final: 0.8889 (m-40) REVERT: G 13 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8167 (pp20) REVERT: G 104 GLU cc_start: 0.8740 (tt0) cc_final: 0.8402 (tt0) REVERT: H 143 GLN cc_start: 0.8520 (tp40) cc_final: 0.7888 (tp-100) REVERT: H 147 ASN cc_start: 0.8554 (m-40) cc_final: 0.8291 (m-40) REVERT: I 121 LYS cc_start: 0.4923 (mmmt) cc_final: 0.4313 (mptt) REVERT: I 122 GLU cc_start: 0.4841 (mm-30) cc_final: 0.4525 (mm-30) REVERT: N 39 ARG cc_start: 0.8334 (mtp85) cc_final: 0.8067 (mtp180) REVERT: N 41 ASP cc_start: 0.8357 (p0) cc_final: 0.8023 (p0) REVERT: N 45 ASN cc_start: 0.9118 (p0) cc_final: 0.8445 (p0) REVERT: N 48 MET cc_start: 0.7717 (ppp) cc_final: 0.6848 (ptp) REVERT: N 71 ILE cc_start: 0.8790 (mp) cc_final: 0.8546 (mm) REVERT: N 85 ILE cc_start: 0.9020 (mm) cc_final: 0.8818 (mp) REVERT: N 117 PHE cc_start: 0.8819 (t80) cc_final: 0.8581 (t80) REVERT: O 9 GLU cc_start: 0.7067 (tm-30) cc_final: 0.6617 (tm-30) REVERT: O 20 MET cc_start: 0.8614 (ttm) cc_final: 0.8106 (ttm) REVERT: O 44 LYS cc_start: 0.8583 (mmtt) cc_final: 0.8183 (mmtt) REVERT: O 59 LYS cc_start: 0.8231 (mtpp) cc_final: 0.7891 (mtmm) REVERT: O 66 LYS cc_start: 0.8628 (tttp) cc_final: 0.7847 (ttmm) REVERT: O 90 GLN cc_start: 0.9092 (mp10) cc_final: 0.8829 (mp10) REVERT: O 91 LEU cc_start: 0.8851 (mt) cc_final: 0.8650 (mt) REVERT: O 94 ARG cc_start: 0.9039 (mtp85) cc_final: 0.8707 (ttm110) REVERT: O 107 ARG cc_start: 0.8473 (mtp85) cc_final: 0.8075 (mtp180) REVERT: O 108 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8398 (mt-10) REVERT: P 9 ASN cc_start: 0.7857 (m-40) cc_final: 0.7608 (m-40) REVERT: P 47 ASP cc_start: 0.8394 (t0) cc_final: 0.7468 (t0) REVERT: P 49 ARG cc_start: 0.8144 (mtm180) cc_final: 0.7602 (mtm-85) REVERT: Q 1 MET cc_start: 0.8307 (ptp) cc_final: 0.7938 (ptp) REVERT: Q 9 TYR cc_start: 0.8725 (m-80) cc_final: 0.8011 (m-80) REVERT: Q 17 LEU cc_start: 0.9152 (mm) cc_final: 0.8697 (mm) REVERT: Q 25 ASP cc_start: 0.8522 (p0) cc_final: 0.8308 (p0) REVERT: Q 37 LEU cc_start: 0.8117 (mt) cc_final: 0.7673 (mt) REVERT: Q 77 LYS cc_start: 0.8774 (mtpp) cc_final: 0.8525 (mttp) REVERT: Q 85 LYS cc_start: 0.8414 (mttp) cc_final: 0.8121 (mmtm) REVERT: Q 128 LYS cc_start: 0.8791 (mtmt) cc_final: 0.8350 (mtmt) REVERT: R 8 ARG cc_start: 0.8872 (mpt-90) cc_final: 0.8275 (ptp90) REVERT: R 9 LYS cc_start: 0.8519 (mttp) cc_final: 0.7506 (mttp) REVERT: R 30 THR cc_start: 0.9307 (OUTLIER) cc_final: 0.8868 (p) REVERT: R 31 HIS cc_start: 0.8308 (m90) cc_final: 0.7685 (m-70) REVERT: R 43 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7145 (mm-30) REVERT: R 83 ILE cc_start: 0.8473 (mm) cc_final: 0.8164 (mp) REVERT: S 32 LEU cc_start: 0.8891 (mt) cc_final: 0.8442 (mp) REVERT: S 83 LYS cc_start: 0.8970 (mtpp) cc_final: 0.8339 (mtpp) REVERT: S 111 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.8223 (mp0) REVERT: T 46 GLU cc_start: 0.7667 (tt0) cc_final: 0.7351 (tt0) REVERT: T 73 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7683 (mt-10) REVERT: T 90 GLN cc_start: 0.7895 (tp-100) cc_final: 0.7653 (tp40) REVERT: U 91 ASP cc_start: 0.8849 (p0) cc_final: 0.8358 (p0) REVERT: V 11 GLN cc_start: 0.8506 (mt0) cc_final: 0.8027 (mt0) REVERT: V 12 TYR cc_start: 0.8643 (m-80) cc_final: 0.8347 (m-80) REVERT: V 19 LYS cc_start: 0.8948 (ptpp) cc_final: 0.8570 (mttm) REVERT: V 71 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9102 (tp) REVERT: V 80 GLN cc_start: 0.8415 (mm-40) cc_final: 0.8058 (mm110) REVERT: V 91 TYR cc_start: 0.8993 (p90) cc_final: 0.8371 (p90) REVERT: W 52 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8325 (tp30) REVERT: X 9 LEU cc_start: 0.8553 (mt) cc_final: 0.8185 (mt) REVERT: X 15 GLU cc_start: 0.9070 (mp0) cc_final: 0.8819 (mp0) REVERT: Y 11 ASP cc_start: 0.7525 (m-30) cc_final: 0.7072 (m-30) REVERT: Y 43 ASN cc_start: 0.8014 (t160) cc_final: 0.7268 (t0) REVERT: Z 6 LYS cc_start: 0.9289 (mtpp) cc_final: 0.9058 (ttmt) REVERT: Z 8 TYR cc_start: 0.8518 (m-10) cc_final: 0.8244 (m-10) REVERT: Z 54 HIS cc_start: 0.8360 (m90) cc_final: 0.7818 (m90) REVERT: Z 65 GLN cc_start: 0.8228 (tp-100) cc_final: 0.7844 (tp-100) REVERT: Z 138 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6655 (tm-30) REVERT: 0 19 LYS cc_start: 0.8746 (mmpt) cc_final: 0.8343 (mmtm) REVERT: 0 38 VAL cc_start: 0.9335 (t) cc_final: 0.9111 (t) REVERT: 1 50 ARG cc_start: 0.8608 (ttm-80) cc_final: 0.8235 (ttm-80) REVERT: 1 56 GLN cc_start: 0.9013 (mm110) cc_final: 0.8705 (mm-40) REVERT: 1 61 ARG cc_start: 0.8037 (mtm180) cc_final: 0.7749 (mtm180) REVERT: 1 96 LYS cc_start: 0.8847 (ttmm) cc_final: 0.8630 (mttt) REVERT: 2 4 SER cc_start: 0.9390 (p) cc_final: 0.9186 (t) REVERT: 2 20 GLU cc_start: 0.9397 (mm-30) cc_final: 0.9108 (mp0) REVERT: 2 27 GLU cc_start: 0.9444 (mt-10) cc_final: 0.9124 (tp30) REVERT: 2 51 ARG cc_start: 0.8811 (ttm110) cc_final: 0.8467 (ttm110) REVERT: 3 4 LEU cc_start: 0.8766 (mp) cc_final: 0.8527 (mp) REVERT: 3 5 LYS cc_start: 0.8860 (ttpp) cc_final: 0.8643 (ttpp) REVERT: 3 35 ARG cc_start: 0.8341 (mmm-85) cc_final: 0.8139 (mmm-85) REVERT: 4 49 PHE cc_start: 0.7702 (OUTLIER) cc_final: 0.7402 (m-80) REVERT: 6 33 LYS cc_start: 0.8104 (mmtt) cc_final: 0.7717 (mmtt) REVERT: 7 6 GLN cc_start: 0.8685 (mm110) cc_final: 0.8395 (mm110) REVERT: 8 21 LYS cc_start: 0.8166 (mttt) cc_final: 0.7624 (mtmt) REVERT: 8 32 LEU cc_start: 0.9445 (mp) cc_final: 0.9107 (mp) REVERT: 9 22 ARG cc_start: 0.7986 (mtt90) cc_final: 0.7725 (mtt90) REVERT: b 8 LYS cc_start: 0.7856 (pmmt) cc_final: 0.7150 (ptmt) REVERT: b 24 TRP cc_start: 0.8150 (p-90) cc_final: 0.7071 (p-90) REVERT: b 25 ASN cc_start: 0.8368 (t0) cc_final: 0.7604 (t0) REVERT: b 146 GLN cc_start: 0.8885 (mt0) cc_final: 0.8653 (mt0) REVERT: b 179 LYS cc_start: 0.9225 (mtpp) cc_final: 0.8819 (mtmt) REVERT: b 211 ILE cc_start: 0.9397 (mt) cc_final: 0.9027 (pt) REVERT: b 220 ASP cc_start: 0.9289 (t70) cc_final: 0.9000 (m-30) REVERT: c 28 GLN cc_start: 0.8730 (mt0) cc_final: 0.8471 (mm-40) REVERT: c 118 GLN cc_start: 0.9062 (mt0) cc_final: 0.8758 (mt0) REVERT: c 135 LYS cc_start: 0.9245 (mtpt) cc_final: 0.8825 (mptt) REVERT: c 139 GLN cc_start: 0.9043 (tp40) cc_final: 0.8570 (tp40) REVERT: c 181 ASN cc_start: 0.8351 (t0) cc_final: 0.8110 (t0) REVERT: c 183 ASP cc_start: 0.8629 (t0) cc_final: 0.7983 (t0) REVERT: c 193 TYR cc_start: 0.8489 (p90) cc_final: 0.8005 (p90) REVERT: d 33 MET cc_start: 0.8682 (tpt) cc_final: 0.8417 (tpt) REVERT: d 50 ARG cc_start: 0.8487 (ttt180) cc_final: 0.8208 (tpp80) REVERT: d 165 MET cc_start: 0.8017 (tpp) cc_final: 0.7753 (tpp) REVERT: d 177 ASP cc_start: 0.7986 (t0) cc_final: 0.7609 (t0) REVERT: d 205 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6596 (mt-10) REVERT: e 45 PHE cc_start: 0.8633 (t80) cc_final: 0.8341 (t80) REVERT: e 47 LYS cc_start: 0.9205 (ptpp) cc_final: 0.8697 (ptpp) REVERT: e 61 TYR cc_start: 0.9327 (m-80) cc_final: 0.8920 (m-80) REVERT: e 65 ASN cc_start: 0.8109 (t0) cc_final: 0.7835 (t0) REVERT: e 82 VAL cc_start: 0.9084 (t) cc_final: 0.8822 (m) REVERT: e 111 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8046 (mt-10) REVERT: f 62 TRP cc_start: 0.7428 (t60) cc_final: 0.7153 (t60) REVERT: g 53 LYS cc_start: 0.8590 (mtpp) cc_final: 0.8277 (mmtm) REVERT: g 64 GLN cc_start: 0.8397 (tm-30) cc_final: 0.8053 (tm-30) REVERT: g 73 MET cc_start: 0.9001 (mmt) cc_final: 0.8787 (mmm) REVERT: g 74 GLU cc_start: 0.9489 (pt0) cc_final: 0.8893 (pm20) REVERT: g 102 ARG cc_start: 0.8521 (ttm110) cc_final: 0.8082 (ttp-110) REVERT: g 106 GLN cc_start: 0.8965 (mt0) cc_final: 0.8531 (mt0) REVERT: g 136 LYS cc_start: 0.9235 (mmtm) cc_final: 0.8828 (tttt) REVERT: g 144 MET cc_start: 0.7144 (mmm) cc_final: 0.6668 (tpt) REVERT: g 155 ARG cc_start: 0.6461 (pmt-80) cc_final: 0.5700 (ptp90) REVERT: h 49 GLU cc_start: 0.8261 (pt0) cc_final: 0.7635 (pt0) REVERT: h 78 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7724 (mm110) REVERT: h 93 VAL cc_start: 0.8260 (t) cc_final: 0.7803 (t) REVERT: h 99 GLU cc_start: 0.8698 (tp30) cc_final: 0.8492 (tp30) REVERT: i 78 LYS cc_start: 0.8989 (tttt) cc_final: 0.8655 (tttp) REVERT: i 114 TYR cc_start: 0.8588 (p90) cc_final: 0.8380 (p90) REVERT: j 13 HIS cc_start: 0.8007 (p-80) cc_final: 0.7646 (p-80) REVERT: j 43 ARG cc_start: 0.7821 (mmm-85) cc_final: 0.7187 (ttp80) REVERT: j 95 GLU cc_start: 0.6328 (tm-30) cc_final: 0.5917 (tm-30) REVERT: k 43 SER cc_start: 0.8970 (t) cc_final: 0.8759 (t) REVERT: k 78 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8219 (tm-30) REVERT: k 104 GLN cc_start: 0.8043 (tt0) cc_final: 0.7581 (tt0) REVERT: l 37 CYS cc_start: 0.9106 (m) cc_final: 0.8599 (m) REVERT: l 50 SER cc_start: 0.8176 (t) cc_final: 0.7930 (t) REVERT: m 12 ASN cc_start: 0.7676 (m-40) cc_final: 0.6763 (t0) REVERT: m 22 ILE cc_start: 0.9352 (mm) cc_final: 0.9139 (mp) REVERT: m 23 TYR cc_start: 0.8096 (t80) cc_final: 0.7809 (t80) REVERT: m 66 LEU cc_start: 0.7451 (mt) cc_final: 0.7060 (mt) REVERT: m 70 LEU cc_start: 0.8711 (tp) cc_final: 0.8215 (tp) REVERT: n 8 GLU cc_start: 0.8485 (tp30) cc_final: 0.8100 (tp30) REVERT: o 13 GLN cc_start: 0.8896 (tm-30) cc_final: 0.8645 (pp30) REVERT: o 48 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8625 (mmmm) REVERT: o 83 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8509 (tm-30) REVERT: p 14 ASN cc_start: 0.9411 (t0) cc_final: 0.8919 (t0) REVERT: p 22 THR cc_start: 0.8747 (t) cc_final: 0.8547 (t) REVERT: p 27 LYS cc_start: 0.7806 (ptmt) cc_final: 0.7447 (pttt) REVERT: p 34 GLU cc_start: 0.8014 (mp0) cc_final: 0.7737 (mp0) REVERT: p 39 TYR cc_start: 0.8877 (t80) cc_final: 0.8249 (t80) REVERT: q 46 ASP cc_start: 0.8421 (t70) cc_final: 0.7646 (t0) REVERT: q 66 SER cc_start: 0.8639 (p) cc_final: 0.8379 (t) REVERT: q 95 TYR cc_start: 0.7916 (m-10) cc_final: 0.7694 (m-10) REVERT: r 33 ASP cc_start: 0.8758 (t0) cc_final: 0.8317 (t0) REVERT: r 51 LEU cc_start: 0.8700 (mt) cc_final: 0.8354 (mt) REVERT: s 5 LEU cc_start: 0.8746 (pp) cc_final: 0.8191 (mt) REVERT: s 12 ASP cc_start: 0.8309 (m-30) cc_final: 0.7666 (m-30) REVERT: s 35 SER cc_start: 0.9316 (m) cc_final: 0.8193 (t) REVERT: s 71 LEU cc_start: 0.8695 (mp) cc_final: 0.8452 (mp) REVERT: u 20 LYS cc_start: 0.8254 (tttm) cc_final: 0.7949 (ttpp) outliers start: 246 outliers final: 183 residues processed: 1940 average time/residue: 1.4170 time to fit residues: 4733.1048 Evaluate side-chains 1918 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1730 time to evaluate : 6.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 108 ASN Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain N residue 22 THR Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 7 TYR Chi-restraints excluded: chain O residue 28 SER Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain P residue 5 ASP Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 59 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 78 LYS Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain S residue 75 GLU Chi-restraints excluded: chain S residue 111 GLU Chi-restraints excluded: chain S residue 112 PHE Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 80 SER Chi-restraints excluded: chain T residue 102 ILE Chi-restraints excluded: chain T residue 104 ASN Chi-restraints excluded: chain T residue 115 ARG Chi-restraints excluded: chain U residue 18 LEU Chi-restraints excluded: chain U residue 29 SER Chi-restraints excluded: chain U residue 38 THR Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain V residue 71 LEU Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 14 SER Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Z residue 137 ILE Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain 0 residue 10 THR Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 80 LEU Chi-restraints excluded: chain 1 residue 86 SER Chi-restraints excluded: chain 1 residue 97 LEU Chi-restraints excluded: chain 2 residue 63 VAL Chi-restraints excluded: chain 2 residue 66 GLU Chi-restraints excluded: chain 3 residue 46 ASN Chi-restraints excluded: chain 4 residue 10 VAL Chi-restraints excluded: chain 4 residue 14 ILE Chi-restraints excluded: chain 4 residue 49 PHE Chi-restraints excluded: chain 5 residue 6 VAL Chi-restraints excluded: chain 5 residue 57 VAL Chi-restraints excluded: chain 6 residue 5 VAL Chi-restraints excluded: chain 6 residue 7 ILE Chi-restraints excluded: chain 6 residue 10 LEU Chi-restraints excluded: chain 6 residue 14 THR Chi-restraints excluded: chain 6 residue 23 THR Chi-restraints excluded: chain 6 residue 36 LEU Chi-restraints excluded: chain 7 residue 43 THR Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain b residue 107 THR Chi-restraints excluded: chain b residue 119 GLU Chi-restraints excluded: chain b residue 150 SER Chi-restraints excluded: chain b residue 187 LEU Chi-restraints excluded: chain b residue 189 ASP Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 198 ASP Chi-restraints excluded: chain b residue 210 SER Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 99 SER Chi-restraints excluded: chain d residue 137 SER Chi-restraints excluded: chain d residue 158 ILE Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 53 LEU Chi-restraints excluded: chain e residue 98 THR Chi-restraints excluded: chain e residue 116 THR Chi-restraints excluded: chain f residue 10 LEU Chi-restraints excluded: chain f residue 19 LEU Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain f residue 85 VAL Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 98 SER Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain h residue 6 ILE Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 35 ILE Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 45 ILE Chi-restraints excluded: chain h residue 46 LYS Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 83 ILE Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain i residue 7 THR Chi-restraints excluded: chain i residue 14 VAL Chi-restraints excluded: chain i residue 47 LEU Chi-restraints excluded: chain i residue 102 LEU Chi-restraints excluded: chain j residue 38 ILE Chi-restraints excluded: chain j residue 48 THR Chi-restraints excluded: chain j residue 49 VAL Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain j residue 89 ASP Chi-restraints excluded: chain j residue 96 ILE Chi-restraints excluded: chain k residue 18 ARG Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 119 CYS Chi-restraints excluded: chain l residue 6 THR Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 62 SER Chi-restraints excluded: chain l residue 66 VAL Chi-restraints excluded: chain l residue 77 LEU Chi-restraints excluded: chain l residue 100 ILE Chi-restraints excluded: chain m residue 16 ASP Chi-restraints excluded: chain m residue 74 VAL Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain o residue 48 LYS Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain o residue 87 ILE Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 33 ILE Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain p residue 53 VAL Chi-restraints excluded: chain p residue 67 THR Chi-restraints excluded: chain q residue 36 ILE Chi-restraints excluded: chain q residue 53 LEU Chi-restraints excluded: chain q residue 60 ILE Chi-restraints excluded: chain q residue 62 SER Chi-restraints excluded: chain q residue 89 LEU Chi-restraints excluded: chain q residue 94 ASN Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain r residue 39 VAL Chi-restraints excluded: chain r residue 72 ARG Chi-restraints excluded: chain r residue 76 LEU Chi-restraints excluded: chain s residue 11 VAL Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 41 VAL Chi-restraints excluded: chain t residue 20 LEU Chi-restraints excluded: chain t residue 63 ILE Chi-restraints excluded: chain t residue 70 SER Chi-restraints excluded: chain t residue 82 SER Chi-restraints excluded: chain u residue 13 ILE Chi-restraints excluded: chain u residue 17 THR Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 224 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1047 random chunks: chunk 941 optimal weight: 30.0000 chunk 716 optimal weight: 10.0000 chunk 494 optimal weight: 0.1980 chunk 105 optimal weight: 20.0000 chunk 454 optimal weight: 10.0000 chunk 639 optimal weight: 10.0000 chunk 955 optimal weight: 0.9980 chunk 1012 optimal weight: 30.0000 chunk 499 optimal weight: 6.9990 chunk 905 optimal weight: 20.0000 chunk 272 optimal weight: 20.0000 overall best weight: 5.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 ASN ** E 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 79 HIS ** U 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 75 ASN ** 0 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 20 HIS ** b 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 130 ASN f 57 GLN ** f 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 ASN ** g 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 58 HIS ** i 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 22 HIS ** k 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 9 GLN ** m 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 26 GLN ** s 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.365 161492 Z= 0.301 Angle : 0.603 29.497 241653 Z= 0.324 Chirality : 0.035 1.903 30609 Planarity : 0.005 0.126 13093 Dihedral : 25.156 178.570 81410 Min Nonbonded Distance : 1.643 Molprobity Statistics. All-atom Clashscore : 61.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.44 % Favored : 93.51 % Rotamer: Outliers : 6.81 % Allowed : 22.19 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.11), residues: 5916 helix: 0.78 (0.12), residues: 1954 sheet: -1.98 (0.14), residues: 1098 loop : -1.22 (0.12), residues: 2864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP g 103 HIS 0.007 0.001 HIS k 116 PHE 0.029 0.002 PHE d 75 TYR 0.016 0.001 TYR d 138 ARG 0.006 0.000 ARG T 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2059 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 329 poor density : 1730 time to evaluate : 6.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 28 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7185 (pm20) REVERT: D 46 GLN cc_start: 0.8444 (mm110) cc_final: 0.8185 (mm110) REVERT: D 53 PHE cc_start: 0.9153 (m-10) cc_final: 0.8918 (m-10) REVERT: D 54 ARG cc_start: 0.7886 (mtp85) cc_final: 0.7592 (mtm180) REVERT: D 84 TYR cc_start: 0.8778 (t80) cc_final: 0.7640 (t80) REVERT: D 146 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7675 (mt-10) REVERT: D 172 TYR cc_start: 0.8405 (m-10) cc_final: 0.7803 (m-80) REVERT: D 186 HIS cc_start: 0.8762 (t-90) cc_final: 0.8536 (t70) REVERT: D 188 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8207 (mm-30) REVERT: D 198 ASN cc_start: 0.8224 (t0) cc_final: 0.7869 (t0) REVERT: D 201 HIS cc_start: 0.9005 (t70) cc_final: 0.8639 (t-90) REVERT: D 226 MET cc_start: 0.8591 (mtm) cc_final: 0.7986 (mtm) REVERT: E 45 THR cc_start: 0.8158 (m) cc_final: 0.7744 (p) REVERT: E 83 ASP cc_start: 0.7886 (m-30) cc_final: 0.7516 (m-30) REVERT: E 154 LYS cc_start: 0.8202 (tppt) cc_final: 0.7856 (tptp) REVERT: F 195 ASP cc_start: 0.8412 (t0) cc_final: 0.8168 (t0) REVERT: F 203 GLN cc_start: 0.9141 (mm-40) cc_final: 0.8865 (mm-40) REVERT: F 204 ASN cc_start: 0.9123 (m-40) cc_final: 0.8807 (m110) REVERT: G 13 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8154 (pp20) REVERT: G 104 GLU cc_start: 0.8687 (tt0) cc_final: 0.8386 (tt0) REVERT: H 41 MET cc_start: 0.6935 (mmm) cc_final: 0.6541 (mmp) REVERT: H 162 ILE cc_start: 0.9498 (mt) cc_final: 0.9111 (tt) REVERT: I 121 LYS cc_start: 0.5044 (mmmt) cc_final: 0.4447 (mptt) REVERT: N 39 ARG cc_start: 0.8165 (mtp85) cc_final: 0.7938 (mtp180) REVERT: N 41 ASP cc_start: 0.8445 (p0) cc_final: 0.8116 (p0) REVERT: N 45 ASN cc_start: 0.9090 (p0) cc_final: 0.8552 (p0) REVERT: N 48 MET cc_start: 0.7769 (ppp) cc_final: 0.6904 (ptp) REVERT: N 71 ILE cc_start: 0.8812 (mp) cc_final: 0.8592 (mm) REVERT: O 12 ASP cc_start: 0.8909 (p0) cc_final: 0.8565 (p0) REVERT: O 20 MET cc_start: 0.8661 (ttm) cc_final: 0.8173 (ttm) REVERT: O 59 LYS cc_start: 0.8285 (mtpp) cc_final: 0.8025 (mtmm) REVERT: O 94 ARG cc_start: 0.9068 (mtp85) cc_final: 0.8774 (ttm110) REVERT: O 107 ARG cc_start: 0.8482 (mtp85) cc_final: 0.8081 (mtp180) REVERT: O 108 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8444 (mt-10) REVERT: P 29 LYS cc_start: 0.8681 (ttpp) cc_final: 0.8375 (tttt) REVERT: P 47 ASP cc_start: 0.8402 (t0) cc_final: 0.7544 (t0) REVERT: P 49 ARG cc_start: 0.8158 (mtm180) cc_final: 0.7684 (mtm-85) REVERT: Q 9 TYR cc_start: 0.8688 (m-80) cc_final: 0.8006 (m-80) REVERT: Q 17 LEU cc_start: 0.9156 (mm) cc_final: 0.8754 (mm) REVERT: Q 25 ASP cc_start: 0.8508 (p0) cc_final: 0.8115 (p0) REVERT: Q 37 LEU cc_start: 0.8097 (mt) cc_final: 0.7664 (mt) REVERT: Q 60 ARG cc_start: 0.8911 (mmm160) cc_final: 0.8610 (mmm160) REVERT: Q 77 LYS cc_start: 0.8807 (mtpp) cc_final: 0.8573 (mttp) REVERT: Q 85 LYS cc_start: 0.8410 (mttp) cc_final: 0.8124 (mmtm) REVERT: Q 111 GLU cc_start: 0.7795 (tp30) cc_final: 0.7458 (tp30) REVERT: Q 128 LYS cc_start: 0.8821 (mtmt) cc_final: 0.8384 (mtmt) REVERT: R 8 ARG cc_start: 0.8965 (mpt-90) cc_final: 0.8596 (mtt-85) REVERT: R 9 LYS cc_start: 0.8543 (mttp) cc_final: 0.7466 (mttp) REVERT: R 30 THR cc_start: 0.9311 (OUTLIER) cc_final: 0.9018 (p) REVERT: R 31 HIS cc_start: 0.8284 (m90) cc_final: 0.7707 (m-70) REVERT: R 43 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7911 (mm-30) REVERT: R 78 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8782 (pttt) REVERT: R 103 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8367 (mtp85) REVERT: S 38 GLN cc_start: 0.8365 (pt0) cc_final: 0.7760 (pt0) REVERT: S 83 LYS cc_start: 0.8963 (mtpp) cc_final: 0.8714 (mtpp) REVERT: T 46 GLU cc_start: 0.7591 (tt0) cc_final: 0.7264 (tt0) REVERT: T 73 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7749 (mt-10) REVERT: T 90 GLN cc_start: 0.8017 (tp-100) cc_final: 0.7789 (tp40) REVERT: U 32 PHE cc_start: 0.8792 (t80) cc_final: 0.8434 (t80) REVERT: V 6 LYS cc_start: 0.8263 (tppt) cc_final: 0.8029 (tppt) REVERT: V 12 TYR cc_start: 0.8718 (m-80) cc_final: 0.8429 (m-80) REVERT: V 19 LYS cc_start: 0.8972 (ptpp) cc_final: 0.8585 (mtpp) REVERT: V 91 TYR cc_start: 0.9026 (p90) cc_final: 0.8536 (p90) REVERT: V 93 GLU cc_start: 0.7461 (tm-30) cc_final: 0.6434 (tm-30) REVERT: V 100 ARG cc_start: 0.8331 (mtm110) cc_final: 0.8022 (mtm110) REVERT: W 40 ASN cc_start: 0.8429 (t0) cc_final: 0.8088 (t0) REVERT: W 52 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8341 (tp30) REVERT: X 9 LEU cc_start: 0.8562 (mt) cc_final: 0.8164 (mt) REVERT: X 15 GLU cc_start: 0.9127 (mp0) cc_final: 0.8735 (mp0) REVERT: Y 11 ASP cc_start: 0.7465 (m-30) cc_final: 0.7038 (m-30) REVERT: Y 43 ASN cc_start: 0.7978 (t160) cc_final: 0.7223 (t0) REVERT: Z 3 TYR cc_start: 0.8624 (m-80) cc_final: 0.8405 (m-80) REVERT: Z 6 LYS cc_start: 0.9215 (mtpp) cc_final: 0.8906 (ttmt) REVERT: Z 8 TYR cc_start: 0.8643 (m-10) cc_final: 0.8370 (m-10) REVERT: Z 44 PHE cc_start: 0.9214 (t80) cc_final: 0.8993 (t80) REVERT: Z 54 HIS cc_start: 0.8486 (m90) cc_final: 0.7460 (m170) REVERT: Z 65 GLN cc_start: 0.8310 (tp-100) cc_final: 0.8099 (tp40) REVERT: Z 78 LYS cc_start: 0.8201 (mtmt) cc_final: 0.7581 (mttp) REVERT: Z 94 GLU cc_start: 0.6950 (pm20) cc_final: 0.6464 (pm20) REVERT: Z 138 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6642 (tm-30) REVERT: 0 19 LYS cc_start: 0.8710 (mmpt) cc_final: 0.8319 (mmtm) REVERT: 0 38 VAL cc_start: 0.9345 (t) cc_final: 0.9049 (m) REVERT: 1 56 GLN cc_start: 0.8996 (mm110) cc_final: 0.8684 (mm-40) REVERT: 1 61 ARG cc_start: 0.8074 (mtm180) cc_final: 0.7580 (mtm180) REVERT: 2 20 GLU cc_start: 0.9393 (mm-30) cc_final: 0.9093 (mp0) REVERT: 2 26 ARG cc_start: 0.8485 (ttm110) cc_final: 0.8052 (mtm110) REVERT: 2 27 GLU cc_start: 0.9412 (mt-10) cc_final: 0.9140 (tp30) REVERT: 2 51 ARG cc_start: 0.8812 (ttm110) cc_final: 0.8458 (ttm110) REVERT: 3 4 LEU cc_start: 0.8854 (mp) cc_final: 0.8631 (mp) REVERT: 3 5 LYS cc_start: 0.8650 (ttpp) cc_final: 0.8163 (ttpp) REVERT: 5 39 MET cc_start: 0.8943 (mmm) cc_final: 0.8510 (mmm) REVERT: 7 6 GLN cc_start: 0.8744 (mm110) cc_final: 0.8520 (mm110) REVERT: 9 22 ARG cc_start: 0.8015 (mtt90) cc_final: 0.7758 (mtt90) REVERT: b 8 LYS cc_start: 0.7812 (pmmt) cc_final: 0.7173 (ptmt) REVERT: b 25 ASN cc_start: 0.8323 (t0) cc_final: 0.8004 (t0) REVERT: c 19 GLU cc_start: 0.8185 (mp0) cc_final: 0.7843 (mp0) REVERT: c 28 GLN cc_start: 0.8684 (mt0) cc_final: 0.8440 (mm-40) REVERT: c 118 GLN cc_start: 0.9066 (mt0) cc_final: 0.8766 (mt0) REVERT: c 131 ARG cc_start: 0.8203 (mtm110) cc_final: 0.7965 (ptt90) REVERT: c 140 ARG cc_start: 0.8406 (ptt-90) cc_final: 0.7950 (ptt180) REVERT: c 181 ASN cc_start: 0.8315 (t0) cc_final: 0.8056 (t0) REVERT: c 183 ASP cc_start: 0.8632 (t0) cc_final: 0.8024 (t0) REVERT: c 193 TYR cc_start: 0.8519 (p90) cc_final: 0.7988 (p90) REVERT: d 33 MET cc_start: 0.8700 (tpt) cc_final: 0.8261 (tpt) REVERT: d 50 ARG cc_start: 0.8695 (ttt180) cc_final: 0.8189 (tpp80) REVERT: d 74 GLN cc_start: 0.8983 (mt0) cc_final: 0.8697 (mt0) REVERT: d 165 MET cc_start: 0.7969 (tpp) cc_final: 0.7704 (tpp) REVERT: d 177 ASP cc_start: 0.8147 (t0) cc_final: 0.7800 (t0) REVERT: d 205 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6576 (mt-10) REVERT: e 47 LYS cc_start: 0.9184 (ptpp) cc_final: 0.8760 (ptpp) REVERT: e 57 LYS cc_start: 0.8846 (ttmp) cc_final: 0.8563 (ttmm) REVERT: e 61 TYR cc_start: 0.9327 (m-80) cc_final: 0.9002 (m-80) REVERT: e 65 ASN cc_start: 0.8158 (t0) cc_final: 0.7895 (t0) REVERT: e 82 VAL cc_start: 0.9032 (t) cc_final: 0.8766 (m) REVERT: e 111 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8057 (mt-10) REVERT: f 62 TRP cc_start: 0.7465 (t60) cc_final: 0.6826 (t60) REVERT: g 53 LYS cc_start: 0.8661 (mtpp) cc_final: 0.8214 (mmtm) REVERT: g 74 GLU cc_start: 0.9488 (pt0) cc_final: 0.8852 (pm20) REVERT: g 89 MET cc_start: 0.7677 (mmt) cc_final: 0.6703 (mmt) REVERT: g 102 ARG cc_start: 0.8527 (ttm110) cc_final: 0.8128 (ttp-110) REVERT: g 106 GLN cc_start: 0.8970 (mt0) cc_final: 0.8519 (mt0) REVERT: g 136 LYS cc_start: 0.9209 (mmtm) cc_final: 0.8812 (tttt) REVERT: g 144 MET cc_start: 0.7162 (mmm) cc_final: 0.6742 (tpt) REVERT: g 155 ARG cc_start: 0.6498 (pmt-80) cc_final: 0.5795 (ptp90) REVERT: h 49 GLU cc_start: 0.8196 (pt0) cc_final: 0.7770 (pt0) REVERT: h 99 GLU cc_start: 0.8777 (tp30) cc_final: 0.8567 (tp30) REVERT: h 132 GLU cc_start: 0.8045 (tt0) cc_final: 0.7787 (tt0) REVERT: i 48 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8250 (mm-30) REVERT: i 113 LYS cc_start: 0.7902 (mmtp) cc_final: 0.7672 (mttm) REVERT: j 13 HIS cc_start: 0.7982 (p-80) cc_final: 0.7705 (p-80) REVERT: j 43 ARG cc_start: 0.7896 (mmm-85) cc_final: 0.7387 (ttt-90) REVERT: j 95 GLU cc_start: 0.6413 (tm-30) cc_final: 0.5915 (tm-30) REVERT: k 43 SER cc_start: 0.8986 (t) cc_final: 0.8758 (t) REVERT: k 93 GLN cc_start: 0.8046 (tp-100) cc_final: 0.7537 (tp-100) REVERT: k 104 GLN cc_start: 0.8061 (tt0) cc_final: 0.7576 (tt0) REVERT: l 37 CYS cc_start: 0.9289 (m) cc_final: 0.8869 (m) REVERT: m 12 ASN cc_start: 0.7732 (m-40) cc_final: 0.6773 (t0) REVERT: m 70 LEU cc_start: 0.8646 (tp) cc_final: 0.8379 (tp) REVERT: n 8 GLU cc_start: 0.8458 (tp30) cc_final: 0.8109 (tp30) REVERT: n 9 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7736 (ttmm) REVERT: n 50 LYS cc_start: 0.8847 (ttmt) cc_final: 0.8538 (ttmm) REVERT: o 13 GLN cc_start: 0.9018 (tm-30) cc_final: 0.8650 (pp30) REVERT: o 83 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8568 (tm-30) REVERT: p 14 ASN cc_start: 0.9449 (t0) cc_final: 0.8897 (t0) REVERT: p 27 LYS cc_start: 0.7803 (ptmt) cc_final: 0.7328 (pttt) REVERT: p 39 TYR cc_start: 0.8909 (t80) cc_final: 0.8206 (t80) REVERT: q 46 ASP cc_start: 0.8392 (t70) cc_final: 0.7634 (t0) REVERT: q 91 ARG cc_start: 0.8720 (mmm-85) cc_final: 0.8308 (mtp-110) REVERT: r 33 ASP cc_start: 0.8808 (t0) cc_final: 0.8390 (t0) REVERT: r 51 LEU cc_start: 0.8825 (mt) cc_final: 0.8469 (mt) REVERT: r 68 LYS cc_start: 0.8665 (tppt) cc_final: 0.8456 (tppt) REVERT: r 84 LYS cc_start: 0.9089 (ptmm) cc_final: 0.8695 (ptmm) REVERT: s 5 LEU cc_start: 0.8756 (pp) cc_final: 0.8199 (mt) REVERT: s 12 ASP cc_start: 0.8417 (m-30) cc_final: 0.7768 (m-30) REVERT: s 35 SER cc_start: 0.9330 (m) cc_final: 0.8240 (t) REVERT: s 71 LEU cc_start: 0.8674 (mp) cc_final: 0.8390 (mp) REVERT: u 20 LYS cc_start: 0.8282 (tttm) cc_final: 0.7979 (ttpp) outliers start: 329 outliers final: 261 residues processed: 1858 average time/residue: 1.4705 time to fit residues: 4714.9604 Evaluate side-chains 1956 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1690 time to evaluate : 6.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 130 ASN Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 122 VAL Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 7 TYR Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 28 SER Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 77 ILE Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain P residue 5 ASP Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 125 VAL Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 54 MET Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 59 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 78 LYS Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 42 ASP Chi-restraints excluded: chain S residue 47 THR Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 75 GLU Chi-restraints excluded: chain S residue 112 PHE Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 38 ASN Chi-restraints excluded: chain T residue 80 SER Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain T residue 102 ILE Chi-restraints excluded: chain T residue 104 ASN Chi-restraints excluded: chain U residue 18 LEU Chi-restraints excluded: chain U residue 29 SER Chi-restraints excluded: chain U residue 38 THR Chi-restraints excluded: chain U residue 44 ASN Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 80 ILE Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain V residue 14 VAL Chi-restraints excluded: chain V residue 92 THR Chi-restraints excluded: chain W residue 13 SER Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 62 HIS Chi-restraints excluded: chain W residue 66 GLU Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 14 SER Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain Y residue 3 VAL Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Z residue 50 GLN Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 125 LEU Chi-restraints excluded: chain Z residue 137 ILE Chi-restraints excluded: chain Z residue 148 ASP Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 165 VAL Chi-restraints excluded: chain 0 residue 10 THR Chi-restraints excluded: chain 0 residue 58 THR Chi-restraints excluded: chain 0 residue 59 LEU Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 74 VAL Chi-restraints excluded: chain 1 residue 86 SER Chi-restraints excluded: chain 1 residue 97 LEU Chi-restraints excluded: chain 2 residue 41 ILE Chi-restraints excluded: chain 2 residue 63 VAL Chi-restraints excluded: chain 2 residue 66 GLU Chi-restraints excluded: chain 3 residue 46 ASN Chi-restraints excluded: chain 4 residue 5 ILE Chi-restraints excluded: chain 4 residue 10 VAL Chi-restraints excluded: chain 4 residue 14 ILE Chi-restraints excluded: chain 5 residue 6 VAL Chi-restraints excluded: chain 5 residue 26 THR Chi-restraints excluded: chain 5 residue 44 THR Chi-restraints excluded: chain 6 residue 5 VAL Chi-restraints excluded: chain 6 residue 10 LEU Chi-restraints excluded: chain 6 residue 14 THR Chi-restraints excluded: chain 6 residue 23 THR Chi-restraints excluded: chain 7 residue 43 THR Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 37 SER Chi-restraints excluded: chain 9 residue 7 VAL Chi-restraints excluded: chain 9 residue 17 ILE Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain b residue 107 THR Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 140 HIS Chi-restraints excluded: chain b residue 160 ASP Chi-restraints excluded: chain b residue 162 ILE Chi-restraints excluded: chain b residue 174 VAL Chi-restraints excluded: chain b residue 187 LEU Chi-restraints excluded: chain b residue 189 ASP Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 195 ASP Chi-restraints excluded: chain b residue 198 ASP Chi-restraints excluded: chain b residue 210 SER Chi-restraints excluded: chain b residue 222 ILE Chi-restraints excluded: chain c residue 3 ASN Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 64 LEU Chi-restraints excluded: chain d residue 99 SER Chi-restraints excluded: chain d residue 116 GLN Chi-restraints excluded: chain d residue 127 THR Chi-restraints excluded: chain d residue 137 SER Chi-restraints excluded: chain d residue 158 ILE Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 98 THR Chi-restraints excluded: chain e residue 144 THR Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 LEU Chi-restraints excluded: chain f residue 19 LEU Chi-restraints excluded: chain f residue 42 GLU Chi-restraints excluded: chain f residue 43 LEU Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain f residue 85 VAL Chi-restraints excluded: chain f residue 90 VAL Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 30 ILE Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 57 GLU Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 98 SER Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain h residue 6 ILE Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 35 ILE Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 45 ILE Chi-restraints excluded: chain h residue 46 LYS Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 83 ILE Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain h residue 120 THR Chi-restraints excluded: chain i residue 7 THR Chi-restraints excluded: chain i residue 14 VAL Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 41 VAL Chi-restraints excluded: chain i residue 47 LEU Chi-restraints excluded: chain i residue 48 GLU Chi-restraints excluded: chain i residue 54 ASP Chi-restraints excluded: chain i residue 77 ILE Chi-restraints excluded: chain i residue 81 ILE Chi-restraints excluded: chain i residue 89 ASN Chi-restraints excluded: chain i residue 102 LEU Chi-restraints excluded: chain j residue 38 ILE Chi-restraints excluded: chain j residue 49 VAL Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain j residue 89 ASP Chi-restraints excluded: chain j residue 96 ILE Chi-restraints excluded: chain k residue 18 ARG Chi-restraints excluded: chain k residue 26 ASN Chi-restraints excluded: chain k residue 28 THR Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain k residue 40 ILE Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 119 CYS Chi-restraints excluded: chain l residue 6 THR Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 58 VAL Chi-restraints excluded: chain l residue 62 SER Chi-restraints excluded: chain l residue 66 VAL Chi-restraints excluded: chain l residue 76 ASN Chi-restraints excluded: chain l residue 89 ARG Chi-restraints excluded: chain l residue 96 VAL Chi-restraints excluded: chain l residue 100 ILE Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 74 VAL Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain n residue 9 LYS Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain p residue 11 SER Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 33 ILE Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain p residue 53 VAL Chi-restraints excluded: chain p residue 67 THR Chi-restraints excluded: chain q residue 36 ILE Chi-restraints excluded: chain q residue 53 LEU Chi-restraints excluded: chain q residue 60 ILE Chi-restraints excluded: chain q residue 89 LEU Chi-restraints excluded: chain q residue 94 ASN Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain r residue 72 ARG Chi-restraints excluded: chain r residue 76 LEU Chi-restraints excluded: chain s residue 18 LYS Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 41 VAL Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain t residue 63 ILE Chi-restraints excluded: chain t residue 82 SER Chi-restraints excluded: chain u residue 8 THR Chi-restraints excluded: chain u residue 13 ILE Chi-restraints excluded: chain u residue 17 THR Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 193 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1047 random chunks: chunk 842 optimal weight: 0.0070 chunk 574 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 753 optimal weight: 20.0000 chunk 417 optimal weight: 10.0000 chunk 863 optimal weight: 5.9990 chunk 699 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 516 optimal weight: 20.0000 chunk 908 optimal weight: 20.0000 chunk 255 optimal weight: 10.0000 overall best weight: 7.2010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 ASN ** E 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 75 ASN Z 151 HIS 0 17 GLN ** 0 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 20 HIS b 37 ASN ** b 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 98 ASN c 110 ASN ** d 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 57 GLN ** f 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 ASN ** g 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 26 GLN ** q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.363 161492 Z= 0.354 Angle : 0.652 29.544 241653 Z= 0.346 Chirality : 0.036 1.892 30609 Planarity : 0.006 0.127 13093 Dihedral : 25.173 178.128 81410 Min Nonbonded Distance : 1.640 Molprobity Statistics. All-atom Clashscore : 64.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.25 % Favored : 92.70 % Rotamer: Outliers : 8.20 % Allowed : 22.28 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.11), residues: 5916 helix: 0.68 (0.12), residues: 1951 sheet: -1.92 (0.14), residues: 1128 loop : -1.27 (0.12), residues: 2837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP g 103 HIS 0.008 0.001 HIS k 116 PHE 0.025 0.002 PHE N 117 TYR 0.022 0.002 TYR Q 26 ARG 0.009 0.001 ARG m 93 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2098 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 396 poor density : 1702 time to evaluate : 6.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: D 16 MET cc_start: 0.8949 (ptm) cc_final: 0.8353 (ptm) REVERT: D 53 PHE cc_start: 0.9170 (m-10) cc_final: 0.8896 (m-10) REVERT: D 54 ARG cc_start: 0.7998 (mtp85) cc_final: 0.7778 (mtm180) REVERT: D 84 TYR cc_start: 0.8839 (t80) cc_final: 0.7656 (t80) REVERT: D 146 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7632 (mt-10) REVERT: D 169 GLU cc_start: 0.8286 (tt0) cc_final: 0.8067 (tt0) REVERT: D 172 TYR cc_start: 0.8436 (m-10) cc_final: 0.7868 (m-80) REVERT: D 198 ASN cc_start: 0.8305 (t0) cc_final: 0.7968 (t0) REVERT: D 201 HIS cc_start: 0.9021 (t70) cc_final: 0.8734 (t-90) REVERT: D 226 MET cc_start: 0.8623 (mtm) cc_final: 0.7970 (mtm) REVERT: D 263 ARG cc_start: 0.8288 (mtm180) cc_final: 0.8080 (mtm110) REVERT: E 45 THR cc_start: 0.8085 (m) cc_final: 0.7677 (p) REVERT: E 83 ASP cc_start: 0.7911 (m-30) cc_final: 0.7522 (m-30) REVERT: E 154 LYS cc_start: 0.8296 (tppt) cc_final: 0.7956 (tptp) REVERT: F 195 ASP cc_start: 0.8396 (t0) cc_final: 0.8138 (t0) REVERT: F 203 GLN cc_start: 0.9150 (mm-40) cc_final: 0.8232 (tm-30) REVERT: F 204 ASN cc_start: 0.9086 (m-40) cc_final: 0.8700 (m110) REVERT: H 41 MET cc_start: 0.7060 (mmm) cc_final: 0.6060 (mmt) REVERT: I 2 LYS cc_start: 0.8387 (tptt) cc_final: 0.8171 (tptp) REVERT: I 121 LYS cc_start: 0.5328 (mmmt) cc_final: 0.4651 (mptt) REVERT: N 41 ASP cc_start: 0.8587 (p0) cc_final: 0.7849 (p0) REVERT: N 45 ASN cc_start: 0.9091 (p0) cc_final: 0.8623 (p0) REVERT: N 48 MET cc_start: 0.7930 (ppp) cc_final: 0.6323 (ptm) REVERT: N 74 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7303 (ttm-80) REVERT: O 12 ASP cc_start: 0.8990 (p0) cc_final: 0.8620 (p0) REVERT: O 20 MET cc_start: 0.8668 (ttm) cc_final: 0.8215 (ttm) REVERT: O 49 ARG cc_start: 0.8336 (ptp90) cc_final: 0.7685 (ptp90) REVERT: O 66 LYS cc_start: 0.8707 (tttp) cc_final: 0.7983 (ttmm) REVERT: O 94 ARG cc_start: 0.9038 (mtp85) cc_final: 0.8653 (ttm110) REVERT: O 107 ARG cc_start: 0.8520 (mtp85) cc_final: 0.8096 (mtp180) REVERT: O 108 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8443 (mt-10) REVERT: P 29 LYS cc_start: 0.8741 (ttpp) cc_final: 0.8456 (tttt) REVERT: P 47 ASP cc_start: 0.8433 (t0) cc_final: 0.7602 (t0) REVERT: P 49 ARG cc_start: 0.8167 (mtm180) cc_final: 0.7685 (mtm-85) REVERT: P 60 MET cc_start: 0.7967 (mmp) cc_final: 0.7700 (mmp) REVERT: P 148 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7917 (pt) REVERT: Q 17 LEU cc_start: 0.9165 (mm) cc_final: 0.8646 (mm) REVERT: Q 37 LEU cc_start: 0.8105 (mt) cc_final: 0.7710 (mt) REVERT: Q 60 ARG cc_start: 0.8913 (mmm160) cc_final: 0.8545 (mmm160) REVERT: Q 85 LYS cc_start: 0.8395 (mttp) cc_final: 0.8135 (mmtm) REVERT: Q 128 LYS cc_start: 0.8843 (mtmt) cc_final: 0.8360 (mtmt) REVERT: R 8 ARG cc_start: 0.9037 (mpt-90) cc_final: 0.8501 (mtt-85) REVERT: R 9 LYS cc_start: 0.8528 (mttp) cc_final: 0.7454 (mttp) REVERT: R 30 THR cc_start: 0.9307 (OUTLIER) cc_final: 0.8861 (p) REVERT: R 31 HIS cc_start: 0.8258 (m90) cc_final: 0.7614 (m-70) REVERT: R 42 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8605 (mtmt) REVERT: R 43 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7792 (mm-30) REVERT: R 103 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.8641 (mtt-85) REVERT: S 83 LYS cc_start: 0.8875 (mtpp) cc_final: 0.8407 (mtpp) REVERT: S 92 TYR cc_start: 0.8870 (OUTLIER) cc_final: 0.8022 (m-80) REVERT: S 111 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8317 (mp0) REVERT: T 46 GLU cc_start: 0.7732 (tt0) cc_final: 0.7337 (tt0) REVERT: T 73 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7931 (mt-10) REVERT: T 84 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8439 (tp40) REVERT: T 90 GLN cc_start: 0.7977 (tp-100) cc_final: 0.7762 (tp40) REVERT: U 24 TYR cc_start: 0.9042 (m-10) cc_final: 0.8309 (m-80) REVERT: U 32 PHE cc_start: 0.8808 (t80) cc_final: 0.8421 (t80) REVERT: U 39 LEU cc_start: 0.8999 (mm) cc_final: 0.8669 (mm) REVERT: V 1 MET cc_start: 0.7180 (tpt) cc_final: 0.6337 (tpt) REVERT: V 12 TYR cc_start: 0.8797 (m-80) cc_final: 0.8543 (m-80) REVERT: V 91 TYR cc_start: 0.9066 (p90) cc_final: 0.8716 (p90) REVERT: V 93 GLU cc_start: 0.7395 (tm-30) cc_final: 0.7138 (tm-30) REVERT: V 100 ARG cc_start: 0.8313 (mtm110) cc_final: 0.8085 (mtm110) REVERT: W 52 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8324 (tp30) REVERT: X 9 LEU cc_start: 0.8503 (mt) cc_final: 0.8071 (mt) REVERT: X 15 GLU cc_start: 0.9147 (mp0) cc_final: 0.8932 (mp0) REVERT: X 93 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7357 (mm-30) REVERT: Y 11 ASP cc_start: 0.7473 (m-30) cc_final: 0.7067 (m-30) REVERT: Y 43 ASN cc_start: 0.7965 (t160) cc_final: 0.7242 (t0) REVERT: Z 8 TYR cc_start: 0.8695 (m-10) cc_final: 0.8461 (m-80) REVERT: Z 54 HIS cc_start: 0.8439 (m90) cc_final: 0.7432 (m90) REVERT: Z 75 ASN cc_start: 0.8873 (m110) cc_final: 0.8517 (m-40) REVERT: Z 138 GLU cc_start: 0.7264 (mt-10) cc_final: 0.6736 (tm-30) REVERT: 0 19 LYS cc_start: 0.8691 (mmpt) cc_final: 0.8264 (mmtm) REVERT: 0 38 VAL cc_start: 0.9367 (t) cc_final: 0.9148 (t) REVERT: 1 50 ARG cc_start: 0.8689 (ttm-80) cc_final: 0.8400 (ttm-80) REVERT: 1 56 GLN cc_start: 0.8988 (mm110) cc_final: 0.8658 (mm-40) REVERT: 2 20 GLU cc_start: 0.9419 (mm-30) cc_final: 0.9098 (mp0) REVERT: 2 27 GLU cc_start: 0.9407 (mt-10) cc_final: 0.9126 (tp30) REVERT: 2 51 ARG cc_start: 0.8826 (ttm110) cc_final: 0.8458 (ttm110) REVERT: 3 4 LEU cc_start: 0.8899 (mp) cc_final: 0.8668 (mp) REVERT: 4 46 GLN cc_start: 0.7098 (OUTLIER) cc_final: 0.5953 (mt0) REVERT: 5 39 MET cc_start: 0.8873 (mmm) cc_final: 0.8319 (mmm) REVERT: 9 22 ARG cc_start: 0.7983 (mtt90) cc_final: 0.7747 (mtt90) REVERT: b 8 LYS cc_start: 0.7800 (pmmt) cc_final: 0.7221 (ptmt) REVERT: b 25 ASN cc_start: 0.8326 (t0) cc_final: 0.8006 (t0) REVERT: b 74 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7185 (ptpp) REVERT: b 170 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8189 (mm-30) REVERT: b 192 SER cc_start: 0.7614 (m) cc_final: 0.7096 (p) REVERT: b 212 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8530 (tp40) REVERT: b 216 SER cc_start: 0.9114 (t) cc_final: 0.8821 (m) REVERT: c 19 GLU cc_start: 0.8185 (mp0) cc_final: 0.7771 (mp0) REVERT: c 28 GLN cc_start: 0.8659 (mt0) cc_final: 0.8425 (mm-40) REVERT: c 118 GLN cc_start: 0.9033 (mt0) cc_final: 0.8721 (mt0) REVERT: c 135 LYS cc_start: 0.9268 (mtpt) cc_final: 0.8784 (mppt) REVERT: c 181 ASN cc_start: 0.8345 (t0) cc_final: 0.8075 (t0) REVERT: c 183 ASP cc_start: 0.8577 (t0) cc_final: 0.7956 (t0) REVERT: c 184 TYR cc_start: 0.9395 (t80) cc_final: 0.9188 (t80) REVERT: c 190 ARG cc_start: 0.7860 (ptp90) cc_final: 0.7633 (ptp-170) REVERT: c 193 TYR cc_start: 0.8681 (p90) cc_final: 0.8089 (p90) REVERT: d 33 MET cc_start: 0.8743 (tpt) cc_final: 0.8408 (tpt) REVERT: d 50 ARG cc_start: 0.8689 (ttt180) cc_final: 0.8211 (tpp80) REVERT: d 60 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8682 (tp30) REVERT: d 74 GLN cc_start: 0.8932 (mt0) cc_final: 0.8629 (mt0) REVERT: d 165 MET cc_start: 0.8053 (tpp) cc_final: 0.7809 (tpp) REVERT: d 177 ASP cc_start: 0.8169 (t0) cc_final: 0.7855 (t0) REVERT: e 47 LYS cc_start: 0.9175 (ptpp) cc_final: 0.8833 (ptpp) REVERT: e 57 LYS cc_start: 0.8896 (ttmp) cc_final: 0.8531 (ttmm) REVERT: e 61 TYR cc_start: 0.9344 (m-80) cc_final: 0.8963 (m-80) REVERT: e 65 ASN cc_start: 0.8226 (t0) cc_final: 0.7946 (t0) REVERT: e 73 ASN cc_start: 0.6956 (t0) cc_final: 0.6753 (t0) REVERT: e 82 VAL cc_start: 0.9025 (t) cc_final: 0.8723 (m) REVERT: e 111 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8132 (mt-10) REVERT: f 62 TRP cc_start: 0.7393 (t60) cc_final: 0.6505 (t60) REVERT: g 53 LYS cc_start: 0.8585 (mtpp) cc_final: 0.8261 (mmtm) REVERT: g 102 ARG cc_start: 0.8553 (ttm110) cc_final: 0.8203 (ttp-110) REVERT: g 106 GLN cc_start: 0.8966 (mt0) cc_final: 0.8517 (mt0) REVERT: g 136 LYS cc_start: 0.9168 (mmtm) cc_final: 0.8714 (ptmt) REVERT: g 144 MET cc_start: 0.7192 (mmm) cc_final: 0.6746 (tpt) REVERT: g 155 ARG cc_start: 0.6519 (pmt-80) cc_final: 0.5801 (ptp90) REVERT: h 34 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8408 (mm-30) REVERT: h 49 GLU cc_start: 0.8252 (pt0) cc_final: 0.7782 (pt0) REVERT: h 99 GLU cc_start: 0.8820 (tp30) cc_final: 0.8606 (tp30) REVERT: h 132 GLU cc_start: 0.8071 (tt0) cc_final: 0.7816 (tt0) REVERT: i 48 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8292 (mm-30) REVERT: i 73 GLN cc_start: 0.8504 (mt0) cc_final: 0.8180 (mt0) REVERT: i 113 LYS cc_start: 0.8125 (mmtp) cc_final: 0.7847 (mttm) REVERT: j 13 HIS cc_start: 0.8078 (p-80) cc_final: 0.7708 (p-80) REVERT: j 43 ARG cc_start: 0.7836 (mmm-85) cc_final: 0.7337 (ttt-90) REVERT: j 95 GLU cc_start: 0.6363 (tm-30) cc_final: 0.5780 (tm-30) REVERT: k 43 SER cc_start: 0.8975 (t) cc_final: 0.8731 (t) REVERT: k 62 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8396 (tm-30) REVERT: k 73 MET cc_start: 0.8647 (mmt) cc_final: 0.8446 (mmt) REVERT: k 78 GLN cc_start: 0.8639 (tm-30) cc_final: 0.8381 (tm-30) REVERT: k 93 GLN cc_start: 0.7986 (tp-100) cc_final: 0.7629 (tp-100) REVERT: k 104 GLN cc_start: 0.8151 (tt0) cc_final: 0.7618 (tt0) REVERT: l 37 CYS cc_start: 0.9160 (m) cc_final: 0.8719 (m) REVERT: m 12 ASN cc_start: 0.7600 (m-40) cc_final: 0.6695 (t0) REVERT: m 67 GLU cc_start: 0.7114 (mm-30) cc_final: 0.6884 (mm-30) REVERT: m 70 LEU cc_start: 0.8581 (tp) cc_final: 0.8323 (tp) REVERT: m 73 GLU cc_start: 0.8693 (pm20) cc_final: 0.8479 (pm20) REVERT: n 3 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7196 (ttm-80) REVERT: n 8 GLU cc_start: 0.8443 (tp30) cc_final: 0.8120 (tp30) REVERT: n 9 LYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7727 (ttmm) REVERT: n 50 LYS cc_start: 0.8945 (ttmt) cc_final: 0.8563 (ttmm) REVERT: o 34 LEU cc_start: 0.9213 (tp) cc_final: 0.8955 (tt) REVERT: o 83 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8472 (tm-30) REVERT: p 14 ASN cc_start: 0.9466 (t0) cc_final: 0.8855 (t0) REVERT: p 27 LYS cc_start: 0.7820 (ptmt) cc_final: 0.7325 (pttt) REVERT: p 39 TYR cc_start: 0.8935 (t80) cc_final: 0.8174 (t80) REVERT: q 46 ASP cc_start: 0.8457 (t70) cc_final: 0.7616 (t0) REVERT: q 91 ARG cc_start: 0.8757 (mmm-85) cc_final: 0.8502 (mtp-110) REVERT: r 33 ASP cc_start: 0.8893 (t0) cc_final: 0.8504 (t0) REVERT: r 38 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8223 (tm-30) REVERT: r 42 ARG cc_start: 0.8683 (mmm160) cc_final: 0.8222 (mmm160) REVERT: r 51 LEU cc_start: 0.8880 (mt) cc_final: 0.8519 (mt) REVERT: r 84 LYS cc_start: 0.9051 (ptmm) cc_final: 0.8699 (ptmm) REVERT: s 5 LEU cc_start: 0.8755 (pp) cc_final: 0.8207 (mt) REVERT: s 12 ASP cc_start: 0.8579 (m-30) cc_final: 0.7871 (m-30) REVERT: s 35 SER cc_start: 0.9321 (m) cc_final: 0.8216 (t) REVERT: u 20 LYS cc_start: 0.8392 (tttm) cc_final: 0.7888 (ttpp) REVERT: u 21 TYR cc_start: 0.7418 (m-80) cc_final: 0.6155 (m-80) REVERT: C 218 MET cc_start: 0.3119 (mtt) cc_final: 0.2542 (mtt) outliers start: 396 outliers final: 325 residues processed: 1861 average time/residue: 1.3319 time to fit residues: 4241.1917 Evaluate side-chains 1993 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 336 poor density : 1657 time to evaluate : 6.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 173 VAL Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 130 ASN Chi-restraints excluded: chain G residue 132 ASN Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 41 GLU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 74 ARG Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain N residue 122 VAL Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 7 TYR Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 28 SER Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 77 ILE Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 114 ILE Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain P residue 5 ASP Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain P residue 125 VAL Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain Q residue 21 THR Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 54 MET Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 138 ASP Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 42 LYS Chi-restraints excluded: chain R residue 59 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 78 LYS Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 103 ARG Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 42 ASP Chi-restraints excluded: chain S residue 47 THR Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 75 GLU Chi-restraints excluded: chain S residue 92 TYR Chi-restraints excluded: chain S residue 112 PHE Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 38 ASN Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 80 SER Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain T residue 102 ILE Chi-restraints excluded: chain T residue 104 ASN Chi-restraints excluded: chain T residue 115 ARG Chi-restraints excluded: chain U residue 18 LEU Chi-restraints excluded: chain U residue 29 SER Chi-restraints excluded: chain U residue 38 THR Chi-restraints excluded: chain U residue 44 ASN Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 80 ILE Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain V residue 14 VAL Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 92 THR Chi-restraints excluded: chain W residue 13 SER Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 53 SER Chi-restraints excluded: chain W residue 62 HIS Chi-restraints excluded: chain W residue 66 GLU Chi-restraints excluded: chain W residue 69 LEU Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 14 SER Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 56 THR Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Z residue 40 ASP Chi-restraints excluded: chain Z residue 45 ASP Chi-restraints excluded: chain Z residue 50 GLN Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 125 LEU Chi-restraints excluded: chain Z residue 137 ILE Chi-restraints excluded: chain Z residue 141 VAL Chi-restraints excluded: chain Z residue 148 ASP Chi-restraints excluded: chain Z residue 165 VAL Chi-restraints excluded: chain 0 residue 10 THR Chi-restraints excluded: chain 0 residue 58 THR Chi-restraints excluded: chain 0 residue 66 VAL Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 1 residue 11 ARG Chi-restraints excluded: chain 1 residue 14 VAL Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 74 VAL Chi-restraints excluded: chain 1 residue 86 SER Chi-restraints excluded: chain 1 residue 97 LEU Chi-restraints excluded: chain 2 residue 12 GLU Chi-restraints excluded: chain 2 residue 41 ILE Chi-restraints excluded: chain 2 residue 63 VAL Chi-restraints excluded: chain 2 residue 66 GLU Chi-restraints excluded: chain 3 residue 8 LEU Chi-restraints excluded: chain 3 residue 54 VAL Chi-restraints excluded: chain 4 residue 5 ILE Chi-restraints excluded: chain 4 residue 10 VAL Chi-restraints excluded: chain 4 residue 14 ILE Chi-restraints excluded: chain 4 residue 46 GLN Chi-restraints excluded: chain 5 residue 6 VAL Chi-restraints excluded: chain 5 residue 26 THR Chi-restraints excluded: chain 5 residue 29 THR Chi-restraints excluded: chain 5 residue 44 THR Chi-restraints excluded: chain 5 residue 57 VAL Chi-restraints excluded: chain 6 residue 5 VAL Chi-restraints excluded: chain 6 residue 10 LEU Chi-restraints excluded: chain 6 residue 14 THR Chi-restraints excluded: chain 6 residue 23 THR Chi-restraints excluded: chain 7 residue 43 THR Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 37 SER Chi-restraints excluded: chain 9 residue 7 VAL Chi-restraints excluded: chain 9 residue 17 ILE Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain b residue 74 LYS Chi-restraints excluded: chain b residue 107 THR Chi-restraints excluded: chain b residue 119 GLU Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 140 HIS Chi-restraints excluded: chain b residue 160 ASP Chi-restraints excluded: chain b residue 162 ILE Chi-restraints excluded: chain b residue 174 VAL Chi-restraints excluded: chain b residue 180 LEU Chi-restraints excluded: chain b residue 187 LEU Chi-restraints excluded: chain b residue 189 ASP Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 196 LEU Chi-restraints excluded: chain b residue 198 ASP Chi-restraints excluded: chain b residue 210 SER Chi-restraints excluded: chain b residue 222 ILE Chi-restraints excluded: chain c residue 3 ASN Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain c residue 144 SER Chi-restraints excluded: chain c residue 164 ARG Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 67 ILE Chi-restraints excluded: chain d residue 99 SER Chi-restraints excluded: chain d residue 116 GLN Chi-restraints excluded: chain d residue 127 THR Chi-restraints excluded: chain d residue 137 SER Chi-restraints excluded: chain d residue 158 ILE Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 53 LEU Chi-restraints excluded: chain e residue 98 THR Chi-restraints excluded: chain e residue 131 ILE Chi-restraints excluded: chain e residue 144 THR Chi-restraints excluded: chain f residue 8 ILE Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 LEU Chi-restraints excluded: chain f residue 19 LEU Chi-restraints excluded: chain f residue 36 ARG Chi-restraints excluded: chain f residue 42 GLU Chi-restraints excluded: chain f residue 43 LEU Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 66 GLU Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain f residue 83 ASP Chi-restraints excluded: chain f residue 85 VAL Chi-restraints excluded: chain f residue 90 VAL Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 24 THR Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 98 SER Chi-restraints excluded: chain h residue 6 ILE Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 45 ILE Chi-restraints excluded: chain h residue 46 LYS Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 83 ILE Chi-restraints excluded: chain h residue 87 SER Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain h residue 93 VAL Chi-restraints excluded: chain h residue 120 THR Chi-restraints excluded: chain i residue 7 THR Chi-restraints excluded: chain i residue 14 VAL Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 41 VAL Chi-restraints excluded: chain i residue 47 LEU Chi-restraints excluded: chain i residue 48 GLU Chi-restraints excluded: chain i residue 54 ASP Chi-restraints excluded: chain i residue 56 LEU Chi-restraints excluded: chain i residue 77 ILE Chi-restraints excluded: chain i residue 102 LEU Chi-restraints excluded: chain i residue 109 VAL Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 38 ILE Chi-restraints excluded: chain j residue 49 VAL Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain j residue 89 ASP Chi-restraints excluded: chain j residue 96 ILE Chi-restraints excluded: chain j residue 98 ILE Chi-restraints excluded: chain k residue 26 ASN Chi-restraints excluded: chain k residue 28 THR Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain k residue 40 ILE Chi-restraints excluded: chain k residue 41 THR Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 108 ILE Chi-restraints excluded: chain k residue 119 CYS Chi-restraints excluded: chain l residue 6 THR Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 18 VAL Chi-restraints excluded: chain l residue 58 VAL Chi-restraints excluded: chain l residue 62 SER Chi-restraints excluded: chain l residue 66 VAL Chi-restraints excluded: chain l residue 76 ASN Chi-restraints excluded: chain l residue 77 LEU Chi-restraints excluded: chain l residue 89 ARG Chi-restraints excluded: chain l residue 96 VAL Chi-restraints excluded: chain l residue 100 ILE Chi-restraints excluded: chain m residue 17 VAL Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain m residue 48 LEU Chi-restraints excluded: chain m residue 74 VAL Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain n residue 3 ARG Chi-restraints excluded: chain n residue 9 LYS Chi-restraints excluded: chain o residue 6 GLU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain p residue 11 SER Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 33 ILE Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain p residue 53 VAL Chi-restraints excluded: chain p residue 67 THR Chi-restraints excluded: chain q residue 36 ILE Chi-restraints excluded: chain q residue 53 LEU Chi-restraints excluded: chain q residue 60 ILE Chi-restraints excluded: chain q residue 66 SER Chi-restraints excluded: chain q residue 89 LEU Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain r residue 39 VAL Chi-restraints excluded: chain r residue 66 LEU Chi-restraints excluded: chain r residue 70 ILE Chi-restraints excluded: chain r residue 72 ARG Chi-restraints excluded: chain r residue 76 LEU Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 41 VAL Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain t residue 63 ILE Chi-restraints excluded: chain t residue 82 SER Chi-restraints excluded: chain t residue 93 GLU Chi-restraints excluded: chain u residue 13 ILE Chi-restraints excluded: chain u residue 17 THR Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 224 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1047 random chunks: chunk 340 optimal weight: 9.9990 chunk 911 optimal weight: 6.9990 chunk 200 optimal weight: 10.0000 chunk 594 optimal weight: 0.5980 chunk 249 optimal weight: 10.0000 chunk 1013 optimal weight: 20.0000 chunk 840 optimal weight: 30.0000 chunk 469 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 335 optimal weight: 10.0000 chunk 531 optimal weight: 5.9990 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN ** R 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 94 ASN ** V 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 65 GLN ** 0 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 42 GLN ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 20 HIS ** b 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 98 ASN c 110 ASN ** d 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 96 GLN ** g 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 ASN ** g 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 78 GLN i 124 GLN ** k 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 117 ASN ** m 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 ASN q 26 GLN ** q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.362 161492 Z= 0.308 Angle : 0.615 29.631 241653 Z= 0.330 Chirality : 0.035 1.897 30609 Planarity : 0.005 0.125 13093 Dihedral : 25.144 178.793 81410 Min Nonbonded Distance : 1.640 Molprobity Statistics. All-atom Clashscore : 63.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.91 % Favored : 93.04 % Rotamer: Outliers : 7.25 % Allowed : 24.35 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.11), residues: 5916 helix: 0.82 (0.12), residues: 1956 sheet: -1.79 (0.15), residues: 1123 loop : -1.19 (0.12), residues: 2837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP g 103 HIS 0.007 0.001 HIS d 123 PHE 0.027 0.002 PHE E 51 TYR 0.021 0.001 TYR 1 71 ARG 0.007 0.000 ARG 7 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2039 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 350 poor density : 1689 time to evaluate : 6.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: D 16 MET cc_start: 0.9026 (ptm) cc_final: 0.8450 (ptm) REVERT: D 53 PHE cc_start: 0.9177 (m-10) cc_final: 0.8931 (m-10) REVERT: D 54 ARG cc_start: 0.8017 (mtp85) cc_final: 0.7809 (mtp180) REVERT: D 84 TYR cc_start: 0.8818 (t80) cc_final: 0.7794 (t80) REVERT: D 146 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7640 (mt-10) REVERT: D 172 TYR cc_start: 0.8341 (m-10) cc_final: 0.7796 (m-80) REVERT: D 198 ASN cc_start: 0.8313 (t0) cc_final: 0.7985 (t0) REVERT: D 201 HIS cc_start: 0.8998 (t70) cc_final: 0.8719 (t-90) REVERT: D 226 MET cc_start: 0.8601 (mtm) cc_final: 0.8066 (mtm) REVERT: D 263 ARG cc_start: 0.8239 (mtm180) cc_final: 0.7937 (mtm110) REVERT: E 45 THR cc_start: 0.8070 (m) cc_final: 0.7655 (p) REVERT: E 83 ASP cc_start: 0.7874 (m-30) cc_final: 0.7467 (m-30) REVERT: E 154 LYS cc_start: 0.8229 (tppt) cc_final: 0.7911 (tptp) REVERT: F 195 ASP cc_start: 0.8391 (t0) cc_final: 0.8129 (t0) REVERT: F 203 GLN cc_start: 0.9165 (mm-40) cc_final: 0.8277 (tm-30) REVERT: F 204 ASN cc_start: 0.9076 (m-40) cc_final: 0.8703 (m110) REVERT: H 41 MET cc_start: 0.7075 (mmm) cc_final: 0.6418 (mmm) REVERT: I 2 LYS cc_start: 0.8380 (tptt) cc_final: 0.8170 (tptp) REVERT: N 41 ASP cc_start: 0.8718 (p0) cc_final: 0.8270 (p0) REVERT: N 45 ASN cc_start: 0.9059 (p0) cc_final: 0.8609 (p0) REVERT: N 48 MET cc_start: 0.7891 (ppp) cc_final: 0.7109 (ptm) REVERT: N 74 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7320 (ttm-80) REVERT: O 12 ASP cc_start: 0.8992 (p0) cc_final: 0.8622 (p0) REVERT: O 20 MET cc_start: 0.8652 (ttm) cc_final: 0.8209 (ttm) REVERT: O 94 ARG cc_start: 0.9050 (mtp85) cc_final: 0.8693 (ttm110) REVERT: O 107 ARG cc_start: 0.8507 (mtp85) cc_final: 0.8087 (mtp180) REVERT: O 108 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8406 (mt-10) REVERT: P 29 LYS cc_start: 0.8751 (ttpp) cc_final: 0.8449 (tttt) REVERT: P 47 ASP cc_start: 0.8427 (t0) cc_final: 0.7597 (t0) REVERT: P 49 ARG cc_start: 0.8172 (mtm180) cc_final: 0.7722 (mtm-85) REVERT: P 148 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7916 (pt) REVERT: Q 17 LEU cc_start: 0.9186 (mm) cc_final: 0.8711 (mm) REVERT: Q 25 ASP cc_start: 0.8594 (p0) cc_final: 0.8165 (p0) REVERT: Q 37 LEU cc_start: 0.8133 (mt) cc_final: 0.7717 (mt) REVERT: Q 60 ARG cc_start: 0.8866 (mmm160) cc_final: 0.8519 (mmm160) REVERT: Q 111 GLU cc_start: 0.7496 (tp30) cc_final: 0.6830 (tp30) REVERT: Q 128 LYS cc_start: 0.8859 (mtmt) cc_final: 0.8425 (mtmt) REVERT: Q 133 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.6806 (mtp85) REVERT: R 8 ARG cc_start: 0.9073 (mpt-90) cc_final: 0.8284 (mtt-85) REVERT: R 9 LYS cc_start: 0.8496 (mttp) cc_final: 0.7465 (mttp) REVERT: R 30 THR cc_start: 0.9322 (OUTLIER) cc_final: 0.9078 (p) REVERT: R 31 HIS cc_start: 0.8229 (m90) cc_final: 0.7659 (m-70) REVERT: R 43 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7737 (mm-30) REVERT: R 78 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8760 (tttt) REVERT: S 11 LYS cc_start: 0.8658 (ttmm) cc_final: 0.8423 (ttmm) REVERT: S 92 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.8053 (m-80) REVERT: T 46 GLU cc_start: 0.7791 (tt0) cc_final: 0.7367 (tt0) REVERT: T 90 GLN cc_start: 0.7952 (tp-100) cc_final: 0.7747 (tp40) REVERT: U 30 LYS cc_start: 0.8925 (mmtt) cc_final: 0.8706 (mmmt) REVERT: U 32 PHE cc_start: 0.8800 (t80) cc_final: 0.8400 (t80) REVERT: U 39 LEU cc_start: 0.8981 (mm) cc_final: 0.8602 (mm) REVERT: V 1 MET cc_start: 0.7106 (tpt) cc_final: 0.6318 (tpt) REVERT: V 12 TYR cc_start: 0.8762 (m-80) cc_final: 0.8535 (m-80) REVERT: V 91 TYR cc_start: 0.9044 (p90) cc_final: 0.8790 (p90) REVERT: V 93 GLU cc_start: 0.7324 (tm-30) cc_final: 0.7066 (tm-30) REVERT: V 100 ARG cc_start: 0.8349 (mtm110) cc_final: 0.8127 (mtm110) REVERT: W 52 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8300 (tp30) REVERT: W 60 ASN cc_start: 0.9199 (t0) cc_final: 0.8857 (t0) REVERT: X 9 LEU cc_start: 0.8569 (mt) cc_final: 0.8155 (mt) REVERT: X 15 GLU cc_start: 0.9133 (mp0) cc_final: 0.8921 (mp0) REVERT: X 60 ARG cc_start: 0.7657 (mtm-85) cc_final: 0.7456 (mtm180) REVERT: X 93 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7256 (mm-30) REVERT: Y 11 ASP cc_start: 0.7589 (m-30) cc_final: 0.7057 (m-30) REVERT: Y 43 ASN cc_start: 0.8010 (t160) cc_final: 0.7284 (t0) REVERT: Z 6 LYS cc_start: 0.9310 (mtpp) cc_final: 0.9009 (ttmt) REVERT: Z 8 TYR cc_start: 0.8759 (m-10) cc_final: 0.8518 (m-10) REVERT: Z 54 HIS cc_start: 0.8338 (m90) cc_final: 0.7288 (m90) REVERT: Z 78 LYS cc_start: 0.8191 (mttp) cc_final: 0.7553 (mttp) REVERT: Z 138 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6735 (tm-30) REVERT: 0 19 LYS cc_start: 0.8668 (mmpt) cc_final: 0.8214 (mmtm) REVERT: 0 38 VAL cc_start: 0.9391 (t) cc_final: 0.9181 (t) REVERT: 1 50 ARG cc_start: 0.8656 (ttm-80) cc_final: 0.8315 (ttm-80) REVERT: 1 56 GLN cc_start: 0.8991 (mm110) cc_final: 0.8680 (mm-40) REVERT: 2 20 GLU cc_start: 0.9412 (mm-30) cc_final: 0.9098 (mp0) REVERT: 2 27 GLU cc_start: 0.9383 (mt-10) cc_final: 0.9131 (tp30) REVERT: 2 51 ARG cc_start: 0.8824 (ttm110) cc_final: 0.8464 (ttm110) REVERT: 3 4 LEU cc_start: 0.8970 (mp) cc_final: 0.8746 (mp) REVERT: 3 5 LYS cc_start: 0.8739 (ttpp) cc_final: 0.8525 (ttpp) REVERT: 4 46 GLN cc_start: 0.7245 (OUTLIER) cc_final: 0.6062 (mt0) REVERT: 5 39 MET cc_start: 0.8894 (mmm) cc_final: 0.8333 (mmm) REVERT: 6 8 LYS cc_start: 0.8457 (mttm) cc_final: 0.7566 (mttt) REVERT: 6 25 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7373 (pttm) REVERT: 9 22 ARG cc_start: 0.7970 (mtt90) cc_final: 0.7743 (mtt90) REVERT: b 7 VAL cc_start: 0.6555 (t) cc_final: 0.6201 (t) REVERT: b 8 LYS cc_start: 0.7835 (pmmt) cc_final: 0.7281 (ptmt) REVERT: b 25 ASN cc_start: 0.8348 (t0) cc_final: 0.8028 (t0) REVERT: b 74 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7146 (ptpp) REVERT: b 122 PHE cc_start: 0.8424 (t80) cc_final: 0.7843 (t80) REVERT: b 147 LYS cc_start: 0.8899 (tttt) cc_final: 0.8519 (ttmt) REVERT: b 170 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8173 (mm-30) REVERT: b 192 SER cc_start: 0.7791 (m) cc_final: 0.7271 (p) REVERT: b 212 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8456 (tp40) REVERT: c 19 GLU cc_start: 0.8091 (mp0) cc_final: 0.7723 (mp0) REVERT: c 28 GLN cc_start: 0.8673 (mt0) cc_final: 0.8428 (mm-40) REVERT: c 104 GLN cc_start: 0.8822 (tp40) cc_final: 0.8595 (tp40) REVERT: c 118 GLN cc_start: 0.9009 (mt0) cc_final: 0.8708 (mt0) REVERT: c 131 ARG cc_start: 0.8151 (mtm110) cc_final: 0.7623 (ptt90) REVERT: c 135 LYS cc_start: 0.9259 (mtpt) cc_final: 0.8777 (mppt) REVERT: c 181 ASN cc_start: 0.8288 (t0) cc_final: 0.8010 (t0) REVERT: c 183 ASP cc_start: 0.8556 (t0) cc_final: 0.7938 (t0) REVERT: c 190 ARG cc_start: 0.7990 (ptp90) cc_final: 0.7579 (ptp-170) REVERT: c 193 TYR cc_start: 0.8715 (p90) cc_final: 0.8064 (p90) REVERT: d 33 MET cc_start: 0.8734 (tpt) cc_final: 0.8235 (tpt) REVERT: d 50 ARG cc_start: 0.8564 (ttt180) cc_final: 0.8191 (tpp80) REVERT: d 74 GLN cc_start: 0.8983 (mt0) cc_final: 0.8685 (mt0) REVERT: d 165 MET cc_start: 0.7993 (tpp) cc_final: 0.7756 (tpp) REVERT: d 177 ASP cc_start: 0.8080 (t0) cc_final: 0.7794 (t0) REVERT: d 205 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6608 (mt-10) REVERT: e 47 LYS cc_start: 0.9082 (ptpp) cc_final: 0.8796 (ptpp) REVERT: e 57 LYS cc_start: 0.8929 (ttmp) cc_final: 0.8543 (ttmm) REVERT: e 61 TYR cc_start: 0.9331 (m-80) cc_final: 0.8932 (m-80) REVERT: e 65 ASN cc_start: 0.8263 (t0) cc_final: 0.7981 (t0) REVERT: e 82 VAL cc_start: 0.9081 (t) cc_final: 0.8782 (m) REVERT: e 84 PHE cc_start: 0.8804 (t80) cc_final: 0.8419 (t80) REVERT: e 111 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8019 (mt-10) REVERT: e 125 SER cc_start: 0.8779 (t) cc_final: 0.8358 (p) REVERT: f 62 TRP cc_start: 0.7370 (t60) cc_final: 0.6573 (t60) REVERT: g 53 LYS cc_start: 0.8687 (mtpp) cc_final: 0.8309 (mmtm) REVERT: g 73 MET cc_start: 0.8848 (mmm) cc_final: 0.8620 (mmm) REVERT: g 106 GLN cc_start: 0.8952 (mt0) cc_final: 0.8551 (mt0) REVERT: g 136 LYS cc_start: 0.9169 (mmtm) cc_final: 0.8720 (ptmt) REVERT: g 155 ARG cc_start: 0.6601 (pmt-80) cc_final: 0.5853 (ptp90) REVERT: h 34 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8416 (mm-30) REVERT: h 49 GLU cc_start: 0.8257 (pt0) cc_final: 0.7695 (pt0) REVERT: h 99 GLU cc_start: 0.8859 (tp30) cc_final: 0.8626 (tp30) REVERT: h 132 GLU cc_start: 0.8085 (tt0) cc_final: 0.7824 (tt0) REVERT: i 48 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8271 (mm-30) REVERT: i 73 GLN cc_start: 0.8451 (mt0) cc_final: 0.8189 (mt0) REVERT: j 13 HIS cc_start: 0.7993 (p-80) cc_final: 0.7759 (p-80) REVERT: j 43 ARG cc_start: 0.7872 (mmm-85) cc_final: 0.7340 (ttt-90) REVERT: j 57 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8511 (ttmm) REVERT: j 95 GLU cc_start: 0.6455 (tm-30) cc_final: 0.5873 (tm-30) REVERT: k 18 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7592 (mtm-85) REVERT: k 43 SER cc_start: 0.8995 (t) cc_final: 0.8759 (t) REVERT: k 62 GLN cc_start: 0.8633 (tm-30) cc_final: 0.8336 (tm-30) REVERT: k 93 GLN cc_start: 0.8057 (tp-100) cc_final: 0.7578 (tp-100) REVERT: k 104 GLN cc_start: 0.8117 (tt0) cc_final: 0.7659 (tt0) REVERT: l 37 CYS cc_start: 0.9158 (m) cc_final: 0.8686 (m) REVERT: l 120 TYR cc_start: 0.8594 (m-80) cc_final: 0.8382 (m-80) REVERT: m 12 ASN cc_start: 0.7690 (m-40) cc_final: 0.6786 (t0) REVERT: m 67 GLU cc_start: 0.6932 (mm-30) cc_final: 0.6720 (mm-30) REVERT: m 70 LEU cc_start: 0.8571 (tp) cc_final: 0.8280 (tp) REVERT: m 82 MET cc_start: 0.7852 (mtt) cc_final: 0.7615 (mtt) REVERT: n 3 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.7128 (ttm-80) REVERT: n 8 GLU cc_start: 0.8407 (tp30) cc_final: 0.8046 (tp30) REVERT: n 9 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7694 (ttmm) REVERT: n 50 LYS cc_start: 0.8945 (ttmt) cc_final: 0.8539 (ttmm) REVERT: o 34 LEU cc_start: 0.9247 (tp) cc_final: 0.8976 (tt) REVERT: o 35 ARG cc_start: 0.9208 (ttm-80) cc_final: 0.8841 (mtm110) REVERT: o 83 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8465 (tm-30) REVERT: p 14 ASN cc_start: 0.9456 (t0) cc_final: 0.8809 (t0) REVERT: p 27 LYS cc_start: 0.7807 (ptmt) cc_final: 0.7334 (pttt) REVERT: p 39 TYR cc_start: 0.8940 (t80) cc_final: 0.8276 (t80) REVERT: q 46 ASP cc_start: 0.8430 (t70) cc_final: 0.7659 (t0) REVERT: q 91 ARG cc_start: 0.8755 (mmm-85) cc_final: 0.8408 (mtp-110) REVERT: r 33 ASP cc_start: 0.8876 (t0) cc_final: 0.8479 (t0) REVERT: r 51 LEU cc_start: 0.8854 (mt) cc_final: 0.8507 (mt) REVERT: r 68 LYS cc_start: 0.8670 (tppt) cc_final: 0.8467 (tppt) REVERT: r 84 LYS cc_start: 0.9080 (ptmm) cc_final: 0.8689 (ptmm) REVERT: s 5 LEU cc_start: 0.8744 (pp) cc_final: 0.8300 (mt) REVERT: s 12 ASP cc_start: 0.8626 (m-30) cc_final: 0.7993 (m-30) REVERT: s 35 SER cc_start: 0.9304 (m) cc_final: 0.8109 (t) REVERT: s 71 LEU cc_start: 0.8694 (mp) cc_final: 0.8406 (mp) REVERT: u 20 LYS cc_start: 0.8486 (tttm) cc_final: 0.8121 (ttpp) outliers start: 350 outliers final: 296 residues processed: 1825 average time/residue: 1.3424 time to fit residues: 4192.4165 Evaluate side-chains 1952 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 310 poor density : 1642 time to evaluate : 6.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 176 ARG Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 130 ASN Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 72 ILE Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 41 GLU Chi-restraints excluded: chain I residue 52 ARG Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 74 ARG Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain N residue 122 VAL Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 7 TYR Chi-restraints excluded: chain O residue 28 SER Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 77 ILE Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 114 ILE Chi-restraints excluded: chain P residue 5 ASP Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 125 VAL Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain Q residue 21 THR Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 54 MET Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 133 ARG Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 59 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 78 LYS Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 42 ASP Chi-restraints excluded: chain S residue 47 THR Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 75 GLU Chi-restraints excluded: chain S residue 92 TYR Chi-restraints excluded: chain S residue 112 PHE Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 38 ASN Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 80 SER Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain T residue 102 ILE Chi-restraints excluded: chain T residue 104 ASN Chi-restraints excluded: chain U residue 18 LEU Chi-restraints excluded: chain U residue 29 SER Chi-restraints excluded: chain U residue 44 ASN Chi-restraints excluded: chain U residue 80 ILE Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain V residue 14 VAL Chi-restraints excluded: chain V residue 92 THR Chi-restraints excluded: chain W residue 13 SER Chi-restraints excluded: chain W residue 17 VAL Chi-restraints excluded: chain W residue 62 HIS Chi-restraints excluded: chain W residue 66 GLU Chi-restraints excluded: chain W residue 69 LEU Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 14 SER Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 75 ASP Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Z residue 34 ASN Chi-restraints excluded: chain Z residue 50 GLN Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 125 LEU Chi-restraints excluded: chain Z residue 137 ILE Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 165 VAL Chi-restraints excluded: chain 0 residue 10 THR Chi-restraints excluded: chain 0 residue 58 THR Chi-restraints excluded: chain 0 residue 59 LEU Chi-restraints excluded: chain 0 residue 66 VAL Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 1 residue 14 VAL Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 74 VAL Chi-restraints excluded: chain 1 residue 80 LEU Chi-restraints excluded: chain 1 residue 85 LEU Chi-restraints excluded: chain 1 residue 86 SER Chi-restraints excluded: chain 1 residue 97 LEU Chi-restraints excluded: chain 2 residue 41 ILE Chi-restraints excluded: chain 2 residue 63 VAL Chi-restraints excluded: chain 2 residue 66 GLU Chi-restraints excluded: chain 3 residue 8 LEU Chi-restraints excluded: chain 3 residue 46 ASN Chi-restraints excluded: chain 3 residue 54 VAL Chi-restraints excluded: chain 4 residue 10 VAL Chi-restraints excluded: chain 4 residue 14 ILE Chi-restraints excluded: chain 4 residue 46 GLN Chi-restraints excluded: chain 5 residue 6 VAL Chi-restraints excluded: chain 5 residue 26 THR Chi-restraints excluded: chain 5 residue 29 THR Chi-restraints excluded: chain 5 residue 44 THR Chi-restraints excluded: chain 6 residue 5 VAL Chi-restraints excluded: chain 6 residue 10 LEU Chi-restraints excluded: chain 6 residue 14 THR Chi-restraints excluded: chain 6 residue 23 THR Chi-restraints excluded: chain 6 residue 25 LYS Chi-restraints excluded: chain 6 residue 40 CYS Chi-restraints excluded: chain 7 residue 43 THR Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 37 SER Chi-restraints excluded: chain 9 residue 2 LYS Chi-restraints excluded: chain 9 residue 7 VAL Chi-restraints excluded: chain 9 residue 17 ILE Chi-restraints excluded: chain 9 residue 26 ILE Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain b residue 74 LYS Chi-restraints excluded: chain b residue 107 THR Chi-restraints excluded: chain b residue 119 GLU Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 140 HIS Chi-restraints excluded: chain b residue 160 ASP Chi-restraints excluded: chain b residue 162 ILE Chi-restraints excluded: chain b residue 174 VAL Chi-restraints excluded: chain b residue 180 LEU Chi-restraints excluded: chain b residue 187 LEU Chi-restraints excluded: chain b residue 189 ASP Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 196 LEU Chi-restraints excluded: chain b residue 198 ASP Chi-restraints excluded: chain b residue 210 SER Chi-restraints excluded: chain b residue 222 ILE Chi-restraints excluded: chain c residue 3 ASN Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain c residue 144 SER Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 99 SER Chi-restraints excluded: chain d residue 127 THR Chi-restraints excluded: chain d residue 137 SER Chi-restraints excluded: chain d residue 158 ILE Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 53 LEU Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain e residue 98 THR Chi-restraints excluded: chain e residue 131 ILE Chi-restraints excluded: chain e residue 144 THR Chi-restraints excluded: chain e residue 148 VAL Chi-restraints excluded: chain f residue 7 ASN Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 LEU Chi-restraints excluded: chain f residue 19 LEU Chi-restraints excluded: chain f residue 42 GLU Chi-restraints excluded: chain f residue 43 LEU Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 66 GLU Chi-restraints excluded: chain f residue 67 MET Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain f residue 85 VAL Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain h residue 6 ILE Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 35 ILE Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 45 ILE Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 83 ILE Chi-restraints excluded: chain h residue 120 THR Chi-restraints excluded: chain h residue 123 GLU Chi-restraints excluded: chain i residue 7 THR Chi-restraints excluded: chain i residue 14 VAL Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 41 VAL Chi-restraints excluded: chain i residue 48 GLU Chi-restraints excluded: chain i residue 54 ASP Chi-restraints excluded: chain i residue 56 LEU Chi-restraints excluded: chain i residue 77 ILE Chi-restraints excluded: chain i residue 81 ILE Chi-restraints excluded: chain i residue 89 ASN Chi-restraints excluded: chain i residue 102 LEU Chi-restraints excluded: chain i residue 109 VAL Chi-restraints excluded: chain i residue 125 TYR Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 47 PHE Chi-restraints excluded: chain j residue 49 VAL Chi-restraints excluded: chain j residue 57 LYS Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain j residue 89 ASP Chi-restraints excluded: chain j residue 96 ILE Chi-restraints excluded: chain k residue 18 ARG Chi-restraints excluded: chain k residue 26 ASN Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 98 LEU Chi-restraints excluded: chain k residue 106 LYS Chi-restraints excluded: chain k residue 117 ASN Chi-restraints excluded: chain k residue 119 CYS Chi-restraints excluded: chain l residue 6 THR Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 58 VAL Chi-restraints excluded: chain l residue 62 SER Chi-restraints excluded: chain l residue 66 VAL Chi-restraints excluded: chain l residue 76 ASN Chi-restraints excluded: chain l residue 77 LEU Chi-restraints excluded: chain l residue 89 ARG Chi-restraints excluded: chain l residue 96 VAL Chi-restraints excluded: chain l residue 100 ILE Chi-restraints excluded: chain m residue 27 LYS Chi-restraints excluded: chain m residue 48 LEU Chi-restraints excluded: chain m residue 74 VAL Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain n residue 3 ARG Chi-restraints excluded: chain n residue 9 LYS Chi-restraints excluded: chain o residue 6 GLU Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain p residue 11 SER Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 33 ILE Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain p residue 53 VAL Chi-restraints excluded: chain q residue 36 ILE Chi-restraints excluded: chain q residue 53 LEU Chi-restraints excluded: chain q residue 60 ILE Chi-restraints excluded: chain q residue 61 GLU Chi-restraints excluded: chain q residue 66 SER Chi-restraints excluded: chain q residue 89 LEU Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain r residue 72 ARG Chi-restraints excluded: chain r residue 76 LEU Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 41 VAL Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain t residue 63 ILE Chi-restraints excluded: chain t residue 70 SER Chi-restraints excluded: chain t residue 93 GLU Chi-restraints excluded: chain u residue 13 ILE Chi-restraints excluded: chain u residue 17 THR Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 224 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1047 random chunks: chunk 976 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 577 optimal weight: 0.8980 chunk 739 optimal weight: 20.0000 chunk 573 optimal weight: 5.9990 chunk 852 optimal weight: 0.2980 chunk 565 optimal weight: 50.0000 chunk 1009 optimal weight: 10.0000 chunk 631 optimal weight: 10.0000 chunk 615 optimal weight: 10.0000 chunk 465 optimal weight: 7.9990 overall best weight: 5.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN ** R 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 94 ASN ** V 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 75 ASN ** 0 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 20 HIS ** b 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 98 ASN c 108 ASN c 110 ASN ** d 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 ASN g 148 ASN ** h 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 117 ASN ** m 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 26 GLN ** q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.362 161492 Z= 0.277 Angle : 0.594 29.656 241653 Z= 0.321 Chirality : 0.034 1.901 30609 Planarity : 0.005 0.125 13093 Dihedral : 25.105 179.378 81410 Min Nonbonded Distance : 1.642 Molprobity Statistics. All-atom Clashscore : 62.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.83 % Favored : 93.14 % Rotamer: Outliers : 7.56 % Allowed : 24.41 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.11), residues: 5916 helix: 0.98 (0.12), residues: 1954 sheet: -1.71 (0.15), residues: 1117 loop : -1.11 (0.12), residues: 2845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP 8 34 HIS 0.006 0.001 HIS d 123 PHE 0.026 0.002 PHE E 51 TYR 0.020 0.001 TYR 1 71 ARG 0.009 0.000 ARG 7 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2040 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 365 poor density : 1675 time to evaluate : 9.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: D 16 MET cc_start: 0.9063 (ptm) cc_final: 0.8479 (ptm) REVERT: D 53 PHE cc_start: 0.9174 (m-10) cc_final: 0.8960 (m-10) REVERT: D 84 TYR cc_start: 0.8778 (t80) cc_final: 0.7796 (t80) REVERT: D 172 TYR cc_start: 0.8319 (m-10) cc_final: 0.7777 (m-80) REVERT: D 198 ASN cc_start: 0.8287 (t0) cc_final: 0.7945 (t0) REVERT: D 201 HIS cc_start: 0.8974 (t70) cc_final: 0.8703 (t-90) REVERT: D 226 MET cc_start: 0.8599 (mtm) cc_final: 0.8085 (mtm) REVERT: E 45 THR cc_start: 0.8046 (m) cc_final: 0.7624 (p) REVERT: E 83 ASP cc_start: 0.7865 (m-30) cc_final: 0.7449 (m-30) REVERT: E 154 LYS cc_start: 0.8241 (tppt) cc_final: 0.7925 (tptp) REVERT: F 195 ASP cc_start: 0.8438 (t0) cc_final: 0.8161 (t0) REVERT: F 203 GLN cc_start: 0.9166 (mm-40) cc_final: 0.8263 (tm-30) REVERT: F 204 ASN cc_start: 0.9047 (m-40) cc_final: 0.8687 (m110) REVERT: H 41 MET cc_start: 0.7015 (mmm) cc_final: 0.6408 (mmm) REVERT: I 2 LYS cc_start: 0.8446 (tptt) cc_final: 0.8229 (tptp) REVERT: I 52 ARG cc_start: 0.6907 (OUTLIER) cc_final: 0.6680 (mtm180) REVERT: N 45 ASN cc_start: 0.9037 (p0) cc_final: 0.8584 (p0) REVERT: N 74 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7359 (ttm-80) REVERT: O 12 ASP cc_start: 0.9009 (p0) cc_final: 0.8651 (p0) REVERT: O 20 MET cc_start: 0.8640 (ttm) cc_final: 0.8221 (ttm) REVERT: O 66 LYS cc_start: 0.8736 (tttp) cc_final: 0.7991 (ttmm) REVERT: O 94 ARG cc_start: 0.9079 (mtp85) cc_final: 0.8726 (ttm110) REVERT: O 107 ARG cc_start: 0.8498 (mtp85) cc_final: 0.8093 (mtp180) REVERT: O 108 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8388 (mt-10) REVERT: P 29 LYS cc_start: 0.8715 (ttpp) cc_final: 0.8349 (tttt) REVERT: P 47 ASP cc_start: 0.8393 (t0) cc_final: 0.7576 (t0) REVERT: P 49 ARG cc_start: 0.8192 (mtm180) cc_final: 0.7759 (mtm-85) REVERT: P 148 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7970 (pt) REVERT: Q 9 TYR cc_start: 0.8760 (m-80) cc_final: 0.8271 (m-80) REVERT: Q 17 LEU cc_start: 0.9194 (mm) cc_final: 0.8790 (mm) REVERT: Q 25 ASP cc_start: 0.8587 (p0) cc_final: 0.8188 (p0) REVERT: Q 37 LEU cc_start: 0.8112 (mt) cc_final: 0.7703 (mt) REVERT: Q 60 ARG cc_start: 0.8837 (mmm160) cc_final: 0.8357 (mmm160) REVERT: Q 111 GLU cc_start: 0.7547 (tp30) cc_final: 0.6950 (tp30) REVERT: Q 128 LYS cc_start: 0.8828 (mtmt) cc_final: 0.8381 (mtmt) REVERT: Q 133 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.6769 (mtp85) REVERT: R 8 ARG cc_start: 0.9050 (mpt-90) cc_final: 0.8221 (mtt-85) REVERT: R 9 LYS cc_start: 0.8468 (mttp) cc_final: 0.7436 (mttp) REVERT: R 30 THR cc_start: 0.9312 (OUTLIER) cc_final: 0.9074 (p) REVERT: R 31 HIS cc_start: 0.8200 (m90) cc_final: 0.7675 (m-70) REVERT: R 43 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7726 (mm-30) REVERT: R 78 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8741 (tttt) REVERT: S 92 TYR cc_start: 0.8926 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: T 46 GLU cc_start: 0.7809 (tt0) cc_final: 0.7404 (tt0) REVERT: T 90 GLN cc_start: 0.7920 (tp-100) cc_final: 0.7715 (tp40) REVERT: T 113 LYS cc_start: 0.8336 (mmmt) cc_final: 0.7978 (mmmt) REVERT: U 30 LYS cc_start: 0.8936 (mmtt) cc_final: 0.8710 (mmmt) REVERT: U 32 PHE cc_start: 0.8806 (t80) cc_final: 0.8462 (t80) REVERT: U 39 LEU cc_start: 0.9017 (mm) cc_final: 0.8631 (mm) REVERT: V 1 MET cc_start: 0.7231 (tpt) cc_final: 0.6535 (tpt) REVERT: V 93 GLU cc_start: 0.7308 (tm-30) cc_final: 0.7052 (tm-30) REVERT: V 100 ARG cc_start: 0.8310 (mtm110) cc_final: 0.8088 (mtm110) REVERT: W 52 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8303 (tp30) REVERT: W 60 ASN cc_start: 0.9212 (t0) cc_final: 0.8893 (t0) REVERT: X 9 LEU cc_start: 0.8555 (mt) cc_final: 0.8140 (mt) REVERT: X 15 GLU cc_start: 0.9139 (mp0) cc_final: 0.8919 (mp0) REVERT: Y 11 ASP cc_start: 0.7675 (m-30) cc_final: 0.7115 (m-30) REVERT: Y 43 ASN cc_start: 0.8029 (t0) cc_final: 0.7315 (t0) REVERT: Z 6 LYS cc_start: 0.9293 (mtpp) cc_final: 0.8991 (ttmt) REVERT: Z 8 TYR cc_start: 0.8786 (m-10) cc_final: 0.8554 (m-10) REVERT: Z 44 PHE cc_start: 0.9197 (t80) cc_final: 0.8897 (t80) REVERT: Z 54 HIS cc_start: 0.8274 (m90) cc_final: 0.7291 (m90) REVERT: Z 78 LYS cc_start: 0.8189 (mttp) cc_final: 0.7556 (mttp) REVERT: Z 138 GLU cc_start: 0.7310 (mt-10) cc_final: 0.6743 (tm-30) REVERT: 0 19 LYS cc_start: 0.8642 (mmpt) cc_final: 0.8175 (mmtm) REVERT: 0 38 VAL cc_start: 0.9401 (t) cc_final: 0.9182 (t) REVERT: 1 50 ARG cc_start: 0.8663 (ttm-80) cc_final: 0.8322 (ttm-80) REVERT: 1 56 GLN cc_start: 0.8996 (mm110) cc_final: 0.8699 (mm-40) REVERT: 2 20 GLU cc_start: 0.9407 (mm-30) cc_final: 0.9066 (mp0) REVERT: 2 27 GLU cc_start: 0.9361 (mt-10) cc_final: 0.9104 (tp30) REVERT: 2 51 ARG cc_start: 0.8819 (ttm110) cc_final: 0.8454 (ttm110) REVERT: 3 38 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7737 (mm-30) REVERT: 4 46 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.5578 (tp-100) REVERT: 5 39 MET cc_start: 0.8925 (mmm) cc_final: 0.8259 (mmm) REVERT: 6 25 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7170 (pttm) REVERT: 7 22 MET cc_start: 0.8794 (tpp) cc_final: 0.8413 (mmt) REVERT: 7 23 ARG cc_start: 0.8835 (ttm110) cc_final: 0.8478 (ttm170) REVERT: 7 47 ARG cc_start: 0.8163 (mtm110) cc_final: 0.7778 (mtm110) REVERT: 8 21 LYS cc_start: 0.8137 (mttt) cc_final: 0.7489 (mtmt) REVERT: b 7 VAL cc_start: 0.6704 (t) cc_final: 0.6363 (t) REVERT: b 8 LYS cc_start: 0.7858 (pmmt) cc_final: 0.7303 (ptmt) REVERT: b 25 ASN cc_start: 0.8349 (t0) cc_final: 0.8031 (t0) REVERT: b 122 PHE cc_start: 0.8350 (t80) cc_final: 0.7965 (t80) REVERT: b 170 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8054 (mm-30) REVERT: b 192 SER cc_start: 0.7811 (m) cc_final: 0.7296 (p) REVERT: b 220 ASP cc_start: 0.9217 (OUTLIER) cc_final: 0.8908 (m-30) REVERT: c 19 GLU cc_start: 0.8046 (mp0) cc_final: 0.7660 (mp0) REVERT: c 28 GLN cc_start: 0.8663 (mt0) cc_final: 0.8419 (mm-40) REVERT: c 104 GLN cc_start: 0.8839 (tp40) cc_final: 0.8604 (tp40) REVERT: c 115 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8262 (mt) REVERT: c 118 GLN cc_start: 0.9001 (mt0) cc_final: 0.8708 (mt0) REVERT: c 181 ASN cc_start: 0.8267 (t0) cc_final: 0.7967 (t0) REVERT: c 183 ASP cc_start: 0.8510 (t0) cc_final: 0.7920 (t0) REVERT: c 190 ARG cc_start: 0.8002 (ptp90) cc_final: 0.7630 (ptp-170) REVERT: c 193 TYR cc_start: 0.8741 (p90) cc_final: 0.8052 (p90) REVERT: d 33 MET cc_start: 0.8786 (tpt) cc_final: 0.8350 (tpt) REVERT: d 50 ARG cc_start: 0.8550 (ttt180) cc_final: 0.8135 (tpp80) REVERT: d 165 MET cc_start: 0.7978 (tpp) cc_final: 0.7737 (tpp) REVERT: d 177 ASP cc_start: 0.8068 (t0) cc_final: 0.7776 (t0) REVERT: e 47 LYS cc_start: 0.9064 (ptpp) cc_final: 0.8830 (ptpp) REVERT: e 57 LYS cc_start: 0.8932 (ttmp) cc_final: 0.8566 (mtpp) REVERT: e 61 TYR cc_start: 0.9339 (m-80) cc_final: 0.9012 (m-80) REVERT: e 65 ASN cc_start: 0.8253 (t0) cc_final: 0.8030 (t0) REVERT: e 82 VAL cc_start: 0.9059 (t) cc_final: 0.8754 (m) REVERT: e 84 PHE cc_start: 0.8797 (t80) cc_final: 0.8392 (t80) REVERT: e 88 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8586 (tttt) REVERT: e 111 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8074 (mt-10) REVERT: e 125 SER cc_start: 0.8773 (t) cc_final: 0.8369 (p) REVERT: f 62 TRP cc_start: 0.7430 (t60) cc_final: 0.6618 (t60) REVERT: g 53 LYS cc_start: 0.8704 (mtpp) cc_final: 0.8301 (mmtm) REVERT: g 106 GLN cc_start: 0.8950 (mt0) cc_final: 0.8551 (mt0) REVERT: g 136 LYS cc_start: 0.9167 (mmtm) cc_final: 0.8716 (ptmt) REVERT: g 155 ARG cc_start: 0.6605 (pmt-80) cc_final: 0.5819 (ptp90) REVERT: h 27 PRO cc_start: 0.8664 (Cg_exo) cc_final: 0.8451 (Cg_endo) REVERT: h 34 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8431 (mm-30) REVERT: h 49 GLU cc_start: 0.8246 (pt0) cc_final: 0.7639 (pt0) REVERT: h 99 GLU cc_start: 0.8899 (tp30) cc_final: 0.8646 (tp30) REVERT: h 132 GLU cc_start: 0.8148 (tt0) cc_final: 0.7869 (tt0) REVERT: i 48 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8278 (mm-30) REVERT: i 73 GLN cc_start: 0.8399 (mt0) cc_final: 0.8152 (mt0) REVERT: j 13 HIS cc_start: 0.8020 (p-80) cc_final: 0.7615 (p-80) REVERT: j 43 ARG cc_start: 0.7893 (mmm-85) cc_final: 0.7338 (ttt-90) REVERT: j 95 GLU cc_start: 0.6433 (tm-30) cc_final: 0.5862 (tm-30) REVERT: k 18 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7765 (mtm-85) REVERT: k 43 SER cc_start: 0.9001 (t) cc_final: 0.8756 (t) REVERT: k 62 GLN cc_start: 0.8652 (tm-30) cc_final: 0.8314 (tm-30) REVERT: k 93 GLN cc_start: 0.7970 (tp-100) cc_final: 0.7519 (tp-100) REVERT: k 104 GLN cc_start: 0.8121 (tt0) cc_final: 0.7626 (tt0) REVERT: k 116 HIS cc_start: 0.7292 (m90) cc_final: 0.7013 (m-70) REVERT: k 123 LYS cc_start: 0.9640 (ttmt) cc_final: 0.9244 (ttmt) REVERT: l 37 CYS cc_start: 0.9124 (m) cc_final: 0.8630 (m) REVERT: m 12 ASN cc_start: 0.7617 (m-40) cc_final: 0.6682 (t0) REVERT: m 67 GLU cc_start: 0.6946 (mm-30) cc_final: 0.6729 (mm-30) REVERT: m 70 LEU cc_start: 0.8600 (tp) cc_final: 0.8287 (tp) REVERT: n 3 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7072 (ttm-80) REVERT: n 8 GLU cc_start: 0.8396 (tp30) cc_final: 0.7986 (tp30) REVERT: n 9 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7647 (ttmm) REVERT: n 50 LYS cc_start: 0.8962 (ttmt) cc_final: 0.8522 (ttmm) REVERT: o 35 ARG cc_start: 0.9239 (ttm-80) cc_final: 0.8917 (mtm110) REVERT: o 83 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8472 (tm-30) REVERT: p 14 ASN cc_start: 0.9441 (t0) cc_final: 0.8776 (t0) REVERT: p 27 LYS cc_start: 0.7807 (ptmt) cc_final: 0.7321 (pttt) REVERT: p 39 TYR cc_start: 0.9016 (t80) cc_final: 0.8320 (t80) REVERT: q 46 ASP cc_start: 0.8363 (t70) cc_final: 0.7715 (t70) REVERT: q 91 ARG cc_start: 0.8787 (mmm-85) cc_final: 0.8561 (mtp-110) REVERT: r 33 ASP cc_start: 0.8865 (t0) cc_final: 0.8464 (t0) REVERT: r 51 LEU cc_start: 0.8850 (mt) cc_final: 0.8501 (mt) REVERT: r 84 LYS cc_start: 0.9095 (ptmm) cc_final: 0.8736 (ptmm) REVERT: s 5 LEU cc_start: 0.8794 (pp) cc_final: 0.8383 (mt) REVERT: s 12 ASP cc_start: 0.8638 (m-30) cc_final: 0.7962 (m-30) REVERT: s 35 SER cc_start: 0.9291 (m) cc_final: 0.8157 (t) REVERT: u 20 LYS cc_start: 0.8528 (tttm) cc_final: 0.8117 (ttpp) outliers start: 365 outliers final: 306 residues processed: 1821 average time/residue: 1.3965 time to fit residues: 4339.5720 Evaluate side-chains 1962 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 322 poor density : 1640 time to evaluate : 6.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain E residue 143 ASN Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 130 ASN Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 41 GLU Chi-restraints excluded: chain I residue 52 ARG Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 74 ARG Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 104 LYS Chi-restraints excluded: chain N residue 122 VAL Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 7 TYR Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 28 SER Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 77 ILE Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 114 ILE Chi-restraints excluded: chain P residue 5 ASP Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 38 GLN Chi-restraints excluded: chain P residue 59 LEU Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 125 VAL Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain Q residue 21 THR Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 54 MET Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 133 ARG Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 59 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 78 LYS Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 42 ASP Chi-restraints excluded: chain S residue 47 THR Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 75 GLU Chi-restraints excluded: chain S residue 92 TYR Chi-restraints excluded: chain S residue 112 PHE Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 38 ASN Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 80 SER Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain T residue 102 ILE Chi-restraints excluded: chain T residue 104 ASN Chi-restraints excluded: chain U residue 18 LEU Chi-restraints excluded: chain U residue 29 SER Chi-restraints excluded: chain U residue 80 ILE Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 110 VAL Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 14 VAL Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 92 THR Chi-restraints excluded: chain W residue 13 SER Chi-restraints excluded: chain W residue 53 SER Chi-restraints excluded: chain W residue 62 HIS Chi-restraints excluded: chain W residue 66 GLU Chi-restraints excluded: chain W residue 69 LEU Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 14 SER Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 75 ASP Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 83 THR Chi-restraints excluded: chain Z residue 50 GLN Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 125 LEU Chi-restraints excluded: chain Z residue 137 ILE Chi-restraints excluded: chain Z residue 148 ASP Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 165 VAL Chi-restraints excluded: chain 0 residue 10 THR Chi-restraints excluded: chain 0 residue 58 THR Chi-restraints excluded: chain 0 residue 59 LEU Chi-restraints excluded: chain 0 residue 66 VAL Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 1 residue 11 ARG Chi-restraints excluded: chain 1 residue 14 VAL Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 74 VAL Chi-restraints excluded: chain 1 residue 80 LEU Chi-restraints excluded: chain 1 residue 86 SER Chi-restraints excluded: chain 2 residue 12 GLU Chi-restraints excluded: chain 2 residue 41 ILE Chi-restraints excluded: chain 2 residue 63 VAL Chi-restraints excluded: chain 2 residue 66 GLU Chi-restraints excluded: chain 3 residue 8 LEU Chi-restraints excluded: chain 3 residue 46 ASN Chi-restraints excluded: chain 3 residue 54 VAL Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 10 VAL Chi-restraints excluded: chain 4 residue 14 ILE Chi-restraints excluded: chain 4 residue 46 GLN Chi-restraints excluded: chain 5 residue 6 VAL Chi-restraints excluded: chain 5 residue 26 THR Chi-restraints excluded: chain 5 residue 29 THR Chi-restraints excluded: chain 5 residue 44 THR Chi-restraints excluded: chain 6 residue 5 VAL Chi-restraints excluded: chain 6 residue 7 ILE Chi-restraints excluded: chain 6 residue 23 THR Chi-restraints excluded: chain 6 residue 25 LYS Chi-restraints excluded: chain 6 residue 40 CYS Chi-restraints excluded: chain 7 residue 43 THR Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 22 VAL Chi-restraints excluded: chain 9 residue 2 LYS Chi-restraints excluded: chain 9 residue 7 VAL Chi-restraints excluded: chain 9 residue 17 ILE Chi-restraints excluded: chain 9 residue 26 ILE Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain b residue 107 THR Chi-restraints excluded: chain b residue 119 GLU Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 140 HIS Chi-restraints excluded: chain b residue 160 ASP Chi-restraints excluded: chain b residue 162 ILE Chi-restraints excluded: chain b residue 174 VAL Chi-restraints excluded: chain b residue 180 LEU Chi-restraints excluded: chain b residue 187 LEU Chi-restraints excluded: chain b residue 189 ASP Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 196 LEU Chi-restraints excluded: chain b residue 198 ASP Chi-restraints excluded: chain b residue 210 SER Chi-restraints excluded: chain b residue 220 ASP Chi-restraints excluded: chain b residue 222 ILE Chi-restraints excluded: chain c residue 3 ASN Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 108 ASN Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain c residue 115 LEU Chi-restraints excluded: chain c residue 144 SER Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 78 LEU Chi-restraints excluded: chain d residue 99 SER Chi-restraints excluded: chain d residue 127 THR Chi-restraints excluded: chain d residue 137 SER Chi-restraints excluded: chain d residue 158 ILE Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 53 LEU Chi-restraints excluded: chain e residue 88 LYS Chi-restraints excluded: chain e residue 131 ILE Chi-restraints excluded: chain e residue 144 THR Chi-restraints excluded: chain f residue 7 ASN Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 LEU Chi-restraints excluded: chain f residue 19 LEU Chi-restraints excluded: chain f residue 40 VAL Chi-restraints excluded: chain f residue 42 GLU Chi-restraints excluded: chain f residue 43 LEU Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 66 GLU Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain f residue 85 VAL Chi-restraints excluded: chain f residue 90 VAL Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain h residue 6 ILE Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 35 ILE Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 45 ILE Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 83 ILE Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain h residue 120 THR Chi-restraints excluded: chain i residue 7 THR Chi-restraints excluded: chain i residue 14 VAL Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 41 VAL Chi-restraints excluded: chain i residue 47 LEU Chi-restraints excluded: chain i residue 48 GLU Chi-restraints excluded: chain i residue 54 ASP Chi-restraints excluded: chain i residue 81 ILE Chi-restraints excluded: chain i residue 89 ASN Chi-restraints excluded: chain i residue 102 LEU Chi-restraints excluded: chain i residue 109 VAL Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 47 PHE Chi-restraints excluded: chain j residue 49 VAL Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain j residue 89 ASP Chi-restraints excluded: chain j residue 96 ILE Chi-restraints excluded: chain k residue 18 ARG Chi-restraints excluded: chain k residue 26 ASN Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain k residue 47 VAL Chi-restraints excluded: chain k residue 98 LEU Chi-restraints excluded: chain k residue 108 ILE Chi-restraints excluded: chain l residue 6 THR Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 18 VAL Chi-restraints excluded: chain l residue 58 VAL Chi-restraints excluded: chain l residue 62 SER Chi-restraints excluded: chain l residue 66 VAL Chi-restraints excluded: chain l residue 76 ASN Chi-restraints excluded: chain l residue 77 LEU Chi-restraints excluded: chain l residue 89 ARG Chi-restraints excluded: chain l residue 96 VAL Chi-restraints excluded: chain l residue 100 ILE Chi-restraints excluded: chain m residue 27 LYS Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain m residue 48 LEU Chi-restraints excluded: chain m residue 74 VAL Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain n residue 3 ARG Chi-restraints excluded: chain n residue 9 LYS Chi-restraints excluded: chain o residue 6 GLU Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain o residue 31 LEU Chi-restraints excluded: chain o residue 32 LEU Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain o residue 87 ILE Chi-restraints excluded: chain p residue 11 SER Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 33 ILE Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain q residue 36 ILE Chi-restraints excluded: chain q residue 53 LEU Chi-restraints excluded: chain q residue 60 ILE Chi-restraints excluded: chain q residue 66 SER Chi-restraints excluded: chain q residue 89 LEU Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain r residue 70 ILE Chi-restraints excluded: chain r residue 72 ARG Chi-restraints excluded: chain r residue 76 LEU Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 40 ILE Chi-restraints excluded: chain s residue 41 VAL Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 63 ILE Chi-restraints excluded: chain t residue 82 SER Chi-restraints excluded: chain u residue 13 ILE Chi-restraints excluded: chain u residue 17 THR Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 224 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1047 random chunks: chunk 624 optimal weight: 3.9990 chunk 402 optimal weight: 0.2980 chunk 602 optimal weight: 8.9990 chunk 303 optimal weight: 10.0000 chunk 198 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 641 optimal weight: 20.0000 chunk 687 optimal weight: 20.0000 chunk 498 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 793 optimal weight: 4.9990 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 HIS ** E 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN ** R 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 94 ASN ** V 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 75 ASN ** 0 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 20 HIS ** b 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 140 HIS ** b 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 98 ASN ** c 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 ASN g 148 ASN ** h 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 117 ASN ** m 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 26 GLN ** q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.362 161492 Z= 0.272 Angle : 0.588 29.653 241653 Z= 0.318 Chirality : 0.034 1.905 30609 Planarity : 0.005 0.125 13093 Dihedral : 25.073 179.777 81410 Min Nonbonded Distance : 1.644 Molprobity Statistics. All-atom Clashscore : 62.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.98 % Favored : 92.97 % Rotamer: Outliers : 7.37 % Allowed : 25.09 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.11), residues: 5916 helix: 1.00 (0.12), residues: 1976 sheet: -1.64 (0.15), residues: 1101 loop : -1.08 (0.12), residues: 2839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP g 103 HIS 0.006 0.001 HIS 1 66 PHE 0.022 0.002 PHE E 51 TYR 0.019 0.001 TYR 1 71 ARG 0.010 0.000 ARG W 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2030 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 356 poor density : 1674 time to evaluate : 6.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: D 16 MET cc_start: 0.9063 (ptm) cc_final: 0.8479 (ptm) REVERT: D 28 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7232 (pm20) REVERT: D 53 PHE cc_start: 0.9175 (m-10) cc_final: 0.8921 (m-80) REVERT: D 54 ARG cc_start: 0.8081 (mtp180) cc_final: 0.7635 (mtm180) REVERT: D 84 TYR cc_start: 0.8795 (t80) cc_final: 0.7816 (t80) REVERT: D 157 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7430 (ptt-90) REVERT: D 172 TYR cc_start: 0.8346 (m-10) cc_final: 0.7815 (m-80) REVERT: D 198 ASN cc_start: 0.8275 (t0) cc_final: 0.7905 (t0) REVERT: D 201 HIS cc_start: 0.8964 (t70) cc_final: 0.8701 (t-90) REVERT: D 226 MET cc_start: 0.8532 (mtm) cc_final: 0.8031 (mtm) REVERT: E 45 THR cc_start: 0.8037 (m) cc_final: 0.7612 (p) REVERT: E 83 ASP cc_start: 0.7844 (m-30) cc_final: 0.7416 (m-30) REVERT: F 195 ASP cc_start: 0.8434 (t0) cc_final: 0.8154 (t0) REVERT: F 203 GLN cc_start: 0.9167 (mm-40) cc_final: 0.8250 (tm-30) REVERT: F 204 ASN cc_start: 0.9040 (m-40) cc_final: 0.8688 (m110) REVERT: H 41 MET cc_start: 0.7040 (mmm) cc_final: 0.6443 (mmm) REVERT: H 163 TYR cc_start: 0.8977 (m-80) cc_final: 0.8640 (m-80) REVERT: N 45 ASN cc_start: 0.9022 (p0) cc_final: 0.8626 (p0) REVERT: N 74 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7323 (ttm-80) REVERT: O 9 GLU cc_start: 0.7161 (tm-30) cc_final: 0.6703 (tm-30) REVERT: O 12 ASP cc_start: 0.9032 (p0) cc_final: 0.8671 (p0) REVERT: O 20 MET cc_start: 0.8633 (ttm) cc_final: 0.8215 (ttm) REVERT: O 66 LYS cc_start: 0.8731 (tttp) cc_final: 0.7992 (ttmm) REVERT: O 94 ARG cc_start: 0.9070 (mtp85) cc_final: 0.8700 (ttm110) REVERT: O 107 ARG cc_start: 0.8537 (mtp85) cc_final: 0.8149 (mtp180) REVERT: O 108 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8392 (mt-10) REVERT: P 29 LYS cc_start: 0.8695 (ttpp) cc_final: 0.8358 (tttt) REVERT: P 47 ASP cc_start: 0.8399 (t0) cc_final: 0.7748 (t0) REVERT: P 49 ARG cc_start: 0.8163 (mtm180) cc_final: 0.7816 (mtm-85) REVERT: P 148 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8039 (pt) REVERT: Q 9 TYR cc_start: 0.8767 (m-80) cc_final: 0.8298 (m-80) REVERT: Q 17 LEU cc_start: 0.9202 (mm) cc_final: 0.8844 (mm) REVERT: Q 25 ASP cc_start: 0.8566 (p0) cc_final: 0.8112 (p0) REVERT: Q 37 LEU cc_start: 0.8113 (mt) cc_final: 0.7708 (mt) REVERT: Q 60 ARG cc_start: 0.8805 (mmm160) cc_final: 0.8308 (mmm160) REVERT: Q 111 GLU cc_start: 0.7548 (tp30) cc_final: 0.7298 (tp30) REVERT: Q 115 MET cc_start: 0.8595 (mmp) cc_final: 0.8384 (mmm) REVERT: Q 139 GLU cc_start: 0.8407 (mp0) cc_final: 0.8121 (mp0) REVERT: R 8 ARG cc_start: 0.9014 (mpt-90) cc_final: 0.8255 (mtt-85) REVERT: R 9 LYS cc_start: 0.8452 (mttp) cc_final: 0.7423 (mttp) REVERT: R 30 THR cc_start: 0.9314 (OUTLIER) cc_final: 0.9075 (p) REVERT: R 31 HIS cc_start: 0.8180 (m90) cc_final: 0.7644 (m-70) REVERT: R 43 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7708 (mm-30) REVERT: R 78 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8747 (tttt) REVERT: S 92 TYR cc_start: 0.8925 (OUTLIER) cc_final: 0.8005 (m-80) REVERT: T 46 GLU cc_start: 0.7820 (tt0) cc_final: 0.7395 (tt0) REVERT: T 90 GLN cc_start: 0.7916 (tp-100) cc_final: 0.7705 (tp40) REVERT: U 30 LYS cc_start: 0.8928 (mmtt) cc_final: 0.8715 (mmmt) REVERT: U 32 PHE cc_start: 0.8808 (t80) cc_final: 0.8465 (t80) REVERT: U 39 LEU cc_start: 0.9037 (mm) cc_final: 0.8665 (mm) REVERT: V 1 MET cc_start: 0.7266 (tpt) cc_final: 0.6610 (tpt) REVERT: V 93 GLU cc_start: 0.7295 (tm-30) cc_final: 0.7033 (tm-30) REVERT: V 100 ARG cc_start: 0.8343 (mtm110) cc_final: 0.8129 (mtm110) REVERT: W 52 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8310 (tp30) REVERT: W 60 ASN cc_start: 0.9219 (t0) cc_final: 0.8912 (t0) REVERT: W 102 HIS cc_start: 0.8105 (m170) cc_final: 0.7899 (m-70) REVERT: X 9 LEU cc_start: 0.8561 (mt) cc_final: 0.8149 (mt) REVERT: X 15 GLU cc_start: 0.9140 (mp0) cc_final: 0.8914 (mp0) REVERT: X 93 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7247 (mm-30) REVERT: Y 11 ASP cc_start: 0.7664 (m-30) cc_final: 0.7128 (m-30) REVERT: Y 43 ASN cc_start: 0.8042 (t0) cc_final: 0.7340 (t0) REVERT: Z 6 LYS cc_start: 0.9290 (mtpp) cc_final: 0.8979 (ttmt) REVERT: Z 8 TYR cc_start: 0.8810 (m-10) cc_final: 0.8577 (m-10) REVERT: Z 44 PHE cc_start: 0.9216 (t80) cc_final: 0.8976 (t80) REVERT: Z 54 HIS cc_start: 0.8170 (m90) cc_final: 0.7143 (m90) REVERT: Z 65 GLN cc_start: 0.8263 (tp-100) cc_final: 0.8008 (tp-100) REVERT: Z 78 LYS cc_start: 0.8201 (mttp) cc_final: 0.7560 (mttp) REVERT: Z 138 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6648 (tm-30) REVERT: 0 12 ASN cc_start: 0.8635 (m110) cc_final: 0.8435 (m-40) REVERT: 0 19 LYS cc_start: 0.8667 (mmpt) cc_final: 0.8204 (mmtm) REVERT: 0 38 VAL cc_start: 0.9401 (t) cc_final: 0.9180 (t) REVERT: 1 50 ARG cc_start: 0.8673 (ttm-80) cc_final: 0.8334 (ttm-80) REVERT: 1 56 GLN cc_start: 0.8996 (mm110) cc_final: 0.8697 (mm-40) REVERT: 2 20 GLU cc_start: 0.9421 (mm-30) cc_final: 0.9067 (mp0) REVERT: 2 27 GLU cc_start: 0.9340 (mt-10) cc_final: 0.9106 (tp30) REVERT: 2 51 ARG cc_start: 0.8819 (ttm110) cc_final: 0.8452 (ttm110) REVERT: 3 57 GLU cc_start: 0.8563 (tt0) cc_final: 0.8304 (tt0) REVERT: 4 46 GLN cc_start: 0.7341 (OUTLIER) cc_final: 0.5555 (tp-100) REVERT: 5 39 MET cc_start: 0.8927 (mmm) cc_final: 0.8259 (mmm) REVERT: 6 25 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7311 (pttm) REVERT: 7 22 MET cc_start: 0.8704 (tpp) cc_final: 0.8432 (mmt) REVERT: 7 23 ARG cc_start: 0.8847 (ttm110) cc_final: 0.8527 (ttm170) REVERT: 8 21 LYS cc_start: 0.8129 (mttt) cc_final: 0.7473 (mtmt) REVERT: b 7 VAL cc_start: 0.6548 (t) cc_final: 0.6286 (t) REVERT: b 8 LYS cc_start: 0.7824 (pmmt) cc_final: 0.7207 (ptmt) REVERT: b 25 ASN cc_start: 0.8368 (t0) cc_final: 0.8048 (t0) REVERT: b 74 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7169 (ptpp) REVERT: b 122 PHE cc_start: 0.8144 (t80) cc_final: 0.7924 (t80) REVERT: b 170 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8122 (mm-30) REVERT: b 192 SER cc_start: 0.7857 (m) cc_final: 0.7343 (p) REVERT: c 19 GLU cc_start: 0.8058 (mp0) cc_final: 0.7623 (mp0) REVERT: c 28 GLN cc_start: 0.8672 (mt0) cc_final: 0.8439 (mm-40) REVERT: c 104 GLN cc_start: 0.8848 (tp40) cc_final: 0.8622 (tp40) REVERT: c 110 ASN cc_start: 0.8870 (m-40) cc_final: 0.8551 (m-40) REVERT: c 115 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8252 (mt) REVERT: c 118 GLN cc_start: 0.8977 (mt0) cc_final: 0.8643 (mt0) REVERT: c 183 ASP cc_start: 0.8527 (t0) cc_final: 0.7955 (t0) REVERT: c 190 ARG cc_start: 0.8036 (ptp90) cc_final: 0.7689 (ptp-170) REVERT: c 193 TYR cc_start: 0.8739 (p90) cc_final: 0.8068 (p90) REVERT: d 33 MET cc_start: 0.8735 (tpt) cc_final: 0.8280 (tpt) REVERT: d 50 ARG cc_start: 0.8544 (ttt180) cc_final: 0.8122 (tpp80) REVERT: d 57 ARG cc_start: 0.8185 (mtt90) cc_final: 0.7917 (mtm-85) REVERT: d 165 MET cc_start: 0.8000 (tpp) cc_final: 0.7752 (tpp) REVERT: d 177 ASP cc_start: 0.8123 (t0) cc_final: 0.7842 (t0) REVERT: e 57 LYS cc_start: 0.8934 (ttmp) cc_final: 0.8563 (mtpp) REVERT: e 61 TYR cc_start: 0.9337 (m-80) cc_final: 0.9032 (m-80) REVERT: e 65 ASN cc_start: 0.8300 (t0) cc_final: 0.8045 (t0) REVERT: e 82 VAL cc_start: 0.9075 (t) cc_final: 0.8774 (m) REVERT: e 84 PHE cc_start: 0.8810 (t80) cc_final: 0.8504 (t80) REVERT: e 88 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8584 (tttt) REVERT: e 111 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8083 (mt-10) REVERT: e 125 SER cc_start: 0.8804 (t) cc_final: 0.8399 (p) REVERT: f 62 TRP cc_start: 0.7379 (t60) cc_final: 0.6561 (t60) REVERT: g 53 LYS cc_start: 0.8628 (mtpp) cc_final: 0.8305 (mmtm) REVERT: g 106 GLN cc_start: 0.8939 (mt0) cc_final: 0.8551 (mt0) REVERT: g 136 LYS cc_start: 0.9158 (mmtm) cc_final: 0.8704 (ptmt) REVERT: g 148 ASN cc_start: 0.8485 (m-40) cc_final: 0.8253 (m-40) REVERT: g 155 ARG cc_start: 0.6689 (pmt-80) cc_final: 0.5933 (ptp-170) REVERT: h 27 PRO cc_start: 0.8679 (Cg_exo) cc_final: 0.8451 (Cg_endo) REVERT: h 34 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8406 (mm-30) REVERT: h 49 GLU cc_start: 0.8235 (pt0) cc_final: 0.7973 (pt0) REVERT: h 99 GLU cc_start: 0.8886 (tp30) cc_final: 0.8632 (tp30) REVERT: i 48 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8272 (mm-30) REVERT: i 73 GLN cc_start: 0.8385 (mt0) cc_final: 0.8139 (mt0) REVERT: j 43 ARG cc_start: 0.7914 (mmm-85) cc_final: 0.7342 (ttt-90) REVERT: j 95 GLU cc_start: 0.6439 (tm-30) cc_final: 0.5867 (tm-30) REVERT: k 18 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7749 (mtm-85) REVERT: k 43 SER cc_start: 0.8992 (t) cc_final: 0.8744 (t) REVERT: k 62 GLN cc_start: 0.8659 (tm-30) cc_final: 0.8338 (tm-30) REVERT: k 93 GLN cc_start: 0.7932 (tp-100) cc_final: 0.7489 (tp-100) REVERT: k 104 GLN cc_start: 0.8105 (tt0) cc_final: 0.7627 (tt0) REVERT: l 37 CYS cc_start: 0.9100 (m) cc_final: 0.8594 (m) REVERT: l 120 TYR cc_start: 0.8562 (m-80) cc_final: 0.8346 (m-80) REVERT: m 12 ASN cc_start: 0.7621 (m-40) cc_final: 0.6687 (t0) REVERT: m 67 GLU cc_start: 0.6873 (mm-30) cc_final: 0.6633 (mm-30) REVERT: m 70 LEU cc_start: 0.8605 (tp) cc_final: 0.8282 (tp) REVERT: m 82 MET cc_start: 0.7796 (mtt) cc_final: 0.7580 (mtt) REVERT: n 3 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7049 (ttm-80) REVERT: n 8 GLU cc_start: 0.8378 (tp30) cc_final: 0.7989 (tp30) REVERT: n 9 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7621 (ttmm) REVERT: n 50 LYS cc_start: 0.8957 (ttmt) cc_final: 0.8503 (ttmm) REVERT: o 35 ARG cc_start: 0.9229 (ttm-80) cc_final: 0.8874 (mtm110) REVERT: o 47 LYS cc_start: 0.8990 (ptpp) cc_final: 0.8764 (pttm) REVERT: o 83 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8479 (tm-30) REVERT: p 14 ASN cc_start: 0.9458 (t0) cc_final: 0.8817 (t0) REVERT: p 27 LYS cc_start: 0.7790 (ptmt) cc_final: 0.7328 (pttt) REVERT: p 39 TYR cc_start: 0.9014 (t80) cc_final: 0.8295 (t80) REVERT: q 46 ASP cc_start: 0.8390 (t70) cc_final: 0.7529 (t0) REVERT: q 91 ARG cc_start: 0.8791 (mmm-85) cc_final: 0.8575 (mtp-110) REVERT: r 33 ASP cc_start: 0.8848 (t0) cc_final: 0.8409 (t0) REVERT: r 51 LEU cc_start: 0.8864 (mt) cc_final: 0.8524 (mt) REVERT: s 5 LEU cc_start: 0.8788 (pp) cc_final: 0.8369 (mt) REVERT: s 12 ASP cc_start: 0.8621 (m-30) cc_final: 0.7941 (m-30) REVERT: s 35 SER cc_start: 0.9280 (m) cc_final: 0.8187 (t) REVERT: u 20 LYS cc_start: 0.8565 (tttm) cc_final: 0.8145 (ttpp) outliers start: 356 outliers final: 308 residues processed: 1814 average time/residue: 1.4308 time to fit residues: 4479.6665 Evaluate side-chains 1976 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 323 poor density : 1653 time to evaluate : 6.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 176 ARG Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 143 ASN Chi-restraints excluded: chain E residue 159 HIS Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 130 ASN Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 41 GLU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 74 ARG Chi-restraints excluded: chain N residue 122 VAL Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 7 TYR Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 28 SER Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 77 ILE Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 114 ILE Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain P residue 5 ASP Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 38 GLN Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 125 VAL Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain Q residue 21 THR Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 54 MET Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 131 ILE Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 59 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 78 LYS Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 42 ASP Chi-restraints excluded: chain S residue 47 THR Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 75 GLU Chi-restraints excluded: chain S residue 92 TYR Chi-restraints excluded: chain S residue 112 PHE Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 38 ASN Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 80 SER Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain T residue 102 ILE Chi-restraints excluded: chain T residue 104 ASN Chi-restraints excluded: chain T residue 115 ARG Chi-restraints excluded: chain U residue 18 LEU Chi-restraints excluded: chain U residue 29 SER Chi-restraints excluded: chain U residue 44 ASN Chi-restraints excluded: chain U residue 80 ILE Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 14 VAL Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 51 VAL Chi-restraints excluded: chain W residue 13 SER Chi-restraints excluded: chain W residue 62 HIS Chi-restraints excluded: chain W residue 66 GLU Chi-restraints excluded: chain W residue 69 LEU Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 14 SER Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 75 ASP Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 83 THR Chi-restraints excluded: chain Z residue 40 ASP Chi-restraints excluded: chain Z residue 50 GLN Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 125 LEU Chi-restraints excluded: chain Z residue 137 ILE Chi-restraints excluded: chain Z residue 141 VAL Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 165 VAL Chi-restraints excluded: chain 0 residue 10 THR Chi-restraints excluded: chain 0 residue 58 THR Chi-restraints excluded: chain 0 residue 59 LEU Chi-restraints excluded: chain 0 residue 66 VAL Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 1 residue 11 ARG Chi-restraints excluded: chain 1 residue 14 VAL Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 74 VAL Chi-restraints excluded: chain 1 residue 80 LEU Chi-restraints excluded: chain 1 residue 86 SER Chi-restraints excluded: chain 2 residue 63 VAL Chi-restraints excluded: chain 2 residue 66 GLU Chi-restraints excluded: chain 3 residue 8 LEU Chi-restraints excluded: chain 3 residue 46 ASN Chi-restraints excluded: chain 3 residue 54 VAL Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 10 VAL Chi-restraints excluded: chain 4 residue 14 ILE Chi-restraints excluded: chain 4 residue 46 GLN Chi-restraints excluded: chain 5 residue 6 VAL Chi-restraints excluded: chain 5 residue 26 THR Chi-restraints excluded: chain 5 residue 29 THR Chi-restraints excluded: chain 5 residue 44 THR Chi-restraints excluded: chain 6 residue 5 VAL Chi-restraints excluded: chain 6 residue 14 THR Chi-restraints excluded: chain 6 residue 23 THR Chi-restraints excluded: chain 6 residue 25 LYS Chi-restraints excluded: chain 6 residue 40 CYS Chi-restraints excluded: chain 7 residue 43 THR Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 37 SER Chi-restraints excluded: chain 8 residue 52 LYS Chi-restraints excluded: chain 9 residue 2 LYS Chi-restraints excluded: chain 9 residue 7 VAL Chi-restraints excluded: chain 9 residue 17 ILE Chi-restraints excluded: chain 9 residue 26 ILE Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain b residue 74 LYS Chi-restraints excluded: chain b residue 107 THR Chi-restraints excluded: chain b residue 115 LEU Chi-restraints excluded: chain b residue 119 GLU Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 150 SER Chi-restraints excluded: chain b residue 160 ASP Chi-restraints excluded: chain b residue 162 ILE Chi-restraints excluded: chain b residue 174 VAL Chi-restraints excluded: chain b residue 187 LEU Chi-restraints excluded: chain b residue 189 ASP Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 196 LEU Chi-restraints excluded: chain b residue 210 SER Chi-restraints excluded: chain b residue 222 ILE Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain c residue 115 LEU Chi-restraints excluded: chain c residue 124 ILE Chi-restraints excluded: chain c residue 144 SER Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 78 LEU Chi-restraints excluded: chain d residue 127 THR Chi-restraints excluded: chain d residue 137 SER Chi-restraints excluded: chain d residue 158 ILE Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 53 LEU Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain e residue 88 LYS Chi-restraints excluded: chain e residue 116 THR Chi-restraints excluded: chain e residue 131 ILE Chi-restraints excluded: chain e residue 144 THR Chi-restraints excluded: chain f residue 7 ASN Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 LEU Chi-restraints excluded: chain f residue 19 LEU Chi-restraints excluded: chain f residue 42 GLU Chi-restraints excluded: chain f residue 43 LEU Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 66 GLU Chi-restraints excluded: chain f residue 67 MET Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain f residue 85 VAL Chi-restraints excluded: chain f residue 90 VAL Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 92 SER Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain h residue 6 ILE Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 35 ILE Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 45 ILE Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 83 ILE Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain h residue 93 VAL Chi-restraints excluded: chain h residue 120 THR Chi-restraints excluded: chain i residue 7 THR Chi-restraints excluded: chain i residue 14 VAL Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 40 LEU Chi-restraints excluded: chain i residue 41 VAL Chi-restraints excluded: chain i residue 47 LEU Chi-restraints excluded: chain i residue 48 GLU Chi-restraints excluded: chain i residue 54 ASP Chi-restraints excluded: chain i residue 81 ILE Chi-restraints excluded: chain i residue 89 ASN Chi-restraints excluded: chain i residue 102 LEU Chi-restraints excluded: chain i residue 109 VAL Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 47 PHE Chi-restraints excluded: chain j residue 49 VAL Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain j residue 89 ASP Chi-restraints excluded: chain j residue 96 ILE Chi-restraints excluded: chain k residue 18 ARG Chi-restraints excluded: chain k residue 26 ASN Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain k residue 47 VAL Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 98 LEU Chi-restraints excluded: chain l residue 6 THR Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 18 VAL Chi-restraints excluded: chain l residue 58 VAL Chi-restraints excluded: chain l residue 62 SER Chi-restraints excluded: chain l residue 66 VAL Chi-restraints excluded: chain l residue 76 ASN Chi-restraints excluded: chain l residue 77 LEU Chi-restraints excluded: chain l residue 82 VAL Chi-restraints excluded: chain l residue 89 ARG Chi-restraints excluded: chain l residue 96 VAL Chi-restraints excluded: chain l residue 100 ILE Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain m residue 48 LEU Chi-restraints excluded: chain m residue 74 VAL Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain n residue 3 ARG Chi-restraints excluded: chain n residue 9 LYS Chi-restraints excluded: chain o residue 6 GLU Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain o residue 87 ILE Chi-restraints excluded: chain p residue 11 SER Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 33 ILE Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain q residue 36 ILE Chi-restraints excluded: chain q residue 53 LEU Chi-restraints excluded: chain q residue 60 ILE Chi-restraints excluded: chain q residue 66 SER Chi-restraints excluded: chain q residue 89 LEU Chi-restraints excluded: chain q residue 94 ASN Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain r residue 66 LEU Chi-restraints excluded: chain r residue 72 ARG Chi-restraints excluded: chain r residue 76 LEU Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 63 ILE Chi-restraints excluded: chain t residue 82 SER Chi-restraints excluded: chain t residue 100 ILE Chi-restraints excluded: chain u residue 13 ILE Chi-restraints excluded: chain u residue 17 THR Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 224 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1047 random chunks: chunk 917 optimal weight: 7.9990 chunk 966 optimal weight: 0.4980 chunk 882 optimal weight: 10.0000 chunk 940 optimal weight: 10.0000 chunk 566 optimal weight: 50.0000 chunk 409 optimal weight: 7.9990 chunk 738 optimal weight: 20.0000 chunk 288 optimal weight: 20.0000 chunk 849 optimal weight: 7.9990 chunk 889 optimal weight: 0.0270 chunk 937 optimal weight: 20.0000 overall best weight: 4.9044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 ASN ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN ** R 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 94 ASN ** V 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 75 ASN ** 0 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 20 HIS ** b 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 98 ASN c 110 ASN ** d 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 ASN h 78 GLN ** k 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 117 ASN ** m 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 26 GLN ** q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.362 161492 Z= 0.272 Angle : 0.588 29.651 241653 Z= 0.318 Chirality : 0.034 1.907 30609 Planarity : 0.005 0.125 13093 Dihedral : 25.061 179.936 81406 Min Nonbonded Distance : 1.644 Molprobity Statistics. All-atom Clashscore : 63.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.98 % Favored : 92.97 % Rotamer: Outliers : 7.41 % Allowed : 25.36 % Favored : 67.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.11), residues: 5916 helix: 1.00 (0.12), residues: 1982 sheet: -1.62 (0.15), residues: 1101 loop : -1.05 (0.12), residues: 2833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP g 103 HIS 0.040 0.001 HIS E 159 PHE 0.025 0.002 PHE N 117 TYR 0.020 0.001 TYR 1 71 ARG 0.008 0.000 ARG k 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2023 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 358 poor density : 1665 time to evaluate : 6.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 MET cc_start: 0.9072 (ptm) cc_final: 0.8487 (ptm) REVERT: D 28 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7225 (pm20) REVERT: D 53 PHE cc_start: 0.9177 (m-10) cc_final: 0.8923 (m-80) REVERT: D 54 ARG cc_start: 0.8083 (mtp180) cc_final: 0.7623 (mtm180) REVERT: D 84 TYR cc_start: 0.8790 (t80) cc_final: 0.7823 (t80) REVERT: D 157 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7377 (ptt-90) REVERT: D 198 ASN cc_start: 0.8236 (t0) cc_final: 0.7899 (t0) REVERT: D 201 HIS cc_start: 0.8966 (t70) cc_final: 0.8709 (t-90) REVERT: D 226 MET cc_start: 0.8538 (mtm) cc_final: 0.8022 (mtm) REVERT: E 45 THR cc_start: 0.8031 (m) cc_final: 0.7605 (p) REVERT: E 83 ASP cc_start: 0.7856 (m-30) cc_final: 0.7423 (m-30) REVERT: F 195 ASP cc_start: 0.8429 (t0) cc_final: 0.8152 (t0) REVERT: F 203 GLN cc_start: 0.9170 (mm-40) cc_final: 0.8248 (tm-30) REVERT: F 204 ASN cc_start: 0.9037 (m-40) cc_final: 0.8687 (m110) REVERT: H 41 MET cc_start: 0.7051 (mmm) cc_final: 0.6460 (mmm) REVERT: H 163 TYR cc_start: 0.8986 (m-80) cc_final: 0.8657 (m-80) REVERT: N 45 ASN cc_start: 0.9027 (p0) cc_final: 0.8645 (p0) REVERT: N 74 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7316 (ttm-80) REVERT: O 12 ASP cc_start: 0.9018 (p0) cc_final: 0.8633 (p0) REVERT: O 20 MET cc_start: 0.8629 (ttm) cc_final: 0.8211 (ttm) REVERT: O 66 LYS cc_start: 0.8732 (tttp) cc_final: 0.7997 (ttmm) REVERT: O 94 ARG cc_start: 0.9042 (mtp85) cc_final: 0.8687 (ttm110) REVERT: O 107 ARG cc_start: 0.8542 (mtp85) cc_final: 0.8164 (mtp180) REVERT: O 108 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8391 (mt-10) REVERT: P 29 LYS cc_start: 0.8720 (ttpp) cc_final: 0.8374 (tttt) REVERT: P 47 ASP cc_start: 0.8423 (t0) cc_final: 0.7790 (t0) REVERT: P 49 ARG cc_start: 0.8144 (mtm180) cc_final: 0.7808 (mtm-85) REVERT: P 148 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8020 (pt) REVERT: Q 9 TYR cc_start: 0.8766 (m-80) cc_final: 0.8316 (m-80) REVERT: Q 17 LEU cc_start: 0.9200 (mm) cc_final: 0.8845 (mm) REVERT: Q 25 ASP cc_start: 0.8465 (p0) cc_final: 0.8105 (p0) REVERT: Q 37 LEU cc_start: 0.8128 (mt) cc_final: 0.7731 (mt) REVERT: Q 60 ARG cc_start: 0.8796 (mmm160) cc_final: 0.8298 (mmm160) REVERT: Q 111 GLU cc_start: 0.7549 (tp30) cc_final: 0.7250 (tp30) REVERT: Q 115 MET cc_start: 0.8564 (mmp) cc_final: 0.8305 (mmm) REVERT: Q 128 LYS cc_start: 0.8734 (mtmt) cc_final: 0.8422 (mtmt) REVERT: Q 139 GLU cc_start: 0.8538 (mp0) cc_final: 0.8222 (mp0) REVERT: R 8 ARG cc_start: 0.9059 (mpt-90) cc_final: 0.8277 (mtt-85) REVERT: R 9 LYS cc_start: 0.8443 (mttp) cc_final: 0.7415 (mttp) REVERT: R 30 THR cc_start: 0.9315 (OUTLIER) cc_final: 0.9073 (p) REVERT: R 31 HIS cc_start: 0.8186 (m90) cc_final: 0.7661 (m-70) REVERT: R 43 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7695 (mm-30) REVERT: R 78 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8746 (tttt) REVERT: S 92 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.7997 (m-80) REVERT: T 46 GLU cc_start: 0.7785 (tt0) cc_final: 0.7361 (tt0) REVERT: T 90 GLN cc_start: 0.7907 (tp-100) cc_final: 0.7699 (tp40) REVERT: U 30 LYS cc_start: 0.8940 (mmtt) cc_final: 0.8729 (mmmt) REVERT: U 32 PHE cc_start: 0.8807 (t80) cc_final: 0.8465 (t80) REVERT: U 39 LEU cc_start: 0.9057 (mm) cc_final: 0.8691 (mm) REVERT: V 1 MET cc_start: 0.7295 (tpt) cc_final: 0.6645 (tpt) REVERT: V 93 GLU cc_start: 0.7388 (tm-30) cc_final: 0.7122 (tm-30) REVERT: V 100 ARG cc_start: 0.8337 (mtm110) cc_final: 0.8121 (mtm110) REVERT: W 52 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8313 (tp30) REVERT: W 60 ASN cc_start: 0.9156 (t0) cc_final: 0.8867 (t0) REVERT: W 102 HIS cc_start: 0.8115 (m170) cc_final: 0.7911 (m-70) REVERT: X 9 LEU cc_start: 0.8542 (mt) cc_final: 0.8131 (mt) REVERT: X 15 GLU cc_start: 0.9132 (mp0) cc_final: 0.8906 (mp0) REVERT: X 93 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7136 (mm-30) REVERT: Y 11 ASP cc_start: 0.7677 (m-30) cc_final: 0.7138 (m-30) REVERT: Y 43 ASN cc_start: 0.8042 (t0) cc_final: 0.7340 (t0) REVERT: Z 6 LYS cc_start: 0.9293 (mtpp) cc_final: 0.8975 (ttmt) REVERT: Z 8 TYR cc_start: 0.8822 (m-10) cc_final: 0.8585 (m-10) REVERT: Z 44 PHE cc_start: 0.9219 (t80) cc_final: 0.9008 (t80) REVERT: Z 54 HIS cc_start: 0.8212 (m90) cc_final: 0.7172 (m90) REVERT: Z 65 GLN cc_start: 0.8272 (tp-100) cc_final: 0.8019 (tp-100) REVERT: Z 78 LYS cc_start: 0.8211 (mttp) cc_final: 0.7566 (mttp) REVERT: Z 138 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6648 (tm-30) REVERT: 0 12 ASN cc_start: 0.8696 (m110) cc_final: 0.8472 (m-40) REVERT: 0 19 LYS cc_start: 0.8654 (mmpt) cc_final: 0.8182 (mmtm) REVERT: 0 38 VAL cc_start: 0.9405 (t) cc_final: 0.9183 (t) REVERT: 1 50 ARG cc_start: 0.8671 (ttm-80) cc_final: 0.8332 (ttm-80) REVERT: 1 56 GLN cc_start: 0.8999 (mm110) cc_final: 0.8703 (mm-40) REVERT: 2 20 GLU cc_start: 0.9419 (mm-30) cc_final: 0.9062 (mp0) REVERT: 2 27 GLU cc_start: 0.9337 (mt-10) cc_final: 0.9096 (tp30) REVERT: 2 51 ARG cc_start: 0.8821 (ttm110) cc_final: 0.8454 (ttm110) REVERT: 3 57 GLU cc_start: 0.8542 (tt0) cc_final: 0.8257 (tt0) REVERT: 4 46 GLN cc_start: 0.7260 (OUTLIER) cc_final: 0.5420 (tp-100) REVERT: 5 39 MET cc_start: 0.8903 (mmm) cc_final: 0.8183 (mmm) REVERT: 5 51 TYR cc_start: 0.8471 (m-10) cc_final: 0.7872 (m-10) REVERT: 6 8 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7766 (mttt) REVERT: 6 25 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7296 (pttm) REVERT: 7 22 MET cc_start: 0.8706 (tpp) cc_final: 0.8437 (mmt) REVERT: 7 23 ARG cc_start: 0.8835 (ttm110) cc_final: 0.8510 (ttm170) REVERT: 8 21 LYS cc_start: 0.8141 (mttt) cc_final: 0.7533 (mtmt) REVERT: 8 34 TRP cc_start: 0.8931 (p90) cc_final: 0.8667 (p90) REVERT: b 7 VAL cc_start: 0.6568 (t) cc_final: 0.6311 (t) REVERT: b 8 LYS cc_start: 0.7755 (pmmt) cc_final: 0.7222 (ptmt) REVERT: b 25 ASN cc_start: 0.8373 (t0) cc_final: 0.8053 (t0) REVERT: b 74 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7174 (ptpp) REVERT: b 140 HIS cc_start: 0.9179 (m-70) cc_final: 0.8886 (m170) REVERT: b 170 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8143 (mm-30) REVERT: b 192 SER cc_start: 0.7870 (m) cc_final: 0.7357 (p) REVERT: c 19 GLU cc_start: 0.8065 (mp0) cc_final: 0.7621 (mp0) REVERT: c 28 GLN cc_start: 0.8670 (mt0) cc_final: 0.8436 (mm-40) REVERT: c 104 GLN cc_start: 0.8852 (tp40) cc_final: 0.8620 (tp40) REVERT: c 115 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8256 (mt) REVERT: c 118 GLN cc_start: 0.8980 (mt0) cc_final: 0.8646 (mt0) REVERT: c 131 ARG cc_start: 0.7913 (mtm110) cc_final: 0.7625 (ptt90) REVERT: c 183 ASP cc_start: 0.8525 (t0) cc_final: 0.7950 (t0) REVERT: c 190 ARG cc_start: 0.8051 (ptp90) cc_final: 0.7712 (ptp-170) REVERT: c 193 TYR cc_start: 0.8756 (p90) cc_final: 0.8089 (p90) REVERT: d 33 MET cc_start: 0.8767 (tpt) cc_final: 0.8299 (tpt) REVERT: d 50 ARG cc_start: 0.8492 (ttt180) cc_final: 0.8123 (tpp80) REVERT: d 165 MET cc_start: 0.8023 (tpp) cc_final: 0.7780 (tpp) REVERT: d 177 ASP cc_start: 0.8147 (t0) cc_final: 0.7873 (t0) REVERT: e 57 LYS cc_start: 0.8930 (ttmp) cc_final: 0.8570 (mtpp) REVERT: e 61 TYR cc_start: 0.9320 (m-80) cc_final: 0.9035 (m-80) REVERT: e 65 ASN cc_start: 0.8283 (t0) cc_final: 0.8078 (t0) REVERT: e 82 VAL cc_start: 0.9037 (t) cc_final: 0.8729 (m) REVERT: e 84 PHE cc_start: 0.8819 (t80) cc_final: 0.8419 (t80) REVERT: e 88 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8576 (tttt) REVERT: e 111 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8115 (mt-10) REVERT: e 125 SER cc_start: 0.8816 (t) cc_final: 0.8405 (p) REVERT: f 62 TRP cc_start: 0.7397 (t60) cc_final: 0.6634 (t60) REVERT: g 53 LYS cc_start: 0.8713 (mtpp) cc_final: 0.8349 (mmtm) REVERT: g 106 GLN cc_start: 0.8939 (mt0) cc_final: 0.8559 (mt0) REVERT: g 136 LYS cc_start: 0.9158 (mmtm) cc_final: 0.8705 (ptmt) REVERT: g 155 ARG cc_start: 0.6684 (pmt-80) cc_final: 0.5931 (ptp-170) REVERT: h 27 PRO cc_start: 0.8618 (Cg_exo) cc_final: 0.8404 (Cg_endo) REVERT: h 34 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8415 (mm-30) REVERT: h 49 GLU cc_start: 0.8213 (pt0) cc_final: 0.7941 (pt0) REVERT: h 99 GLU cc_start: 0.8890 (tp30) cc_final: 0.8638 (tp30) REVERT: i 48 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8273 (mm-30) REVERT: i 73 GLN cc_start: 0.8375 (mt0) cc_final: 0.8151 (mt0) REVERT: j 43 ARG cc_start: 0.7938 (mmm-85) cc_final: 0.7303 (ttt-90) REVERT: j 95 GLU cc_start: 0.6445 (tm-30) cc_final: 0.5897 (tm-30) REVERT: k 18 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7780 (mtm-85) REVERT: k 43 SER cc_start: 0.9002 (t) cc_final: 0.8754 (t) REVERT: k 62 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8338 (tm-30) REVERT: k 93 GLN cc_start: 0.7910 (tp-100) cc_final: 0.7464 (tp-100) REVERT: k 104 GLN cc_start: 0.8151 (tt0) cc_final: 0.7690 (tt0) REVERT: k 123 LYS cc_start: 0.9603 (ttmt) cc_final: 0.9214 (ttmt) REVERT: l 37 CYS cc_start: 0.9096 (m) cc_final: 0.8584 (m) REVERT: l 120 TYR cc_start: 0.8559 (m-80) cc_final: 0.8347 (m-80) REVERT: m 12 ASN cc_start: 0.7626 (m-40) cc_final: 0.6682 (t0) REVERT: m 67 GLU cc_start: 0.6756 (mm-30) cc_final: 0.6538 (mm-30) REVERT: m 70 LEU cc_start: 0.8589 (tp) cc_final: 0.8261 (tp) REVERT: m 82 MET cc_start: 0.7807 (mtt) cc_final: 0.7597 (mtt) REVERT: n 3 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.6997 (ttm-80) REVERT: n 8 GLU cc_start: 0.8363 (tp30) cc_final: 0.7987 (tp30) REVERT: n 9 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7577 (ttmm) REVERT: n 50 LYS cc_start: 0.8969 (ttmt) cc_final: 0.8516 (ttmm) REVERT: o 35 ARG cc_start: 0.9237 (ttm-80) cc_final: 0.8875 (mtm110) REVERT: o 47 LYS cc_start: 0.8980 (ptpp) cc_final: 0.8751 (pttm) REVERT: o 83 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8482 (tm-30) REVERT: p 14 ASN cc_start: 0.9460 (t0) cc_final: 0.8838 (t0) REVERT: p 27 LYS cc_start: 0.7790 (ptmt) cc_final: 0.7327 (pttt) REVERT: p 39 TYR cc_start: 0.9019 (t80) cc_final: 0.8304 (t80) REVERT: q 46 ASP cc_start: 0.8383 (t70) cc_final: 0.7517 (t0) REVERT: q 91 ARG cc_start: 0.8797 (mmm-85) cc_final: 0.8580 (mtp-110) REVERT: r 33 ASP cc_start: 0.8848 (t0) cc_final: 0.8412 (t0) REVERT: r 51 LEU cc_start: 0.8900 (mt) cc_final: 0.8554 (mt) REVERT: s 5 LEU cc_start: 0.8785 (pp) cc_final: 0.8372 (mt) REVERT: s 12 ASP cc_start: 0.8622 (m-30) cc_final: 0.7916 (m-30) REVERT: s 35 SER cc_start: 0.9287 (m) cc_final: 0.8187 (t) REVERT: u 20 LYS cc_start: 0.8613 (tttm) cc_final: 0.8279 (ttpp) outliers start: 358 outliers final: 328 residues processed: 1810 average time/residue: 1.3544 time to fit residues: 4193.3784 Evaluate side-chains 1999 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 344 poor density : 1655 time to evaluate : 6.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 176 ARG Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 40 GLU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 143 ASN Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 130 ASN Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain I residue 41 GLU Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 74 ARG Chi-restraints excluded: chain N residue 122 VAL Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 7 TYR Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 28 SER Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 77 ILE Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 114 ILE Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain P residue 5 ASP Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 125 VAL Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain Q residue 21 THR Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 54 MET Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain Q residue 116 GLU Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 131 ILE Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 59 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 78 LYS Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 42 ASP Chi-restraints excluded: chain S residue 47 THR Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 75 GLU Chi-restraints excluded: chain S residue 92 TYR Chi-restraints excluded: chain S residue 112 PHE Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 38 ASN Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 80 SER Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain T residue 102 ILE Chi-restraints excluded: chain T residue 104 ASN Chi-restraints excluded: chain T residue 115 ARG Chi-restraints excluded: chain U residue 18 LEU Chi-restraints excluded: chain U residue 29 SER Chi-restraints excluded: chain U residue 44 ASN Chi-restraints excluded: chain U residue 80 ILE Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 14 VAL Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 35 LEU Chi-restraints excluded: chain V residue 51 VAL Chi-restraints excluded: chain V residue 94 LEU Chi-restraints excluded: chain W residue 13 SER Chi-restraints excluded: chain W residue 62 HIS Chi-restraints excluded: chain W residue 66 GLU Chi-restraints excluded: chain W residue 69 LEU Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 14 SER Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 75 ASP Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 83 THR Chi-restraints excluded: chain Z residue 40 ASP Chi-restraints excluded: chain Z residue 45 ASP Chi-restraints excluded: chain Z residue 50 GLN Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 125 LEU Chi-restraints excluded: chain Z residue 137 ILE Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 165 VAL Chi-restraints excluded: chain 0 residue 10 THR Chi-restraints excluded: chain 0 residue 58 THR Chi-restraints excluded: chain 0 residue 59 LEU Chi-restraints excluded: chain 0 residue 66 VAL Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 1 residue 11 ARG Chi-restraints excluded: chain 1 residue 14 VAL Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 74 VAL Chi-restraints excluded: chain 1 residue 86 SER Chi-restraints excluded: chain 2 residue 63 VAL Chi-restraints excluded: chain 2 residue 66 GLU Chi-restraints excluded: chain 3 residue 4 LEU Chi-restraints excluded: chain 3 residue 8 LEU Chi-restraints excluded: chain 3 residue 46 ASN Chi-restraints excluded: chain 3 residue 54 VAL Chi-restraints excluded: chain 4 residue 10 VAL Chi-restraints excluded: chain 4 residue 14 ILE Chi-restraints excluded: chain 4 residue 46 GLN Chi-restraints excluded: chain 5 residue 6 VAL Chi-restraints excluded: chain 5 residue 26 THR Chi-restraints excluded: chain 5 residue 29 THR Chi-restraints excluded: chain 5 residue 44 THR Chi-restraints excluded: chain 6 residue 5 VAL Chi-restraints excluded: chain 6 residue 7 ILE Chi-restraints excluded: chain 6 residue 8 LYS Chi-restraints excluded: chain 6 residue 23 THR Chi-restraints excluded: chain 6 residue 25 LYS Chi-restraints excluded: chain 6 residue 40 CYS Chi-restraints excluded: chain 7 residue 43 THR Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 37 SER Chi-restraints excluded: chain 8 residue 52 LYS Chi-restraints excluded: chain 9 residue 2 LYS Chi-restraints excluded: chain 9 residue 7 VAL Chi-restraints excluded: chain 9 residue 17 ILE Chi-restraints excluded: chain 9 residue 26 ILE Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain b residue 74 LYS Chi-restraints excluded: chain b residue 80 ILE Chi-restraints excluded: chain b residue 107 THR Chi-restraints excluded: chain b residue 115 LEU Chi-restraints excluded: chain b residue 119 GLU Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 160 ASP Chi-restraints excluded: chain b residue 162 ILE Chi-restraints excluded: chain b residue 174 VAL Chi-restraints excluded: chain b residue 180 LEU Chi-restraints excluded: chain b residue 187 LEU Chi-restraints excluded: chain b residue 189 ASP Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 196 LEU Chi-restraints excluded: chain b residue 210 SER Chi-restraints excluded: chain b residue 212 GLN Chi-restraints excluded: chain b residue 222 ILE Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain c residue 115 LEU Chi-restraints excluded: chain c residue 144 SER Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 78 LEU Chi-restraints excluded: chain d residue 127 THR Chi-restraints excluded: chain d residue 137 SER Chi-restraints excluded: chain d residue 158 ILE Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 53 LEU Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain e residue 88 LYS Chi-restraints excluded: chain e residue 98 THR Chi-restraints excluded: chain e residue 131 ILE Chi-restraints excluded: chain e residue 144 THR Chi-restraints excluded: chain f residue 7 ASN Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 LEU Chi-restraints excluded: chain f residue 19 LEU Chi-restraints excluded: chain f residue 42 GLU Chi-restraints excluded: chain f residue 43 LEU Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 66 GLU Chi-restraints excluded: chain f residue 67 MET Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain f residue 85 VAL Chi-restraints excluded: chain f residue 90 VAL Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 92 SER Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain h residue 6 ILE Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 35 ILE Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 45 ILE Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 83 ILE Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain h residue 93 VAL Chi-restraints excluded: chain h residue 120 THR Chi-restraints excluded: chain h residue 123 GLU Chi-restraints excluded: chain i residue 7 THR Chi-restraints excluded: chain i residue 14 VAL Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 41 VAL Chi-restraints excluded: chain i residue 47 LEU Chi-restraints excluded: chain i residue 48 GLU Chi-restraints excluded: chain i residue 54 ASP Chi-restraints excluded: chain i residue 81 ILE Chi-restraints excluded: chain i residue 89 ASN Chi-restraints excluded: chain i residue 102 LEU Chi-restraints excluded: chain i residue 109 VAL Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 38 ILE Chi-restraints excluded: chain j residue 47 PHE Chi-restraints excluded: chain j residue 49 VAL Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain j residue 89 ASP Chi-restraints excluded: chain j residue 96 ILE Chi-restraints excluded: chain k residue 18 ARG Chi-restraints excluded: chain k residue 26 ASN Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain k residue 47 VAL Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 98 LEU Chi-restraints excluded: chain k residue 106 LYS Chi-restraints excluded: chain k residue 117 ASN Chi-restraints excluded: chain l residue 6 THR Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 18 VAL Chi-restraints excluded: chain l residue 58 VAL Chi-restraints excluded: chain l residue 62 SER Chi-restraints excluded: chain l residue 66 VAL Chi-restraints excluded: chain l residue 76 ASN Chi-restraints excluded: chain l residue 77 LEU Chi-restraints excluded: chain l residue 82 VAL Chi-restraints excluded: chain l residue 89 ARG Chi-restraints excluded: chain l residue 96 VAL Chi-restraints excluded: chain l residue 100 ILE Chi-restraints excluded: chain m residue 27 LYS Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain m residue 48 LEU Chi-restraints excluded: chain m residue 74 VAL Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain n residue 3 ARG Chi-restraints excluded: chain n residue 9 LYS Chi-restraints excluded: chain o residue 6 GLU Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain o residue 32 LEU Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain o residue 87 ILE Chi-restraints excluded: chain p residue 11 SER Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 33 ILE Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain q residue 36 ILE Chi-restraints excluded: chain q residue 53 LEU Chi-restraints excluded: chain q residue 60 ILE Chi-restraints excluded: chain q residue 61 GLU Chi-restraints excluded: chain q residue 66 SER Chi-restraints excluded: chain q residue 89 LEU Chi-restraints excluded: chain q residue 94 ASN Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain r residue 62 GLU Chi-restraints excluded: chain r residue 72 ARG Chi-restraints excluded: chain r residue 76 LEU Chi-restraints excluded: chain s residue 15 LEU Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 63 ILE Chi-restraints excluded: chain t residue 82 SER Chi-restraints excluded: chain t residue 100 ILE Chi-restraints excluded: chain u residue 13 ILE Chi-restraints excluded: chain u residue 17 THR Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 224 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1047 random chunks: chunk 617 optimal weight: 6.9990 chunk 994 optimal weight: 20.0000 chunk 606 optimal weight: 5.9990 chunk 471 optimal weight: 5.9990 chunk 691 optimal weight: 20.0000 chunk 1043 optimal weight: 20.0000 chunk 960 optimal weight: 10.0000 chunk 830 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 641 optimal weight: 20.0000 chunk 509 optimal weight: 4.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 HIS ** E 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS ** F 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 94 ASN ** V 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 75 ASN ** 0 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 20 HIS ** b 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 98 ASN c 110 ASN ** d 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 141 GLN ** f 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 ASN ** h 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 26 GLN ** q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.362 161492 Z= 0.333 Angle : 0.620 29.622 241653 Z= 0.331 Chirality : 0.035 1.898 30609 Planarity : 0.005 0.126 13093 Dihedral : 25.050 179.996 81406 Min Nonbonded Distance : 1.643 Molprobity Statistics. All-atom Clashscore : 64.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.52 % Favored : 92.43 % Rotamer: Outliers : 7.66 % Allowed : 25.32 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.11), residues: 5916 helix: 0.95 (0.12), residues: 1981 sheet: -1.61 (0.15), residues: 1096 loop : -1.09 (0.12), residues: 2839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP g 103 HIS 0.020 0.001 HIS k 116 PHE 0.030 0.002 PHE N 117 TYR 0.020 0.001 TYR 1 71 ARG 0.011 0.000 ARG e 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2014 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 370 poor density : 1644 time to evaluate : 6.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 16 MET cc_start: 0.9094 (ptm) cc_final: 0.8518 (ptm) REVERT: D 28 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7211 (pm20) REVERT: D 53 PHE cc_start: 0.9185 (m-10) cc_final: 0.8941 (m-80) REVERT: D 84 TYR cc_start: 0.8807 (t80) cc_final: 0.7828 (t80) REVERT: D 157 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7410 (ptt-90) REVERT: D 172 TYR cc_start: 0.8330 (m-10) cc_final: 0.7830 (m-80) REVERT: D 198 ASN cc_start: 0.8239 (t0) cc_final: 0.7903 (t0) REVERT: D 201 HIS cc_start: 0.8989 (t70) cc_final: 0.8731 (t-90) REVERT: D 226 MET cc_start: 0.8545 (mtm) cc_final: 0.8025 (mtm) REVERT: E 45 THR cc_start: 0.8034 (m) cc_final: 0.7612 (p) REVERT: E 83 ASP cc_start: 0.7876 (m-30) cc_final: 0.7439 (m-30) REVERT: F 59 TYR cc_start: 0.8655 (m-80) cc_final: 0.8291 (m-10) REVERT: F 195 ASP cc_start: 0.8449 (t0) cc_final: 0.8173 (t0) REVERT: F 203 GLN cc_start: 0.9170 (mm-40) cc_final: 0.8255 (tm-30) REVERT: F 204 ASN cc_start: 0.9046 (m-40) cc_final: 0.8700 (m110) REVERT: H 41 MET cc_start: 0.7075 (mmm) cc_final: 0.6486 (mmm) REVERT: H 163 TYR cc_start: 0.8996 (m-80) cc_final: 0.8670 (m-80) REVERT: N 45 ASN cc_start: 0.9050 (p0) cc_final: 0.8646 (p0) REVERT: N 74 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7356 (ttm-80) REVERT: O 12 ASP cc_start: 0.9028 (p0) cc_final: 0.8643 (p0) REVERT: O 20 MET cc_start: 0.8646 (ttm) cc_final: 0.8226 (ttm) REVERT: O 66 LYS cc_start: 0.8740 (tttp) cc_final: 0.8004 (ttmm) REVERT: O 90 GLN cc_start: 0.9085 (mp10) cc_final: 0.8858 (pm20) REVERT: O 94 ARG cc_start: 0.9045 (mtp85) cc_final: 0.8669 (ttm110) REVERT: O 107 ARG cc_start: 0.8527 (mtp85) cc_final: 0.8139 (mtp180) REVERT: O 108 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8377 (mt-10) REVERT: P 29 LYS cc_start: 0.8730 (ttpp) cc_final: 0.8383 (tttt) REVERT: P 47 ASP cc_start: 0.8433 (t0) cc_final: 0.7817 (t0) REVERT: P 49 ARG cc_start: 0.8157 (mtm180) cc_final: 0.7822 (mtm-85) REVERT: Q 9 TYR cc_start: 0.8765 (m-80) cc_final: 0.8306 (m-80) REVERT: Q 17 LEU cc_start: 0.9216 (mm) cc_final: 0.8855 (mm) REVERT: Q 25 ASP cc_start: 0.8534 (p0) cc_final: 0.8119 (p0) REVERT: Q 37 LEU cc_start: 0.8129 (mt) cc_final: 0.7734 (mt) REVERT: Q 60 ARG cc_start: 0.8776 (mmm160) cc_final: 0.8287 (mmm160) REVERT: Q 111 GLU cc_start: 0.7542 (tp30) cc_final: 0.6704 (tp30) REVERT: Q 115 MET cc_start: 0.8562 (mmp) cc_final: 0.8190 (mmm) REVERT: Q 128 LYS cc_start: 0.8728 (mtmt) cc_final: 0.8399 (mtmt) REVERT: Q 133 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.6754 (mtp85) REVERT: Q 139 GLU cc_start: 0.8505 (mp0) cc_final: 0.8169 (mp0) REVERT: R 8 ARG cc_start: 0.9074 (mpt-90) cc_final: 0.8286 (mtt-85) REVERT: R 9 LYS cc_start: 0.8453 (mttp) cc_final: 0.7435 (mttp) REVERT: R 30 THR cc_start: 0.9314 (OUTLIER) cc_final: 0.9070 (p) REVERT: R 31 HIS cc_start: 0.8208 (m90) cc_final: 0.7678 (m-70) REVERT: R 43 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7697 (mm-30) REVERT: R 78 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8749 (tttt) REVERT: S 92 TYR cc_start: 0.8869 (OUTLIER) cc_final: 0.8044 (m-80) REVERT: T 46 GLU cc_start: 0.7832 (tt0) cc_final: 0.7412 (tt0) REVERT: T 90 GLN cc_start: 0.7925 (tp-100) cc_final: 0.7719 (tp40) REVERT: T 99 LEU cc_start: 0.9046 (mt) cc_final: 0.8827 (mt) REVERT: U 30 LYS cc_start: 0.8943 (mmtt) cc_final: 0.8735 (mmmt) REVERT: U 32 PHE cc_start: 0.8806 (t80) cc_final: 0.8407 (t80) REVERT: U 39 LEU cc_start: 0.9071 (mm) cc_final: 0.8702 (mm) REVERT: V 1 MET cc_start: 0.7304 (tpt) cc_final: 0.6677 (tpt) REVERT: V 93 GLU cc_start: 0.7414 (tm-30) cc_final: 0.7183 (tm-30) REVERT: V 100 ARG cc_start: 0.8327 (mtm110) cc_final: 0.7917 (mtm110) REVERT: W 52 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8320 (tp30) REVERT: W 60 ASN cc_start: 0.9167 (t0) cc_final: 0.8878 (t0) REVERT: X 9 LEU cc_start: 0.8569 (mt) cc_final: 0.8154 (mt) REVERT: X 15 GLU cc_start: 0.9145 (mp0) cc_final: 0.8921 (mp0) REVERT: X 93 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7148 (mm-30) REVERT: Y 11 ASP cc_start: 0.7669 (m-30) cc_final: 0.7133 (m-30) REVERT: Y 43 ASN cc_start: 0.8049 (t0) cc_final: 0.7352 (t0) REVERT: Z 6 LYS cc_start: 0.9288 (mtpp) cc_final: 0.8963 (ttmt) REVERT: Z 8 TYR cc_start: 0.8857 (m-10) cc_final: 0.8624 (m-10) REVERT: Z 54 HIS cc_start: 0.8208 (m90) cc_final: 0.7174 (m90) REVERT: Z 78 LYS cc_start: 0.8222 (mttp) cc_final: 0.7575 (mttp) REVERT: Z 138 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6582 (tm-30) REVERT: 0 12 ASN cc_start: 0.8616 (m110) cc_final: 0.8408 (m-40) REVERT: 0 19 LYS cc_start: 0.8672 (mmpt) cc_final: 0.8207 (mmtm) REVERT: 0 38 VAL cc_start: 0.9408 (t) cc_final: 0.9189 (t) REVERT: 1 50 ARG cc_start: 0.8685 (ttm-80) cc_final: 0.8348 (ttm-80) REVERT: 1 56 GLN cc_start: 0.8999 (mm110) cc_final: 0.8691 (mm-40) REVERT: 2 20 GLU cc_start: 0.9419 (mm-30) cc_final: 0.9063 (mp0) REVERT: 2 27 GLU cc_start: 0.9336 (mt-10) cc_final: 0.9068 (tp30) REVERT: 2 51 ARG cc_start: 0.8824 (ttm110) cc_final: 0.8452 (ttm110) REVERT: 3 57 GLU cc_start: 0.8514 (tt0) cc_final: 0.8271 (tt0) REVERT: 4 46 GLN cc_start: 0.7268 (OUTLIER) cc_final: 0.5419 (tp-100) REVERT: 5 39 MET cc_start: 0.8897 (mmm) cc_final: 0.8187 (mmm) REVERT: 6 8 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7817 (mttt) REVERT: 6 25 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7310 (pttm) REVERT: 7 22 MET cc_start: 0.8735 (tpp) cc_final: 0.8439 (mmt) REVERT: 7 23 ARG cc_start: 0.8854 (ttm110) cc_final: 0.8528 (ttm170) REVERT: 8 21 LYS cc_start: 0.8147 (mttt) cc_final: 0.7529 (mtmt) REVERT: 8 34 TRP cc_start: 0.8952 (p90) cc_final: 0.8685 (p90) REVERT: b 8 LYS cc_start: 0.7778 (pmmt) cc_final: 0.7196 (ptmt) REVERT: b 25 ASN cc_start: 0.8371 (t0) cc_final: 0.8052 (t0) REVERT: b 74 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7194 (ptpp) REVERT: b 140 HIS cc_start: 0.9172 (m-70) cc_final: 0.8888 (m170) REVERT: b 170 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8147 (mm-30) REVERT: b 192 SER cc_start: 0.7887 (m) cc_final: 0.7368 (p) REVERT: b 220 ASP cc_start: 0.9196 (OUTLIER) cc_final: 0.8887 (m-30) REVERT: c 19 GLU cc_start: 0.8080 (mp0) cc_final: 0.7638 (mp0) REVERT: c 28 GLN cc_start: 0.8670 (mt0) cc_final: 0.8436 (mm-40) REVERT: c 104 GLN cc_start: 0.8850 (tp40) cc_final: 0.8614 (tp40) REVERT: c 115 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8519 (mt) REVERT: c 118 GLN cc_start: 0.8992 (mt0) cc_final: 0.8733 (mt0) REVERT: c 183 ASP cc_start: 0.8516 (t0) cc_final: 0.7928 (t0) REVERT: c 190 ARG cc_start: 0.8061 (ptp90) cc_final: 0.7727 (ptp-170) REVERT: c 193 TYR cc_start: 0.8776 (p90) cc_final: 0.8107 (p90) REVERT: d 33 MET cc_start: 0.8754 (tpt) cc_final: 0.8282 (tpt) REVERT: d 50 ARG cc_start: 0.8504 (ttt180) cc_final: 0.8123 (tpp80) REVERT: d 65 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7396 (ttt90) REVERT: d 165 MET cc_start: 0.7994 (tpp) cc_final: 0.7761 (tpp) REVERT: d 177 ASP cc_start: 0.8156 (t0) cc_final: 0.7879 (t0) REVERT: e 57 LYS cc_start: 0.8927 (ttmp) cc_final: 0.8556 (mtpp) REVERT: e 61 TYR cc_start: 0.9336 (m-80) cc_final: 0.9040 (m-80) REVERT: e 65 ASN cc_start: 0.8352 (t0) cc_final: 0.8087 (t0) REVERT: e 82 VAL cc_start: 0.9061 (t) cc_final: 0.8748 (m) REVERT: e 88 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8577 (tttt) REVERT: e 111 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8140 (mt-10) REVERT: e 125 SER cc_start: 0.8837 (t) cc_final: 0.8419 (p) REVERT: f 62 TRP cc_start: 0.7415 (t60) cc_final: 0.6626 (t60) REVERT: g 53 LYS cc_start: 0.8718 (mtpp) cc_final: 0.8344 (mmtm) REVERT: g 64 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7997 (tm-30) REVERT: g 106 GLN cc_start: 0.8946 (mt0) cc_final: 0.8570 (mt0) REVERT: g 136 LYS cc_start: 0.9156 (mmtm) cc_final: 0.8706 (ptmt) REVERT: g 155 ARG cc_start: 0.6688 (pmt-80) cc_final: 0.5931 (ptp-170) REVERT: h 27 PRO cc_start: 0.8622 (Cg_exo) cc_final: 0.8410 (Cg_endo) REVERT: h 34 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8433 (mm-30) REVERT: h 49 GLU cc_start: 0.8225 (pt0) cc_final: 0.7948 (pt0) REVERT: h 99 GLU cc_start: 0.8880 (tp30) cc_final: 0.8628 (tp30) REVERT: i 48 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8283 (mm-30) REVERT: i 73 GLN cc_start: 0.8396 (mt0) cc_final: 0.8173 (mt0) REVERT: j 43 ARG cc_start: 0.7947 (mmm-85) cc_final: 0.7309 (ttt-90) REVERT: j 95 GLU cc_start: 0.6454 (tm-30) cc_final: 0.5905 (tm-30) REVERT: k 18 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7789 (mtm-85) REVERT: k 43 SER cc_start: 0.9016 (t) cc_final: 0.8771 (t) REVERT: k 62 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8347 (tm-30) REVERT: k 93 GLN cc_start: 0.7915 (tp-100) cc_final: 0.7476 (tp-100) REVERT: k 104 GLN cc_start: 0.8127 (tt0) cc_final: 0.7689 (tt0) REVERT: k 123 LYS cc_start: 0.9606 (ttmt) cc_final: 0.9222 (ttmt) REVERT: l 37 CYS cc_start: 0.9086 (m) cc_final: 0.8580 (m) REVERT: l 120 TYR cc_start: 0.8593 (m-80) cc_final: 0.8368 (m-80) REVERT: m 12 ASN cc_start: 0.7655 (m-40) cc_final: 0.6707 (t0) REVERT: m 67 GLU cc_start: 0.6799 (mm-30) cc_final: 0.6565 (mm-30) REVERT: m 82 MET cc_start: 0.7808 (mtt) cc_final: 0.7590 (mtt) REVERT: n 3 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.6995 (ttm-80) REVERT: n 8 GLU cc_start: 0.8382 (tp30) cc_final: 0.8011 (tp30) REVERT: n 9 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7602 (ttmm) REVERT: n 50 LYS cc_start: 0.8981 (ttmt) cc_final: 0.8518 (ttmm) REVERT: o 35 ARG cc_start: 0.9239 (ttm-80) cc_final: 0.8839 (mtm110) REVERT: o 47 LYS cc_start: 0.8984 (ptpp) cc_final: 0.8766 (pttm) REVERT: o 83 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8507 (tm-30) REVERT: p 14 ASN cc_start: 0.9462 (t0) cc_final: 0.8840 (t0) REVERT: p 27 LYS cc_start: 0.7807 (ptmt) cc_final: 0.7323 (pttt) REVERT: p 39 TYR cc_start: 0.9016 (t80) cc_final: 0.8291 (t80) REVERT: q 46 ASP cc_start: 0.8386 (t70) cc_final: 0.7517 (t0) REVERT: q 91 ARG cc_start: 0.8799 (mmm-85) cc_final: 0.8563 (mtp-110) REVERT: r 33 ASP cc_start: 0.8860 (t0) cc_final: 0.8429 (t0) REVERT: r 51 LEU cc_start: 0.8907 (mt) cc_final: 0.8557 (mt) REVERT: s 5 LEU cc_start: 0.8790 (pp) cc_final: 0.8375 (mt) REVERT: s 12 ASP cc_start: 0.8635 (m-30) cc_final: 0.7924 (m-30) REVERT: s 35 SER cc_start: 0.9300 (m) cc_final: 0.8170 (t) REVERT: u 20 LYS cc_start: 0.8636 (tttm) cc_final: 0.8296 (ttpp) REVERT: C 218 MET cc_start: 0.2240 (mtt) cc_final: 0.1923 (mtt) outliers start: 370 outliers final: 342 residues processed: 1802 average time/residue: 1.3451 time to fit residues: 4145.9465 Evaluate side-chains 1994 residues out of total 5008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 360 poor density : 1634 time to evaluate : 5.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 176 ARG Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 190 TYR Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain E residue 4 ILE Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 143 ASN Chi-restraints excluded: chain E residue 159 HIS Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 48 THR Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 78 SER Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 130 ASN Chi-restraints excluded: chain G residue 159 VAL Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 40 THR Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 74 ARG Chi-restraints excluded: chain N residue 76 SER Chi-restraints excluded: chain N residue 104 LYS Chi-restraints excluded: chain N residue 122 VAL Chi-restraints excluded: chain N residue 136 GLU Chi-restraints excluded: chain O residue 7 TYR Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 28 SER Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 75 SER Chi-restraints excluded: chain O residue 77 ILE Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 114 ILE Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain P residue 5 ASP Chi-restraints excluded: chain P residue 25 SER Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain P residue 88 LEU Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 125 VAL Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain Q residue 21 THR Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 52 VAL Chi-restraints excluded: chain Q residue 54 MET Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 94 VAL Chi-restraints excluded: chain Q residue 110 THR Chi-restraints excluded: chain Q residue 116 GLU Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 131 ILE Chi-restraints excluded: chain Q residue 133 ARG Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 36 THR Chi-restraints excluded: chain R residue 59 ASP Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 78 LYS Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 47 THR Chi-restraints excluded: chain S residue 69 VAL Chi-restraints excluded: chain S residue 75 GLU Chi-restraints excluded: chain S residue 92 TYR Chi-restraints excluded: chain S residue 112 PHE Chi-restraints excluded: chain T residue 9 LEU Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 31 SER Chi-restraints excluded: chain T residue 38 ASN Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 80 SER Chi-restraints excluded: chain T residue 83 ILE Chi-restraints excluded: chain T residue 102 ILE Chi-restraints excluded: chain T residue 104 ASN Chi-restraints excluded: chain U residue 18 LEU Chi-restraints excluded: chain U residue 29 SER Chi-restraints excluded: chain U residue 44 ASN Chi-restraints excluded: chain U residue 80 ILE Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 14 VAL Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 35 LEU Chi-restraints excluded: chain V residue 51 VAL Chi-restraints excluded: chain V residue 94 LEU Chi-restraints excluded: chain W residue 13 SER Chi-restraints excluded: chain W residue 23 LEU Chi-restraints excluded: chain W residue 53 SER Chi-restraints excluded: chain W residue 62 HIS Chi-restraints excluded: chain W residue 66 GLU Chi-restraints excluded: chain W residue 69 LEU Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 14 SER Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 75 ASP Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 83 THR Chi-restraints excluded: chain Z residue 40 ASP Chi-restraints excluded: chain Z residue 50 GLN Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain Z residue 100 VAL Chi-restraints excluded: chain Z residue 125 LEU Chi-restraints excluded: chain Z residue 141 VAL Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 165 VAL Chi-restraints excluded: chain 0 residue 10 THR Chi-restraints excluded: chain 0 residue 58 THR Chi-restraints excluded: chain 0 residue 59 LEU Chi-restraints excluded: chain 0 residue 66 VAL Chi-restraints excluded: chain 1 residue 4 VAL Chi-restraints excluded: chain 1 residue 11 ARG Chi-restraints excluded: chain 1 residue 14 VAL Chi-restraints excluded: chain 1 residue 59 THR Chi-restraints excluded: chain 1 residue 74 VAL Chi-restraints excluded: chain 1 residue 86 SER Chi-restraints excluded: chain 2 residue 12 GLU Chi-restraints excluded: chain 2 residue 63 VAL Chi-restraints excluded: chain 2 residue 66 GLU Chi-restraints excluded: chain 3 residue 8 LEU Chi-restraints excluded: chain 3 residue 46 ASN Chi-restraints excluded: chain 3 residue 54 VAL Chi-restraints excluded: chain 4 residue 10 VAL Chi-restraints excluded: chain 4 residue 14 ILE Chi-restraints excluded: chain 4 residue 46 GLN Chi-restraints excluded: chain 5 residue 6 VAL Chi-restraints excluded: chain 5 residue 26 THR Chi-restraints excluded: chain 5 residue 29 THR Chi-restraints excluded: chain 5 residue 44 THR Chi-restraints excluded: chain 6 residue 5 VAL Chi-restraints excluded: chain 6 residue 7 ILE Chi-restraints excluded: chain 6 residue 8 LYS Chi-restraints excluded: chain 6 residue 10 LEU Chi-restraints excluded: chain 6 residue 14 THR Chi-restraints excluded: chain 6 residue 23 THR Chi-restraints excluded: chain 6 residue 25 LYS Chi-restraints excluded: chain 6 residue 40 CYS Chi-restraints excluded: chain 7 residue 43 THR Chi-restraints excluded: chain 7 residue 46 VAL Chi-restraints excluded: chain 8 residue 6 THR Chi-restraints excluded: chain 8 residue 37 SER Chi-restraints excluded: chain 8 residue 52 LYS Chi-restraints excluded: chain 9 residue 2 LYS Chi-restraints excluded: chain 9 residue 6 SER Chi-restraints excluded: chain 9 residue 7 VAL Chi-restraints excluded: chain 9 residue 17 ILE Chi-restraints excluded: chain 9 residue 26 ILE Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain b residue 74 LYS Chi-restraints excluded: chain b residue 80 ILE Chi-restraints excluded: chain b residue 107 THR Chi-restraints excluded: chain b residue 136 VAL Chi-restraints excluded: chain b residue 160 ASP Chi-restraints excluded: chain b residue 162 ILE Chi-restraints excluded: chain b residue 174 VAL Chi-restraints excluded: chain b residue 180 LEU Chi-restraints excluded: chain b residue 187 LEU Chi-restraints excluded: chain b residue 189 ASP Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 196 LEU Chi-restraints excluded: chain b residue 210 SER Chi-restraints excluded: chain b residue 212 GLN Chi-restraints excluded: chain b residue 216 SER Chi-restraints excluded: chain b residue 220 ASP Chi-restraints excluded: chain b residue 222 ILE Chi-restraints excluded: chain c residue 3 ASN Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 20 SER Chi-restraints excluded: chain c residue 112 SER Chi-restraints excluded: chain c residue 115 LEU Chi-restraints excluded: chain c residue 144 SER Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 58 LEU Chi-restraints excluded: chain d residue 65 ARG Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 78 LEU Chi-restraints excluded: chain d residue 127 THR Chi-restraints excluded: chain d residue 137 SER Chi-restraints excluded: chain d residue 158 ILE Chi-restraints excluded: chain d residue 203 VAL Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 53 LEU Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain e residue 88 LYS Chi-restraints excluded: chain e residue 98 THR Chi-restraints excluded: chain e residue 131 ILE Chi-restraints excluded: chain e residue 144 THR Chi-restraints excluded: chain f residue 7 ASN Chi-restraints excluded: chain f residue 9 VAL Chi-restraints excluded: chain f residue 10 LEU Chi-restraints excluded: chain f residue 19 LEU Chi-restraints excluded: chain f residue 42 GLU Chi-restraints excluded: chain f residue 43 LEU Chi-restraints excluded: chain f residue 65 VAL Chi-restraints excluded: chain f residue 66 GLU Chi-restraints excluded: chain f residue 67 MET Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 75 LEU Chi-restraints excluded: chain f residue 85 VAL Chi-restraints excluded: chain f residue 90 VAL Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 22 LEU Chi-restraints excluded: chain g residue 33 ASP Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 92 SER Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain h residue 6 ILE Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 35 ILE Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 45 ILE Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 83 ILE Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain h residue 93 VAL Chi-restraints excluded: chain h residue 120 THR Chi-restraints excluded: chain i residue 7 THR Chi-restraints excluded: chain i residue 14 VAL Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 40 LEU Chi-restraints excluded: chain i residue 41 VAL Chi-restraints excluded: chain i residue 47 LEU Chi-restraints excluded: chain i residue 48 GLU Chi-restraints excluded: chain i residue 54 ASP Chi-restraints excluded: chain i residue 81 ILE Chi-restraints excluded: chain i residue 89 ASN Chi-restraints excluded: chain i residue 102 LEU Chi-restraints excluded: chain i residue 109 VAL Chi-restraints excluded: chain j residue 23 ILE Chi-restraints excluded: chain j residue 38 ILE Chi-restraints excluded: chain j residue 47 PHE Chi-restraints excluded: chain j residue 49 VAL Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain j residue 89 ASP Chi-restraints excluded: chain j residue 96 ILE Chi-restraints excluded: chain k residue 18 ARG Chi-restraints excluded: chain k residue 26 ASN Chi-restraints excluded: chain k residue 33 THR Chi-restraints excluded: chain k residue 47 VAL Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 98 LEU Chi-restraints excluded: chain k residue 106 LYS Chi-restraints excluded: chain k residue 117 ASN Chi-restraints excluded: chain l residue 6 THR Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 18 VAL Chi-restraints excluded: chain l residue 58 VAL Chi-restraints excluded: chain l residue 62 SER Chi-restraints excluded: chain l residue 66 VAL Chi-restraints excluded: chain l residue 76 ASN Chi-restraints excluded: chain l residue 77 LEU Chi-restraints excluded: chain l residue 82 VAL Chi-restraints excluded: chain l residue 89 ARG Chi-restraints excluded: chain l residue 96 VAL Chi-restraints excluded: chain l residue 100 ILE Chi-restraints excluded: chain m residue 27 LYS Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain m residue 48 LEU Chi-restraints excluded: chain m residue 74 VAL Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain n residue 3 ARG Chi-restraints excluded: chain n residue 9 LYS Chi-restraints excluded: chain o residue 6 GLU Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain o residue 31 LEU Chi-restraints excluded: chain o residue 32 LEU Chi-restraints excluded: chain o residue 60 VAL Chi-restraints excluded: chain o residue 87 ILE Chi-restraints excluded: chain p residue 11 SER Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 22 THR Chi-restraints excluded: chain p residue 33 ILE Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain q residue 31 LEU Chi-restraints excluded: chain q residue 36 ILE Chi-restraints excluded: chain q residue 53 LEU Chi-restraints excluded: chain q residue 60 ILE Chi-restraints excluded: chain q residue 61 GLU Chi-restraints excluded: chain q residue 66 SER Chi-restraints excluded: chain q residue 89 LEU Chi-restraints excluded: chain q residue 94 ASN Chi-restraints excluded: chain r residue 37 VAL Chi-restraints excluded: chain r residue 39 VAL Chi-restraints excluded: chain r residue 62 GLU Chi-restraints excluded: chain r residue 66 LEU Chi-restraints excluded: chain r residue 72 ARG Chi-restraints excluded: chain r residue 76 LEU Chi-restraints excluded: chain s residue 15 LEU Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 63 ILE Chi-restraints excluded: chain t residue 82 SER Chi-restraints excluded: chain t residue 100 ILE Chi-restraints excluded: chain u residue 13 ILE Chi-restraints excluded: chain u residue 17 THR Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 224 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1047 random chunks: chunk 659 optimal weight: 10.0000 chunk 884 optimal weight: 5.9990 chunk 254 optimal weight: 10.0000 chunk 765 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 831 optimal weight: 0.9980 chunk 348 optimal weight: 4.9990 chunk 854 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 chunk 153 optimal weight: 10.0000 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 29 ASN ** R 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 94 ASN ** V 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 75 ASN ** 0 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 20 HIS ** b 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 141 GLN ** f 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 ASN ** h 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 117 ASN ** m 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 26 GLN ** q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.084707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.068150 restraints weight = 523480.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.069909 restraints weight = 163599.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.071064 restraints weight = 86698.189| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.363 161492 Z= 0.320 Angle : 0.616 29.621 241653 Z= 0.330 Chirality : 0.035 1.903 30609 Planarity : 0.005 0.126 13093 Dihedral : 25.063 179.894 81406 Min Nonbonded Distance : 1.643 Molprobity Statistics. All-atom Clashscore : 64.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.52 % Favored : 92.43 % Rotamer: Outliers : 7.68 % Allowed : 25.51 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.11), residues: 5916 helix: 0.94 (0.12), residues: 1981 sheet: -1.62 (0.15), residues: 1099 loop : -1.09 (0.12), residues: 2836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP g 103 HIS 0.040 0.001 HIS E 159 PHE 0.025 0.002 PHE N 117 TYR 0.020 0.001 TYR 1 71 ARG 0.009 0.000 ARG k 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 55633.65 seconds wall clock time: 967 minutes 16.26 seconds (58036.26 seconds total)